Genomic analysis of the virulome and resistome of high-risk Escherichia coli clones in Peru

Abstract Introduction Globally, there has been a reported increase in the frequency of certain Escherichia coli strains carrying a broad repertoire of antimicrobial resistance genes, classified as high-risk clones. The aim of this study was to characterize the virulome and resistome of ESBL-producing E. coli strains isolated from human patients and to determine the prevalence of high-risk clones circulating in Peru. Methods A total of 134 ESBL-producing E. coli strains recovered from faecal samples were sequenced and analysed alongside 351 publicly available genomes from previous studies to assign phylogroups, pathotypes and sequence types (STs), as well as to predict virulence and antimicrobial resistance genes. Results All known E. coli phylogroups were detected, with Phylogroups A and B1 being the most frequent. Only 26% of the strains were classified as diarrhoeagenic pathotypes. Based on MLST analysis, the strains were assigned to 160 distinct STs, of which 8 have been previously identified as high-risk clones. Notably, ST10 was the most prevalent ST in the dataset and has been classified as a high-risk clone. Phylogenetic analysis revealed no clear association between E. coli phylogroups and pathotypes. In contrast, high-risk clones were primarily non-diarrhoeagenic and carried a wide array of virulence genes associated with extraintestinal infections, along with multiple antimicrobial resistance genes, particularly blaTEM, blaCTX-M, sul2, tetA and sul1 as well as the resistance-associated mutations gyrA (S83L) and parC. Conclusions These findings underscore the wide genomic diversity observed among E. coli strains, including multidrug-resistant and high-risk clones with significant potential to cause infections that pose a serious public health threat.