title: Identifying associations in Escherichia coli antimicrobial resistance patterns using additive Bayesian networks.
abstract: While the genesis of antimicrobial resistance (AMR) in animal production is a high profile topic in the media and the scientific community, it is still not well understood. The epidemiology of AMR is complex. This complexity is demonstrated by extensive biological and evolutionary mechanisms which are potentially impacted by farm management and husbandry practices - the risk factors. Many parts of this system have yet to be fully described. Notably, the occurrence of multiple resistance patterns is the rule rather than exception - the multivariate problem. A first essential step in the development of any comprehensive risk factor analysis - whose goal is the prevention or reduction of AMR - is to describe those associations between different patterns of resistance which are systematic. That is, have sufficient statistical support for these patterns to be considered robust features of the underlying epidemiological system, and whose presence must therefore be incorporated into any risk factor analysis of AMR for it to be meaningful with respect to the farm environment. Presented here is a case study that seeks to identify systematic associations between patterns of resistance to 13 different antimicrobials in Escherichia coli isolates obtained from composite finisher (>80 kg) pig faecal samples obtained from Canada's five major pork producing provinces. The use of a Bayesian network analysis approach allowed us to identify many systematic associations between individual antimicrobial resistances. Sixteen of these resistances are corroborated with existing literature. These associations are distributed between several important classes of antimicrobials including the β-lactams, folate biosynthesis inhibitors, tetracyclines, aminoglycosides and quinolones. This study presents an exciting first step towards the larger and far more ambitious goal of developing generic and holistic risk factor analyses for on-farm occurrence of AMR. Analyses of this nature would combine multivariate response variables (joint patterns of resistance) with multi-factorial causal factors from within the livestock production environment thereby permitting a more complete understanding of the epidemiology of antimicrobial resistance.
authors.affiliation: Laboratory for Foodborne Zoonoses, Public Health Agency of Canada, Groupe de Recherche en Épidémiologie et Santé Publique (GREZOSP), 3200 Sicotte C.P. 5000, St-Hyacinthe, QC J2S 7C6, Canada. antoinette.ludwig@phac-aspc.gc.ca
authors.forename: Antoinette
authors.initials: A
authors.lastname: Ludwig
authors.forename: Philippe
authors.initials: P
authors.lastname: Berthiaume
authors.forename: Patrick
authors.initials: P
authors.lastname: Boerlin
authors.forename: Sheryl
authors.initials: S
authors.lastname: Gow
authors.forename: David
authors.initials: D
authors.lastname: Léger
authors.forename: Fraser I
authors.initials: FI
authors.lastname: Lewis
mesh_terms: D000818:Animals; D000900:Anti-Bacterial Agents / Q000494:pharmacology*; D001499:Bayes Theorem; D002170:Canada; D024901:Drug Resistance, Multiple, Bacterial; D004926:Escherichia coli / Q000187:drug effects*; D004927:Escherichia coli Infections / Q000453:epidemiology / Q000382:microbiology / Q000662:veterinary*; D005243:Feces / Q000382:microbiology; D015999:Multivariate Analysis; D012307:Risk Factors; D012621:Seasons; D013552:Swine; D013553:Swine Diseases / Q000453:epidemiology* / Q000382:microbiology*
chemical_list: D000900:Anti-Bacterial Agents