Anthropogenic and environmental factors associated with high prevalence of mcr-1 carriage in humans across China

MCR-1-positve E. coli (MCRPEC) have been reported in human worldwide; however, thus far it’s prevalence is low and potential sources for human mcr-1 carriage have not yet been identified. Herein, we analysed a nationwide epidemiological data set on MCRPEC in humans throughout China and assessed factors associated with MCRPEC carriage using natural and national anthropogenic data. We identified 774 non-duplicate MCRPEC isolates from 774 stool samples collected from 5,159 healthy individuals in 30 provinces/municipalities in 2016, with a prevalence of MCRPEC ranging from 3.7% to 32.7% (average of 15.0%), substantially higher than previously reported. MCRPEC carriage was associated with provincial regions, production of sheep and freshwater aquaculture, annual consumption of total meat, pork and mutton, and daily intake of aquaculture products. MCRPEC was significantly more prevalent in provinces with higher aquaculture industries. WGS analysis revealed that the MCRPEC isolates were clustered into four distinct lineages, two of which were dominant and harbored most of the MCRPEC isolates. The high prevalence of MCRPEC in community poses a substantial risk for colistin usage in clinical practice and suggests the need for intestinal screening of mcr-1 carriers in intensive care units in Chinese hospitals. Furthermore, our data suggests that aquaculture is a significant reservoir of mcr-1.