title: High Heterogeneity of Escherichia coli Sequence Types Harbouring ESBL/AmpC Genes on IncI1 Plasmids in the Colombian Poultry Chain.
abstract: BACKGROUND
  Escherichia coli producing ESBL/AmpC enzymes are unwanted in animal production chains as they may pose a risk to human and animal health. Molecular characterization of plasmids and strains carrying genes that encode these enzymes is essential to understand their local and global spread.
  
  
  OBJECTIVE
  To investigate the diversity of genes, plasmids and strains in ESBL/AmpC-producing E. coli from the Colombian poultry chain isolated within the Colombian Integrated Program for Antimicrobial Resistance Surveillance (Coipars).
  
  
  METHODS
  A total of 541 non-clinical E. coli strains from epidemiologically independent samples and randomly isolated between 2008 and 2013 within the Coipars program were tested for antimicrobial susceptibility. Poultry isolates resistant to cefotaxime (MIC ≥ 4 mg/L) were screened for ESBL/AmpC genes including blaCTX-M, blaSHV, blaTEM, blaCMY and blaOXA. Plasmid and strain characterization was performed for a selection of the ESBL/AmpC-producing isolates. Plasmids were purified and transformed into E. coli DH10B cells or transferred by conjugation to E. coli W3110. When applicable, PCR Based Replicon Typing (PBRT), plasmid Multi Locus Sequence Typing (pMLST), plasmid Double Locus Sequence Typing (pDLST) and/or plasmid Replicon Sequence Typing (pRST) was performed on resulting transformants and conjugants. Multi Locus Sequence Typing (MLST) was used for strain characterization.
  
  
  RESULTS
  In total, 132 of 541 isolates were resistant to cefotaxime and 122 were found to carry ESBL/AmpC genes. Ninety-two harboured blaCMY-2 (75%), fourteen blaSHV-12 (11%), three blaSHV-5 (2%), five blaCTX-M-2 (4%), one blaCTX-M-15 (1%), one blaCTX-M-8 (1%), four a combination of blaCMY-2 and blaSHV-12 (4%) and two a combination of blaCMY-2 and blaSHV-5 (2%). A selection of 39 ESBL/AmpC-producing isolates was characterized at the plasmid and strain level. ESBL/AmpC genes from 36 isolates were transferable by transformation or conjugation of which 22 were located on IncI1 plasmids. These IncI1 plasmids harboured predominantly blaCMY-2 (16/22), and to a lesser extend blaSHV-12 (5/22) and blaCTX-M-8 (1/22). Other plasmid families associated with ESBL/AmpC-genes were IncK (4/33), IncHI2 (3/33), IncA/C (2/33), IncΒ/O (1/33) and a non-typeable replicon (1/33). Subtyping of IncI1 and IncHI2 demonstrated IncI1/ST12 was predominantly associated with blaCMY-2 (12/16) and IncHI2/ST7 with blaCTX-M-2 (2/3). Finally, 31 different STs were detected among the 39 selected isolates.
  
  
  CONCLUSIONS
  Resistance to extended spectrum cephalosporins in E. coli from Colombian poultry is mainly caused by blaCMY-2 and blaSHV-12. The high diversity of strain Sequence Types and the dissemination of homogeneous IncI1/ST12 plasmids suggest that spread of the resistance is mainly mediated by horizontal gene transfer.
authors.affiliation: Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, the Netherlands.|Colombian Integrated Program for Antimicrobial Resistance Surveillance - Coipars, Corporación Colombiana de Investigación Agropecuaria - Corpoica, Cundinamarca, Colombia.
authors.forename: Luis Ricardo
authors.identifier: http://orcid.org/0000-0003-3580-2719
authors.initials: LR
authors.lastname: Castellanos
authors.affiliation: Colombian Integrated Program for Antimicrobial Resistance Surveillance - Coipars, Corporación Colombiana de Investigación Agropecuaria - Corpoica, Cundinamarca, Colombia.
authors.forename: Pilar
authors.initials: P
authors.lastname: Donado-Godoy
authors.affiliation: Instituto Colombiano Agropecuario - ICA, Bogotá, Colombia.
authors.forename: Maribel
authors.initials: M
authors.lastname: León
authors.affiliation: Colombian Integrated Program for Antimicrobial Resistance Surveillance - Coipars, Corporación Colombiana de Investigación Agropecuaria - Corpoica, Cundinamarca, Colombia.|Department of Biological Sciences, Los Andes University, Bogotá, Colombia.
authors.forename: Viviana
authors.initials: V
authors.lastname: Clavijo
authors.affiliation: Colombian Integrated Program for Antimicrobial Resistance Surveillance - Coipars, Corporación Colombiana de Investigación Agropecuaria - Corpoica, Cundinamarca, Colombia.
authors.forename: Alejandra
authors.initials: A
authors.lastname: Arevalo
authors.affiliation: Colombian Integrated Program for Antimicrobial Resistance Surveillance - Coipars, Corporación Colombiana de Investigación Agropecuaria - Corpoica, Cundinamarca, Colombia.
authors.forename: Johan F
authors.initials: JF
authors.lastname: Bernal
authors.affiliation: Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, the Netherlands.
authors.forename: Arjen J
authors.initials: AJ
authors.lastname: Timmerman
authors.affiliation: Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, the Netherlands.|Wageningen Bioveterinary Research, Lelystad, the Netherlands.
authors.forename: Dik J
authors.initials: DJ
authors.lastname: Mevius
authors.affiliation: Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, the Netherlands.|Wageningen Bioveterinary Research, Lelystad, the Netherlands.
authors.forename: Jaap A
authors.initials: JA
authors.lastname: Wagenaar
authors.affiliation: Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, the Netherlands.
authors.forename: Joost
authors.initials: J
authors.lastname: Hordijk
mesh_terms: D000818:Animals; D000900:Anti-Bacterial Agents / Q000494:pharmacology; D001426:Bacterial Proteins / Q000235:genetics* / Q000378:metabolism; D002645:Chickens / Q000382:microbiology; D003105:Colombia / Q000453:epidemiology; D062665:Epidemiological Monitoring; D004926:Escherichia coli / Q000145:classification / Q000187:drug effects / Q000235:genetics* / Q000302:isolation & purification; D004927:Escherichia coli Infections / Q000188:drug therapy / Q000453:epidemiology / Q000635:transmission / Q000662:veterinary*; D015964:Gene Expression Regulation, Bacterial; D022761:Gene Transfer, Horizontal; D018740:Genetic Heterogeneity; D006801:Humans; D010802:Phylogeny; D010957:Plasmids / Q000737:chemistry / Q000378:metabolism*; D011200:Poultry / Q000382:microbiology; D011201:Poultry Diseases / Q000188:drug therapy / Q000453:epidemiology / Q000382:microbiology / Q000635:transmission; D018440:beta-Lactam Resistance / Q000235:genetics*; D001618:beta-Lactamases / Q000235:genetics* / Q000378:metabolism; D047090:beta-Lactams / Q000494:pharmacology
chemical_list: D000900:Anti-Bacterial Agents; D001426:Bacterial Proteins; D047090:beta-Lactams; C048795:AmpC beta-lactamases; D001618:beta-Lactamases