# US 2019/0376111 A1 · Antimicrobial cartridges and processes for multiplexed antimicrobial susceptibility testing

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- Number: US 2019/0376111 A1
- Document ID: US20190376111A1
- Status: Published application
- Kind: A1
- Application number: 16/435,184
- Filed: 2019-06-07
- Published: 2019-12-12
- Earliest claimed: 2018-06-08
- Assignees: Selux Diagnostics, Inc.
- Applicants: Selux Diagnostics, Inc.
- Inventors: Eric Stern; Kelly Flentie; Aleksandar Vacic; Frederick P. Floyd; Sarah A. Scott
- Web page: https://patentgrep.com/patent/US20190376111A1

## CPC

- C12Q 1/18: Testing for antimicrobial activity of a material
- B01L 3/5085: {for multiple samples, e.g. microtitration plates}
- C12Q 1/025: {for testing or evaluating the effect of chemical or biological compounds, e.g. drugs, cosmetics (antimicrobial activity C12Q1/18)}
- C12Q 1/04: Determining presence or kind of microorganism; Use of selective media for testing antibiotics or bacteriocides; Compositions containing a chemical indicator therefor {(C12Q1/6897 takes precedence)}
- C12Q 1/06: Quantitative determination
- B01L 2200/16: Reagents, handling or storing thereof
- C12Q 2545/101: with an internal standard/control
- C12Q 2547/10: the purpose being preventing contamination
- C12Q: MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS (immunoassay G01N33/53); COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
- B01L: CHEMICAL OR PHYSICAL LABORATORY APPARATUS FOR GENERAL USE

## Abstract

The present invention provides, among other things, cartridges for multiplexed antimicrobial susceptibility testing (AST), single cartridges useful for both AST and quality control of AST, and systems and methods relating thereto.

## Claims

### Claim 1

A cartridge for performing antimicrobial susceptibility testing (AST) of microorganisms derived from human samples and/or quality control (QC) microorganisms, comprising:
(a) a first plurality of reservoirs comprising at least 8, 10, 12, 14, 16, 18, 20, 22 or 25 different antimicrobials, a plurality of antimicrobials being present at a plurality of different amounts or concentrations across different reservoirs, thereby defining a dilution series; and
(c) an arrangement of a plurality of these dilution series into “QC blocks,” such that each block comprises a plurality of antimicrobials that may utilize the same QC microorganism.

### Claim 2 (depends on 1)

The cartridge of claim 1, comprising at least 96 or at least 384 reservoirs.

### Claim 3 (depends on 1)

The cartridge of claim 1, wherein one or more dilution series of antimicrobials spans one or more QC blocks.

### Claim 4 (depends on 1)

The cartridge of claim 1, wherein a plurality of antimicrobial dilution series comprise sufficient dilution extents to include a minimum inhibitory concentration (MIC) of the indicated QC organism.

### Claim 5 (depends on 1)

The cartridge of claim 1, wherein each dilution series includes at least one concentration below the lower of:
a) a lowest clinical breakpoint for which the antimicrobial has an indication or
b) the lower end of a QC range for the indicated QC microorganism.

### Claim 6

(canceled)

### Claim 7

(canceled)

### Claim 8

(canceled)

### Claim 9 (depends on 1)

The cartridge of claim 1, wherein each dilution series includes at least one concentration above the higher of the highest clinical breakpoint for which the antimicrobial has an indication and the higher end of the QC range for the organism of the QC block.

### Claim 10

(canceled)

### Claim 11

(canceled)

### Claim 12

(canceled)

### Claim 13 (depends on 1)

The cartridge of claim 1, wherein a range of predicted MICs of the antimicrobial for a patient sample are not identical to a range of predicted MICs of the antimicrobial for a QC organism.

### Claim 14 (depends on 1)

The cartridge of claim 1, wherein two or more reservoirs of the cartridge comprise a sufficient quantity of an antimicrobial compound to inhibit the growth of a plurality of gram-negative microorganisms.

### Claim 15 (depends on 14)

The cartridge of claim 14, wherein the antimicrobial compound present at high concentration is a carbapenem.

### Claim 16 (depends on 1)

The cartridge of claim 1, comprising at least one sufficient growth reservoir in each QC block of the panel.

