title: The EpiQuant Framework for Computing Epidemiological Concordance of Microbial Subtyping Data.
abstract: A fundamental assumption in the use and interpretation of microbial subtyping results for public health investigations is that isolates that appear to be related based on molecular subtyping data are expected to share commonalities with respect to their origin, history, and distribution. Critically, there is currently no approach for systematically assessing the underlying epidemiology of subtyping results. Our aim was to develop a method for directly quantifying the similarity between bacterial isolates using basic sampling metadata and to develop a framework for computing the epidemiological concordance of microbial typing results. We have developed an analytical model that summarizes the similarity of bacterial isolates using basic parameters typically provided in sampling records, using a novel framework (EpiQuant) developed in the R environment for statistical computing. We have applied the EpiQuant framework to a data set comprising 654 isolates of the enteric pathogenCampylobacter jejunifrom Canadian surveillance data in order to examine the epidemiological concordance of clusters obtained by using two leadingC. jejunisubtyping methods. The EpiQuant framework can be used to directly quantify the similarity of bacterial isolates based on basic sample metadata. These results can then be used to assess the concordance between microbial epidemiological and molecular data, facilitating the objective assessment of subtyping method performance and paving the way for the improved application of molecular subtyping data in investigations of infectious disease.
authors.affiliation: Department of Biological Sciences, University of Lethbridge, Lethbridge, Alberta, Canada.|National Microbiology Laboratory at Lethbridge, Public Health Agency of Canada, Lethbridge, Alberta, Canada.
authors.forename: Benjamin M
authors.initials: BM
authors.lastname: Hetman
authors.affiliation: National Microbiology Laboratory at Lethbridge, Public Health Agency of Canada, Lethbridge, Alberta, Canada.
authors.forename: Steven K
authors.initials: SK
authors.lastname: Mutschall
authors.affiliation: Department of Biological Sciences, University of Lethbridge, Lethbridge, Alberta, Canada.
authors.forename: James E
authors.initials: JE
authors.lastname: Thomas
authors.affiliation: National Microbiology Laboratory at Lethbridge, Public Health Agency of Canada, Lethbridge, Alberta, Canada.
authors.forename: Victor P J
authors.initials: VPJ
authors.lastname: Gannon
authors.affiliation: National Microbiology Laboratory at Winnipeg, Public Health Agency of Canada, Winnipeg, Manitoba, Canada.
authors.forename: Clifford G
authors.initials: CG
authors.lastname: Clark
authors.affiliation: Centre for Foodborne, Environmental and Zoonotic Infectious Diseases, Public Health Agency of Canada, Guelph, Ontario, Canada.
authors.forename: Frank
authors.initials: F
authors.lastname: Pollari
authors.affiliation: National Microbiology Laboratory at Lethbridge, Public Health Agency of Canada, Lethbridge, Alberta, Canada eduardo.taboada@canada.ca.
authors.forename: Eduardo N
authors.identifier: 0000-0001-8373-3653
authors.initials: EN
authors.lastname: Taboada
mesh_terms: D002169:Campylobacter Infections / Q000453:epidemiology* / Q000382:microbiology; D016123:Campylobacter jejuni / Q000145:classification* / Q000235:genetics* / Q000302:isolation & purification; D002170:Canada / Q000453:epidemiology; D016680:Genome, Bacterial / Q000235:genetics; D006801:Humans; D015233:Models, Statistical; D017720:Molecular Epidemiology / Q000379:methods*; D058889:Molecular Typing / Q000379:methods*
keywords: Campylobacter jejuni; ecological epidemiology; epidemiological concordance; molecular epidemiology; molecular subtyping; sampling metadata; whole-genome sequencing