Rapid Emergence, Subsidence, and Molecular Detection of Escherichia coli Sequence Type 1193-fimH64 (ST1193-H64), a New Disseminated Multidrug-resistant Commensal and Extraintestinal Pathogen

Abstract

Escherichia coli sequence type ST1193 is an emerging multidrug-resistant pathogen. We performed longitudinal and cross-sectional surveillance for ST1193 among clinical and fecal E. coli isolates from Minneapolis Veterans Affairs Medical Center (VAMC) patients and their household members, other Minnesota centers, and national VAMCs, and compared these ST1193 isolates with archival human and canine ST1193 isolates from Australia (2008). We also developed and validated extensively a novel multiplex PCR assay for ST1193 and its characteristic fimH64 (type-1 fimbriae adhesin) allele. We found that ST1193-H64, which was uniformly fluoroquinolone-resistant, appeared to emerge in the USA in a geographically staggered fashion beginning around 2011. Its prevalence among clinical and fecal E. coli isolates at the Minneapolis VAMC rose rapidly beginning in 2013 and peaked in early 2017, then plateaued or declined. In comparison with other ST14 complex (STc14) isolates, ST1193-H64 isolates were more extensively multidrug-resistant, whereas their virulence genotypes were less extensive, but included (uniquely) K1 capsule and fimH64. Pulsed-field gel electrophoresis separated ST1193-H64 isolates from other STc14 isolates and showed genetic commonality between archival Australian vs. recent United States isolates, fecal vs. clinical isolates, and human vs. canine isolates. Three main ST1193 pulsotypes differed significantly for resistance profile and capsular type; emergent pulsotype 2123 was associated with trimethoprim-sulfamethoxazole resistance and K1 (vs. K5) capsule. These findings clarify ST1193-H64's temporal prevalence trends as a fluoroquinolone-resistant pathogen and commensal, document clonal subsets with distinctive geographic, temporal, resistance, and virulence gene associations, and establish a new laboratory tool for rapid and simple detection of ST1193-H64.