Appl Environ Microbiol. 2021 Mar 5:AEM.00087-21. doi: 10.1128/AEM.00087-21. Online ahead of print.
We investigated the prevalence and transmission of NDM-producing Enterobacteriaceae 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 bla NDM and bla NDM-positive bacteria were characterized based on WGS data from the Illumina and ONT platforms. Of 117 samples analyzed, the carriage rates for NDM-positive Enterobacteriaceae were 47.1, 18 and 50% in geese, inanimate environments (sewage, soil, fodder and dust) and mouse samples, respectively. Two variants (4 bla NDM-1 and 40 bla NDM-5) were found among 44 bla NDM-positive Enterobacteriaceae, which belonged to 8 species and Escherichia coli was the most prevalent (50%). WGS analysis revealed that bla NDM co-existed with diverse antibiotic resistance genes (ARGs). Population structure analysis showed that most E. coli and Enterobacter sp. isolates were highly heterogeneous while most Citrobacter sp. and P. stuartii isolates possessed extremely high genetic similarity. Additionally, bla NDM-5-positive ST4358/ST48 E. coli isolates were found to be clonally spread between the geese and 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 (n=40) and untypable pM2-1-like plasmids (n=4) mediated bla NDM spread. pM2-1-like plasmids possessed diverse ARGs including bla 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 Enterobacteriaceae. The bla NDM contamination of wild mice and the novel pM2-1-like plasmid described in this study likely adds to the risk for dissemination of bla NDM and associated resistance genes.Importance: The carbapenem-resistant bacteria, in particular NDM-producing Enterobacteriaceae, has 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 Enterobacteriaceae. However, the dissemination of NDM-producing bacteria in the waterfowl farm has been less well explored. Our study demonstrated that horizontal spread of bla NDM-carrying plasmids and the partial clonal spread of bla NDM-positive Enterobacteriaceae contributed to widespread contamination of bla NDM in the goose farm ecosystem, including mouse. Furthermore, we found a novel and transferable bla NDM-1-carrying 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 bla NDM-producing Enterobacteriaceae among diverse niches in the farm ecosystem.