Deciphering mechanisms of bla(NDM) gene transmission between human and animals: a genomics study of bacterial isolates from various sources in China, 2015 to 2017

BACKGROUND: In China, the bla(NDM) gene has been recovered from human bacterial isolates since 2011. After 2014, detections of this gene in animal and food bacterial isolates have increasingly been reported. AIM: We aimed to understand how bla(NDM)-bearing bacteria could spread between humans, animals, and animal-derived food. METHODS: A total of 288 non-duplicate Escherichia coli strains, including 130 bla(NDM)-carrying and 158 bla(NDM)-negative strains were collected from clinical (humans), food-producing animals (pigs) and food (retail pork) sources between 2015 and 2017. The strains were whole genome sequenced. Core-genome-multilocus-sequence-typing was conducted. To investigate if sequence types (STs) found in human, animal or food samples could have a prior origin in a clinical, animal or food-borne animal reservoir, discriminant analysis of principal components (DAPC) was used. Plasmids bearing bla(NDM) were characterised. RESULTS: The 130 bla(NDM)-carrying E. coli strains comprised a total of 60 STs, with ST167 (10/51), ST77 (6/33) and ST48 (6/46) being most prevalent in clinical, animal and food sources, respectively. Some ST10 and ST167 strains were respectively found among all three sources sampled, suggesting they might enable transfer of bla(NDM) between sources. DAPC analysis indicated possible transmissions of ST167 from humans to animals and ST10 from animals to human. In 114 of 130 bla(NDM)-carrying isolates, bla(NDM) was located on an IncX3 plasmid. CONCLUSION: This study in a Chinese context suggests that cross-species transmission of certain STs of E. coli harbouring bla(NDM) on mobile elements, may facilitate the spread of carbapenem-resistant Enterobacteriaceae. Stringent monitoring of bla(NDM)-bearing E. coli in ecosystems is important.