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Emergence of NDM-5-producing ST405 and NDM-1-producing ST10 Escherichia coli in bloodstream infections in Apulia, Italy, 2023–2025

Year: 2026

Type: article

Abstract: NDM-producing Escherichia coli ( E. coli ) are emerging across Europe, especially clones ST405 (NDM-5) and ST10 (NDM-1). Data from Southern Italy remain scarce. We investigated NDM-producing E. coli bloodstream infections (BSIs) detected through regional Carbapenem-resistant Enterobacteriaceae (CRE) surveillance in Apulia, 2014–2025. Within the regional CRE surveillance (2014–2025), all carbapenem-resistant (CR) E. coli BSI isolates were collected and screened for carbapenemase genes (GeneXpert: blaKPC, blaVIM, blaNDM, blaIMP, blaOXA-48). NDM-positive isolates (2023–2025) underwent Illumina whole-genome sequencing (WGS). Core-genome SNP analysis assessed clonal relatedness. Resistance, virulence genes, and plasmid replicons were characterized using ResFinder, VirulenceFinder, and PlasmidFinder, respectively. Among 50 CR E. coli BSI isolates, bla KPC and bla NDM were detected in 23/50 (46.0%) and 11/50 (22.0%), respectively; 16/50 (32.0%) had carbapenem resistance mechanisms not identified by the PCR panel. All bla NDM -positive isolates were detected from 2023 onwards. Nine NDM-producing isolates were sequenced: eight bla NDM-5 E. coli ST405 (phylogroup D, O102:H6, fimH29) and one bla NDM-1 E. coli ST10 (phylogroup A, O9:H9, fimH54). All were multidrug-resistant yet colistin-susceptible. ST405 isolates co-harboured bla OXA-1 , bla CTX-M-15 , sul1 , aac(6')-Ib-cr , catB3 , dfrA17 , and tet(B) , and carried multiple virulence genes including fimH , papC , traT , fyuA , iutA/iucC and chuA , consistent with a hypervirulent multidrug resistance (MDR) profile. Core-genome SNP analysis showed a tight cluster of six ST405 isolates from one hospital (< 30 SNPs), and two unrelated ST405 isolates from different hospitals. ST405 strains carried IncFIA, IncFIB(AP001918), IncFII and Col(BS512) plasmids; the ST10 isolate carried IncFIB(pQil). We report the emergence of the high-risk MDR E. coli strains NDM-5 ST405 and NDM-5 ST10 in cases of BSI in Apulia. Integration of WGS into regional CRE surveillance is essential to detect high-risk clones and guide infection control and stewardship interventions.

Source: Scientific Reports

DOI: 10.1038/s41598-026-54754-z