Dissemination of Cephalosporin Resistance Genes between Escherichia coli Strains from Farm Animals and Humans by Specific Plasmid Lineages

Abstract

Third-generation cephalosporins are a class of β-lactam antibiotics that are often used for the treatment of human infections caused by Gram-negative bacteria, especially Escherichia coli. Worryingly, the incidence of human infections caused by third-generation cephalosporin-resistant E. coli is increasing worldwide. Recent studies have suggested that these E. coli strains, and their antibiotic resistance genes, can spread from food-producing animals, via the food-chain, to humans. However, these studies used traditional typing methods, which may not have provided sufficient resolution to reliably assess the relatedness of these strains. We therefore used whole-genome sequencing (WGS) to study the relatedness of cephalosporin-resistant E. coli from humans, chicken meat, poultry and pigs. One strain collection included pairs of human and poultry-associated strains that had previously been considered to be identical based on Multi-Locus Sequence Typing, plasmid typing and antibiotic resistance gene sequencing. The second collection included isolates from farmers and their pigs. WGS analysis revealed considerable heterogeneity between human and poultry-associated isolates. The most closely related pairs of strains from both sources carried 1263 Single-Nucleotide Polymorphisms (SNPs) per Mbp core genome. In contrast, epidemiologically linked strains from humans and pigs differed by only 1.8 SNPs per Mbp core genome. WGS-based plasmid reconstructions revealed three distinct plasmid lineages (IncI1- and IncK-type) that carried cephalosporin resistance genes of the Extended-Spectrum Beta-Lactamase (ESBL)- and AmpC-types. The plasmid backbones within each lineage were virtually identical and were shared by genetically unrelated human and animal isolates. Plasmid reconstructions from short-read sequencing data were validated by long-read DNA sequencing for two strains. Our findings failed to demonstrate evidence for recent clonal transmission of cephalosporin-resistant E. coli strains from poultry to humans, as has been suggested based on traditional, low-resolution typing methods. Instead, our data suggest that cephalosporin resistance genes are mainly disseminated in animals and humans via distinct plasmids.

Host-Specific Patterns of Genetic Diversity among IncI1-Iγ and IncK Plasmids Encoding CMY-2 β-Lactamase in Escherichia coli Isolates from Humans, Poultry Meat, Poultry, and Dogs in Denmark

“…The sequenced IncI1-I␥/ST2, IncI1-I␥/ST12, and IncK plasmids were highly similar (99% identity; 88% to 100% coverage) to plasmids detected in Enterobacteriaceae isolated from dogs (I1-I␥/ ST2) and poultry (IncI1-I␥/ST12 and IncK) in the United States, the Netherlands, and Norway (14,(41)(42)(43). The recovery of highly similar plasmids from different E. coli lineages and from unrelated individuals of the same host species suggests that these plasmids may possess traits enhancing adaptation of E. coli to the intestinal tracts of specific animal hosts.…”

“…In Sweden, similar bla CMY-2 -carrying IncK plasmids were detected in genetically unrelated E. coli isolates from broilers, broiler meat, and human clinical isolates, suggesting possible plasmid-mediated zoonotic transmission of bla CMY-2 (12,13). In the Netherlands, highly related IncI1-I␥ and IncK plasmids harboring bla CMY-2 were found in human, broiler, and broiler meat isolates (14,15). Additionally, this resistance determinant occurs at high frequencies among E. coli isolates from dogs with an AmpC phenotype (16).…”

Environmental adaptation and vertical dissemination of ESBL‐/pAmpC‐producing Escherichia coli in an integrated broiler production chain in the absence of an antibiotic treatment

“…In contrast, isolates of the parent flock were collected only 17 days earlier but the SNP differences between isolates of the parent flock and the fattening flock were about 10.5 SNPs Mbp −1 . The number of SNP differences between the strains of the fattening period is higher than the numbers published for clonal outbreaks of enterohemorrhagic E. coli (EHEC) (de Been et al ., 2014; Berenger et al ., 2015; Rusconi et al ., 2016) but overall lower than those described for interspecies transmissions of clonal ST‐410 E. coli strains (Schaufler et al ., 2016b). These findings suggest that ESBL‐/pAmpC‐resistant E. coli were more likely transferred from the parent flock into the production chain via an earlier event but not directly along the investigated batch of broiler chicken.…”

Analysis of high levels of multidrug resistant Escherichia coli from healthy broiler chickens in Western Algeria

“…Further, a high rate of multiresistant in E. coli fecal isolates from poultry, poultry farmers and poultry slaughterers has been shown in the Netherlands (Van Den Bogaard et al, 2001). Spread of antibiotic resistance plasmids (De Been et al, 2014) or of antibiotic-resistant microorganisms from poultry to humans (Thorsteinsdottir et al, 2010) has been reported. Of special, concern is the detection of high level of resistance to quinolone and fluoroquinolones in healthy broiler chickens.…”