The role of plasmids in carbapenem resistant E. coli in Alameda County, California

Abstract

Background: Antimicrobial resistant infections continue to be a leading global public health crisis. Mobile genetic elements, such as plasmids, have been shown to play a major role in the dissemination of antimicrobial resistance (AMR) genes. Despite its ongoing threat to human health, surveillance of AMR in the United States is often limited to phenotypic resistance. Genomic analyses are important to better understand the underlying resistance mechanisms, assess risk, and implement appropriate prevention strategies. This study aimed to investigate the extent of plasmid mediated antimicrobial resistance that can be inferred from short read sequences of carbapenem resistant E. coli (CR-Ec) in Alameda County, California. E. coli isolates from healthcare locations in Alameda County were sequenced using an Illumina MiSeq and assembled with Unicycler. Genomes were categorized according to predefined multilocus sequence typing (MLST) and core genome multilocus sequence typing (cgMLST) schemes. Resistance genes were identified and corresponding contigs were predicted to be plasmid-borne or chromosome-borne using two bioinformatic tools (MOB-suite and mlplasmids).

Results: Among 82 of CR-Ec identified between 2017 and 2019, twenty-five sequence types (STs) were detected. ST131 was the most prominent (n = 17) followed closely by ST405 (n = 12). bla_CTX-M were the most common ESBL genes and just over half (18/30) of these genes were predicted to be plasmid-borne by both MOB-suite and mlplasmids. Three genetically related groups of E. coli isolates were identified with cgMLST. One of the groups contained an isolate with a chromosome-borne bla_CTX-M-15 gene and an isolate with a plasmid-borne bla_CTX-M-15 gene.

Conclusions: This study provides insights into the dominant clonal groups driving carbapenem resistant E. coli infections in Alameda County, CA, USA clinical sites and highlights the relevance of whole-genome sequencing in routine local genomic surveillance. The finding of multi-drug resistant plasmids harboring high-risk resistance genes is of concern as it indicates a risk of dissemination to previously susceptible clonal groups, potentially complicating clinical and public health intervention.

Keywords: Carbapenem resistance; ESBLs; Plasmids; Short-read whole genome sequencing; bla CTX−M−15.

Fig. 1

Relative abundance of antimicrobial resistance genes across E. coli sequence types Legend: Relative abundance is the total count of a resistance gene in the ST divided by the total number of resistance genes in the ST. The mean value of relative abundance was calculated for isolates within the same ST and resistance group. Clonal groups were categorized due to clinical relevancy as documented in previous literature [–37]

Fig. 2

Proportion of plasmid bound antimicrobial resistance genes (ARGs). Legend: Antimicrobial resistance genes were detected using the ResFinder database in ABRicate and contigs were determined to be plasmid or chromosomal using mlplasmids v1.0 and MOB-suite v3.0.3

Fig. 3

Neighbor-joining tree of 30 CTX-producing E. coli isolates based on a cgMLST EnteroBase scheme including 2513 genes Legend: The tree was built using cgMLSTFinder v.1.1 and T-Rex webserver and visualized with iTOL v.6.4.3. Different MLST clusters are highlighted in various shades of grey. Isolate pairs with the same cgMLST sequence type are highlighted in pink. The color-coded rings represent the contig type containing the CTX gene as called by mlplasmids and MOB-suite (outer ring) and the CTX gene (inner ring)