Genomic characterization of extended-spectrum β-lactamase-producing Enterobacterales isolated from abdominal surgical patients

Abstract

Extended-spectrum β-lactamase-producing Enterobacterales (ESBL-PE) are a serious global health problem. Rectal swabs of 104 patients who underwent abdominal surgery were screened for ESBL-producing isolates of Escherichia coli (EPE) and Klebsiella pneumoniae (EPK), which were recovered from 31 patients. Sequence types (STs) and resistance genes were screened for by whole genome sequencing of 46 isolates (EPE=32, EPK =10, and 4 Enterobacter spp.) from 17 patients. All but seven of the isolates were assigned to recognised STs. Eighteen EPEC strains were of unique STs, but EPKP strains were mainly ST14 or ST15. Eight patients harboured strains of the same ST before and after abdominal surgery. The most prevalent resistant genes in E. coli were blaEC (69.57%), blaCTX-M (65.22%) and blaTEM (36.95%), while blaSHV was present in only K. pneumoniae (41.30%). Overall, genes encoding beta-lactamases of classes A (blaCTX-M, blaTEM, blaZ), C (blaSHV, blaMIR and blaDHA), and D (blaOXA) were identified, with the most prevalent variants being blaCTX-M-15, blaTEM-1B, blaSHV-28, and blaOXA-1. Interestingly, blaCMY-2, the most common pAmpC β-lactamase genes reported worldwide, and mobile colistin resistance genes, mcr-10-1, were also identified. The presence of the genes blaCMY-2 and mcr-10-1 is concerning as they may constitute a potentially high risk of pan-resistant post-surgical infections. It is imperative that healthcare professionals monitor intra-abdominal surgical site infections to prevent transmission of faecal ESBL carriage in high-risk patients.