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1. WO2020117650 - APPARATUS, SYSTEMS, AND METHODS FOR QUANTIFYING INFECTIOUS AGENTS

Note: Text based on automatic Optical Character Recognition processes. Please use the PDF version for legal matters

[ EN ]

APPARATUS, SYSTEMS, AND METHODS FOR QUANTIFYING INFECTIOUS

AGENTS

CROSS-REFERENCE TO RELATED APPLICATION

[0001] This application claims the benefit of U.S. Provisional Application No.

62/774,631 filed on December 3, 2018, the entirety of which is incorporated herein by reference.

TECHNICAL FIELD

[0002] The present disclosure relates generally to in vitro quantification of

microorganisms or infectious agents and, more specifically, to apparatus, systems, and methods for determining the concentration of microorganisms or infectious agents in biological samples.

BACKGROUND

[0003] Infections caused by anti-infective resistant microorganisms or infectious agents are a significant problem for healthcare professionals in hospitals, nursing homes, and other healthcare environments. Rapid detection of the susceptibility of such infectious agents to antibiotics or other anti-infectives is crucial in order to prevent the spread of their resistance profiles. The first step in most anti-infective susceptibility testing protocols is to accurately quantify the amount of infectious agents in a particular sample.

[0004] Existing methods and instruments used to quantify infectious agents include costly and labor intensive microbial culturing techniques. However, those methods often require manual interpretation by skilled personnel and are prone to technical or clinician error. In addition, certain biological samples suspected of harboring infectious agents, such as samples containing animal or human blood, are often difficult to assess using prevailing optical techniques given the samples’ opacity. Moreover, such optical techniques often require bulky and expensive detection equipment.

[0005] As a result of the above limitations and restrictions, there is a need for improved apparatus, systems, and methods to quickly and effectively quantify infectious agents in a wide variety of biological samples.

SUMMARY

[0006] A method of determining a concentration of an infectious agent of an unknown strain in a target sample is disclosed. The method comprises diluting a first aliquot of the target sample comprising the infectious agents of the unknown strain by a first dilution factor (DFi) to yield a first diluted sample and diluting a second aliquot of the target sample comprising the infectious agents of the unknown strain by a second dilution factor (DF2) to yield a second diluted sample. The first aliquot and the second aliquot of the sample can be diluted with growth media. The method also comprises determining a first time-to-detection (TTDi) representing the time it takes a solution characteristic of the first diluted sample to undertake a predetermined threshold change and determining a second time-to-detection (TTD2) representing the time it takes the solution characteristic of the second diluted sample to undertake the predetermined threshold change. The method further comprises calculating an average calibration curve slope (maVg) and an average calibration curve y-intercept (bav ) from equation parameters obtained from multiple calibration curves representing growth behavior of one or more infectious agents of different known strains. The method also comprises calculating a corrected calibration curve slope (mcorr) using at least the TTD2, the TTDi, the DF2, and the DFi and calculating a corrected calibration curve y-intercept (bcorr) using at least the bavg, the mcorr, and the mav . The method further comprises determining the concentration of the infectious agent of the unknown strain in the target sample using at least the mcorr, the bcorr, and either the TTDi and the DFi or the TTD2 and the DF2.

[0007] The one or more infectious agents of the different known strains can comprise at least a first infectious agent and a second infectious agent. In some embodiments, the first infectious agent is a different species from the second infectious agent. In other embodiments, the infectious agents of the different known strains are the same species as the infectious agent of the unknown strain.

[0008] The method further comprises generating the multiple calibration curves prior to calculating the maVg and the bav by preparing cultures comprising the one or more infectious agents of the different known strains. The prepared cultures comprise different initial concentrations (Nimtiai) of an infectious agent of a known strain. The method further comprises monitoring, using one or more sensors, changes in the solution characteristics of each of the prepared cultures over time and determining a calibration time-to-detection (TTD calibration) of each of the prepared cultures representing the time it takes the solution characteristic of each of the prepared cultures to undertake the predetermined threshold change. The method further comprises fitting each of the multiple calibration curves to TTDcaiibration data and Ninitial data related to a specific known strain using the relationship:

TTDcalibration = nistram_specific X loga(Ninitial) + bstrain_specific· In this relationship,“a” is any positive real number other than 1,“mstrain_spedfic” is a strain- specific calibration curve slope, and“bstram_spedfic” is a strain- specific calibration curve y-intercept.

[0009] In some embodiments, calculating the maVg comprises taking an average of multiple mstrain_spedfic values and calculating the bavg comprises taking an average of multiple bstrain_spedfic values. Moreover, calculating the mCOrr comprises involves using the relationship:


[0010] In some embodiments, calculating the bcorr comprises using the relationship:


[0011] Determining the concentration of the infectious agent of the unknown strain (Conctarget) can comprise using the relationship:


[0012] Determining the concentration of the infectious agent of the unknown strain (Conctarget) can comprise using the relationship:

TTD2 - bcorr

Conctarget = DF2 x a mcorr

[0013] In some embodiments, the solution characteristic can be an oxidation reduction potential (ORP) and the solution characteristic can be monitored by at least one computing

device communicatively coupled to at least a first ORP sensor and a second ORP sensor. Each of the first ORP sensor and the second ORP sensor can comprise a redox-active material. The first ORP sensor can be in fluid communication with the first diluted sample and the second ORP sensor can be in fluid communication with the second diluted sample. The ORP can be monitored in the absence of any added reporter molecules in any of the first diluted sample or the second diluted sample.

[0014] The first ORP sensor and the second ORP sensor can each comprise at least an active electrode and a reference electrode. The predetermined threshold change can be a change in the ORP of between approximately -100 mV and -700 mV. The redox-active material can comprise a gold layer, a platinum layer, a metal oxide layer, a carbon layer, or a combination thereof.

[0015] In other embodiments, the solution characteristic can be pH and the solution characteristic can be monitored by at least one computing device communicatively coupled to at least a first pH sensor and a second pH sensor. Each of the first pH sensor and the second pH sensor can comprise a functionalization layer. The first pH sensor can be in fluid communication with the first diluted sample and the second pH sensor can be in fluid communication with the second diluted sample.

[0016] The first pH sensor and the second pH sensor each can comprise at least an active electrode and a reference electrode. The predetermined threshold change can be approximately a change in pH of between approximately -0.01 to -3.0.

[0017] The target sample can comprise a bodily fluid, a wound swab or sample, a rectal swab or sample, another type of biological sample, a culture derived therefrom, or a combination thereof. The bodily fluid can comprise urine, blood, sputum, saliva, breast milk, spinal fluid, semen, vaginal secretions, synovial fluid, pleural fluid, peritoneal fluid, pericardial fluid, amniotic fluid, cultures of bodily fluid that have tested positive for infectious agent growth, or a combination thereof. The infectious agent can comprise bacteria, fungus, mold, or a combination thereof.

[0018] A system to determine a concentration of an infectious agent of an unknown strain in a target sample, comprising a metering conduit configured to dilute a first aliquot of the target sample comprising the infectious agent of the unknown strain by a first dilution factor (DFi) to yield a first diluted sample and dilute a second aliquot of the target sample comprising the infectious agent of the unknown strain by a second dilution factor (DF2) to yield a second diluted sample. The first aliquot and the second aliquot of the target sample can be diluted with growth media. The system can also comprise a first sensor configured to detect a change in a solution characteristic of the first diluted sample and a second sensor configured to detect a change in the solution characteristic of the second diluted sample. The system can further comprise one or more sample delivery conduits configured to introduce the first diluted sample to the first sensor and introduce the second diluted sample to the second sensor and a computing device communicatively coupled to the first sensor and the second sensor. The computing device can comprise one or more processors. The one or more processors can be programmed to determine a first time-to-detection (TTDi) representing the time it takes the solution characteristic of the first diluted sample to undertake a predetermined threshold change and determine a second time-to-detection (TTD2) representing the time it takes the solution characteristic of the second diluted sample to undertake the predetermined threshold change. The one or more processor can also be programmed to calculate a corrected calibration curve slope (mcorr) using at least the TTD2, the TTDi, the DF2, and the DFi and calculate an average calibration curve slope (maVg) and an average calibration curve y-intercept (bav ) from equation parameters obtained from multiple calibration curves representing growth behavior of infectious agents of different known strains. Furthermore, the one or more processors can be programmed to calculate a corrected calibration curve y-intercept (bcorr) using at least the mCOrr, the mavg, and the bavg and determine the concentration of the infectious agent of the unknown strain in the target sample using at least the mcorr, the bcorr, and either the TTDi and the DFi or the TTD2 and the DF2.

[0019] The one or more infectious agents of the different known strains can comprise at least a first infectious agent and a second infectious agent. The first infectious agent can be a different species from the second infectious agent. In other embodiments, the one or more infectious agents of the different known strains can be the same species as the infectious agent of the unknown strain.

[0020] The one or more processors of the computing device can be programmed to generate the multiple calibration curves prior to calculating the mav and the bav by monitoring, via one or more sensors communicatively coupled to the computing device, changes in the solution characteristics of prepared cultures comprising the one or more infectious agents of the different known strains. The prepared cultures can comprise different initial concentrations (Nmitial) of an infectious agent of a known strain.

[0021] The one or more processors can also be programmed to determine a calibration time-to-detection (TTDcaiibration) of each of the prepared cultures representing the time it takes the solution characteristic of each of the prepared cultures to undertake the predetermined threshold change. Moreover, the one or more processors can be

programmed to fit each of the multiple calibration curves to TTDcaiibration data and Nmitial data related to a specific known strain using the relationship:

TTDcaiibration = nistram_specific X loga(Ninitial) + bstrain_specific,

[0022] In this relationship,“a” is any positive real number other than 1,“mstrain_specific” is a strain- specific calibration curve slope, and“bstrain_specific” is a strain- specific calibration curve y-intercept.

[0023] The one or more processors can also be programmed to calculate the mav by taking an average of multiple mstrain_specific values and calculate the bavg by taking an average of multiple bstrain_specific values. The one or more processors can also be programmed to calculate the mcorr using the relationship:


[0024] Furthermore, the one or more processors can be programmed to calculate the bcorr using the relationship:

h Ucorr


[0025] In addition, the one or more processors can be programmed to determine the concentration of the target infectious agent of the unknown strain (Conctarget) using the relationship:


[0026] The one or more processors can also be programmed to determine the concentration of the target infectious agent of the unknown strain (Conctarget) using the relationship:

TTD2 - bcorr

Conctarget = DF2 X a mcorr

[0027] In some embodiments, the solution characteristic can be an oxidation reduction potential (ORP) and both the first sensor and the second sensor can be ORP sensors. In these embodiments, each of the first sensor and the second sensor can comprise a redox-active material. Moreover, the predetermined threshold change can be a change in the ORP of between approximately -100 mV and -700 mV. The redox-active material can comprise a gold layer, a platinum layer, a metal oxide layer, a carbon layer, or a combination thereof.

[0028] In other embodiments, the solution characteristic can be pH and both the first sensor and the second sensor can be pH sensors. In these embodiments, each of the first sensor and the second sensor comprise a functionalization layer.

[0029] The predetermined threshold change can be approximately a change in pH of between approximately -0.01 to -3.0. Moreover, the first sensor and the second sensor can each comprise at least an active electrode and a reference electrode.

[0030] In some embodiments, the target sample can comprise a bodily fluid, a wound swab or sample, a rectal swab or sample, another type of biological sample, a sample culture derived therefrom, or a combination thereof. The bodily fluid can comprise urine, blood, sputum, saliva, breast milk, spinal fluid, semen, vaginal secretions, synovial fluid, pleural fluid, peritoneal fluid, pericardial fluid, amniotic fluid, cultures of bodily fluid that have tested positive for infectious agent growth, or a combination thereof. The infectious agent can comprise bacteria, fungus, mold, or a combination thereof.

BRIEF DESCRIPTION OF THE DRAWINGS

[0031] Fig. 1 illustrates certain steps of an example method for determining the concentration of an infectious agent in a target sample.

[0032] Fig. 2 illustrates additional steps of the example method for determining the concentration of an infectious agent in a target sample.

[0033] Fig. 3A illustrates growth curves of cultures of infectious agents of a particular strain at different starting concentrations.

[0034] Fig. 3B illustrates a strain- specific calibration curve fitted to data obtained from the strain- specific growth curves.

[0035] Fig. 3C illustrates a reference calibration curve and multiple strain- specific calibration curves for a particular species of an infectious agent.

[0036] Fig. 3D illustrates two sample growth curves of diluted aliquots of a target sample comprising an infectious agent of an unknown strain.

[0037] Fig. 3E illustrates the reference calibration curve of Fig. 3C in relation to a corrected calibration curve generated using the methods described herein.

[0038] Fig. 4A illustrates additional strain- specific growth curves of infectious agent cultures of different starting concentrations.

[0039] Fig. 4B illustrates a strain- specific calibration curve fitted to data obtained from the additional strain- specific growth curves.

[0040] Fig. 4C illustrates another example of a reference calibration curve and multiple strain- specific calibration curves for a particular infectious agent species.

[0041] Fig. 4D illustrates two sample growth curves of diluted aliquots of another target sample comprising an infectious agent of an unknown strain.

[0042] Fig. 4E illustrates the reference calibration curve of Fig. 4C in relation to a corrected calibration curve generated using the methods described herein.

[0043] Fig. 5A illustrates a reference calibration curve and multiple calibration curves for infectious agents of multiple species.

[0044] Fig. 5B illustrates two sample growth curves of diluted aliquots of an additional target sample comprising an infectious agent of an unknown strain.

[0045] Fig. 5C illustrates the reference calibration curve of Fig. 5A in relation to a corrected calibration curve generated using the methods described herein.

[0046] Fig. 6 illustrates one embodiment of a system and devices for determining the concentration of an infectious agent in a target sample.

[0047] Fig. 7A illustrates a schematic of one embodiment of an ORP sensor used as part of the methods and systems described herein.

[0048] Fig.7B illustrates a schematic of another embodiment of the ORP sensor used as part of the methods and systems described herein.

[0049] Fig. 8A illustrates a schematic of one embodiment of a pH sensor used as part of the methods and systems described herein.

[0050] Fig. 8B illustrates a schematic of another embodiment of the pH sensor used as part of the methods and systems described herein.

[0051] Fig. 9A illustrates a schematic of one embodiment of a combined ORP and pH sensor used as part of the methods and systems described herein.

