Temporal Dynamics of Genetically Heterogeneous Extended-Spectrum Cephalosporin ResistantEscherichia coliBloodstream Infections

Abstract

ABSTRACTExtended-spectrum cephalosporin resistantEscherichia coli(ESC-R-Ec) is an urgent public health threat with sequence type clonal complex 131 (STc131), phylogroup B2 strains being particularly concerning as the dominant cause of ESC-R-Ecinfections. To address the paucity of recent ESC-R-Ecmolecular epidemiology data in the United States, we used whole genome sequencing (WGS) to fully characterize a large cohort of invasive ESC-R-Ecat a tertiary care cancer center in Houston, Texas collected from 2016-2020. During the study timeframe, there were 1154 indexE. colibloodstream infections (BSIs) of which 389 (33.7%) were ESC-R-Ec. Using time series analyses, we identified a temporal dynamic of ESC-R-Ecdistinct from ESC-susceptibleE. coli(ESC-S-Ec), with cases peaking in the last six months of the calendar year. WGS of 297 ESC-R-Ecstrains revealed that while STc131 strains accounted for ∼45% of total BSIs, the proportion of STc131 strains remained stable across the study time frame with infection peaks driven by genetically heterogeneous ESC-R-Ecclonal complexes.BlaCTX-Mvariants accounted for most β-lactamases conferring the ESC-R phenotype (89%; 220/248 index ESC-R-Ec), and amplification ofblaCTX-Mgenes was widely detected in ESC-R-Ecstrains, particularly in carbapenem non-susceptible, recurrent BSI strains.BlaCTX-M-55was significantly enriched within phylogroup A strains, and we identifiedblaCTX-M-55plasmid-to-chromosome transmission occurring across non-B2 strains. Our data provide important information regarding the current molecular epidemiology of invasive ESC-R-Ecinfections at a large tertiary care cancer center and provide novel insights into the genetic basis of observed temporal variability for these clinically important pathogens.IMPORTANCEGiven thatE. coliis the leading cause of worldwide ESC-REnterobacteralesinfections, we sought to assess the current molecular epidemiology of ESC-R-Ecusing a WGS analysis of many BSIs over a five-year period. We identified fluctuating temporal dynamics of ESC-R-Ecinfections, which has also recently been identified in other geographical regions such as Israel. Our WGS data allowed us to visualize the stable nature of STc131 over the study period and demonstrate a limited, but genetically diverse group of ESC-R-Ecclonal complexes are detected during infection peaks. Additionally, we provide a widespread assessment of β-lactamase gene copy number in ESC-R-Ecinfections and delineate mechanisms by which such amplifications are achieved in a diverse array of ESC-R-Ecstrains. These data suggest that serious ESC-R-Ecinfections are driven by a diverse array of strains in our cohort and impacted by environmental factors suggesting that community-based monitoring could inform novel preventative measures.