# US 2014/0193824 A1 · High-Resolution Clonal Typing of Escherichia coli

> Agents: this data is available as JSON from the patentgrep API and MCP server — see https://patentgrep.com/llms.txt

- Number: US 2014/0193824 A1
- Document ID: US20140193824A1
- Status: Published application
- Kind: A1
- Application number: 14/146,427
- Filed: 2014-01-02
- Published: 2014-07-10
- Earliest claimed: 2013-01-04
- Inventors: Evgeni V. SOKURENKO; James R. JOHNSON; Scott WEISSMAN; Veronika TCHESNOKOVA
- Web page: https://patentgrep.com/patent/US20140193824A1

## CPC

- C12Q 1/689: for bacteria
- C12Q 2600/106: Pharmacogenomics, i.e. genetic variability in individual responses to drugs and drug metabolism
- 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

## Abstract

The present invention provides methods and compositions for high-resolution clonal typing of Escherichia coli.

## Claims

### Claim 1

A method of typing Escherichia coli in a sample comprising:
(a) determining a nucleic acid sequence in the sample of Escherichia coli (E. coli) type 1 fimbrial adhesion (fimH) gene and a further E. coli gene selected from the group consisting of fumC, adk, gyrB, icd, mdh, purA, and recA to identify a clonotype of the sample; and
(b) typing E. coli present in the sample based on the clonotype.

### Claim 2 (depends on 1)

The method of claim 1, wherein the sample is a biological sample from a subject, and wherein the typing indicates presence of antibiotic resistant E. coli in the subject, or is used to diagnose or prognose a disease state in the subject.

### Claim 3 (depends on 2)

The method of claim 2, wherein the typing indicates that the subject is infected with antibiotic resistant E. coli.

### Claim 4 (depends on 2)

The method of claim 2, wherein the subject is at risk of having a urinary tract infection, and wherein the typing is used to diagnose a urinary tract infection in the subject.

### Claim 5 (depends on 2)

The method of claim 2, wherein the subject is at risk of having sepsis, and wherein the typing is used to diagnose sepsis in the subject.

### Claim 6 (depends on 2)

The method of claim 2, wherein the subject has a urinary tract infection, and wherein the typing is used to prognose the urinary tract infection in the subject.

### Claim 7 (depends on 2)

The method of claim 2, wherein the subject has sepsis, and wherein the typing is used to prognose the sepsis in the subject.

### Claim 8 (depends on 3)

The method of claim 3, wherein the typing indicates efficacy of an antibiotic treatment for the subject.

### Claim 9 (depends on 8)

The method of claim 8, wherein the typing indicates efficacy of ampicillin (AMP), tetracycline (TET), ampicillin-sulbactam (A/S), trimethoprimsulfamethoxazole (T/S), amoxicillin-clavulanate (A/K), cefazolin (CZ), ciprofloxacin (CIP), gentamicin (GM), nitrofurantoin (NIT), ceftriaxone (CTR) and/or piperacillin-tazobactam (PTZ) in the subject.

### Claim 10 (depends on 2)

The method of claim 2, wherein the typing is carried out after the subject has undergone treatment for the disease state or the infection with antibiotic resistant E. coli, and wherein the typing indicates efficacy of the treatment.

### Claim 11 (depends on 2)

The method of claim 2, wherein the biological sample is selected from the group consisting of urine, blood, wound, tissue, saliva, sputum, feces, spinal fluid, plasma, peritoneal fluid, ascites, pleural fluid, joint fluid, abscess material, pus, tracheal secretions, bile, exudate, corneal scraping, bone, drainage and biopsy material.

### Claim 12 (depends on 2)

The method of claim 2, wherein the biological sample is urine.

### Claim 13 (depends on 1)

The method of claim 1, wherein the further E. coli gene is fumC.

### Claim 14 (depends on 1)

The method of claim 1, wherein determining the fimH gene nucleic acid sequence comprises amplifying and determining a sequence of a portion of the fimH gene, wherein the portion of the fimH gene is amplified by an oligonucleotide primer pair consisting of 5′-CACTCAGGGAACCATTCAGGCA-3′ (SEQ ID NO: 01) and 5′-CTTATTGATAAACAAAAGTCAC-3′ (SEQ ID NO: 02).

### Claim 15 (depends on 14)

The method of claim 14, wherein determining the fumC gene nucleic acid sequence comprises amplifying and determining a sequence of a portion of the fumC gene, wherein the portion of the fumC gene is amplified by an oligonucleotide primer pair that amplifies a fumC fragment of 500 nucleotides or less.

### Claim 16 (depends on 1)

The method of claim 1, wherein determining the nucleic acid sequences comprises quantitative polymerase chain reaction (qPCR).

### Claim 17

A composition consisting of between 2-5 oligonucleotide primer pairs, wherein:
(a) a first primer pair selectively amplifies a region of a fimH gene; and
(b) a second primer pair selectively amplifies a region of a gene selected from the group consisting of fumC, adk, gyrB, icd, mdh, purA, and recA.

### Claim 18 (depends on 17)

The composition of claim 17, wherein the first primer pair consists of 5′-CACTCAGGGAACCATTCAGGCA-3′ (SEQ ID NO: 01) and 5′-CTTATTGATAAACAAAAGTCAC-3′ (SEQ ID NO: 02).