Epidemiological Characterisation of bla(NDM)-Positive Enterobacterales from Food-Producing Animal Farms in Southwest China

Carbapenems are atypical β-lactam antibiotics with a broade antibacterial spectrum and strong antibacterial activity; however, the emergence and spread of carbapenemases have led to a decline in their effectiveness. New Delhi metallo-β-lactamase (NDM) is an important carbapenemase that has attracted widespread attention and poses a major threat to public health. To investigate the epidemiological characteristics of bla(NDM) in swine and chicken farms in southwestern China, we isolated 102 bla(NDM)-positive Enterobacterales strains from 18 farms in Sichuan and Yunnan provinces in 2021, with Escherichia coli and Klebsiella spp. being the main reservoirs of bla(NDM), variant bla(NDM)-5 being the most prevalent, and all strains being multi-drug resistant. Whole-genome sequencing analysis of 102 bla(NDM)-positive Enterobacterales strains revealed that bla(NDM) had spread primarily through its carriers on the same farm and among the 18 farms in this study. A high degree of genetic similarity between animal-derived bla(NDM)-positive Escherichia coli strains and human-derived strains was also identified, suggesting a potential mutual transmission between them. Nanopore sequencing results indicated that bla(NDM) is predominantly present on the IncX3 plasmid, that an insertion sequence might be important for recombination in the bla(NDM) genetic environment, and that most of the plasmids carrying bla(NDM) are transferable. Collectively, our results enrich the current epidemiological information regarding bla(NDM) in pig and chicken farms in Southwest China, revealing its transmission pattern, as well as the potential risk of transmission to humans, which could help to better understand and control the spread of bla(NDM).