[0052] Fig. 9B illustrates a schematic of another embodiment of a combined ORP and pH sensor used as part of the methods and systems described herein.

DETAILED DESCRIPTION

[0053] Variations of the devices, systems, and methods described herein are best understood from the detailed description when read in conjunction with the accompanying drawings. It is emphasized that, according to common practice, the various features of the drawings may not be to scale. On the contrary, the dimensions of the various features may be arbitrarily expanded or reduced for clarity and not all features may be visible or labeled in every drawing. The drawings are taken for illustrative purposes only and are not intended to define or limit the scope of the claims to that which is shown.

[0054] Fig. 1 illustrates one embodiment of a method 100 for determining the concentration of an infectious agent 102 in a target sample 104. In some embodiments, the method 100 can be used to determine the concentration of an infectious agent 102 of a known species but an unknown strain. For example, the species of the infectious agent 102 in the target sample 104 can be determined using biochemical tests using specific substrates (both for metabolism and as substrates for specific enzymes), mass spectrometry, genotyping, phenotypic analysis from culture plates, test kits comprising engineered phages, or a combination thereof.

[0055] Once the species of the infectious agent 102 in the target sample 104 is determined, the method 100 can comprise introducing aliquots of the target sample 104 into reaction vessels 106 in step 1A. The reaction vessels 106 can refer to one or more test tubes, reaction tubes, wells of a high throughput assay plate or well plate such as a 96-well plate, a 192-well plate, or a 384-well plate, culture plates or dishes, microfluidic conduits, or other suitable containers for housing biological samples. One or more fluid delivery conduits 108 can inject, deliver, or otherwise introduce the aliquots of the target sample 104 to the reaction vessels 106. In some embodiments, the species of the infectious agent 102 in the target sample 104 does not need to be determined prior to introducing aliquots of the target sample 104 into reaction vessels 106 in step 1A.

[0056] In additional embodiments not shown in Fig. 1, a stimulus solution can be added to the target sample 104 before introducing aliquots of the target sample 104 to the reaction vessels 106. The stimulus solution can be a nutrient or growth solution. In these and other embodiments, the target sample 104 can also be filtered before step 1A. This filtering step can involve filtering the target sample 104 using an instance of a filter, a microfluidic filter, or a combination thereof to filter out debris, inorganic material, and larger cellular components including blood cells or epithelial cells from the target sample [0057] The target sample 104 can comprise at least one of a biological sample, a bodily fluid, a wound swab or sample, a rectal swab or sample, and a bacterial culture derived from the biological sample, the bodily fluid, the wound swab or sample, or the rectal swab or sample. The bodily fluid can comprise urine, blood, serum, plasma, saliva, sputum, semen, breast milk, joint fluid, spinal fluid such as cerebrospinal fluid, wound material, mucus, fluid accompanying stool, re-suspended rectal or wound swabs, vaginal secretions, synovial fluid, pleural fluid, peritoneal fluid, pericardial fluid, amniotic fluid, cultures of bodily fluid or samples that have tested positive for an infectious agent or infectious agent growth such as blood culture that has tested positive for an infectious agent or infectious agent growth (i.e., positive blood culture), or a combination thereof.

[0058] The infectious agents 102 that can be quantified using the methods or systems disclosed herein can be any metabolizing single- or multi-cellular organism including bacteria and fungi. In certain embodiments, the infectious agent 102 can be bacteria selected from the genera Acinetobacter, Acetobacter, Actinomyces, Aerococcus,

Aeromonas, Agrobacterium, Anaplasma, Azorhizobium, Azotobacter, Bacillus,

Bacteriodes, Bartonella, Bordetella, Borrelia, Brucella, Burkholderia,

Calymmatobacterium, Campylobacter, Chlamydia, Chlamydophila, Citrobacter,

Clostridium, Corynebacterium, Coxiella, Ehrlichia, Enterobacter, Enterococcus,

Escherichia, Francisella, Fusobacterium, Gardnerella, Haemophilus, Helicobacter,

Klebsiella, Lactobacillus, Legionella, Listeria, Methanobacterium, Microbacterium, Micrococcus, Morganella, Moraxella, Mycobacterium, Mycoplasma, Neisseria, Pandoraea, Pasteurella, Pep to streptococcus, Porphyromonas, Prevotella, Proteus, Providencia,

Pseudomonas, Ralstonia, Raoultella, Rhizobium, Rickettsia, Rochalimaea, Rothia,

Salmonella, Serratia, Shewanella, Shigella, Spirillum, Staphylococcus, Strenotrophomonas, Streptococcus, Streptomyces, Treponema, Vibrio, Wolbachia, Yersinia, or a combination thereof. In other embodiments, the infectious agent 102 can be one or more fungi selected from the genera Candida or Cryptococcus or mold.

[0059] Other specific bacteria that can be quantified using the methods and systems disclosed herein can comprise Staphylococcus aureus, Staphylococcus lugdunensis, coagulase-negative Staphylococcus species (including but not limited to Staphylococcus epidermidis, Staphylococcus haemolyticus, Staphylococcus hominis, Staphylococcus capitis, not differentiated), Enterococcus faecalis, Enterococcus faecium (including but not limited to Enterococcus faecium and other Enterococcus spp., not differentiated, excluding Enterococcus faecalis), Streptococcus pneumoniae, Streptococcus pyogenes, Streptococcus

agalactiae, Streptococcus spp., (including but not limited to Streptococcus mitis,

Streptococcus pyogenes, Streptococcus gallolyticus, Streptococcus agalactiae,

Streptococcus pneumoniae, not differentiated), Pseudomonas aeruginosa, Acinetobacter baumannii, Klebsiella spp. (including but not limited to Klebsiella pneumoniae, Klebsiella oxytoca, not differentiated), Escherichia coli, Enterobacter spp. (including but not limited to Enterobacter cloacae, Enterobacter aerogenes, not differentiated), Proteus spp.

(including but not limited to Proteus mirabilis, Proteus vulgaris, not differentiated), Citrobacter spp. (including but not limited to Citrobacter freundii, Citrobacter koseri, not differentiated), Serratia marcescens, Candida albicans, Candida glabrata, and Candida tropicalis.

[0060] Other more specific bacteria that can be quantified can comprise Acinetobacter baumannii, Actinobacillus spp., Actinomycetes, Actinomyces spp. (including but not limited to Actinomyces israelii and Actinomyces naeslundii), Aeromonas spp. (including but not limited to Aeromonas hydrophila, Aeromonas veronii biovar sobria (Aeromonas sobria), and Aeromonas caviae), Anaplasma phagocytophilum, Alcaligenes xylosoxidans, Actinobacillus actinomycetemcomitans, Bacillus spp. (including but not limited to Bacillus anthracis, Bacillus cereus, Bacillus subtilis, Bacillus thuringiensis, and Bacillus

stearothermophilus), Bacteroides spp. (including but not limited to Bacteroides fragilis), Bartonella spp. (including but not limited to Bartonella bacilliformis and Bartonella henselae, Bifidobacterium spp., Bordetella spp. (including but not limited to Bordetella pertussis, Bordetella parapertussis, and Bordetella bronchiseptica), Borrelia spp. (including but not limited to Borrelia recurrentis, and Borrelia burgdorferi), Brucella sp. (including but not limited to Brucella abortus, Brucella canis, Brucella melintensis and Brucella suis), Burkholderia spp. (including but not limited to Burkholderia pseudomallei and

Burkholderia cepacia), Campylobacter spp. (including but not limited to Campylobacter jejuni, Campylobacter coli, Campylobacter lari and Campylobacter fetus), Capnocytophaga spp., Cardiobacterium hominis, Chlamydia trachomatis, Chlamydophila pneumoniae, Chlamydophila psittaci, Citrobacter spp. Coxiella burnetii, Corynebacterium spp.

(including but not limited to, Corynebacterium diphtheriae, Corynebacterium jeikeum and Corynebacterium), Clostridium spp. (including but not limited to Clostridium perfringens, Clostridium difficile, Clostridium botulinum and Clostridium tetani), Eikenella corrodens, Enterobacter spp. (including but not limited to Enterobacter aerogenes, Enterobacter agglomerans, Enterobacter cloacae and Escherichia coli, including opportunistic

Escherichia coli, including but not limited to enterotoxigenic E. coli, enteroinvasive E. coli, enteropathogenic E. coli, enterohemorrhagic E. coli, enteroaggregative E. coli and uropathogenic E. coli) Enterococcus spp. (including but not limited to Enterococcus faecalis and Enterococcus faecium) Ehrlichia spp. (including but not limited to Ehrlichia chafeensia and Ehrlichia canis), Erysipelothrix rhusiopathiae, Eubacterium spp.,

Francisella tularensis, Fusobacterium nucleatum, Gardnerella vaginalis, Gemella morbillorum, Haemophilus spp. (including but not limited to Haemophilus influenzae, Haemophilus ducreyi, Haemophilus aegyptius, Haemophilus parainfluenzae, Haemophilus haemolyticus and Haemophilus parahaemolyticus, Helicobacter spp. (including but not limited to Helicobacter pylori, Helicobacter cinaedi and Helicobacter fennelliae), Kingella kingii, Klebsiella spp. (including but not limited to Klebsiella pneumoniae, Klebsiella granulomatis and Klebsiella oxytoca), Lactobacillus spp., Listeria monocytogenes, Leptospira interrogans, Legionella pneumophila, Leptospira interrogans,

Pep to streptococcus spp., Moraxella catarrhalis, Morganella spp., Mobihmcus spp., Micrococcus spp., Mycobacterium spp. (including but not limited to Mycobacterium leprae, Mycobacterium tuberculosis, Mycobacterium intracellulare, Mycobacterium avium, Mycobacterium bovis, and Mycobacterium marinum), Mycoplasm spp. (including but not limited to Mycoplasma pneumoniae, Mycoplasma hominis, and Mycoplasma genitalium), Nocardia spp. (including but not limited to Nocardia asteroides, Nocardia cyriacigeorgica and Nocardia brasiliensis), Neisseria spp. (including but not limited to Neisseria gonorrhoeae and Neisseria meningitidis), Pasteurella multocida, Plesiomonas shigelloides. Prevotella spp., Porphyromonas spp., Prevotella melaninogenica, Proteus spp. (including but not limited to Proteus vulgaris and Proteus mirabilis), Providencia spp. (including but not limited to Providencia alcalifaciens, Providencia rettgeri and Providencia stuartii), Pseudomonas aeruginosa, Propionibacterium acnes, Rhodococcus equi, Rickettsia spp. (including but not limited to Rickettsia rickettsii, Rickettsia akari and Rickettsia prowazekii, Orientia tsutsugamushi (formerly: Rickettsia tsutsugamushi) and Rickettsia typhi), Rhodococcus spp., Serratia marcescens, Stenotrophomonas maltophilia, Salmonella spp. (including but not limited to Salmonella enterica, Salmonella typhi, Salmonella paratyphi, Salmonella enteritidis, Salmonella cholerasuis and Salmonella typhimurium), Serratia spp. (including but not limited to Serratia marcesans and Serratia liquifaciens), Shigella spp. (including but not limited to Shigella dysenteriae, Shigella flexneri, Shigella boydii and Shigella sonnei), Staphylococcus spp. (including but not limited to

Staphylococcus aureus, Staphylococcus epidermidis, Staphylococcus hemolyticus, Staphylococcus saprophyticus), Streptococcus spp. (including but not limited to

Streptococcus pneumoniae (for example chloramphenicol-resistant serotype 4

Streptococcus pneumoniae, spectinomycin-resistant serotype 6B Streptococcus

pneumoniae, streptomycin-resistant serotype 9V Streptococcus pneumoniae, erythromycin-resistant serotype 14 Streptococcus pneumoniae, optochin-resistant serotype 14

Streptococcus pneumoniae, rifampicin-resistant serotype 18C Streptococcus pneumoniae, tetracycline -resistant serotype 19F Streptococcus pneumoniae, penicillin-resistant serotype 19F Streptococcus pneumoniae, and trimethoprim-resistant serotype 23F Streptococcus pneumoniae, chloramphenicol-resistant serotype 4 Streptococcus pneumoniae,

spectinomycin-resistant serotype 6B Streptococcus pneumoniae, streptomycin-resistant serotype 9V Streptococcus pneumoniae, optochin-resistant serotype 14 Streptococcus pneumoniae, rifampicin-resistant serotype 18C Streptococcus pneumoniae, penicillin-resistant serotype 19F Streptococcus pneumoniae, or trimethoprim-resistant serotype 23F Streptococcus pneumoniae), Streptococcus agalactiae, Streptococcus mutans,

Streptococcus pyogenes, Group A streptococci, Streptococcus pyogenes, Group B streptococci, Streptococcus agalactiae, Group C streptococci, Streptococcus anginosus, Streptococcus equismilis, Group D streptococci, Streptococcus bovis, Group F

streptococci, and Streptococcus anginosus Group G streptococci), Spirillum minus, Streptobacillus moniliformi, Treponema spp. (including but not limited to Treponema carateum, Treponema petenue, Treponema pallidum and Treponema endemicum,

Tropheryma whippelii, Ureaplasma urealyticum, Veillonella sp., Vibrio spp. (including but not limited to Vibrio cholerae, Vibrio parahemolyticus, Vibrio vulnificus, Vibrio parahaemolyticus, Vibrio vulnificus, Vibrio alginolyticus, Vibrio mimicus, Vibrio hollisae, Vibrio fluvialis, Vibrio metchnikovii, Vibrio damsela and Vibrio fumisii), Yersinia spp. (including but not limited to Yersinia enterocolitica, Yersinia pestis, and Yersinia pseudotuberculosis) and Xanthomonas maltophilia among others.

[0061] Furthermore, other infectious agents 102 that can be quantified can comprise fungi or mold including, but not limited to, Candida spp. (including but not limited to Candida albicans, Candida glabrata, Candida tropicalis, Candida parapsilosis, and Candida krusei), Aspergillus spp. (including but not limited to Aspergillus fumigatous, Aspergillus flavus, Aspergillus clavatus), Cryptococcous spp. (including but not limited to

Cryptococcus neoformans, Cryptococcus gattii, Cryptococcus laurentii, and Cryptococcus albidus), Fusarium spp. (including but not limited to Fusarium oxysporum, Fusarium solani, Fusarium verticillioides, and Fusarium proliferatum), Rhizopus oryzae, Penicillium mameffei, Coccidiodes immitis, and Blastomyces dermatitidis.