### Claim 17 (depends on 1)

The cartridge of claim 1, comprising two orthogonal axes defining first and second directions.

### Claim 18 (depends on 17)

The cartridge of claim 17, wherein the dilution series for each of the plurality of antimicrobials are oriented in the first direction and wherein a microorganism sample is inoculated into the cartridge in the second direction.

### Claim 19 (depends on 17)

The cartridge of claim 17, wherein the dilution series for each of the plurality of antimicrobials are oriented in the first direction and wherein a microorganism sample is inoculated into the cartridge in the first direction.

### Claim 20 (depends on 18)

The cartridge of claim 18, wherein a plurality of the dilution series are oriented in the first direction and each QC block comprises a plurality of dilution series which are adjacent to each other across the second direction.

### Claim 21 (depends on 19)

The cartridge of claim 19, wherein a plurality of the dilution series are oriented in the first direction and each QC block comprises a plurality of dilution series which are adjacent to each other across the second direction.

### Claim 22 (depends on 17)

The cartridge of claim 17, wherein the dilution series for each of the plurality of antimicrobials are oriented in the first direction, and a microorganism sample is inoculated in the first direction.

### Claim 23 (depends on 1)

The cartridge of claim 1, in which one or more of the antimicrobials is selected from a list consisting of: Amikacin, Amikacin-fosfomycin, Amoxicillin, Amoxicillin-clavulanate, Ampicillin, Ampicillin-sulbactam, Azithromycin, Azithromycin-Avibactam, Azlocillin, Aztreonam, Aztreonam-avibactam, Besifloxacin, Biapenem, Cadazolid, Carbenicillin, Cefaclor, Cefamandole, Cefazolin, Cefdinir, Cefditoren, Cefepime, Cefepime-tazobactam, Cefetamet, Cefiderocol, Cefixime, Cefmetazole, Cefonicid, Cefoperazone, Cefotaxime, Cefotetan, Cefoxitin, Ceftolozane-tazobactam, Cefpodoxime, Cefprozil, Ceftaroline, Ceftaroline-avibactam, Ceftazidime, Ceftazidime-avibactam, Ceftibuten, Ceftizoxime, Ceftobiprole, Ceftolozane-tazobactam, Ceftriaxone, Cefuroxime, Cephalothin, Chloramphenicol, Cinoxacin, Ciprofloxacin, Clarithromycin, Clinafloxacin, Clindamycin, Colistin, Dalbavancin, Daptomycin, Delafloxacin, Dirithromycin, Doripenem, Doxycycline, Enoxacin, Eravacycline, Ertapenem, Erythromycin, Faropenem, Fidaxomicin, Finafloxacin, Fleroxacin, Fosfomycin, Fusidic acid, Garenoxacin, Gatifloxacin, Gemifloxacin, Gentamicin, Gepotidacin, Grepafloxacin, Iclaprim, Imipenem, Imipenem-Relebactam, Kanamycin, Lefamulin, Levofloxacin, Levonadifloxacin, Linezolid, Linopristin-flopristin, Lomefloxacin, Loracarbef, Mecillinam, Meropenem, Methicillin, Mezlocillin, Minocycline, Moxalactam, Moxifloxacin, Nafcillin, Nalidixic acid, Netilmicin, Nitrofurantoin, Norfloxacin, Ofloxacin, Omadacycline, Oritavancin, Oxacillin, Penicillin, Piperacillin, Piperacillin-tazobactam, Plazomicin, Polymyxin B, Quinupristin-dalfopristin, Razupenem, Rifampin, Solithromycin, Sparfloxacin, Sulfisoxazole, Sulopenem, Tedizolid, Teicoplanin, Televancin, Telithromycin, Tetracycline, Ticarcillin, Ticarcillin-clavulanate, Tigecycline, Tobramycin, Trimethoprim, Trimethoprim-sulfamethoxazole, Trospectomycin, Vancomycin, Aculeacin A, Amphotericin B, Caspofungin, Clotrimazole, Fluconazole, Flucytosine, 5-Fluorocytosine, Griseofulvin, Itraconazole, Ketoconazole, Nystatin, Sordarin, Terbinafine, Vaborbactam-meropenem, Voriconazole and a salt or hydrate form thereof.

