New Delhi Metallo-β-Lactamase Plasmidomes of Intensive Care Unit Clinical and Environmental Enterobacterales Isolates.

BACKGROUND

There are limited data on the molecular epidemiology of New Delhi metallo-β-lactamase (NDM)-producing carbapenem-resistant Enterobacterales (CRE) in Latin America, despite the high burden of NDM-CRE in the region. This study characterized bla NDM-harboring plasmids from CRE from patients and the environment of an Argentine hospital.

METHOD: We performed whole-genome sequencing of 40 environmental isolates (Klebsiella complex, n = 11; Enterobacter cloacae, complex n = 16; Citrobacter freundii, n = 10; Serratia marcescens, n = 3) and 4 clinical isolates (Klebsiella pneumoniae, n = 4) recovered from the environment and rectal surveillance samples of patients in the same intensive care units (ICUs) at a tertiary care center in Argentina, July 2023-February 2024, respectively. Representative genomic groups underwent Oxford Nanopore sequencing and hybrid genome assembly for complete plasmid characterization. Resolved bla NDM-harboring plasmids were compared across species and publicly available reference sequences to characterize plasmid relatedness and dissemination patterns.

RESULTS

Ten representative genomic groups were identified across species, including 7 defined sequence types and 3 assigned in this study. bla NDM-1 and bla NDM-5 were present in 72.5% (29/40) and 27.5% (11/40) of environmental isolates, respectively (all 4 clinical isolates were bla NDM-5). Hybrid assembly of the representative genomic groups revealed bla NDM-1 was located on highly conserved plasmids belonging to the IncC incompatibility group across multiple CRE species. bla NDM-5 was restricted to Klebsiella spp. and was associated with structurally diverse plasmids including IncF- and IncHI1B/IncFIB-type backbones in both environmental and patient isolates.

CONCLUSIONS

These findings highlight the ICU environment as a reservoir for bla NDM plasmids.