[0062] The fluid delivery conduits 108 can include tubes, pumps, containers, or microfluidic channels for delivering buffers, reagents, fluid samples including the target sample 104, or a combination thereof to and between devices, apparatus, or containers in the system. For example, as shown in Fig. 1, the fluid delivery conduits 108 can refer to parts of a pump such as a syringe pump. In other embodiments, the fluid delivery conduits 108 can include or refer to at least part of a hydraulic pump, a pneumatic pump, a peristaltic pump, a vacuum pump or a positive pressure pump, a manual or mechanical pump, or a combination thereof. In additional embodiments, the fluid delivery conduits 108 can include or refer to at least part of an injection cartridge, a pipette, a capillary, a dispenser bottle, or a combination thereof. The fluid delivery conduits 108 can also be part of a vacuum system configured to draw fluid to or through channels, tubes, or passageways under vacuum. Moreover, the fluid delivery conduits 108 can include or refer to at least part of a multichannel delivery system or pipette.

[0063] The method 100 can further comprise diluting aliquots of the target sample 104 in step IB. For example, step IB can comprise diluting a first aliquot of the target sample 104 by a first dilution factor (DFi) to yield a first diluted sample 110A. Step IB can also comprise diluting a second aliquot of the target sample 104 by a second dilution factor (DF2) to yield a second diluted sample 110B. The second diluted sample 110B can also be obtained by serially or subsequently diluting a previously diluted sample. The first aliquot and the second aliquot can be diluted using a dilutive solution 112.

[0064] In some embodiments, the dilutive solution 112 can comprise growth media or a growth inducer. In these and other embodiments, the dilutive solution 112 can be a solution containing bacto-tryptone, tryptic soy digest, yeast extract, beef extract, cation-adjusted Mueller Hinton Broth (CAMHB), glucose supplemented Mueller Hinton broth (MHG), starch, acid hydrolysate of casein, calcium chloride, magnesium chloride, sodium chloride, blood or lysed blood including lysed horse blood (LHB), CAMHB-LHB, glucose or other carbohydrates, or a combination thereof. The growth inducer can comprise a carbon-based inducer, a nitrogen-based inducer, a mineral, a trace element, a biological growth factor, or any combination thereof. For example, the growth inducer can include but is not limited to a carbohydrate such as glucose or starches, ammonia, magnesium, amino acids, casamino acids, vitamins, peptides, blood, or a combination thereof. In one example embodiment, the dilutive solution 112 can comprise tryptone, yeast extract, sodium chloride, starch, and glucose.

[0065] In some embodiments, any one of DFi and DF2 can be between about 1 : 1 to about 1:10. In these and other embodiments, any one of DFi and DF2 can also be between about 1:10 to about 1:100. In these and other embodiments, any one of DFi and DF2 can also be between about 1:100 to about 1 : 103. In these and other embodiments, any one of DFi and DF2 can also be between about 1 : 103 to about 1 : 107. In these and other embodiments, any one of DFi and DF2 can also be greater than 1 : 107. For example, the first aliquot of the target sample 104 can be diluted with the dilutive solution 112 by a dilution factor of 1:10 to yield the first diluted sample 110A and the second aliquot of the target sample 104 can be diluted with the dilutive solution 112 by a dilution factor of 1:100 to yield the second diluted sample 110B.

[0066] Although Fig. 1 illustrates two aliquots of the target sample 104 being diluted in step IB, it is contemplated by this disclosure that additional aliquots of the target sample 104 can be diluted to different dilution ratios to yield additional diluted samples (e.g., a third diluted sample, a fourth diluted sample, etc.). The additional diluted samples can be used to generate additional corrected calibration curve equation parameters to improve the accuracy of the method. For example, the additional diluted samples can be used to generate additional corrected calibration curve slopes (i.e., additional mcorr values) that can be averaged to yield a more accurate corrected calibration curve slope. As another example, the additional diluted samples can be used to identify outliers and therefore enable a more careful selection of which mcorr values to use for the corrected calibration curve slope.

[0067] The method 100 can further comprise introducing the diluted samples to sensors 116 or exposing the sensors 116 to the diluted samples such that the diluted samples are in fluid communication with a redox-active material 708 (see Figs. 7A and 7B) or a functionalization layer 806 (see Figs. 8A and 8B) of the sensors 116 in step 1C. For example, the first diluted sample 110A can be introduced to a first sensor (one of the sensors 116) and the second diluted sample 110B can be introduced to a second sensor (another one of the sensors 116). The sensors 116 can be configured to respond to a change in a solution characteristic of the diluted samples. In some embodiments, the sensors 116 can be oxidation reduction potential (ORP) sensors configured to respond to a change in the ORP of the diluted samples. In other embodiments, the sensors 116 can be pH sensors configured to respond to a change in the pH of the diluted samples.

[0068] The method 100 can also comprise incubating the diluted samples at an elevated temperature for a period of time in step ID. The diluted samples can be incubated in the same reaction vessels 106 or transferred to different reaction vessels 106 or containers. For example, the first diluted sample 110A and the second diluted sample 110B can be heated to a temperature of between about 30 °C and about 40 °C (e.g., 35 °C ± 2 °C) and allowed to incubate for an incubation period 114. The incubation period 114 can range from 15 minutes to over one hour. In other embodiments, the incubation period 114 can be less than 15 minutes or up to 48 hours. The diluted samples can be incubated while exposed to or otherwise in fluid communication with at least part of the sensors 116.

[0069] In the example embodiment shown in Fig. 1, exposing a sensor 116 to a diluted sample (any of the first diluted sample 110A or the second diluted sample 110B) can involve directly immersing at least part of a handheld or probe instance of the sensor 116 into the diluted sample. In this embodiment, the handheld or probe instance of the sensor 116 can be a handheld OPR sensor or a handheld pH sensor coupled to a standalone parameter analyzer 118, such as a voltmeter or multimeter. In another example

embodiment shown in Fig. 6, introducing the diluted sample to the sensor 116 can involve injecting, delivering, or otherwise introducing the diluted sample to a well or container comprising the sensor 116 fabricated on a substrate. The sensors 116 will be discussed in more detail in the following sections.

[0070] The method 100 can further comprise monitoring the solution characteristics of the diluted samples with one or more computing devices 120 coupled to the parameter analyzers 118 or coupled directly to the sensors 116. The solution characteristics of the diluted samples can be monitored in the absence of any exogenous reporter molecules added to the diluted samples.

[0071] Although Fig. 1 shows the parameter analyzers 118 as separate standalone devices from the computing device 120, it is contemplated by this disclosure and it should be understood by one of ordinary skill in the art that the parameter analyzer 118 and the computing device 120 can be integrated into one device. As illustrated in Fig. 1, computing device 120 can be a mobile device, a handheld device, a tablet device, a laptop or desktop computer. In some embodiments, the parameter analyzers 118 can wirelessly communicate a signal or result to computing device 120.

[0072] The solution characteristics of the diluted samples can change as the amount of electro-active redox species or the amount of ions change due to the energy use, oxygen uptake or release, growth, or metabolism of the infectious agents 102 in the diluted

samples. For example, the amount of electro-active redox species in the diluted samples can change as a result of cellular activity (e.g., microbial aerobic or anaerobic respiration) undertaken by the infectious agents 102 in the diluted samples. Also, as an example, the amount of H+ ions in the diluted samples can change as a result of cellular activity undertaken by the infectious agents 102 in the diluted samples.

[0073] As a more specific example, the amount of electron donors from Table 1 below (e.g., the amount of energy carriers such as nicotinamide adenine dinucleotide (NADH) and flavin adenine dinucleotide (FADFb)) in the diluted samples can change due to the growth of the infectious agents 102 in the diluted samples. Also, as another more specific example, the amount of oxygen depleted in the diluted samples due to aerobic respiration can change due to the growth of the infectious agents 102 in the diluted samples.

TABLE 1: Below is a“redox tower” visualizing potential electron donors and acceptors which can be utilized by infectious agents during the course of metabolism. An electron donor will have a greater negative potential than the electron acceptor. In aerobic respiration for example, O2 can serve as a terminal electron acceptor whereas in anaerobic respiration, the terminal electron acceptor can comprise NO3 , Fe3+, Mn4+, SO42 , or CO2.


[0074] The method 100 can further comprise determining a first time-to-detection (TTDi) representing the time it takes a solution characteristic of the first diluted sample 110A to undertake a predetermined threshold change 122 in step IE. In addition, step IE can also comprise determining a second time-to-detection (TTD2) representing the time it takes a solution characteristic of the second diluted sample 110B to undertake the same predetermined threshold change 122. For example, when the solution characteristic is ORP, the predetermined threshold change 122 can be between about D 100 mV and A700mV. As a more specific example, a predetermined ORP threshold level (Vth) can be set at -lOOmV and the time-to-detection can represent the time it takes the ORP of a diluted sample to reach - lOOmV from 0 mV. As an additional example, when the solution characteristic is pH, the predetermined threshold change 122 can be between about ApH 0.01 and ApH 3.0. As a more specific example, a predetermined pH threshold level (pHth) can be set at pH 6.7 and the time-to-detection can represent the time it takes the pH of a diluted sample to reach pH 6.7 from a normalized pH of 7.0 (ApH -0.3).

[0075] The method 100 can further comprise calculating an average calibration curve slope (maVg) and an average calibration curve y-intercept (bav ) from equation parameters obtained from multiple calibration curves 204 representing growth behavior of infectious agents 202 of different known strains. An example method 200 of generating the multiple calibration curves 204 and calculating the mavg and the bav will be discussed in the following sections with respect to Fig. 2. In some embodiments, the infectious agents 202 used to generate the multiple calibration curves 204 can be the same species as the infectious agent 102 of the unknown strain in the target sample 104. In other embodiments, at least one of the infectious agents 202 used to generate the multiple calibration curves 204 can be of a different species from the infectious agent 102 of the unknown strain in the target sample 104. As will be discussed in the following sections, generating the multiple calibration curves 204 and calculating the mav and the bav can be done at any point prior to step 1G. For example, generating the multiple calibration curves 204 and calculating the mav and the bav can be done contemporaneously with any of steps 1A, IB, 1C, ID, IE, or IF of method 100. Alternatively, generating the multiple calibration curves 204 and

calculating the maVg and the bavg can be done prior to step 1A and the multiple calibration curves 204, the mav , and the bav can be stored in a memory of computing device 120 or a database accessible to the computing device 120.

[0076] The method 100 can also comprise calculating a corrected calibration curve slope (mCOrr) using at least the TTD2, the TTDi, the DF2, and the DFi in step IF. As will be discussed in more detail in the following sections, mCOrr can be calculated using Equation 1 below:

.

Equation


[0077] The method 100 can further comprise calculating a corrected calibration curve y-intercept (bcorr) using at least the bav , the mcorr, and the mavg in step 1G. As will be discussed in more detail in the following sections, mcorr can be calculated using Equation 2 below:

Equation 2: bCOrr = mcorr X bavg

mavg

[0078] The method 100 can further comprise determining the concentration of the infectious agent 102 of the unknown strain in the target sample 104 (hereinafter, Conctarget) using at least the mCOrr, the bcorr, and either the TTDi and the DFi or the TTD2 and the DF2. As will be discussed in more detail in the following sections, Conctarget can be calculated using either Equation 3 or Equation 4 below:

TTD1 bcorr .

Equation 3 : Conctarget = DFi X a1 mcorr

Equation 4: Conctarget

[0079] In Equations 3 and 4 above, the variable“a” can be any positive real number other than E Using the method 100 described herein, a laboratory or hospital can determine the concentration of the infectious agent 102 in a target sample 104 between about 60 minutes and 120 minutes. In other embodiments, the concentration of the infectious agent 102 can be determined between about 5 minutes and 60 minutes.

[0080] In some embodiments, one or more of the aforementioned steps of the method 100 can be stored as machine-executable instructions or logical commands in a non

transitory machine-readable medium (e.g., a memory or storage unit) of the computing device 120 or another device communicatively or electrically coupled to the computing device 120. Any of the parameter analyzer 118, the computing device 120, or another device coupled to the parameter analyzer 118 or the computing device 120 can comprise one or more processors or controllers configured to execute the aforementioned

instructions or logical commands.

[0081] The steps depicted in Fig. 1 do not require the particular order shown to achieve the desired result. Moreover, certain steps or processes may be omitted or occur in parallel in order to achieve the desired result. In addition, any of the systems or devices disclosed herein can be used in lieu of devices or systems shown in the steps of Fig. 1.

[0082] Fig. 2 illustrates an example method 200 for generating the multiple calibration curves 204 and calculating the maVg and the baVg from equation parameters obtained from the multiple calibration curves 204. As previously discussed, the infectious agents 202 used to generate the multiple calibration curves 204 can be the same species as the infectious agent 102 in the target sample 104. In other embodiments, at least one of the infectious agents 202 used to generate the multiple calibration curves 204 can be of a different species from the infectious agent 102 in the target sample 104.

[0083] The method 200 can comprise preparing cultures 206 comprising infectious agents 202 of different known strains in step 2A. For example, the infectious agent 102 in the target sample 104 can be determined to be of the species Staphylococcus Aureus (SAu). In this example embodiment, the infectious agents 202 used to prepare the multiple calibration curves 204 can be different known strains of SAu such as wild-type strain SAu (SAu_WT), CDC483 strain SAu (SAu_CDC483), ATCC43300 strain SAu

(SAu_ATCC43300), and CDC475 strain SAu (SAu_CDC475). The prepared cultures 206 can comprise different initial concentrations (Nmitmi) of an infectious agent 202 of a particular known strain. For example, step 2A can comprise preparing cultures of SAu_WT at initial concentrations of 1 x 104 CFU/mL, 1 x 105 CFU/mL, 1 x 106 CFU/mL, 1 x 107 CFU/mL, and 1 x 108 CFU/mL. A dilutive solution (such as the dilutive solution 112) can be used to dilute an initial prepared culture 206 of an infectious agent 202 to obtain additional cultures with different starting concentrations. For example, the prepared cultures can be infectious agent liquid cultures prepared by re-suspending infectious agent colonies from an infectious agent culture plate into growth media to reach the

aforementioned concentrations by measuring the optical density (O.D.) of the solution

(e.g., O.D. measured at a wavelength of 600 nm). As a more specific example, the prepared cultures can be liquid bacterial cultures prepared by inoculating bacterial colonies from a bacterial culture plate into growth media to reach the aforementioned concentrations measured by O.D.

