Whole-Genome Analysis of bla(NDM)-Bearing Proteus mirabilis Isolates and mcr-1-Positive Escherichia coli Isolates Carrying bla(NDM) from the Same Fresh Vegetables in China

The global spread of colistin or carbapenem-resistant Enterobacteriaceae (CRE) has been a pressing threat to public health. Members of Enterobacteriaceae, especially Proteus mirabilis and Escherichia coli, have been prevalent foodborne pathogens and such pathogens from fresh vegetables have triggered foodborne illness in China. However, reports about CRE, especially P. mirabilis from fresh vegetables, are still lacking. In this study, we identified five bla(NDM)-positive P. mirabilis and five bla(NDM)-positive generic E. coli concurrently from five fresh vegetables in two markets from China, and four of the five E. coli also carried mcr-1. The 10 isolates were characterized with methods including antimicrobial susceptibility testing, conjugation, whole-genome sequencing and phylogenetic analysis. All 10 isolates were multidrug-resistant (MDR). bla(NDM-5) in five E. coli isolates and one P. mirabilis carrying bla(NDM-5) was located on similarly transferable IncX3 plasmids, while transferably untypable plasmids were the carriers of bla(NDM-1) in four P. mirabilis isolates from different types of vegetables/markets. mcr-1 in the four bla(NDM)-(5)-positive E. coli was located on similarly non-conjugative IncHI2 MDR plasmids lacking transfer region. Notably, ISCR1 complex class 1 integron capable of capturing bla(NDM-1) was found on all untypable plasmids from P. mirabilis, and five copies of ISCR1 complex class 1 integron containing bla(NDM-1) even occurred in one P. mirabilis, which showed high-level carbapenem resistance. Plasmid and phylogenetic analysis revealed that the bla(NDM)-positive P. mirabilis and E. coli from fresh vegetables might be derived from animals and transmitted to humans via the food chain. The concurrence of bla(NDM)-positive P. mirabilis and E. coli carrying both mcr-1 and bla(NDM) in different types of fresh vegetables eaten raw is alarming and threatens food safety. Sustained surveillance of these foodborne pathogens among fresh vegetables is urgent to ensure the health of food consumers. We report for the first time the concurrence of bla(NDM)-positive P. mirabilis and mcr-1-bearing E. coli carrying bla(NDM) from the same fresh vegetables.