title: AreEscherichia coliPathotypes Still Relevant in the Era of Whole-Genome Sequencing?
abstract: The empirical and pragmatic nature of diagnostic microbiology has given rise to several different schemes to subtypeE.coli, including biotyping, serotyping, and pathotyping. These schemes have proved invaluable in identifying and tracking outbreaks, and for prognostication in individual cases of infection, but they are imprecise and potentially misleading due to the malleability and continuous evolution ofE. coli. Whole genome sequencing can be used to accurately determineE. colisubtypes that are based on allelic variation or differences in gene content, such as serotyping and pathotyping. Whole genome sequencing also provides information about single nucleotide polymorphisms in the core genome ofE. coli, which form the basis of sequence typing, and is more reliable than other systems for tracking the evolution and spread of individual strains. A typing scheme forE. colibased on genome sequences that includes elements of both the core and accessory genomes, should reduce typing anomalies and promote understanding of how different varieties ofE. colispread and cause disease. Such a scheme could also define pathotypes more precisely than current methods.
authors.affiliation: Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, The University of MelbourneParkville, VIC, Australia; Murdoch Childrens Research Institute, Royal Children's HospitalParkville, VIC, Australia.
authors.forename: Roy M
authors.initials: RM
authors.lastname: Robins-Browne
authors.affiliation: Centre for Systems Genomics, The University of MelbourneParkville, VIC, Australia; Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, The University of MelbourneParkville, VIC, Australia.
authors.forename: Kathryn E
authors.initials: KE
authors.lastname: Holt
authors.affiliation: Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, The University of MelbourneParkville, VIC, Australia; Centre for Systems Genomics, The University of MelbourneParkville, VIC, Australia; Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, The University of MelbourneParkville, VIC, Australia.
authors.forename: Danielle J
authors.initials: DJ
authors.lastname: Ingle
authors.affiliation: Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, The University of Melbourne Parkville, VIC, Australia.
authors.forename: Dianna M
authors.initials: DM
authors.lastname: Hocking
authors.affiliation: Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, The University of Melbourne Parkville, VIC, Australia.
authors.forename: Ji
authors.initials: J
authors.lastname: Yang
authors.affiliation: Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, The University of Melbourne Parkville, VIC, Australia.
authors.forename: Marija
authors.initials: M
authors.lastname: Tauschek
mesh_terms: D018829:Adhesins, Bacterial / Q000235:genetics; D015373:Bacterial Typing Techniques / Q000379:methods; D001483:Base Sequence; D004269:DNA, Bacterial / Q000235:genetics; D003967:Diarrhea / Q000382:microbiology; D004196:Disease Outbreaks; D054324:Enterohemorrhagic Escherichia coli / Q000145:classification / Q000235:genetics / Q000302:isolation & purification; D054308:Enteropathogenic Escherichia coli / Q000145:classification / Q000235:genetics / Q000302:isolation & purification; D054307:Enterotoxigenic Escherichia coli / Q000235:genetics; D004926:Escherichia coli / Q000145:classification* / Q000235:genetics* / Q000302:isolation & purification / Q000472:pathogenicity*; D004927:Escherichia coli Infections / Q000382:microbiology; D029968:Escherichia coli Proteins / Q000191:economics*; D019143:Evolution, Molecular; D019204:GTP-Binding Proteins / Q000191:economics*; D005798:Genes, Bacterial; D016680:Genome, Bacterial; D006801:Humans; D058889:Molecular Typing / Q000379:methods*; D010802:Phylogeny; D020641:Polymorphism, Single Nucleotide; D016601:RNA-Binding Proteins / Q000191:economics*; D017422:Sequence Analysis, DNA; D012703:Serotyping / Q000379:methods; D014774:Virulence / Q000235:genetics
chemical_list: D018829:Adhesins, Bacterial; D004269:DNA, Bacterial; D029968:Escherichia coli Proteins; D016601:RNA-Binding Proteins; C068027:era protein, E coli; D019204:GTP-Binding Proteins
keywords: E. coli; bacterial typing; diarrhoea; pathogenesis; pathotype; sequence type; whole genome sequence