[0084] The method 200 can also comprise introducing the prepared cultures 206 to sensors 116 or exposing the sensors 116 to the prepared cultures 206 such that the prepared cultures 206 are in fluid communication with a redox-active material 708 (see Figs. 7A and 7B) or a functionalization layer 806 (see Figs. 8 A and 8B) of the sensors 116 in step 2B. The sensors 116 can be configured to respond to a change in a solution characteristic of the prepared cultures 206 over time. In some embodiments, the sensors 116 can be oxidation reduction potential (ORP) sensors configured to respond to a change in the ORP of the prepared cultures 206. In other embodiments, the sensors 116 can be pH sensors configured to respond to a change in the pH of the prepared cultures 206. The method 200 can further comprise monitoring the solution characteristics of the prepared cultures 206 with one or more computing devices 120 coupled to the parameter analyzers 118 or coupled directly to the sensors 116. The solution characteristics of the prepared cultures 206 can be monitored in the absence of any exogenous reporter molecules added to the prepared cultures 206.

[0085] The method 200 can further comprise determining a calibration time-to-detection (TTDcaiibration) of each of the prepared cultures 206 representing the time it takes the solution characteristic of each of the prepared cultures 206 to undertake a

predetermined threshold change 122 in step 2C. For example, when the solution

characteristic is ORP, the predetermined threshold change 122 can be between about AlOOmV and A700mV. As a more specific example, a predetermined ORP threshold level (Vth) can be set at -lOOmV and the TTD calibration can represent the time it takes the ORP of a prepared culture 206 to reach - lOOmV from 0 mV. As an additional example, when the solution characteristic is pH, the predetermined threshold change 122 can be between about ApH 0.01 and ApH 3.0. As a more specific example, a predetermined pH threshold level (pHth) can be set at pH 6.7 and the TTDcaiibration can represent the time it takes the pH of a prepared culture 206 to reach pH 6.7 from a normalized pH of 7.0 (ApH -0.3). In all such embodiments, the same predetermined threshold change 122 used with respect to step 2C is also used with respect to step IE of Fig. 1.

[0086] The method 200 can further comprise plotting TTDcaiibration data against Ninitial data for each of the prepared cultures 206 of a particular known strain in step 2D. For

example, TTDcaiibration data for SAu_WT can be plotted against Nmitiai data for SAu_WT. Step 2D can also comprise fitting a calibration curve 204 to TTDcaiibration data and Nmitiai data using a curve-fitting technique. In some embodiments, the curve-fitting technique can be least-squares curve-fitting technique or algorithm. In other embodiments, the curve fitting technique can be a logarithmic regression curve-fitting technique. In other embodiments, a polynomial curve fitting technique can also be used.

[0087] For example, a calibration curve 204 can be fitted to the TTDcaiibration data and Ninitial data for a particular known strain using Equation 5 below:

Equation 5: TTDcaiibration = mstrain_specific X loga( initial) + bstrain_specific

[0088] In Equation 5 above, the variable“a” can be any positive real number other than 1. In addition, in Equation 5 above, the curve fitting parameters mstrain_spedfic and bstrain_specific can refer to a strain- specific calibration curve slope and a strain-specific calibration curve y-intercept, respectively. The same process can be repeated for other known strains of an infectious agent 202. For example, the same process can be repeated for multiple strains of SAu such as SAu_WT, SAu_CDC483, SAu_ATCC43300, and SAu_CDC475 such that unique pairs of mstrain_spedfic and bstrain_spedfic are calculated for each of SAu_WT, SAu_CDC483, SAu_ATCC43300, and SAu_CDC475.

[0089] In addition to calculating curve fitting parameters mstrain_spedfic and

bstrain_spedfic for known strains of the same species, steps 2A, 2B, 2C, and 2D can also be undertaken to calculate mstrain_spedfic and bstrain_spedfic for known strains of infectious agents 202 of different species. For example, as will be discussed in more detail in the following sections, unique pairs of mstrain_spedfic and bstrain_spedfic can also be calculated for different known strains of Escherichia Coli (Eco), Enterobacter Cloacae (ECl), Enterobacter Aerogenes (EAe), and Klebsiella Pneumoniae (KPn).

[0090] The method 200 can also comprise calculating an average calibration curve slope (mav ) in step 2E by taking an average of the multiple mstrain_spedfic values calculated from step 2D. Step 2E can also comprise calculating an average calibration curve y-intercept (bav ) by taking an average of the multiple bstrain_spedfic values calculated from step 2D. In some embodiments, all of the mstrain_spedfic values used to calculate the mavg and all of the bstrain_spedfic values used to calculate the baVg can be obtained from calibration curves 204 fitted to data obtained from multiple strains of the same species of infectious agent 202. For example, the maVg and the bav can be calculated from

mstrain_specific values and bstrain_specific values calculated for SAu_WT, SAu_CDC483, SAu_ATCC43300, and SAu_CDC475.

[0091] In other embodiments, the mstrain_spedfic values used to calculate the mav and the bstrain_spedfic values used to calculate the bav can be obtained from calibration curves 204 fitted to data obtained from infectious agents 202 of different species. For example, the mavg and the bavg can be calculated from mstrain_specific values and bstrain_spedfic values calculated for SAu_WT, wild-type strain ECo (ECo_WT), wild-type strain EAe

(EAe_WT), wild-type strain KPn (KPn_WT), and CDC8 strain ECl (EC1_CDC 8). Also, as additional examples, the mav and the bav can be calculated from mstrain_specific values and bstrain_spedfic values calculated for infectious agents 202 of the same family or the same genus.

[0092] Although method 200 is shown separate from method 100, it is contemplated by this disclosure and it should be understood by one of ordinary skill in the art that method 200 can be considered sub-steps or pre-steps of method 100. Moreover, the steps depicted in Fig. 2 do not require the particular order shown to achieve the desired result. Moreover, certain steps or processes may be omitted or occur in parallel in order to achieve the desired result. In addition, any of the systems or devices disclosed herein can be used in lieu of devices or systems shown in the steps of Fig. 2.

[0093] Figs. 3A to 3E illustrate an example application of the methods described herein for determining the concentration of an unknown strain of SAu in a target sample 104. Fig. 3A illustrates multiple growth curves 300 representing a change in the solution

characteristic of prepared cultures 206 of a known strain of SAu (in this case, wild-type SAu). The growth curves 300 can be recorded by monitoring the sensor output of one or more ORP sensors (including, but not limited to, the sensors 116) in fluid communication with the prepared cultures 206. The prepared cultures 206 can comprise different initial concentrations (Nmitial) of SAu_WT (e.g., 1 x 104 CFU/mL, 1 x 105 CFU/mL, 1 x 106 CFU/mL, 1 x 107 CFU/mL, and 1 x 108 CFU/mL of SAu_WT).

[0094] The sensor output (voltage output in this case) can be a potential difference between an active electrode and a reference electrode such as the external reference

electrode or the on-chip reference electrode (see Figs. 7 A and 7B). The voltage output of the one or more ORP sensors can change as the ORP of each of the prepared cultures 206 changes over time.

[0095] The voltage output can decrease as the solution characteristic of the prepared cultures 206 change due to the energy use, oxygen uptake or release, growth, or metabolism of the infectious agents 202 in solution. In some embodiments, the growth curve can follow a sigmoidal pattern or shape, a step function or shape, or other patterns or shapes. Over longer time scales, the growth curve can begin to increase or become more positive.

[0096] For example, the voltage output of the ORP sensor can decrease to a negative potential over time as the solution characteristic of each of the prepared cultures 206 changes as a result of cellular activity undertaken by the infectious agents 202 in solution. As a more specific example, the solution characteristic of the prepared cultures 206 can change as the amount of energy carriers (such as nicotinamide adenine dinucleotide (NADH) and flavin adenine dinucleotide (FADFh)) in the sampled solution changes due to the growth of the infectious agents 202. Also, as another more specific example, the amount of oxygen depleted in the prepared cultures 206 can change due to the growth of the infectious agents 202 (e.g., SAu_WT) in solution.

[0097] Although outputs for ORP sensors are shown in Figs. 3A-3E, it is contemplated by this disclosure that pH sensors can also be used in lieu of or in combination with ORP sensors. The pH sensors can be configured to respond to a change in the pH of the prepared cultures 206.

[0098] Fig. 3A also illustrates that a calibration time-to-detection (TTDcaiibration) can also be recorded for each of the prepared cultures 206. The TTDcaiibration represents the time it takes the solution characteristic of each of the prepared cultures 206 to undertake a predetermined threshold change 122. For example, as shown in Fig. 3A, the time it takes the ORP of each of the prepared cultures 206 of SAu_WT to reach a predetermined threshold voltage of -100 mV (from a starting voltage of 0 V) can be recorded by the parameter analyzer 118, the computing device 120, or a combination thereof.

[0099] Fig. 3B illustrates a strain- specific calibration curve 302 (in this case, the SAu_WT calibration curve) fitted to TTDcaiibration and Njnjtja] data obtained from the strain-specific growth curves 300 of Fig. 3A. For example, TTDcaiibration data and Nmitial data can be plotted on a semi-log plot (or linear- logarithmic plot) 304 as shown in Fig. 3B. The

strain-specific calibration curve 302 can be fitted to the TTDcaiibration and Nmitiai data using curve-fitting techniques. In one embodiment, the curve-fitting technique can be a least- squares curve fitting technique. In other embodiments, the curve-fitting technique can be a logarithmic regression or polynomial curve-fitting technique. The strain-specific calibration curve 302 can refer to one of the multiple calibration curves 204 discussed with respect to Fig. 2.

[0100] In one embodiment, the strain- specific calibration curve 302 for SAu_WT can be fitted to the TTDcaiibration and Nmitiai data using Equation 5 above. In this and other embodiments (i.e., the prepared cultures 206 are cultures of SAu_WT), the curve fitting parameters mstrain_spedfic and bstrain_spedfic can refer to a SAu_WT calibration curve slope and a SAu_WT calibration curve y-intercept, respectively.

[0101] The same process can be repeated for other known strains of an infectious agent 202 of a particular species. For example, the same process can be repeated for other known strains of SAu such as SAu_CDC483, SAu_ATCC43300, and SAu_CDC475 such that unique pairs of mstrain_spedfic and bstrain_spedfic are calculated for each of SAu_WT, SAu_CDC483, SAu_ATCC43300, and SAu_CDC475.

[0102] Table 2 below shows calibration curve slopes and calibration curve y-intercepts calculated for different strains of SAu including SAu_WT, SAu_CDC483,

SAu_ATCC43300, and SAu_CDC475. Table 2 also shows that an average calibration curve slope (maVg) can be calculated by taking an average of the various SAu calibration curve slopes. In addition, Table 2 also shows that an average calibration curve y-intercept (baVg) can be calculated by taking an average of the various SAu calibration curve y- intercepts.

TABLE 2: SAu Calibration Curve Parameters


[0103] The various SAu calibration curve slopes and y-intercepts along with the maVg and the bav values can be stored in a database on a memory device of the computing device 120 or stored in another database accessible to the computing device 120. Such stored values can be used to quantify a target sample 104 that immediately tests positive for SAu but where the particular strain or growth characteristic of SAu is initially unknown.

[0104] Fig. 3C illustrates an SAu reference calibration curve 306 plotted on the same axes as multiple strain- specific SAu calibration curves 302 used to generate the slope and y-intercept of the SAu reference calibration curve 306. For example, the SAu reference calibration curve 306 can be generated using Equation 5 above but with mstram_specific and bstrain_specific in the equation replaced by mavg and bav , respectively.

[0105] Fig. 3D illustrates two sample growth curves 308 of diluted aliquots of a target sample 104 comprising SAu of an unknown strain. As shown in Fig. 3D, the first aliquot of the target sample 104 can be diluted by a dilution factor (DFi) of 1:10 to yield a first diluted sample and the second aliquot of the target sample 104 can be diluted by a dilution factor (DF2) of 1:100 to yield a second diluted sample. The first aliquot and the second aliquot can be diluted using a dilutive solution (such as the dilutive solution 112). Fig. 3D also illustrates that the solution characteristics of the two diluted samples can change as the amount of electro-active redox species in the samples changes due to the energy use, oxygen uptake or release, growth, or metabolism of the unknown strain of SAu in the diluted samples.

[0106] A predetermined ORP threshold level (Vth) can be set at -lOOmV and the time it takes the solution characteristic of each of the first diluted sample and the second diluted sample to reach this Vth can be recorded. The time it takes the first diluted sample to undertake a predetermined threshold change from 0 mV to -100 mV (also referred to as the TTDi) can be recorded. For example, Fig. 3D shows the TTDi as 190 minutes. Moreover, the time it takes the second diluted sample to undertake a predetermined threshold change from 0 mV to -100 mV (referred to as the TTD2) can be recorded. For example, Fig. 3D shows the TTD2 as 310 minutes. As shown in Fig. 3D, the sample growth curve 308 of the second diluted sample can be time shifted with respect to the first diluted sample since a more dilute sample takes longer to reach a detectable level.

[0107] Fig. 3E illustrates the SAu reference calibration curve 306 of Fig. 3C in relation to a corrected SAu calibration curve 310. The corrected SAu calibration curve 310 can be used to more accurately determine a concentration of the unknown strain of SAu in the target sample 104 compared to the SAu reference calibration curve 306. The corrected SAu calibration curve 310 can be generated by applying a correction factor (CF) to certain equation parameters of the SAu reference calibration curve 306.

[0108] For example, a computing device 120 can calculate a corrected calibration curve slope (mCOrr) using Equation 1 provided above and where TTD2 = 310 minutes, TTDi =

190 minutes, DF2 = 100, DFi = 10, and a = 10:


mcorr— 120

[0109] In the calculation above, the variable“a” can be equal to 10 when 10 is used as the base of the log function in Equation 5 above. As previously discussed,“a” can be any positive real number other than 1.

[0110] The computing device 120 can also calculate a corrected calibration curve y-intercept (bcorr) using Equation 2 provided above, the calculated mcorr value, and the stored maVg and baVg values for SAu:

V, _ mcorr ,

Ucorr— Uavg

mavg

bcorr


625.2

bcorr = 1027.73

[0111] The value obtained by dividing mcorrby mav (the ratio of m values) can also be considered a correction factor or CF (that is CF example, another way of

expressing Equation 2 above can be:

bcorr = C F X bavg

[0112] With the mCOrr and bCOrr values calculated, the concentration of the unknown strain of SAu in the target sample 104 (Conctarget) can be calculated using either Equation 3 or Equation 4 above.

