Carbapenem Resistant E. coli in Alameda County

This study provided a framework for analyzing short-read whole genome sequencing using 82 carbapenem resistant E. coli isolated from clinical sites in Alameda County, California from 2017 to 2019. Using the sequencing data, we were able to identify prominent high risk clonal groups as defined by MLST, investigate the distribution of carbapenem and ESBL resistance genes across clonal groups, establish the frequency of plasmid localizations of the AMR genes and view movement of blaCTX-M genes across epidemiologically related isolates. We were limited in determining relative colocalization of plasmid-borne AMR genes and the prevalence of plasmid replicon types. Long read sequencing is needed to supplement analysis of clinical isolates of interest in routine surveillance, but screening using short-read sequences is a cost-effective way to investigate clonal relationships of AMR isolates in routine genomic surveillance.