Find in Library

The prevalence of carbapenem-resistant <i>Enterobacterales</i> (CRE) has been increasing since the year 2000 and is considered a serious public health threat according to the Centers for Disease Control and Prevention. Limited studies have genotyped Carbapenem-resistant <i>Escherichia coli</i> using whole genome sequencing to characterize the most common lineages and resistance and virulence genes. The aim of this study was to characterize sequence data from carbapenem-resistant <i>E. coli</i> isolates (<i>n</i> = 82) collected longitudinally by the Alameda County Public Health Laboratory (ACPHL) between 2017 and 2019. <i>E. coli</i> genomes were screened for antibiotic resistance genes (ARGs) and extraintestinal pathogenic <i>E. coli</i> virulence factor genes (VFGs). The carbapenem-resistant <i>E. coli</i> lineages were diverse, with 24 distinct sequence types (STs) represented, including clinically important STs: ST131, ST69, ST95, and ST73. All Ambler classes of Carbapenemases were present, with NDM-5 being most the frequently detected. Nearly all isolates (90%) contained genes encoding resistance to third-generation cephalosporins; <i>bla</i>_CTX-M genes were most common. The number of virulence genes present within pandemic STs was significantly higher than the number in non-pandemic lineages (<i>p</i> = 0.035). Virulence genes <i>fim</i>A (92%), <i>tra</i>t (71%), <i>kps</i>M (54%), and <i>iut</i>A (46%) were the most prevalent within the isolates. Considering the public health risk associated with CRE, these data enhance our understanding of the diversity of clinically important <i>E. coli</i> that are circulating in Alameda County, California.