[0113] For example, using Equation 3 and with DFi = 10 and TTDi = 190 minutes, the Conctarget can be calculated as:


Conctarget = lO7 98 CFU/mL

Conctarget = 9.5 X 107 CFU/mL

[0114] Similarly, using Equation 4 and with DF2 = 100 and TTD2 = 310 minutes, the Conctarget can be calculated as:

Conctarget = 100

Conctarget = lO7 98 CFU/mL

Conctarget = 9.5 X 107 CFU/mL

[0115] To highlight the importance of the correction steps described above, the Conctarget can also be calculated using Equations 3 and 4 but with mcorr substituted with maVg and bcorr substituted with bav :


ConCtarget = 00 X - 73.0

ConC target = 10(6 32)

Conctarget = 2.1 X 106 CFU/mL

[0116] As can be seen by the concentration amounts calculated using the maVg and bav values, the concentration amount is inconsistent across the two dilutions. In addition, the improved accuracy of the correction steps is apparent when the concentration of the unknown strain of SAu in the target sample 104 or Conctarget is calculated to be approximately 1.0 X 108 CFU/mL using other prevailing methods.

[0117] Figs. 4A to 4E illustrate an example application of the methods described herein for determining the concentration of an unknown strain of ECl in a target sample 104. Fig. 4A illustrates multiple growth curves 400 representing a change in the solution

characteristic of prepared cultures 206 of a known strain of ECl (in this case, wild-type strain ECl or EC1_WT). The growth curves 400 can be recorded by monitoring the sensor output of one or more ORP sensors (including, but not limited to, the sensors 116) in fluid communication with the prepared cultures 206. The prepared cultures 206 can comprise different initial concentrations (Nmitial) of EC1_WT (e.g., 1 x 104 CFU/mL, 1 x 105 CFU/mL, 1 x 106 CFU/mL, 1 x 107 CFU/mL, and 1 x 108 CFU/mL of EC1_WT).

[0118] The sensor output (voltage output in this case) can be a potential difference between an active electrode and a reference electrode such as the external reference electrode or the on-chip reference electrode (see Figs. 7A and 7B). The voltage output of the one or more ORP sensors can change as the ORP of each of the prepared cultures 206 changes over time.

[0119] The voltage output can decrease as the solution characteristic of the prepared cultures 206 change due to the energy use, oxygen uptake or release, growth, or metabolism of the infectious agents 202 in solution. In some embodiments, the growth curve can follow a sigmoidal pattern or shape, a step function or shape, or other patterns or shapes. Over longer time scales, the growth curve can begin to increase or become more positive.

[0120] For example, the voltage output of the ORP sensor can decrease over time as the solution characteristic of each of the prepared cultures 206 changes as a result of cellular activity undertaken by the infectious agents 202 in solution. As a more specific example, the solution characteristic of the prepared cultures 206 can change as the amount of energy carriers (such as nicotinamide adenine dinucleotide (NADH) and flavin adenine dinucleotide (FADEb)) in the sampled solution changes due to the growth of the infectious agents 202. Also, as another more specific example, the amount of oxygen depleted in the prepared cultures 206 can change due to the growth of the infectious agents 202 (e.g., EC1_WT) in solution.

[0121] Although outputs for ORP sensors are shown in Figs. 4A-4E, it is contemplated by this disclosure that pH sensors can also be used in lieu of or in combination with ORP sensors. The pH sensors can be configured to respond to a change in the pH of the prepared cultures 206.

[0122] Fig. 4A also illustrates that a calibration time-to-detection (TTDcaiibration) can also be recorded for each of the prepared cultures 206 of EC1_WT. The TTDcaiibration represents the time it takes the solution characteristic of each of the prepared cultures 206 to undertake a predetermined threshold change 122. For example, as shown in Fig. 4A, the time it takes the ORP of each of the prepared cultures 206 of EC1_WT to reach a predetermined threshold voltage of -100 mV (from a starting voltage of 0 V) can be recorded by the parameter analyzer 118, the computing device 120, or a combination thereof.

[0123] Fig. 4B illustrates a strain- specific calibration curve 402 (in this case, the EC1_WT calibration curve) fitted to TTD calibration and Nmitial data obtained from the strain-specific growth curves 400 of Fig. 4A. For example, TTDcaiibration data and Nmitial data can be plotted on a semi-log plot (or linear- logarithmic plot) 404 as shown in Fig. 4B. The strain- specific calibration curve 402 can be fitted to the TTDcaiibration and Nmitial data using curve-fitting techniques. In one embodiment, the curve-fitting technique can be a least-squares curve fitting technique. In other embodiments, the curve-fitting technique can be a logarithmic regression or polynomial curve-fitting technique. The strain-specific calibration curve 402 can refer to one of the multiple calibration curves 204 discussed with respect to Fig. 2.

[0124] In one embodiment, the strain- specific calibration curve 402 for EC1_WT can be fitted to the TTDcaiibration and Nmitial data using Equation 5 above. In this and other embodiments (i.e., the prepared cultures 206 are cultures of EC1_WT), the curve fitting parameters mstrain_specific and bstrain_specific can refer to an EC1_WT calibration curve slope and an EC1_WT calibration curve y-intercept, respectively.

[0125] The same process can be repeated for other known strains of an infectious agent 202 of a particular species. For example, the same process can be repeated for other known strains of ECl such as the CDC 32 type strain of ECl or EC1_CDC32, the ATCC2341 strain of ECl or EC1_ATCC2341, and the CDC 93 type strain of ECl or EC1_CDC93 such that unique pairs of mstrain_specific and bstrain_specific are calculated for each of EC1_WT, ECLCDC32, ECLATCC2341, and EC1_CDC93.

[0126] Table 3 below shows calibration curve slopes and calibration curve y-intercepts calculated for different strains of ECl including EC1_WT, EC1_CDC32, EC1_ATCC2341, and EC1_CDC93. Table 3 also shows that an average calibration curve slope (maVg) can be

calculated by taking an average of the various ECl calibration curve slopes. In addition, Table 3 also shows that an average calibration curve y-intercept (bav ) can be calculated by taking an average of the various ECl calibration curve y-intercepts.

TABLE 3: ECl Calibration Curve Parameters

[0127] The various ECl calibration curve slopes and y-intercepts along with the maVg and the bavg values can be stored in a database on a memory device of the computing device 120 or stored in another database accessible to the computing device 120. Such stored values can be used to quantify a target sample 104 that immediately tests positive for ECl but where the particular strain of ECl is initially unknown.

[0128] Fig. 4C illustrates an ECl reference calibration curve 406 plotted on the same axes as multiple strain- specific ECl calibration curves 402 used to generate the slope and y-intercept of the ECl reference calibration curve 406. For example, the ECl reference calibration curve 406 can be generated using Equation 5 above but with mstrain_specific and bstrain_specific in the equation replaced by mav and bav , respectively.

[0129] Fig. 4D illustrates two sample growth curves 408 of diluted aliquots of a target sample 104 comprising ECl of an unknown strain. As shown in Fig. 4D, the first aliquot of the target sample 104 can be diluted by a dilution factor (DFi) of 1: 10 to yield a first diluted sample and the second aliquot of the target sample 104 can be diluted by a dilution factor (DF2) of 1: 100 to yield a second diluted sample. The first aliquot and the second aliquot can be diluted using a dilutive solution (such as the dilutive solution 112). Fig. 4D also illustrates that the solution characteristics of the two diluted samples can change as the amount of electro-active redox species in the samples changes due to the energy use,

oxygen uptake or release, growth, or metabolism of the unknown strain of ECl in the diluted samples.

[0130] A predetermined ORP threshold level (Vth) can be set at -lOOmV and the time it takes the solution characteristic of each of the first diluted sample and the second diluted sample to reach this Vth can be recorded. The time it takes the first diluted sample to undertake a predetermined threshold change from 0 mV to -100 mV (also referred to as the TTDi) can be recorded. For example, Fig. 4D shows the TTDi as 100 minutes. Moreover, the time it takes the second diluted sample to undertake a predetermined threshold change from 0 mV to -100 mV (referred to as the TTD2) can be recorded. For example, Fig. 4D shows the TTD2 as 190 minutes. As shown in Fig. 4D, the sample growth curve 408 of the second diluted sample can be time shifted with respect to the first diluted sample since a more dilute sample takes longer to reach a detectable level.

[0131] Fig. 4E illustrates the ECl reference calibration curve 406 of Fig. 4C in relation to a corrected ECl calibration curve 410. The corrected ECl calibration curve 410 can be used to more accurately determine a concentration of the unknown strain of ECl in the target sample 104 compared to the ECl reference calibration curve 406. The corrected ECl calibration curve 410 can be generated by applying a correction factor (CF) to certain equation parameters of the ECl reference calibration curve 406.

[0132] For example, a computing device 120 can calculate a corrected calibration curve slope (mCOrr) using Equation 1 provided above and where TTD2 = 190 minutes, TTDi =

100 minutes, DF2 = 100, DFi = 10, and a = 10:


rUcorr =— 90

[0133] In the calculation above, the variable“a” can be equal to 10 when 10 is used as the base of the log function in Equation 5 above. As previously discussed,“a” can be any positive real number other than 1.

[0134] The computing device 120 can also calculate a corrected calibration curve y-intercept (bcorr) using Equation 2 provided above, the calculated mcorr value, and the stored niavg and baVg values for ECl:

tn corr

bcorr m X b avg

avg

-90

bcorr— X 504.2

61.95

bcorr = 732.49

[0135] The value obtained by dividing mcorrby maVg (the ratio of m values) can also be considered a correction factor or CF (that is CF
example, another way of m avg

expressing Equation 2 above can be:

bcorr = CF X b avg

[0136] With the mcorr and bcorr values calculated, the concentration of the unknown strain of ECl in the target sample 104 (Conctarget) can be calculated using either Equation 3 or Equation 4 above.

[0137] For example, using Equation 3 and with DFi = 10 and TTDi = 100 minutes, the Conctarget can be calculated as:


Conctarget = 108 03 CFU/mL

Conctarget = 1.1 X 108 CFU/mL

[0138] Similarly, using Equation 4 and with DF2 = 100 and TTD2 = 190 minutes, the Conctarget can be calculated as:

Conctarget = 100

Conctarget = 108 03 CFU/mL

Conctarget = 1.1 X 108 CFU/mL

[0139] To highlight the importance of the correction steps described above, the Conctarget can also be calculated using Equations 3 and 4 but with mcorr substituted with maVg and bcorr substituted with bav :


Conctarget = 10(7 52)

Conctarget = 3.3 X 107 CFU/mL

TTR2 - bavg

Conctarget = DF2 X a mavS

ConCtarget = 100

CoilCtarget = 10(7 °7)

Conctarget = 1.2 X 107 CFU/mL

[0140] As can be seen by the concentration amounts calculated using the maVg and bav values, the concentration amount is inconsistent across the two dilutions. In addition, the improved accuracy of the correction steps is apparent when the concentration of the unknown strain of ECl in the target sample 104 or Conctarget is calculated to be

approximately 1.0 X 108 CFU/mL using other prevailing methods.

[0141] Figs. 5A-5C illustrate an example application of the methods described herein for determining the concentration of an unknown strain of an infectious agent 102 in a target sample 104 using an inter-species reference calibration curve 500. The inter-species reference calibration curve 500 can be generated from multiple calibration curves 502 (such as multiple strain- specific calibration curves) representing the growth behavior of multiple species of infectious agents.

[0142] For example, at least one of the infectious agents 202 used to generate the multiple calibration curves 502 can be of a different species from the infectious agent 102 of the unknown strain in the target sample 104. In some embodiments, the method used to determine the concentration of the unknown strain of the infectious agent 102 can begin by determining at least one of the species, the genus, the family, the order, the class, the phylum, the kingdom, and the domain of the infectious agent 102 in the target sample 104. In these and other embodiments, the computing device 120 can then select the appropriate calibration curves 502 used to generate the inter-species reference calibration curve 500 based on at least one of the species, the genus, the family, the order, the class, the phylum, the kingdom, and the domain of the infectious agent 102 in the target sample 104. For example, the target sample 104 can be determined to comprise bacteria from the phylum Proteobacteria. In this example, the computing device 120 can generate the inter- species reference calibration curve 500 using calibration curves 502 representing different types of bacteria within the phylum Proteobacteria. In another example, the target sample 104 can be determined to comprise an infectious agent 102 from the domain Bacteria. In this

example, the computing device 120 can generate the inter-species reference calibration curve 500 using calibration curves 502 representing different types of bacteria from across multiple phyla or encompassing both Gram-positive and Gram-negative bacteria.

[0143] Fig. 5A illustrates the inter-species reference calibration curve 500 plotted on the same axes as multiple calibration curves 502 of multiple infectious agent species. In addition, Table 4 below shows calibration curve slopes and calibration curve y-intercepts calculated for different strains of ECo, EAe, KPn, ECl, and SAu. For example, calibration curve slopes and calibration curve y-intercepts can be calculated for Eco_WT, EAe_WT, KPn_WT, EC1_CDC8, and SAu_WT. Table 4 below also shows that an average calibration curve slope (maVg) can be calculated for the inter-species reference calibration curve 500 by taking an average of the various calibration curve slopes. Moreover, Table 4 shows that an average calibration curve y-intercept (bav ) can be calculated for the inter-species reference calibration curve 500 by taking an average of the various calibration curve y-intercepts.

TABLE 4: Calibration Curve Parameters of Multiple Calibration Curves Across Different Species

[0144] The various calibration curve slopes and y-intercepts along with the mavg and the bav values provided in Table 4 above can be stored in a database on a memory device of the computing device 120 or stored in another database accessible to the computing device 120. The inter-species reference calibration curve 500 can be generated using Equation 5 above but with mstrain_specific and bstrain_speci ric in the equation replaced by mav and bav , respectively.

[0145] Fig. 5B illustrates two sample growth curves 502 of diluted aliquots of a target sample 104 comprising an infectious agent 102 of an unknown strain. As shown in Fig. 5B,

the first aliquot of the target sample 104 can be diluted by a dilution factor (DFi) of 1: 10 to yield a first diluted sample and the second aliquot of the target sample 104 can be diluted by a dilution factor (DF2) of 1: 100 to yield a second diluted sample. The first aliquot and the second aliquot can be diluted using a dilutive solution (such as the dilutive solution 112). Fig. 5B also illustrates that the solution characteristics of the two diluted samples can change as the amount of electro-active redox species in the samples changes due to the energy use, oxygen uptake or release, growth, or metabolism of the unknown infectious agent 102 in the diluted samples.

