Molecular Epidemiology of Escherichia coli Producing CTX-M and pAmpC β-Lactamases from Dairy Farms Identifies a Dominant Plasmid Encoding CTX-M-32 but No Evidence for Transmission to Humans in the Same Geographical Region

Abstract

Third-generation cephalosporin resistance (3GC-R) in <i>Escherichia coli</i> is a rising problem in human and farmed-animal populations. We conducted whole-genome sequencing analysis of 138 representative 3GC-R isolates previously collected from dairy farms in southwest England and confirmed by PCR to carry acquired 3GC-R genes. This analysis identified <i>bla</i>_CTX-M (131 isolates encoding CTX-M-1, -14, -15, -and 32 and the novel variant CTX-M-214), <i>bla</i>_CMY-2 (6 isolates), and <i>bla</i>_DHA-1 (1 isolate). A highly conserved plasmid was identified in 73 isolates, representing 27 <i>E. coli</i> sequence types. This novel ∼220-kb IncHI2 plasmid carrying <i>bla</i>_CTX-M-32 was sequenced to closure and designated pMOO-32. It was found experimentally to be stable in cattle and human transconjugant <i>E. coli</i> even in the absence of selective pressure and was found by multiplex PCR to be present on 26 study farms representing a remarkable range of transmission over 1,500 square kilometers. However, the plasmid was not found among human urinary <i>E. coli</i> isolates we recently characterized from people living in the same geographical location, collected in parallel with farm sampling. There were close relatives of two <i>bla</i>_CTX-M plasmids circulating among eight human and two cattle isolates, and a closely related <i>bla</i>_CMY-2 plasmid was found in one cattle and one human isolate. However, phylogenetic evidence of recent sharing of 3GC-R strains between farms and humans in the same region was not found.<b>IMPORTANCE</b> Third-generation cephalosporins (3GCs) are critically important antibacterials, and 3GC resistance (3GC-R) threatens human health, particularly in the context of opportunistic pathogens such as <i>Escherichia coli</i> There is some evidence for zoonotic transmission of 3GC-R <i>E. coli</i> through food, but little work has been done examining possible transmission via interaction of people with the local near-farm environment. We characterized acquired 3GC-R <i>E. coli</i> found on dairy farms in a geographically restricted region of the United Kingdom and compared these with <i>E. coli</i> from people living in the same region, collected in parallel. While there is strong evidence for recent farm-to-farm transmission of 3GC-R strains and plasmids-including one epidemic plasmid that has a remarkable capacity to be transmitted-there was no evidence that 3GC-R <i>E. coli</i> found on study farms had a significant impact on circulating 3GC-R <i>E. coli</i> strains or plasmids in the local human population.