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 <i>bla</i>_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 <i>bla</i>_NDM gene within these markets under the One Health approach. This study investigated the prevalence of the <i>bla</i>_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 <i>bla</i>_NDM-positive strains, comprising 218 <i>Escherichia coli</i> strains, 4 <i>Enterobacter cloacae</i> strains, 7 <i>Klebsiella pneumoniae</i>, 2 <i>Klebsiella aerogenes</i>, 1 <i>Providencia rettgeri</i>, and 1 <i>Proteus mirabilis</i> were isolated from two live poultry markets in Jiangsu, China. Among the <i>bla</i>_NDM-positive strains, multiple variants were identified, primarily <i>bla</i>_NDM-5, followed by <i>bla</i>_NDM-1, <i>bla</i>_NDM-13, <i>bla</i>_NDM-27, and <i>bla</i>_NDM-39. The coexistence of <i>bla</i>_NDM-5 and <i>mcr-1</i> was detected in five <i>E. coli</i> strains. Additionally, we found one <i>E. coli</i> strain in which <i>bla</i>_NDM-5 coexisted with <i>estT</i> and <i>tet</i>(X4), and another <i>E. coli</i> strain where <i>bla</i>_NDM-5 coexisted with <i>estT</i>. Spearman correlation analysis of publicly available genomes revealed that the genetic element preferences of <i>bla</i>_NDM variants vary significantly across species (|R| > 0.3, <i>p</i> < 0.05). The element preferences of <i>E. coli</i> strains carrying <i>bla</i>_NDM-5 are similar to those of <i>Klebsiella pneumoniae</i> harboring <i>bla</i>_NDM-1. In <i>Klebsiella aerogenes</i>, <i>Enterobacter cloacae</i>, and <i>Proteus mirabilis</i>, strains carrying <i>bla</i>_NDM-1, have opposite genetic element preferences when compared with strains harboring <i>bla</i>_NDM-5 or <i>bla</i>_NDM-7. Notably, we report the first evidence of the <i>bla</i>_NDM-1 gene transfer mediated by IS<i>Kpn13</i>, IS<i>Spu2</i>, and MITE<i>Kpn1</i>. The findings highlight that live poultry markets are important transmission hotspots of AMR and thus require continuous surveillance.