[0146] A predetermined ORP threshold level (Vth) can be set at -lOOmV and the time it takes the solution characteristic of each of the first diluted sample and the second diluted sample to reach this Vth can be recorded. The time it takes the first diluted sample to undertake a predetermined threshold change from 0 mV to -100 mV (also referred to as the TTDi) can be recorded. For example, Fig. 5B shows the TTDi as 180 minutes. Moreover, the time it takes the second diluted sample to undertake a predetermined threshold change from 0 mV to -100 mV (referred to as the TTD2) can be recorded. For example, Fig. 5B shows the TTD2 as 310 minutes. As shown in Fig. 5B, the sample growth curve 502 of the second diluted sample can be time shifted with respect to the first diluted sample since a more dilute sample takes longer to reach a detectable level.

[0147] Fig. 5C illustrates the inter-species reference calibration curve 500 of Fig. 5A in relation to a corrected inter-species calibration curve 504. The corrected inter-species calibration curve 504 can be used to more accurately determine a concentration of an unknown infectious agent 102 in a target sample 104 compared to the inter-species reference calibration curve 500. The corrected inter-species calibration curve 504 can be generated by applying a correction factor (CF) to certain equation parameters of the inter species reference calibration curve 500.

[0148] For example, a computing device 120 can calculate a corrected calibration curve slope (mcorr) using Equation 1 provided above and where TTD2 = 310 minutes, TTDi =

180 minutes, DF2 = 100, DFi = 10, and a = 10:


mcorr— 130

[0149] In the calculation above, the variable“a” can be equal to 10 when 10 is used as the base of the log function in Equation 5 above. As previously discussed,“a” can be any positive real number other than 1.

[0150] The computing device 120 can also calculate a corrected calibration curve y-intercept (bCOrr) using Equation 2 provided above, the calculated mcorr value, and the stored maVg and bav values:


-130

b ',corr— X 614.3

73.2

bcorr = 1090.97

[0151] The value obtained by dividing mcorrby maVg (the ratio of m values) can also be considered a correction factor or CF (that is CF example, another way of

expressing Equation 2 above can be:

bcorr— C F X b; avg

[0152] With the mcorr and bcorr values calculated, the concentration of the unknown infectious agent 102 in the target sample 104 (Conctarget) can be calculated using either Equation 3 or Equation 4 above.

[0153] For example, using Equation 3 and with DFi = 10 and TTDi = 180 minutes, the Conctarget can be calculated as:

Conctarget = 10 X 10 -130

Conctarget = 108 01 CFU/mL

Conctarget = 1.0 X 108 CFU/mL

[0154] Similarly, using Equation 4 and with DF2 = 100 and TTD2 = 310 minutes, the Conctarget can be calculated as:

Conctarget = 100

Conctarget = 108 01 CFU/mL

Conctarget = 1.0 X 108 CFU/mL

[0155] To highlight the importance of the correction steps described above, the Conctarget can also be calculated using Equations 3 and 4 but with mcorr substituted with maVg and bcorr substituted with bavg:

Conctarget

Conctarget = 10 X 10^
-73.2


Conctarget = 8.5 X 106 CFU/mL

TTR2 - bavg

Conctarget = DF2 X a mavS

ConCtarget = 100 X 10
- 73.2

ConC target = 10(6 16)

Conctarget = 1.4 X 106 CFU/mL

[0156] As can be seen by the concentration amounts calculated using the mavg and bavg values, the concentration amount is inconsistent across the two dilutions. In addition, the improved accuracy of the correction steps is apparent when the concentration of the unknown infectious agent 102 in the target sample 104 or Conctarget is calculated to be approximately 1.0 X 108 CFU/mL using other prevailing methods.

[0157] Fig. 6 illustrates one embodiment of a system 600 for determining the concentration of an infectious agent 102 in a target sample 104. It is contemplated by this disclosure, and it should be understood by one or ordinary skill in the art, that the system 600 can be used to undertake any of the steps of method 100 or method 200 described in the preceding sections.

[0158] Fig. 6 illustrates that the system 600 can comprise one or more sensors 116 fabricated or positioned on a surface of or within a substrate 602. The substrate 602 can also have a sample receiving surface 604 or port, one or more metering conduits 606, and one or more sample delivery conduits 608, defined on the surface of or within the substrate 602. The sample receiving surface 604 or port can be in fluid communication with the one or more metering conduits 606, the one or more sample delivery conduits 608, or a combination thereof. In addition, the one or more sample delivery conduits 608 can also be in fluid communication with each of the sensors 116.

[0159] The substrate 602 can be comprised of a polymeric material, a metal, a ceramic, a semiconductor material, an insulator, or a combination thereof. In one embodiment, the sample receiving surface 604 can be a flat surface for receiving the target sample 104. In other embodiments, the sample receiving surface 604 can be a concave or tapered surface of a well, divot, dish, or container. For example, the target sample 104 can be injected, pipetted, pumped, spotted, or otherwise introduced to the sample receiving surface 604.

[0160] The one or more metering conduits 606 can be channels, passageways, capillaries, tubes, parts therein, or combinations thereof for delivering the dilutive solution 112 to the target sample 104 on the sample receiving surface 604. For example, the one or more metering conduits 606 can refer to channels, passageways, capillaries, or tubes defined on the substrate 602. Also, for example, the one or more metering conduits 606 can refer to channels, passageways, capillaries, or tubes serving as part of hydraulic pump, a pneumatic pump, peristaltic pump, a vacuum or positive pressure pump, a manual or mechanical pump, a syringe pump, or a combination thereof. For example, the one or more metering conduits 606 can be microfluidic channels or tubes or channels serving as part of a vacuum system.

[0161] In some embodiments, the one or more metering conduits 606 can be configured to dilute aliquots of the target sample 104 with the dilutive solution 112 to a dilution ratio between about 1:1 to about 1 : 107. In other embodiments, the one or more metering conduits 606 can be configured to dilute aliquots of the target sample 104 to a dilution ratio beyond 1 : 107.

[0162] For example, the system 600 can be used to undertake step IB of the method 100. The one or more metering conduits 606 can be used to dilute a first aliquot of the target sample 104 by DFi to yield a first diluted sample. In addition, the one or more metering conduits 606 can also be used to dilute a second aliquot of the target sample 104 by DF2 to yield a second diluted sample.

[0163] The one or more sample delivery conduits 608 can also introduce the diluted samples to the sensors 116 such that the diluted samples are in fluid communication with at least part of the sensors 116. The sample delivery conduits 608 can refer to channels, passageways, capillaries, tubes, parts therein, or combinations thereof for delivering the diluted samples to the sensors 116. For example, the one or more sample delivery conduits 608 can introduce the first diluted sample to the first sensor and introduce the second

diluted sample to the second sensor. The sample delivery conduits 608 can serve the same function as the fluid delivery conduits 108 of Fig. 1.

[0164] As shown in the example embodiment of Fig. 6, the one or more sample delivery conduits 608 can also comprise growth media 610 or growth inducer. The growth media 610 or growth inducer can be the same growth media or growth inducer discussed in connection with Fig. 1. For example, the sample delivery conduits 608 can be covered or coated by a lyophilized or dried form of the growth media 610 or the growth inducer. In other embodiments, the sample delivery conduits 608 can contain growth media 610 or grow inducer in an aqueous form. In these and other embodiments, the dilutive solution 112 delivered by the one or more metering conduits 606 can be a saline solution, deionized water, or a combination thereof. The dilutive solution 112 can dilute the target sample 104 and deliver the diluted sample through the sample delivery conduits 608 to the sensors 116 such that the diluted samples mix with the growth media 610 en route to the sensors 116. In other embodiments not shown in the figures, at least one layer of the sensor 116 or a surface in a vicinity of the sensor 116 can be coated or covered by the growth media 610 in lyophilized or dried form and the diluted samples can mix with the growth media 610 when the diluted samples are in fluid communication with the part of the sensor 116 or part of the area covered by the growth media 610.

[0165] Although not shown in Fig. 6, the system 600 can also comprise an incubating component configured to heat the substrate 602 or portions therein, the diluted samples, or a combination thereof. For example, the incubating component can heat the diluted samples to a temperature of between about 30 °C and about 40 °C (e.g., 35 °C ± 2 °C) for a period of time.

[0166] In addition, one or more parameter analyzers 118 can also be fabricated or located on the substrate 602 and electrically or communicatively coupled to the one or more sensors 116. In other embodiments, the one or more parameter analyzers 118 can be standalone devices such as a voltmeter or a multimeter electrically coupled to the sensors 116. Moreover, one or more computing devices 120 can also be electrically or

communicatively coupled to the one or more parameter analyzers 118, the one or more sensor 116, or a combination thereof. In some embodiments, the computing device 120 and the parameter analyzer 118 can be integrated into one device.

[0167] The sensors 116 can be configured to respond to a change in a solution characteristic of the diluted samples. For example, the first sensor can be configured to detect a change in the solution characteristic of the first diluted sample and the second sensor can be configured to detect a change in the solution characteristic of the second diluted sample. In some embodiments, the sensors 116 can be oxidation reduction potential (ORP) sensors configured to respond to a change in the ORP of the diluted samples (ORP sensors will be discussed in more detail in the following sections with respect to Figs. 7 A and 7B). In other embodiments, the sensors 116 can be pH sensors configured to respond to a change in the pH of the diluted samples (pH sensors will be discussed in more detail in the following sections with respect to Figs. 8A and 8B).

[0168] The substrate 602, the sensors 116, the parameter analyzers 118, the sample receiving surface 604, the metering conduits 606, the sample delivery conduits 608, or a combination thereof can be part of a cartridge, a test strip, an integrated circuit, a micro-electro-mechanical system (MEMS) device, a microfluidic chip, or a combination thereof. In these and other embodiments, the substrate 602 can be part of a lab-on-a-chip (LOC) device. In all such embodiments, the sensors 116 can comprise components of such circuits, chips, or devices including, but not limited to, one or more transistors, gates, or other electrical components.

[0169] As shown in Fig. 6, one or more computing device 120 can be electrically or communicatively coupled to the sensors 116, the one or more parameter analyzers 118, or a combination thereof. In some embodiments, the computing device 120 can be a mobile device, a handheld device, a tablet device, a laptop or desktop computer. In these and other embodiments, the parameter analyzers 118, the sensors 116, or a combination thereof can wirelessly communicate a signal or result to computing device 120.

[0170] The computing device 120 can comprise one or more processors programmed to store and evaluate information or data received from the sensors 116, the one or more parameter analyzers 118, or a combination thereof. For example, the one or more processors of the computing device 120 can be programmed to monitor the solution characteristics of the diluted samples in fluid communication with the sensors 116. The one or more processors of the computing device 120 can undertake any of the steps IE, IF, 1G, and 1H of method 100 including determining a first time-to-detection (TTDi) representing the time it takes the solution characteristic of the first diluted sample to undertake a predetermined threshold change and determining a second time-to-detection (TTD2) representing the time it takes the solution characteristic of the second diluted sample to undertake the predetermined threshold change. In addition, the one or more processors of the computing device 120 can also calculate a corrected calibration curve slope (mcorr) using at least the TTD2, the TTDi, the DF2, and the DFi and calculate an average calibration curve slope (maVg) and an average calibration curve y-intercept (baVg) from equation parameters obtained from multiple calibration curves representing growth behavior of infectious agents of different known strains.

[0171] Moreover, the one or more processors of the computing device 120 can calculate a corrected calibration curve y-intercept (bcorr) using at least the mcorr, the mav , and the bav and determine the concentration of the infectious agent 102 in the target sample 104 using either the mcorr, the bcorr, the TTDi, and the DFi or the mcorr, the bcorr, the TTD2, and the DF2.

[0172] Although Fig. 6 shows two sensors 116 on the substrate 602, it is contemplated by this disclosure that more than two sensors 116 can be fabricated or otherwise positioned on the substrate 602. In addition, the number of sample receiving surfaces 604, metering conduits 606, and sample delivery conduits 608 can also be increased and multiple target samples 104 can be quantified simultaneously or concurrently such that the system 600 is a multiplex system.

[0173] It should be understood by one or ordinary skill in the art that the system 600 can be used to undertake the example quantification procedures detailed in Figs. 3A-3E, Figs. 4A-4E, and Figs. 5A-5C. Moreover, a variant of the system 600 having multiple sample receiving surfaces 604 or ports, metering conduits 606, and sample delivery conduits 608 can also be used to undertake the calibration steps 2A-2E of method 200 shown in Fig. 2.

[0174] Fig. 7A illustrates a schematic of one embodiment of an ORP sensor 700 used as part of the methods and systems described herein. The sensor 700 of Fig. 7A can be or refer to any of the sensors 116 depicted in Figs. 1, 2, and 6 (including any of the sensors 116 referred to as the first sensor or the second sensor). The sensor 700 can be an electrochemical cell comprising an active electrode 701 and an external reference electrode 702. In some embodiments of the sensor 700, the active electrode 701 and the external reference electrode 702 are the only electrodes of the sensor 700.

[0175] The active electrode 701 can extend from or be disposed on a substrate layer 704. The substrate layer 704 can be composed of, but is not limited to, any non-conducting material such as a polymer, an oxide, a ceramic, or a composite thereof. The

electrochemical cell can be surrounded or contained by walls 706 configured to retain a sampled solution 710. The walls 706 can be made of an inert or non-conductive material.

[0176] The sampled solution 710 can refer to any of the diluted samples or an aliquot thereof. At least part of the external reference electrode 702 can be in fluid communication or in fluid contact with the sampled solution 710. For example, the external reference electrode 702 can extend into or be immersed in the sampled solution 710. The external reference electrode 702 can also have a stable or well-known internal voltage and the sensor 700 can use the external reference electrode 702 to determine or measure a relative change in the potential of the active electrode 701. In one embodiment, the external reference electrode 702 can be a standalone probe or electrode. In other embodiments, the external reference electrode 702 can be coupled to the parameter analyzer 118. In some embodiments, multiple sensors (including but not limited to the first sensor and the second sensor) can share and use the same external reference electrode 702.

[0177] In one embodiment, the external reference electrode 702 can be a silver/silver chloride (Ag/AgCl) electrode. In other embodiments, the external reference electrode 702 can comprise a saturated calomel reference electrode (SCE) or a copper-copper (II) sulfate electrode (CSE). The external reference electrode 702 can also be a pseudo -reference electrode including any metal that is not part of the active electrode such as platinum, silver, gold, or a combination thereof; any metal oxide or semiconductor oxide material such as aluminum oxide, iridium oxide, silicon oxide; or any conductive polymer electrodes such as polypyrrole, polyaniline, polyacetylene, or a combination thereof.

