title: Novel genetic markers define a subgroup of pathogenic Escherichia coli strains belonging to the B2 phylogenetic group.
abstract: The B2 phylogenetic group of Escherichia coli contains important pathogens such as extraintestinal pathogenic, adherent-invasive, and uropathogenic strains. In this study, we used comparative genomics and statistical methods to identify genetic variations that define a subset of pathogenic strains belonging to the B2 phylogenetic group. An initial proof of concept analysis indicated that five of the 62 E. coli strains available in the Kyoto Encyclopedia of Genes and Genomes database showed close association with B2 adherent-invasive E. coli, forming a subgroup within the B2 phylogenetic group. The tool, kSNP which uses a k-mer approach, and the statistical phenotype prediction tool PPFS2 were then employed to identify 29 high-resolution SNPs, which reaffirmed this grouping. PPFS2 analysis also provided indications that the clustering of this subgroup was highly consistent, and thus, could have a strong phenotypic basis rather than being only evolutionary. Protein homology analyses identified three proteins to be conserved across this subgrouping, two CRISPR-Cas proteins and a hypothetical protein. Functional analyses of these genetic and protein variations may provide insights into the phenotype of these strains.
authors.affiliation: Systems Biology Initiative, School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, NSW 2052, Australia.
authors.forename: Nandan P
authors.initials: NP
authors.lastname: Deshpande
authors.affiliation: Systems Biology Initiative, School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, NSW 2052, Australia School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, NSW 2052, Australia Ramaciotti Centre for Gene Function Analysis, The University of New South Wales, Sydney, NSW 2052, Australia.
authors.forename: Marc R
authors.initials: MR
authors.lastname: Wilkins
authors.affiliation: School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, NSW 2052, Australia.
authors.forename: Hazel M
authors.initials: HM
authors.lastname: Mitchell
authors.affiliation: School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, NSW 2052, Australia n.kaakoush@unsw.edu.au.
authors.forename: Nadeem O
authors.initials: NO
authors.lastname: Kaakoush
mesh_terms: D056808:Biostatistics; D016000:Cluster Analysis; D019295:Computational Biology; D017124:Conserved Sequence; D004926:Escherichia coli / Q000145:classification* / Q000235:genetics*; D005819:Genetic Markers; D005838:Genotype; D010641:Phenotype; D010802:Phylogeny; D020641:Polymorphism, Single Nucleotide; D017386:Sequence Homology, Amino Acid
chemical_list: D005819:Genetic Markers
keywords: B2 phylogenetic group; Escherichia coli; biomarker; comparative genomics; single nucleotide polymorphism