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

Abstract

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.

Keywords: blaNDM; carbapenem resistance; genomic analysis; live poultry; transmission.

Figure 1

The phylogenetic tree and ARG heatmap of 29 E. coli isolates. The phylogenetic tree was generated by FastTree based on core gene alignment using Roary and was visualized using Chiplot. Isolates from different sources are highlighted in different colors. The three columns of information marked next to the strain names are isolation source, ST type (identified by MLST), and serotype (identified by ECTyper). The three sets of heatmaps show the presence of ARGs in the strains. The outermost bar chart shows the number of virulence genes in the isolates based on the VFDB core dataset.

Figure 2

Plasmid profile of the bla_NDM-5-containing IncX3-type plasmid. Plasmid slices (assembled contigs, not complete plasmids) from this study were compared with a plasmid (CP033399.1) derived from E. coli. The GC skew and GC content are depicted in an inward-to-outward sequence. The outermost arrows colored in red indicate the positions and transcriptional orientations of the open reading frames.

Figure 3

Genetic environments of several bla_NDM variants in assembled genomes and genomes from the database. (A) Different types of genetic environments of bla_NDM variants in assembled genomes. Different genetic elements are highlighted in different colors. (B) Primary genetic contexts of bla_NDM-1 across different species. In different species, the transfer of bla_NDM-1 is mediated by various IS elements.