Global molecular epidemiology of carbapenem-resistant Escherichia coli (2002–2017)

Brian D Johnston, Paul Thuras, Stephen B Porter, Melissa Anacker, Brittany VonBank, Paula Snippes Vagnone, Medora Witwer, Mariana Castanheira, James R Johnson

Research output: Contribution to journalArticlepeer-review

12 Scopus citations


The emergence of carbapenem-resistant (CR) Escherichia coli obliges an assessment of such strains’ molecular epidemiology. Accordingly, we characterized in detail a globally distributed collection of CR E. coli isolates, then explored for associations between geographical origin and bacterial traits, and between different bacterial traits. We used established PCR-based assays and broth microdilution MIC determinations to characterize 343 global CR (i.e., non-susceptible to ≥ 1 carbapenem) extraintestinal E. coli isolates (2002–2017) for diverse molecular traits—including phylogroups, sequence types (STs), beta-lactamase genes, and 51 virulence genes—and susceptibility to 12 relevant antimicrobial agents. The study population was tremendously diverse according to all assessed variables. Nonetheless, certain geographically aligned, unifying themes emerged. These included an association of an Asia/West Pacific origin with non-B2/D/F phylogroups and STs, lower molecularly inferred virulence, more extensive resistance, and specific resistance genes (notably, metallo-beta-lactamases). Likewise, U.S. isolates from the central region, vs. other regions, were more virulent-appearing and more often from phylogroup B2 and ST131, but less extensively resistant and more often carbapenemase-gene negative. The global CR E. coli population is highly diverse according to multiple characteristics and varies significantly by geographical region. This predictably will pose challenges for prevention and management, and obliges ongoing surveillance.

Original languageEnglish (US)
JournalEuropean Journal of Clinical Microbiology and Infectious Diseases
Early online dateJul 19 2021
StatePublished - Jul 19 2021

Bibliographical note

Funding Information:
This work was supported in part by investigator-initiated grants from Allergan, Cipla/Achaogen, Melinta, Merck, Shionogi, and Tetraphase. It was also supported by Office of Research and Development, Department of Veterans Affairs. The sponsors had no role in study design, data collection, data analysis, writing the manuscript, or the decision to publish.

Publisher Copyright:
© 2021, This is a U.S. government work and not under copyright protection in the U.S.; foreign copyright protection may apply.


  • Antimicrobial resistance
  • Beta lactamases
  • CMY-2
  • CTX-M
  • Carbapenem resistance
  • Escherichia coli
  • Fluoroquinolone resistance
  • KPC
  • Molecular epidemiology
  • NDM
  • OXA-48
  • ST131
  • Sequence types


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