### Claim 24 (depends on 1)

The cartridge of claim 1, wherein one or more QC organisms are selected from:
Staphylococcus aureus ssp. aureus (ATCC 29213);
Enterococcus faecalis (ATCC 29212); Escherichia coli (ATCC 25922);
Klebsiella pneumoniae ssp. pneumoniae (ATCC 700603);
Klebsiella pneumoniae (ATCC BAA2814);
Pseudomonas aeruginosa (ATCC 27853); E. faecalis (ATCC 51299); S. aureus (BAA-1708); S. aureus (BAA-977); S. aureus (ATCC 43300); Streptococcus pneumoniae (ATCC 49619) and Trichothecium plasmoparae (ATCC 13353).

### Claim 25

(canceled)

### Claim 26

(canceled)

### Claim 27

(canceled)

### Claim 28

(canceled)

### Claim 29

(canceled)

### Claim 30

(canceled)

### Claim 31

A method of performing AST or providing quality control (QC) for an AST with a cartridge comprising at least 96 or at least 384 reservoirs and at least 8 unique antimicrobials, each present in a plurality of concentrations defining a dilution series that spans both an expected clinical breakpoint range and an expected QC organism breakpoint range, the method comprising:
inoculating the cartridge with either a patient-derived sample comprising a microorganism or at least one QC organism for an antimicrobial present on the cartridge;
incubating the cartridge under conditions promoting microorganism growth for a period between 2 and 24 hours; and
performing one or more assays to determine, for the test sample or QC organism, a minimum inhibitory concentration (MIC) for a plurality of antimicrobials on the cartridge.

### Claim 32 (depends on 31)

The method of claim 31, wherein:
a) if the cartridge is inoculated with a patient-derived sample, the step of determining the MICs for the test sample comprises comparing microorganism growth at antimicrobial concentrations within the clinical breakpoint range; and
b) if the cartridge is inoculated with a QC organism, the step of determining the MICs for the QC organism comprises comparing QC organism growth at antimicrobial concentrations within the expected QC range.

### Claim 33 (depends on 31)

The method of claim 31, wherein each antimicrobial dilution series is replicated two or more times and the cartridge is inoculated with two or more patient derived samples.

### Claim 34 (depends on 31)

The method of claim 31, wherein the cartridge is inoculated with a patient-derived sample comprising a gram-negative microorganism, and at least two reservoirs in the cartridge are inoculated at a higher concentration than the other reservoirs of the cartridge.

### Claim 35

(canceled)

### Claim 36 (depends on 31)

The method of claim 31, further comprising the step of comparing the MIC of the antimicrobial for the QC organism to a reference range and, if the MIC is not within the reference range, signaling to a user of the AST system that the MIC for the antimicrobial is out of range.

### Claim 37

(canceled)

### Claim 38

(canceled)

### Claim 39

(canceled)

### Claim 40

(canceled)

### Claim 41 (depends on 1)

A kit for performing antimicrobial susceptibility testing (AST), comprising
a cartridge according to claim 1; and
instructions for performing:
(a) an AST method comprising the steps of:
inoculating the cartridge with a patient derived sample; and
assessing, based on a comparison of cell growth in differing antimicrobial concentrations, one of a minimum inhibitory concentration (MIC) of an antimicrobial, and a susceptibility to an antimicrobial; and
(b) a quality control (QC) method comprising the steps of:
inoculating the cartridge with at least one QC organism specified for an antimicrobial present on the cartridge; and
assessing, based on a comparison of cell growth in differing antimicrobial concentrations and a normal range for the QC organism, whether a MIC of an antimicrobial is within the normal range for the QC organism.

### Claim 42 (depends on 41)

The kit of claim 41 wherein the AST method is automated.

### Claim 43 (depends on 41)

The kit of claim 41 wherein the dilution series are oriented in the same direction such that the inoculation of the cartridge with the patient derived sample does not cause contamination within the cartridge.

### Claim 44 (depends on 41)

The kit of claim 41 wherein a plurality of QC organisms are used to provide quality control for the antimicrobials present on the cartridge, wherein a plurality of different wells in the cartridge are inoculated with the plurality of QC organisms simultaneously.