Occurrence and Transmission of <i>bla</i> _NDM -Carrying <i>Enterobacteriaceae</i> from Geese and the Surrounding Environment on a Commercial Goose Farm

Abstract

We investigated the prevalence and transmission of NDM-producing <i>Enterobacteriaceae</i> in fecal samples of geese and environmental samples from a goose farm in southern China. The samples were cultivated on MacConkey agar plates supplemented with meropenem. Individual colonies were examined for <i>bla</i>_NDM, and <i>bla</i>_NDM-positive bacteria were characterized based on whole-genome sequencing (WGS) data from the Illumina and Oxford Nanopore Technologies (ONT) platforms. Of 117 samples analyzed, the carriage rates for New Delhi metallo-β-lactamase (NDM)-positive <i>Enterobacteriaceae</i> were 47.1, 18, and 50% in geese, inanimate environments (sewage, soil, fodder, and dust), and mouse samples, respectively. Two variants (<i>bla</i>_NDM-1 and <i>bla</i>_NDM-5, in 4 and 40 isolates, respectively) were found among 44 <i>bla</i>_NDM-positive <i>Enterobacteriaceae</i>; these variants belonged to eight species, and <i>Escherichia coli</i> was the most prevalent (50%). WGS analysis revealed that <i>bla</i>_NDM coexisted with diverse antibiotic resistance genes (ARGs). Population structure analysis showed that most <i>E. coli</i> and <i>Enterobacter</i> sp. isolates were highly heterogeneous, while most <i>Citrobacter</i> sp. and <i>P. stuartii</i> isolates possessed extremely high genetic similarities. In addition, <i>bla</i>_NDM-5-positive ST4358/ST48 <i>E. coli</i> isolates were found to be clonally spread between geese and the environment and were highly genetically similar to those reported from ducks, farm environments, and humans in China. Plasmid analysis indicated that IncX3 pHNYX644-1-like (<i>n</i> = 40) and untypeable pM2-1-like plasmids (<i>n</i> = 4) mediated <i>bla</i>_NDM spread. pM2-1-like plasmids possessed diverse ARGs, including <i>bla</i>_NDM-1, the arsenical and mercury resistance operons, and the maltose operon. Our findings revealed that the goose farm is a reservoir for NDM-positive <i>Enterobacteriaceae</i> The <i>bla</i>_NDM contamination of wild mice and the novel pM2-1-like plasmid described here likely adds to the risk for dissemination of <i>bla</i>_NDM and associated resistance genes.<b>IMPORTANCE</b> Carbapenem-resistant bacteria, in particular NDM-producing <i>Enterobacteriaceae</i>, have become a great threat to global public. These bacteria have been found not only in hospital and community environments but also among food animal production chains, which are recognized as reservoirs for NDM-producing <i>Enterobacteriaceae</i> However, the dissemination of NDM-producing bacteria in waterfowl farms has been less well explored. Our study demonstrates that the horizontal spread of <i>bla</i>_NDM-carrying plasmids and the partial clonal spread of <i>bla</i>_NDM-positive <i>Enterobacteriaceae</i> contribute to the widespread contamination of <i>bla</i>_NDM in the goose farm ecosystem, including mice. Furthermore, we found a novel and transferable <i>bla</i>_NDM-1-carrying multidrug resistance (MDR) plasmid that possessed multiple environmental adaptation-related genes. The outcomes of this study contribute to a better understanding of the prevalence and transmission of <i>bla</i>_NDM-carrying <i>Enterobacteriaceae</i> among diverse niches in the farm ecosystem.