Global genomic epidemiology of NDM-5-producing Escherichia coli ST410 strains

Carbapenem-resistant Enterobacteriaceae (CRE) pose a major public health threat due to extensive drug resistance and nosocomial spread. This study characterised the genome sequence of a multidrug-resistant Escherichia coli strain EC6030 carrying bla_NDM-5 recovered from a 10-month-old patient, and investigated its relationship to global bla_NDM-5-positive E. coli.

Whole-genome sequencing was performed to analyses antimicrobial resistance genes, virulence determinants, plasmid content and the genetic context of bla_NDM-5 in EC6030. A total of 7606 bla_NDM-5-carrying E. coli genomes were retrieved from the NCBI RefSeq database. Core-genome multilocus sequence typing, minimum-spanning tree analysis and SNP-based phylogenetic analysis were used to assess global distribution and genetic relatedness.

EC6030 was resistant to multiple antimicrobial agents, including β-lactams, carbapenems, fluoroquinolones, trimethoprim-sulfamethoxazole, chloramphenicol and tetracycline, but remained susceptible to amikacin and gentamicin. Genomic analysis assigned EC6030 to ST410 and phylogroup C. The bla_NDM-5 gene was located on a 46,161 bp IncX3 plasmid flanked by multiple insertion sequences. This plasmid showed high sequence similarity to previously reported bla_NDM-carrying plasmids among E. coli and Klebsiella pneumoniae isolates in the public database. Globally, bla_NDM-5-carrying E. coli strains are most prevalent in Asia, primarily from clinical specimens, and occur sporadically. The closest relative to EC6030 is a ST410 strain P24_WM1_05.20, recovered from the United Kingdom in 2020 which differing by 61 SNPs.

These findings highlight the clinical significance and potential clonal and plasmid-mediated dissemination of bla_NDM-5-carrying E. coli ST410 lineage and support strengthened genomic surveillance, antimicrobial stewardship and infection control strategies globally.