Genomic Surveillance of Ceftriaxone-ResistantEscherichia coliin Western New York Suggests the Extended-Spectrum beta-Lactamasebla(CTX-M-27)Is Emerging on Distinct Plasmids in ST38

Extended-spectrum beta-lactamase (ESBL)-producingEnterobacteriaceaepose significant treatment and infection prevention challenges.Escherichia colisequence type (ST) 131 associated with thebla(CTX-M-15)gene has been the dominant lineage of ESBL-producingE. coliin the US and worldwide. In this study, our objective was to determine the beta-lactamase profile, means of dissemination, prevalence, and the clonal identity of ESBL-producingE. coliin our region of Western New York. Whole-genome SNP-based phylogenomics was used to assess 89 ceftriaxone-resistant (CTR)E. coli. Isolates were collected from both inpatients and outpatients and from urine and sterile-sites over a 2 month period in 2017 or throughout the year, respectively. ST131 was the predominant ST (46.0%), followed by ST38 (15.7%). Thebla(CTX-M-15)gene was commonly found in 53.7% of ST131 isolates, whereas thebla(CTX-M-27)gene was found in 26.8% of ST131, though was significantly associated with ST38, and was found in 71.4% of those strains. When compared to ST131, ST38E. coliexhibited increased frequency of resistance to nitrofurantoin and decreased frequency of resistance to ciprofloxacin and ampicillin-sulbactam. Using Nanopore long-read sequencing technology, an analysis of the ESBL genetic context showed that thebla(CTX-M-15)gene was chromosomal in 68.2% of ST131, whereas thebla(CTX-M-27)gene was plasmid-borne in all ST131 and 90% of ST38 isolates. Notably, thebla(CTX-M-27)gene in ST38 resided on highly-related (99.0-100.0% identity and 65.0-98.0% query coverage) conjugative IncF plasmids of distinct plasmid multi-locus sequence types (pMLSTs) from those in ST131. Furthermore, ST131 and ST38 were found to harbor different antibiotic resistance gene and virulence factor profiles. These findings raise the possibility of an emerging ESBL-producingE. colilineage in our region.