A Novel 7-single nucleotide polymorphism-based clonotyping test allows rapid prediction of antimicrobial susceptibility of extraintestinal Escherichia coli directly from urine specimens

Veronika Tchesnokova, Hovhannes Avagyan, Mariya Billig, Sujay Chattopadhyay, Pavel Aprikian, Diana Chan, Julietta Pseunova, Elena Rechkina, Kim Riddell, Delia Scholes, Ferric C. Fang, James R. Johnson, Evgeni V. Sokurenko

Research output: Contribution to journalArticlepeer-review

13 Scopus citations

Abstract

Background. Escherichia coli is a highly clonal pathogen. Extraintestinal isolates belong to a limited number of genetically related groups, which often exhibit characteristic antimicrobial resistance profiles. Methods. We developed a rapid clonotyping method for extraintestinal E coli based on detection of the presence or absence of 7 single nucleotide polymorphisms (SNPs) within 2 genes (fumC and fimH). A reference set of 2559 E coli isolates, primarily of urinary origin, was used to predict the resolving power of the 7-SNP-based typing method, and 582 representative strains from this set were used to evaluate test robustness. Results. Fifty-four unique SNP combinations ("septatypes") were identified in the reference strains. These septatypes yielded a clonal group resolution power on par with that of traditional multilocus sequence typing. In 72% of isolates, septatype identity predicted sequence type identity with at least 90% (mean, 97%) accuracy. Most septatypes exhibited highly distinctive antimicrobial susceptibility profiles. The 7-SNP-based test could be performed with high specificity and sensitivity using single or multiplex conventional polymerase chain reaction (PCR) and quantitative PCR. In the latter format, E coli presence and septatype identity were determined directly in urine specimens within 45 minutes with bacterial loads as low as 102 colony-forming units/mL and, at clinically significant bacterial loads, with 100% sensitivity and specificity. Conclusion. 7-SNP-based typing of E coli can be used for both epidemiological studies and clinical diagnostics, which could greatly improve the empirical selection of antimicrobial therapy.

Original languageEnglish (US)
Article numberofw002
JournalOpen Forum Infectious Diseases
Volume3
Issue number1
DOIs
StatePublished - Jan 1 2016

Bibliographical note

Funding Information:
Financial support. This material was supported by the National Institutes of Health (grant nos. R01AI106007 [to E. V. S.] and R41AI116114 [to ID Genomics, Inc]) and the Office of Research and Development, Medical Research Service, Department of Veterans Affairs (grant no. 1 I01 CX000192 01; to J. R. J.).

Keywords

  • Antibiotic resistance
  • Clonal typing
  • Escherichia coli
  • Personal therapy
  • Point-of-care testing

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