Clonal Lineages and Virulence Factors of Carbapenem Resistant E. coli in Alameda County, California, 2017-2019

Abstract

The prevalence of carbapenem-resistant Enterobacterales (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 Escherichia coli 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 E. coli isolates (n = 82) collected longitudinally by the Alameda County Public Health Laboratory (ACPHL) between 2017 and 2019. E. coli genomes were screened for antibiotic resistance genes (ARGs) and extraintestinal pathogenic E. coli virulence factor genes (VFGs). The carbapenem-resistant E. coli 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; bla_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 (p = 0.035). Virulence genes fimA (92%), trat (71%), kpsM (54%), and iutA (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 E. coli that are circulating in Alameda County, California.

Keywords: E. Coli; antibiotic resistance; carbapenem; genomic analysis.

Figure 1

Maximum likelihood phylogenetic tree of 82 carbapenem resistant E. coli isolates from Alameda County Health systems 2017–2019, derived from a core alignment of 18,587 core SNP’s. The tree was generated using the general time reversible model with FigTree. A, B1, B2, C, D, E, and F are insilico ClermonTyper phylogenetic groups. The presence of any carbapenemase genes and the count of ExPEC virulence genes per isolate are indicated. The pandemic sequence types are annotated. “Other” sequence types include all sequence types other than ST131, ST69, ST405, and ST10 detected in the sample group.

Figure 2

Distribution of putative extraintestinal pathogenic E. coli (ExPEC) virulence factor genes (VFGs) compared to non-ExPEC associated VFGs among E. coli STs from Alameda County, CA hospital patients from 2017–2019. (A) Putative ExPEC virulence genes representing 19 sub types from seven virulence gene families (afa, fim, hlyD, iutA, kpsM, traT, pap, sfa) were selected for sub-analysis. The average number of ExPEC VFGs among all STs was calculated and displayed as the dashed blue y-intercept line, with a value of 35.68 ExPEC VFGs per ST. (B) The relative abundance of each virulence gene is the total length of the virulence gene sequence divided by the total genome sequence length. The mean value of relative abundance was calculated by ST.