[0178] The active electrode 701 can comprise multiple conductive layers (e.g., a stack of metallic layers) and a redox-active material 708 or layer such as a gold layer, a platinum layer, a metal oxide layer, a carbon layer, or a combination thereof on top of the multiple conductive layers. In some embodiments, the metal oxide layer can comprise an iridium oxide layer, a ruthenium oxide layer, or a combination thereof. The parameter analyzer 118 can be coupled to the active electrode 701 and the external reference electrode 702.

[0179] The parameter analyzer 118, the computing device 120, or a combination thereof can determine the ORP of the sampled solution 710 by measuring the potential difference between the external reference electrode 702 and the active electrode 701 instantly or over a period of time. As shown in Fig. 7A, the parameter analyzer 118 can be a voltmeter or any other type of high-impedance amplifier or sourcemeter. The voltmeter can measure a relative change in an equilibrium potential at an interface between the redox-active material 708 of the active electrode 701 and the sampled solution 710 containing electro-active redox species. The parameter analyzer 118 can also be used to apply a voltage or current to the active electrodes and the external reference electrode 702.

[0180] The solution characteristic of the sampled solution 710 can change as the amount of electro-active redox species changes due to the energy use, oxygen uptake or release, growth, or metabolism of the infectious agents in solution. For example, the amount of electro-active redox species in the sampled solution 710 can change as a result of cellular activity undertaken by the infectious agents in solution. As a more specific example, the amount of electron donors from Table 1 (e.g., the amount of energy carriers such as nicotinamide adenine dinucleotide (NADH) and flavin adenine dinucleotide (FADFh)) in the sampled solution 710 can change due to the growth or lack thereof of the infectious agents in solution. Also, as another more specific example, the amount of oxygen depleted in the sampled solution 710 can change due to the growth or lack thereof of the infectious agents in solution.

[0181] In one embodiment, the active electrode 701 can comprise a metallic layer. The metallic layer can comprise a gold layer, a platinum layer, or a combination thereof. The active electrode 701 can also comprise multiple layers comprising a semiconductor layer having a redox-active metal oxide layer, such as iridium oxide or ruthenium oxide on top of the multiple layers. In other embodiments, the active electrode 701 can comprise one or more metallic layers, one or more redox-active metal oxide layers, one or more

semiconductor layers, or any combination or stacking arrangement thereof.

[0182] Fig. 7B illustrates a schematic of another embodiment of an ORP sensor 700 used as part of the methods and systems described herein. The sensor 700 of Fig. 7B can be or refer to any of the sensors 116 depicted in Figs. 1, 2, and 6 (including any of the sensors 116 referred to as the first sensor or the second sensor). The sensor 700 can have an on-chip reference electrode 712 disposed on the substrate layer 704 in lieu of the external reference electrode 702 of Fig. 7A. In some embodiments of the sensor 700, the active electrode 701 and the on-chip reference electrode 712 are the only electrodes of the sensor 700. The parameter analyzer 118 can also be used to apply a voltage or current to the active electrodes and the on-chip reference electrode 712.

[0183] In these and other embodiments, the on-chip reference electrode 712 can be coated by a polymeric coating. For example, the on-chip reference electrode 712 can be coated by a polyvinyl chloride (PVC) coating, a perfluoro sulfonate coating (e.g.,

Nafion™), or a combination thereof.

[0184] The on-chip reference electrode 712 can serve the same purpose as the external reference electrode 702 except be fabricated on or integrated with the substrate layer 704. The on-chip reference electrode 712 can be located adjacent to or near the active electrode 701. The sensor 700 of Fig. 7B can serve the same function as the sensor 700 of Fig. 7A. Similar to the active electrode 701 of Fig. 7B, the on-chip reference electrode 712 can also be in fluid communication or communication with the sampled solution 710 retained within walls 706.

[0185] The on-chip reference electrode 712 can be comprised of a metal, a

semiconductor material, or a combination thereof. The metal of the on-chip reference electrode 712 can be covered by an oxide layer, a silane layer, a polymer layer, or a combination thereof. In another embodiment, the on-chip reference electrode 712 can be a metal combined with a metal salt such as an Ag/AgCl on-chip reference electrode. In another embodiment, the on-chip reference electrode can be a miniaturized electrode with a well-defined potential. In some embodiments, multiple sensors can share and use the same on-chip reference electrode 712. The on-chip reference electrode 712 can comprise a saturated calomel reference electrode (SCE) or a copper-copper (II) sulfate electrode (CSE). The on-chip reference electrode 712 can also comprise a pseudo-reference electrode including any metal that is not part of the active electrode such as platinum, silver, gold, or a combination thereof; any metal oxide or semiconductor oxide material such as aluminum oxide, iridium oxide, silicon oxide; or any conductive polymer electrodes such as polypyrrole, polyaniline, polyacetylene, or a combination thereof.

[0186] Fig. 8A illustrates a schematic of one embodiment of a pH sensor 800 used as part of the methods and systems described herein. The sensor 800 of Fig. 8A can be or refer to any of the sensors 116 depicted in Figs. 1, 2, and 6 (including any of the sensors 116 referred to as the first sensor or the second sensor). The sensor 800 can be or comprise an electrochemical cell comprising container walls 802, an active electrode 801positioned on a substrate layer 810, and an external reference electrode 804. The active electrode 801 can comprise a functionalization layer 806 and a conductor layer 808. The sensor 800 can be configured to receive or be in fluid contact with a solution 812. For example, the sensor 800 can receive and retain the solution 812 within the container walls 802 as shown in Fig. 8A. In other embodiments not shown in the figures but contemplated by this disclosure, one or more layers of the sensor 800 can be in fluid contact with the solution 812 even though the solution 812 is not retained within the container walls 802 of the sensor 800 or the sensor 800 has no container walls 802.

[0187] In all such embodiments, the solution 812 can be any of the diluted samples or aliquots thereof. The sensor 800 can be connected or coupled to the parameter analyzer 118. In one embodiment, the parameter analyzer 118 can be coupled to both the external

reference electrode 804 and the conductor layer 808. In other embodiments, the parameter analyzer 118 can be coupled to the external reference electrode 804, the conductor layer 808, as well as other layers. As shown in Fig. 8A, the external reference electrode 804 can extend into the solution 812.

[0188] When the parameter analyzer 118 is coupled to the external reference electrode 804, the conductor layer 808, or another layer, the parameter analyzer 118 can measure a difference in the electrical characteristic of the solution 812. The external reference electrode 804 can have a stable and well-known internal reference potential and can also act as a differential noise filter for removing electrical noise from measurements taken by the sensor 800. An operator or clinician can use this setup to determine or record a relative change in the electrical characteristic of the sensor 800 rather than having to ascertain an absolute change. An operator or clinician can also use the external reference electrode 804 to determine or record a relative difference between the electrical characteristics of multiple sensors 800. In one embodiment, the external reference electrode 804 can be a standalone probe or electrode. In other embodiments, the external reference electrode 804 can be coupled to the parameter analyzer 118 or a computing device 120 (not shown) connected to the parameter analyzer 118. The parameter analyzer 118 can also be used to apply a voltage or current to the active electrodes and the external reference electrode 804.

[0189] In one embodiment, the external reference electrode 804 can be a silver/silver chloride (Ag/AgCl) electrode. In other embodiments, the external reference electrode 804 can be, but is not limited to, a saturated calomel reference electrode (SCE) or a copper-copper (II) sulfate electrode (CSE).

[0190] The substrate layer 808 can be composed of, but is not limited to, any non conducting material such as a polymer, an oxide, a ceramic, or a composite thereof. As depicted in Fig. 8A, the conductor layer 808 can be disposed on or cover the substrate layer 810.

[0191] The conductor layer 808 can be composed of, but is not limited to, a metal, a semiconducting material, a metal/metal- salt, or a combination thereof. For example, the conductor layer 808 can be composed of, but is not limited to, silicon, gold, silver, aluminum, platinum, or a composite thereof. The conductor layer 808 can also be an organic semiconductor, a carbon nanotube, graphene, an organic conductor such as those derived from polyacetylene, polyaniline, Quinacridone, Poly(3,4-ethylenedioxythiophene) or PEDOT, PEDOT: polystyrene sulfonate (PSS), or a combination thereof. The conductor layer 808 can be composed of any conducting material which allows an electrical property change to be measured, including, but is not limited to, a voltage change, a capacitance change, a conductance change, and/or a current change measured through the conductor layer 808, the functionalization layer 806, and the solution 812 to the external reference electrode 804.

[0192] As depicted in Fig. 8A, the functionalization layer 806 can be disposed on or cover the conductor layer 808. The functionalization layer 806 can comprise oxides, silanes, DNA, proteins, antibodies, self-assembled mono layers (SAMs), oxides, buffered hydrogels, PVC, parylene, polyACE, or any other biochemically active materials. The functionalization layer 806 can be configured to facilitate the sensor 800 from interacting with ions, analytes, or other molecules or byproducts in the solution 812. For example, the functionalization layer 806 can be a pH-sensitive layer or pH-active layer.

[0193] In one example, the functionalization layer 806 can comprise hydroxyl groups which can interact with hydrogen ions (H+) in the solution 812. This interaction can generate a change in the electrical characteristic between the sensor 800 and the external reference electrode 804 as detected by the parameter analyzer 118. In one embodiment, this interaction can create a measurable change in the electrical characteristic of the sensor 800 at the interface between the solution 812 and the functionalization layer 806 or the interface between the solution 812 and the conductor layer 808.

[0194] For example, the parameter analyzer 118 can be a voltmeter and the voltmeter can detect a voltage (potential) change (AV) at or near the functionalization layer 806 exposed to the solution 812. The voltage change can be determined with respect to the external reference electrode 804 extending into or in contact with the solution 812. In this embodiment, the functionalization layer 806 and the conductor layer 808 can be considered part of a working or active electrode 801.

[0195] As depicted in Fig. 8A, the solution 812, the functionalization layer 806, and the conductor layer 808 can be surrounded by the container walls 802. The container walls 802 can be made of an inert or non-conductive material. The container walls 802 can comprise, but is not limited to, a polymeric material such as polyvinyl chloride (PVC), poly(methyl methacrylate) (PMMA), polydimethylsiloxane (PDMS), a ceramic, glass, or a combination thereof.

[0196] Fig. 8B illustrates a schematic of another embodiment of the pH sensor 800 used as part of the methods and systems described herein. The sensor 800 can be or refer to any of the sensors 116 depicted in Figs. 1, 2, and 6 (including any of the sensors 116 referred to as the first sensor or the second sensor).

[0197] In this embodiment, the sensor 800 can comprise an active electrode 814 or an indicator electrode and an on-chip reference electrode 816. In this embodiment, the active electrode 814 (i.e., the active electrode) and the on-chip reference electrode 816 can be disposed on the same substrate layer 810. The substrate layer 810 can be composed of the same material as the substrate layer 810 depicted in Fig. 8 A.

[0198] The solution 812 can flow over or be exposed to both the active electrode 814 and the on-chip reference electrode 816 simultaneously. In this embodiment, the active electrode 814 and the on-chip reference electrode 816 can be separated by a container wall 802 or container divide.

[0199] The active electrode 814 can comprise the functionalization layer 806 disposed on or covering the conductor layer 808. The functionalization layer 806 can comprise oxides, silanes, DNA, proteins, hydroxyl group, antibodies, oxides, self-assembled mono layers (SAMs), buffered hydrogels, PVC, parylene, polyACE, or any other biochemically active materials.

[0200] As shown in Fig. 8B, a passivation layer 818 can be disposed on or cover the conductor layer 808. The passivation layer 818 can be configured to prevent the on-chip reference electrode 816 from interacting with analytes, ions, or other molecules or byproducts in the solution 812. For example, the passivation layer 818 can be a pH-insensitive layer. The passivation layer 818 can comprise silanes, self-assembled monolayers (SAMs), buffered hydrogels, parylene, polyACE, or any other biochemically inert material.

[0201] In this embodiment, the parameter analyzer 118 can have a lead connection wire, such as a copper wire, connected to the conductor layer 808 of the active electrode 814 and another lead connection wire connected to the conductor layer 808 of the on-chip reference electrode 816. The parameter analyzer 118 can also be used to apply a voltage or current to the active electrodes and the on-chip reference electrode 816.

[0202] In this and other embodiments, the sensor 800 shown in Fig. 8B miniaturizes the sensor set-up shown in Fig. 8A. The on-chip reference electrode 816 obviates the need for an external reference electrode, such as the external reference electrode 804. The on-chip reference electrode 816 can also be a silver/silver chloride (Ag/AgCl) electrode. In other embodiments, the on-chip reference electrode 816 can be, but is not limited to, a saturated calomel reference electrode (SCE) or a copper-copper (II) sulfate electrode (CSE). The on-chip reference electrode 816 provides similar functionality as that of the external reference electrode 804 in this embodiment of the sensor 800. The passivation layer 818 of the on-chip reference electrode 816 prevents the conductor layer 808 covered by the passivation layer 818 from interacting with the ions, analytes, or other molecules or byproducts in the solution 812. This allows a reader or another device from being able to differentiate the electrical signals obtained by the parameter analyzer 118. In some embodiments, the passivation layer 818 can refer to an on-chip reference electrode 816 with a well-defined potential. In other embodiments, the on-chip reference electrode 816 can be without a passivation layer 818.

[0203] In one embodiment where the conductor layer 808 is used as a reference electrode, the conductor layer 808 can be a metal covered with a metal salt such as a metal chloride. In another embodiment, the conductor layer 808 can also be covered with an oxide. For example, the conductor layer 808 can be a silver/silver chloride contact. In this embodiment, the conductor layer 808 can be covered by, but is not limited to, a passivation layer 818 such as a KCL electrolyte gel or KCL solution, to prevent the conductor layer 808 from interacting with analytes, ions, or other molecules or byproducts in the solution 812 and to act as a reference electrode.

