Dissemination of cephalosporin resistance genes between Escherichia coli strains from farm animals and humans by specific plasmid lineages

PLoS Genet. 2014 Dec 18;10(12):e1004776. doi: 10.1371/journal.pgen.1004776. eCollection 2014 Dec.


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.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Anti-Bacterial Agents / pharmacology
  • Cephalosporin Resistance / genetics*
  • Chickens / microbiology
  • DNA, Bacterial / genetics
  • Escherichia coli / drug effects
  • Escherichia coli / genetics*
  • Escherichia coli Infections / drug therapy
  • Food Contamination / analysis
  • Food Microbiology
  • Meat / microbiology
  • Phylogeny
  • Plasmids / genetics*
  • Polymorphism, Single Nucleotide
  • Sequence Analysis, DNA
  • Swine / microbiology


  • Anti-Bacterial Agents
  • DNA, Bacterial

Grant support

This work was supported by The European Union Seventh Framework (http://ec.europa.eu/research/fp7/) Programmes “Evolution and Transfer of Antibiotic Resistance” (EvoTAR; FP7-HEALTH-2011-single-stage; grant number 282004; to MdB, VFL, MdT, RJLW, FdlC, and WvS), and “Plaswires” (FP7 ICT 2009 4; grant number 248919; to VFL, MdT, and FdlC), the Spanish Ministry of Education (http://www.mecd.gob.es/portada-mecd/) (BFU2011 26608; to VFL, MdT, and FdlC), and The Netherlands Organisation for Research and Development ZonMw (http://www.nwo.nl/) (Contract number 50-51700-98-053; to WD). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.