Characterisation of multidrug-resistant Shiga toxin-producing Escherichia coli cultured from pigs in China: co-occurrence of extended spectrum β-lactamase and mcr-1 encoding genes on plasmids. Colistin resistant MDR STEC

The identification of Enterobacteriaceae harbouring the plasmid-mediated transferable colistin resistance mcr-1 gene presents a new challenge to public health. The aim of this study was to characterise multidrug-resistant Shiga toxin-producing Escherichia coli (STEC) harbouring mcr-1 encoding genes on plasmids cultured from pigs in China. Using CHROMagar ECC plates combined the stx PCR detection method, 93 STEC isolates were recovered from 326 fecal, 351 small intestinal contents and 326 colon contents samples of healthy pigs in 2011 and 2012 in China. Among which, ten STEC isolates were colistin resistant with MIC values of 8-12 mg/L. Ten colistin resistant STEC were identified among 93 STEC isolates cultured from pigs with MIC values of 8-12 mg/L. The mcr-1 gene was detected by PCR in these isolates and sequencing of the resulting amplicons showed a 100% identity with the mcr-1 sequence first reported. High-molecular weight plasmid profiles were determined by S1-nuclease digestion followed by pulsed-field gel electrophoresis (PFGE) and these plasmids were typed by PBRT (PCR-based replicon typing). Whole genome sequences (WGS) for two isolates [STEC-CQ09 O116:H11/ST88 and -CQ10 O2:H32/ST3628] were determined using the Illumina MiSeq platform. Based on whole genome sequencing and PCR-based genotyping assays, several resistance-encoding genes were identified and these included AmpC β-lactamases encoded by blaCMY-2, blaCFE-1 in STEC-CQ09 and blaCMY-104 in STEC-CQ10; extended spectrum β-lactamase-encoding genes including blaCTX-M-55 in STEC-CQ09 and blaCTX-M-65 with blaTEM-1 in STEC-CQ10. The colistin resistance gene of STEC-CQ09 was successfully transferable by conjugation experiments. These data highlight the need to monitor the use of colistin in treatment of both human and animal populations, and the need for active surveillance to support improvements in infection control practices to limit its further dissemination.