[0204] Fig. 9A illustrates a schematic of one embodiment of a sensor 900 used as part of the methods and systems described herein. The sensor 900 of Fig. 9A can be or refer to any of the sensors 116 depicted in Figs. 1, 2, and 6 (including any of the sensors 116 referred to as the first sensor or the second sensor). The sensor 900 can be or comprise an electrochemical cell having container walls 902, a first active electrode 904 and a second active electrode 906 positioned on a substrate layer 908, and an external reference electrode 910. Although two active electrodes are shown in Fig. 9A, it is contemplated by this disclosure and it should be understood by one of ordinary skill in the art that three or more active electrodes or multiple reference electrodes can be positioned on one substrate layer.

[0205] The first active electrode 904 can comprise a redox-active material 912 disposed or otherwise positioned on a conductor layer 914. The second active electrode 906 can comprise a functionalization layer 916 disposed or otherwise positioned on a conductor layer 914. In some embodiments, the functionalization layer 916 can be a pH sensitive layer. In these and other embodiments, the first active electrode 904 can serve as part of an ORP sensor and the second active electrode 906 can serve as part of a pH sensor.

[0206] The containers walls 902 of the sensor 900 can be configured to receive and retain a sampled solution 918. The container walls 902 can be made of an inert or non-conductive material. The container walls 902 can comprise, but is not limited to, a

polymeric material such as polyvinyl chloride (PVC), poly(methyl methacrylate) (PMMA), polydimethylsiloxane (PDMS), a ceramic, glass, or a combination thereof.

[0207] In other embodiments not shown in the figures but contemplated by this disclosure, one or more layers of the sensor 900 can be in fluid contact or communication with the sampled solution 918 even though the sampled solution 918 is not retained within the container walls 902 of the sensor 900 or the sensor 900 has no container walls 902. The sampled solution 918 can be any of the diluted samples described herein or aliquots thereof.

[0208] As shown in Fig. 9A, one or more parameter analyzers 118 can be coupled to both the external reference electrode 910 and the conductor layers 914 of the first active electrode 904 and the second active electrode 906. The parameter analyzer 118 can be coupled to the external reference electrode 910 and the conductor layers 914 through one or more other layers of the sensor 900. The parameter analyzer 118 can be coupled to the first active electrode 904, the second active electrode 906, the external reference electrode 910, and any other active or reference electrodes and multiplex the signal from each of the electrodes in parallel or one after the other.

[0209] At least part of the external reference electrode 910 can be in fluid

communication or in fluid contact with the sampled solution 918. As shown in Fig. 9A, at least part of the external reference electrode 910 can extend into or be immersed in the sampled solution 918.

[0210] The external reference electrode 910 can also have a stable or well-known internal voltage and can also act as a differential noise filter for removing electrical noise from measurements taken using the sensor 900. In one embodiment, the external reference electrode 910 can be a standalone probe or electrode coupled to the parameter analyzer 118. In other embodiments, the external reference electrode 910 can be integrated with the parameter analyzer 118. As shown in Fig. 9A, the first active electrode 904 and the second active electrode 906 can be coupled to and share the same external reference electrode 910. Although Fig. 9A shows the first active electrode 904 and the second active electrode 906 coupled to separate parameter analyzers 118, it is contemplated by this disclosure and it should be understood by one of ordinary skill in the art that the first active electrode 904 and the second active electrode 906 can be coupled to the same parameter analyzer 118.

[0211] In one embodiment, the external reference electrode 910 can be or comprise a silver/silver chloride (Ag/AgCl) electrode. In other embodiments, the external reference electrode 910 can be or comprise a saturated calomel reference electrode (SCE) or a

copper-copper (II) sulfate electrode (CSE). The external reference electrode 910 can also be a pseudo-reference electrode including any metal that is not part of the active electrode such as platinum, silver, gold, or a combination thereof; any metal oxide or semiconductor oxide material such as aluminum oxide, iridium oxide, silicon oxide; or any conductive polymer electrodes such as polypyrrole, polyaniline, polyacetylene, or a combination thereof.

[0212] As depicted in Fig. 9A, each of the first active electrode 904 and the second active electrode 906 can comprise at least one conductor layer 914 disposed or otherwise positioned on the substrate layer 908. The substrate layer 908 can be composed of, but is not limited to, any non-conducting material such as a polymer, an oxide, a ceramic, or a composite thereof.

[0213] The conductor layer 914 can be composed of, but is not limited to, a metal, a semiconducting material, a metal/metal- salt, or a combination thereof. For example, the conductor layer 914 can be composed of, but is not limited to, silicon, gold, silver, aluminum, platinum, or a composite thereof. The conductor layer 914 can also be an organic semiconductor, a carbon nanotube, graphene, an organic conductor such as those derived from polyacetylene, polyaniline, Quinacridone, Poly(3,4-ethylenedioxythiophene) or PEDOT, PEDOT: polystyrene sulfonate (PSS), or a combination thereof. The conductor layer 914 can be composed of any conducting material which allows an electrical property change to be measured, including, but is not limited to, a voltage change, a capacitance change, a conductance change, and/or a current change measured through the conductor layer 914, the redox-active material 912 or the functionalization layer 916, and the sampled solution 918. The conductor layer 914 can also refer to multiple conductive layers such as a stack of metallic layers. For example, the metallic layers can comprise gold layers, platinum layers, or a combination thereof.

[0214] The first active electrode 904 can comprise a redox-active material 912 or layer disposed or otherwise covering a conductor layer 914. The redox-active material 912 can comprise a gold layer, a platinum layer, a metal oxide layer, a carbon layer, or a combination thereof on top of the conductor layer 914 (or multiple conductor layers 914).

In some embodiments, the metal oxide layer can comprise an iridium oxide layer, a ruthenium oxide layer, or a combination thereof.

[0215] The parameter analyzer 118 (or another device coupled to the parameter analyzer 118, such as the computing device 120, not shown) coupled to the first active electrode 904 and the external reference electrode 910 can determine the ORP of the

sampled solution 918 by measuring the potential difference between the external reference electrode 910 and the first active electrode 904.

[0216] In some embodiments, the parameter analyzer 118 can be a voltmeter or any other type of high-impedance amplifier or sourcemeter. The parameter analyzer 118 can measure a relative change in an equilibrium potential at an interface between the redox-active material 912 and the sampled solution 918 containing the electro-active redox species. The parameter analyzer 118 can also measure a relative change in the equilibrium potential at an interface between the conductor layer 914 and the sampled solution 918 containing the electro-active redox species. The change in the equilibrium potential can be measured with respect to the external reference electrode 910. The parameter analyzer 118 can also be used to apply a voltage or current to the external reference electrode 910 or the active electrodes.

[0217] The solution characteristic of the sampled solution 918 can change as the amount of electro-active redox species changes due to the energy use, oxygen uptake or release, growth, or metabolism of the infectious agents in solution. For example, the amount of electro-active redox species in the sampled solution 918 can change as a result of cellular activity undertaken by the infectious agents in solution. As a more specific example, the amount of electron donors (e.g., the amount of energy carriers such as nicotinamide adenine dinucleotide (NADH) and flavin adenine dinucleotide (FADFh)) in the sampled solution 918 can change due to the growth or lack thereof of the infectious agents in solution. Also, as another more specific example, the amount of oxygen depleted in the sampled solution 918 can change due to the growth or lack thereof of the infectious agents in solution.

[0218] The second active electrode 906 can comprise a functionalization layer 916 disposed or otherwise covering a conductor layer 914. The functionalization layer 916 can comprise oxides, silanes, DNA, proteins, antibodies, self-assembled mono layers (SAMs), oxides, buffered hydrogels, PVC, parylene, polyACE, or any other biochemically active materials. The functionalization layer 916 can be a pH-sensitive layer or pH-active layer configured to interact with ions, analytes, or other molecules or byproducts in the sampled solution 918. For example, the functionalization layer 916 can comprise hydroxyl groups which can interact with hydrogen ions (H+) in the sampled solution 918.

[0219] The parameter analyzer 118 (or another device coupled to the parameter analyzer 118, such as the computing device 120, not shown) coupled to the second active electrode 906 and the external reference electrode 910 can determine the pH of the sampled solution 918 by measuring the potential difference between the external reference electrode 910 and the second active electrode 906.

[0220] The parameter analyzer 118 can measure a relative change in an equilibrium potential at an interface between the functionalization layer 916 and the sampled solution 918 containing the ions, analytes, or other molecules. The parameter analyzer 118 can also measure a relative change in the equilibrium potential at an interface between the conductor layer 914 and the sampled solution 918 containing the ions, analytes, or other molecules. The solution characteristic of the sampled solution 918 can change as the amount of ions, analytes, or other molecules changes due to the energy use, oxygen uptake or release, growth, or metabolism of the infectious agents in solution. For example, the amount of hydrogen ions (H+) in the sampled solution 918 can change as a result of cellular activity undertaken by the infectious agents in solution. The change in the equilibrium potential can be measured with respect to the external reference electrode 910. In these instances, what is measured by the parameter analyzer 118 (or the computing device 120 coupled to the parameter analyzer 118, not shown) is a relative change in the electrical characteristic of the sensor 900.

[0221] Fig. 9B illustrates a schematic of another embodiment of the sensor 900 used as part of the methods and systems described herein. The sensor 900 of Fig. 9B can be or refer to any of the sensors 116 depicted in Figs. 1, 2, and 6 (including any of the sensors 116 referred to as the first sensor or the second sensor).

[0222] The sensor 900 can be or comprise an electrochemical cell having container walls 902, a first active electrode 904 and a second active electrode 906 positioned on a substrate layer 908, and an on-chip reference electrode 920 positioned on the same substrate layer 908. Although two active electrodes are shown in Fig. 9B, it is

contemplated by this disclosure and it should be understood by one of ordinary skill in the art that three or more active electrodes or multiple reference electrodes can be positioned on one substrate layer.

[0223] The container walls 902, the first active electrode 904, the second active electrode 906, and the substrate layer 908 of Fig. 9B can be the same as the container walls 902, the first active electrode 904, the second active electrode 906, and the substrate layer 908, respectively, of Fig. 9A. The sampled solution 918 can be in fluid communication or otherwise exposed to the on-chip reference electrode 920, the first active electrode 904, and the second active electrode 906 at the same time.

[0224] Although not shown in Fig. 9B, a passivation layer can be disposed on or cover the on-chip reference electrode 920. The passivation layer can be configured to prevent the on-chip reference electrode 920 from interacting with redox-active species, analytes, ions, or other molecules in the sampled solution 918. For example, the passivation layer can be a pH-insensitive layer. The passivation layer can comprise silanes, self-assembled monolayers (SAMs), buffered hydrogels, parylene, poly ACE, or any other biochemically inert material.

[0225] In this embodiment, the parameter analyzer 118 can have a lead connection wire, such as a copper wire, coupled to the conductor layers 914 of the active electrodes and another lead connection wire connected to the on-chip reference electrode 920. The parameter analyzer 118 can be coupled to the first active electrode 904, the second active electrode 906, the on-chip reference electrode 920, and any other active or reference electrodes and multiplex the signal from each of the electrodes in parallel or one after the other. The parameter analyzer 118 can also be used to apply a voltage or current to the on-chip reference electrode 920 or the active electrodes.

[0226] In this and other embodiments, the sensor 900 shown in Fig. 9B miniaturizes the sensor set-up shown in Fig. 9A. The on-chip reference electrode 920 obviates the need for an external reference electrode, such as the external reference electrode 910. The on-chip reference electrode 920 can also be a silver/silver chloride (Ag/AgCl) electrode. In other embodiments, the on-chip reference electrode 920 can be, but is not limited to, a saturated calomel reference electrode (SCE) or a copper-copper (II) sulfate electrode (CSE). The on-chip reference electrode 920 provides similar functionality as that of the external reference electrode 910.

[0227] In one embodiment, a conductor layer 914 can be used as an on-chip reference electrode 920. The conductor layer 914 serving as the on-chip reference electrode 920 can be a metal covered with a metal salt such as a metal chloride. In another embodiment, the conductor layer 914 serving as the on-chip reference electrode 920 can also be covered with an oxide. For example, the conductor layer 914 can be a silver/silver chloride contact. In some embodiments, the conductor layer 914 can be covered by a passivation layer such as a KCL electrolyte gel or KCL solution to prevent the conductor layer 914 from interacting with redox-active species, analytes, ions, or other molecules in the sampled solution 918 and to act as a reference electrode.

[0228] Each of the individual variations or embodiments described and illustrated herein has discrete components and features which may be readily separated from or

combined with the features of any of the other variations or embodiments. Modifications may be made to adapt a particular situation, material, composition of matter, process, process act(s) or step(s) to the objective(s), spirit or scope of the present invention.

[0229] Methods recited herein may be carried out in any order of the recited events that is logically possible, as well as the recited order of events. For example, the flowcharts or process flows depicted in the figures do not require the particular order shown to achieve the desired result. Moreover, additional steps or operations may be provided or steps or operations may be eliminated to achieve the desired result.

[0230] It will be understood by one of ordinary skill in the art that all or a portion of the methods disclosed herein may be embodied in a non-transitory machine readable or accessible medium comprising instructions readable or executable by a processor or processing unit of a computing device or other type of machine.

[0231] Furthermore, where a range of values is provided, every intervening value between the upper and lower limit of that range and any other stated or intervening value in that stated range is encompassed within the invention. Also, any optional feature of the inventive variations described may be set forth and claimed independently, or in combination with any one or more of the features described herein.

[0232] All existing subject matter mentioned herein (e.g., publications, patents, patent applications and hardware) is incorporated by reference herein in its entirety except insofar as the subject matter may conflict with that of the present invention (in which case what is present herein shall prevail). The referenced items are provided solely for their disclosure prior to the filing date of the present application. Nothing herein is to be construed as an admission that the present invention is not entitled to antedate such material by virtue of prior invention.

[0233] Reference to a singular item, includes the possibility that there are plural of the same items present. More specifically, as used herein and in the appended claims, the singular forms“a,”“an,”“said” and“the” include plural referents unless the context clearly dictates otherwise. It is further noted that the claims may be drafted to exclude any optional element. As such, this statement is intended to serve as antecedent basis for use of such exclusive terminology as“solely,”“only” and the like in connection with the recitation of claim elements, or use of a“negative” limitation. Unless defined otherwise, all technical and scientific terms used herein have the same meaning as commonly understood by one of ordinary skill in the art to which this invention belongs.

[0234] This disclosure is not intended to be limited to the scope of the particular forms set forth, but is intended to cover alternatives, modifications, and equivalents of the variations or embodiments described herein. Further, the scope of the disclosure fully encompasses other variations or embodiments that may become obvious to those skilled in the art in view of this disclosure. The scope of the present invention is limited only by the appended claims.