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 blaNDM 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 blaNDM gene within these markets under the One Health approach. This study investigated the prevalence of the blaNDM 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 blaNDM-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 blaNDM-positive strains, multiple variants were identified, primarily blaNDM-5, followed by blaNDM-1, blaNDM-13, blaNDM-27, and blaNDM-39. The coexistence of blaNDM-5 and mcr-1 was detected in five E. coli strains. Additionally, we found one E. coli strain in which blaNDM-5 coexisted with estT and tet(X4), and another E. coli strain where blaNDM-5 coexisted with estT. Spearman correlation analysis of publicly available genomes revealed that the genetic element preferences of blaNDM variants vary significantly across species (|R| > 0.3, p < 0.05). The element preferences of E. coli strains carrying blaNDM-5 are similar to those of Klebsiella pneumoniae harboring blaNDM-1. In Klebsiella aerogenes, Enterobacter cloacae, and Proteus mirabilis, strains carrying blaNDM-1, have opposite genetic element preferences when compared with strains harboring blaNDM-5 or blaNDM-7. Notably, we report the first evidence of the blaNDM-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.