Genomic Insights into Carbapenem-Resistant Organisms Producing New Delhi Metallo-β-Lactamase in Live Poultry Markets

New Delhi metallo-β-lactamase (NDM) is an enzyme that can degrade a wide range of β-lactam antibiotics. The widespread dissemination of the bla_NDM gene, which encodes NDM, in animal-derived settings poses a threat to public health security. Live poultry markets represent critical nodes in public health surveillance. However, there is currently limited reporting on the spread of the bla_NDM gene within these markets under the One Health approach. This study investigated the prevalence of the bla_NDM gene in live poultry markets and, by integrating newly sequenced genomes with publicly available database entries, performed an in-depth analysis of its association networks with other genetic elements across species. A total of 233 bla_NDM-positive strains, comprising 218 Escherichia coli strains, 4 Enterobacter cloacae strains, 7 Klebsiella pneumoniae, 2 Klebsiella aerogenes, 1 Providencia rettgeri, and 1 Proteus mirabilis were isolated from two live poultry markets in Jiangsu, China. Among the bla_NDM-positive strains, multiple variants were identified, primarily bla_NDM-5, followed by bla_NDM-1, bla_NDM-13, bla_NDM-27, and bla_NDM-39. The coexistence of bla_NDM-5 and mcr-1 was detected in five E. coli strains. Additionally, we found one E. coli strain in which bla_NDM-5 coexisted with estT and tet(X4), and another E. coli strain where bla_NDM-5 coexisted with estT. Spearman correlation analysis of publicly available genomes revealed that the genetic element preferences of bla_NDM variants vary significantly across species (|R| > 0.3, p < 0.05). The element preferences of E. coli strains carrying bla_NDM-5 are similar to those of Klebsiella pneumoniae harboring bla_NDM-1. In Klebsiella aerogenes, Enterobacter cloacae, and Proteus mirabilis, strains carrying bla_NDM-1, have opposite genetic element preferences when compared with strains harboring bla_NDM-5 or bla_NDM-7. Notably, we report the first evidence of the bla_NDM-1 gene transfer mediated by ISKpn13, ISSpu2, and MITEKpn1. The findings highlight that live poultry markets are important transmission hotspots of AMR and thus require continuous surveillance.