Predictive diagnostics for Escherichia coli infections based on the clonal association of antimicrobial resistance and clinical outcome

Veronika Tchesnokova, Mariya Billig, Sujay Chattopadhyay, Elena Linardopoulou, Pavel Aprikian, Pacita L. Roberts, Veronika Skrivankova, Brian Johnston, Alena Gileva, Irina Igusheva, Angus Toland, Kim Riddell, Peggy Rogers, Xuan Qin, Susan Butler-Wu, Brad T. Cookson, Ferric C. Fang, Barbara Kahl, Lance B. Price, Scott J. WeissmanAjit Limaye, Delia Scholes, James R. Johnson, Evgeni V. Sokurenko

Research output: Contribution to journalArticlepeer-review

55 Scopus citations


The ability to identify bacterial pathogens at the subspecies level in clinical diagnostics is currently limited. We investigated whether splitting Escherichia coli species into clonal groups (clonotypes) predicts antimicrobial susceptibility or clinical outcome. A total of 1,679 extraintestinal E. coli isolates (collected from 2010 to 2012) were collected from one German and 5 U.S. clinical microbiology laboratories. Clonotype identity was determined by fumC and fimH (CH) sequencing. The associations of clonotype with antimicrobial susceptibility and clinical variables were evaluated. CH typing divided the isolates into>200 CH clonotypes, with 93% of the isolates belonging to clonotypes with≥2 isolates. Antimicrobial susceptibility varied substantially among clonotypes but was consistent across different locations. Clonotype-guided antimicrobial selection significantly reduced "drug-bug" mismatch compared to that which occurs with the use of conventional empirical therapy. With trimethoprim-sulfamethoxazole and fluoroquinolones, the drug-bug mismatch was predicted to decrease 62% and 78%, respectively. Recurrent or persistent urinary tract infection and clinical sepsis were significantly correlated with specific clonotypes, especially with CH40-30 (also known as H30), a recently described clonotype within sequence type 131 (ST131). We were able to clonotype directly from patient urine samples within 1 to 3 h of obtaining the specimen. In E. coli, subspecies-level identification by clonotyping can be used to significantly improve empirical predictions of antimicrobial susceptibility and clinical outcomes in a timely manner.

Original languageEnglish (US)
Pages (from-to)2991-2999
Number of pages9
JournalJournal of Clinical Microbiology
Issue number9
StatePublished - Sep 2013
Externally publishedYes

ASJC Scopus subject areas

  • Microbiology (medical)


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