First report of an Escherichia coli strain from swine carrying an OXA-181 carbapenemase and the colistin resistance determinant MCR-1.

ABSTRACT

Plasmid-mediated resistance to carbapenems and colistin in Enterobacteriaceae represents an emerging public health threat. Although animals have been identified as a relevant source of multidrug-resistant (MDR) bacteria, there are only a few reports on the presence of carbapenemases in animal isolates. In this study, 7850 faecal Escherichia coli isolates obtained from 2160 pigs were screened for carbapenem non-susceptibility using Mueller-Hinton agar supplemented with meropenem. Eleven isolates showed growth on meropenem-containing agar but only two proved positive by PCR for a carbapenemase gene, namely blaOXA-48-like. The two isolates were obtained from different pigs housed at the same farm in Italy and were not genetically related by multilocus sequence typing (MLST), comprising ST359 and ST641. Whole-genome sequencing revealed the presence of blaOXA-181 in both isolates; in addition, the colistin resistance gene mcr-1 and aminoglycoside resistance gene armA were found in one isolate. The blaOXA-181 resistance gene was located on a 51.5-kb non-conjugative plasmid of replicon type IncX3 and the mcr-1 gene on a 33.3-kb transferable IncX4 plasmid. The high nucleotide similarity (>99%) of plasmids pEcIHIT31346-OXA-181 and pEcIHIT31346-MCR-1 to published plasmids from various human and animal sources suggests that specific antibiotic resistance plasmids are circulating among E. coli strains worldwide and across vertebrate species barriers. Although carbapenems are not licensed for use in livestock and the overall prevalence of carbapenemases in porcine E. coli appears to be low, the current findings indicate that even pigs can host MDR strains with accumulated plasmid-mediated resistance against several last-line antibiotics.