title: In silicoserotyping ofE. colifrom short read data identifies limited novel O-loci but extensive diversity of O:H serotype combinations within and between pathogenic lineages.
abstract: The lipopolysaccharide (O) and flagellar (H) surface antigens ofEscherichia coliare targets for serotyping that have traditionally been used to identify pathogenic lineages. These surface antigens are important for the survival ofE. coliwithin mammalian hosts. However, traditional serotyping has several limitations, and public health reference laboratories are increasingly moving towards whole genome sequencing (WGS) to characterize bacterial isolates. Here we present a method to rapidly and accurately serotypeE. coliisolates from raw, short read WGS data. Our approach bypasses the need forde novogenome assembly by directly screening WGS reads against a curated database of alleles linked to known and novelE. coliO-groups and H-types (the EcOH database) using the software package srst2. We validated the approach by comparingin silicoresults for 197 enteropathogenicE. coliisolates with those obtained by serological phenotyping in an independent laboratory. We then demonstrated the utility of our method to characterize isolates in public health and clinical settings, and to explore the genetic diversity of >1500E. coligenomes from multiple sources. Importantly, we showed that transfer of O- and H-antigen loci betweenE. colichromosomal backbones is common, with little evidence of constraints by host or pathotype, suggesting thatE. coli 'strain space' may be virtually unlimited, even within specific pathotypes. Our findings show that serotyping is most useful when used in combination with strain genotyping to characterize microevolution events within an inferred population structure.
authors.affiliation: 2​Centre for Systems Genomics, University of Melbourne, Parkville, Victoria 3010, Australia.|1​Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Parkville, Victoria 3010, Australia.|3​Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria 3010, Australia.
authors.forename: Danielle J
authors.initials: DJ
authors.lastname: Ingle
authors.affiliation: 4​Microbiological Diagnostic Unit Public Health Laboratory, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Victoria 3010, Australia.
authors.forename: Mary
authors.initials: M
authors.lastname: Valcanis
authors.affiliation: 4​Microbiological Diagnostic Unit Public Health Laboratory, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Victoria 3010, Australia.
authors.forename: Alex
authors.initials: A
authors.lastname: Kuzevski
authors.affiliation: 1​Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Parkville, Victoria 3010, Australia.
authors.forename: Marija
authors.initials: M
authors.lastname: Tauschek
authors.affiliation: 2​Centre for Systems Genomics, University of Melbourne, Parkville, Victoria 3010, Australia.|5​School of BioSciences, University of Melbourne, Victoria 3010, Australia.
authors.forename: Michael
authors.initials: M
authors.lastname: Inouye
authors.affiliation: 1​Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Parkville, Victoria 3010, Australia.
authors.forename: Tim
authors.initials: T
authors.lastname: Stinear
authors.affiliation: 6​Department of Medicine, University of Maryland School of Medicine, Baltimore, MD 21201, USA.
authors.forename: Myron M
authors.initials: MM
authors.lastname: Levine
authors.affiliation: 1​Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Parkville, Victoria 3010, Australia.|7​Murdoch Childrens Research Institute, Royal Children's Hospital, Victoria 3010, Australia.
authors.forename: Roy M
authors.initials: RM
authors.lastname: Robins-Browne
authors.affiliation: 2​Centre for Systems Genomics, University of Melbourne, Parkville, Victoria 3010, Australia.|3​Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria 3010, Australia.
authors.forename: Kathryn E
authors.initials: KE
authors.lastname: Holt
mesh_terms: D000818:Animals; D000942:Antigens, Bacterial / Q000235:genetics; D003198:Computer Simulation; D004926:Escherichia coli / Q000145:classification / Q000235:genetics* / Q000472:pathogenicity*; D029968:Escherichia coli Proteins / Q000235:genetics*; D014644:Genetic Variation; D019081:O Antigens / Q000235:genetics; D010802:Phylogeny; D017422:Sequence Analysis, DNA; D065288:Serogroup; D012703:Serotyping
chemical_list: D000942:Antigens, Bacterial; D029968:Escherichia coli Proteins; C022863:H antigen; D019081:O Antigens
keywords: E. coli; diversity; genotype; phenotype; serotype