title: 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.
authors.affiliation: Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands.
authors.forename: Mark
authors.initials: M
authors.lastname: de Been
authors.affiliation: Instituto de Biomedicina y Biotecnología de Cantabria, Universidad de Cantabria-Sodercan-CSIC, Santander, Spain.
authors.forename: Val F
authors.initials: VF
authors.lastname: Lanza
authors.affiliation: Instituto de Biomedicina y Biotecnología de Cantabria, Universidad de Cantabria-Sodercan-CSIC, Santander, Spain.
authors.forename: María
authors.initials: M
authors.lastname: de Toro
authors.affiliation: Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands.
authors.forename: Jelle
authors.initials: J
authors.lastname: Scharringa
authors.affiliation: Institute for Risk Assessment Sciences, Division of Environmental Epidemiology, Utrecht University, Utrecht, The Netherlands.
authors.forename: Wietske
authors.initials: W
authors.lastname: Dohmen
authors.affiliation: BGI-Shenzhen, Shenzhen, China.
authors.forename: Yu
authors.initials: Y
authors.lastname: Du
authors.affiliation: BGI-Shenzhen, Shenzhen, China.
authors.forename: Juan
authors.initials: J
authors.lastname: Hu
authors.affiliation: BGI-Shenzhen, Shenzhen, China.
authors.forename: Ying
authors.initials: Y
authors.lastname: Lei
authors.affiliation: BGI-Europe, Copenhagen, Denmark.
authors.forename: Ning
authors.initials: N
authors.lastname: Li
authors.affiliation: Norwegian High-Throughput Sequencing Centre, Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, Oslo, Norway.
authors.forename: Ave
authors.initials: A
authors.lastname: Tooming-Klunderud
authors.affiliation: Institute for Risk Assessment Sciences, Division of Environmental Epidemiology, Utrecht University, Utrecht, The Netherlands.
authors.forename: Dick J J
authors.initials: DJ
authors.lastname: Heederik
authors.affiliation: Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands.
authors.forename: Ad C
authors.initials: AC
authors.lastname: Fluit
authors.affiliation: Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands.
authors.forename: Marc J M
authors.initials: MJ
authors.lastname: Bonten
authors.affiliation: Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands.
authors.forename: Rob J L
authors.initials: RJ
authors.lastname: Willems
authors.affiliation: Instituto de Biomedicina y Biotecnología de Cantabria, Universidad de Cantabria-Sodercan-CSIC, Santander, Spain.
authors.forename: Fernando
authors.initials: F
authors.lastname: de la Cruz
authors.affiliation: Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands.
authors.forename: Willem
authors.initials: W
authors.lastname: van Schaik
mesh_terms: D000818:Animals; D000900:Anti-Bacterial Agents / Q000494:pharmacology; D018550:Cephalosporin Resistance / Q000235:genetics*; D002645:Chickens / Q000382:microbiology; D004269:DNA, Bacterial / Q000235:genetics; D004926:Escherichia coli / Q000187:drug effects / Q000235:genetics*; D004927:Escherichia coli Infections / Q000188:drug therapy; D005506:Food Contamination / Q000032:analysis; D005516:Food Microbiology; D008460:Meat / Q000382:microbiology; D010802:Phylogeny; D010957:Plasmids / Q000235:genetics*; D020641:Polymorphism, Single Nucleotide; D017422:Sequence Analysis, DNA; D013552:Swine / Q000382:microbiology
chemical_list: D000900:Anti-Bacterial Agents; D004269:DNA, Bacterial