Occurrence and Genomic Characterization of ESBL-Producing, MCR-1-Harboring Escherichia coli in Farming Soil

Abstract

The emergence and spread of the mobile colistin resistance gene (<i>mcr-1</i>) has become a major global public health concern. So far, this gene has been widely detected in food animals, pets, food, and humans. However, there is little information on the contamination of <i>mcr-1</i>-containing bacteria in farming soils. In August 2016, a survey of ESBL-producing <i>Escherichia coli</i> isolated from farming soils was conducted in Shandong Province, China. We observed colistin resistance in 12 of 53 (22.6%) ESBL-producing Enterobacteriaceae isolates from farming soil. Six <i>mcr-1</i>-positive <i>E. coli</i> strains originating from a livestock-intensive area were found. The isolates belonged to four different STs (ST2060, ST3014, ST6756, and ST1560) and harbored extensive additional resistance genes. An <i>E. coli</i> with <i>bla</i>_NDM-1 was also detected in a soil sample from the same area. Comparative whole genome sequencing and S1-PFGE analysis indicated that <i>mcr-1</i> was chromosomally encoded in four isolates and located on IncHI2 plasmids in two isolates. To our knowledge, we report the first isolation of <i>mcr-1</i> in ESBL-producing <i>E. coli</i> from farming soils. This work highlights the importance of active surveillance of colistin-resistant organisms in soil. Moreover, investigations addressing the influence of animal manure application on the transmission of <i>mcr-1-</i>producing bacteria are also warranted.