rhs Genes Are Potential Markers for Multilocus Sequence Typing of Escherichia coli O157:H7 Strains
- 15 September 2009
- journal article
- Published by American Society for Microbiology in Applied and Environmental Microbiology
- Vol. 75 (18), 5853-5862
- https://doi.org/10.1128/aem.00859-09
Abstract
DNA sequence-based molecular subtyping methods such as multilocus sequence typing (MLST) are commonly used to generate phylogenetic inferences for monomorphic pathogens. The development of an effective MLST scheme for subtyping Escherichia coli O157:H7 has been hindered in the past due to the lack of sequence variation found within analyzed housekeeping and virulence genes. A recent study suggested that rhs genes are under strong positive selection pressure, and therefore in this study we analyzed these genes within a diverse collection of E. coli O157:H7 strains for sequence variability. Eighteen O157:H7 strains from lineages I and II and 15 O157:H7 strains from eight clades were included. Examination of these rhs genes revealed 44 polymorphic loci (PL) and 10 sequence types (STs) among the 18 lineage strains and 280 PL and 12 STs among the 15 clade strains. Phylogenetic analysis using rhs genes generally grouped strains according to their known lineage and clade classifications. These findings also suggested that O157:H7 strains from clades 6 and 8 fall into lineage I/II and that strains of clades 1, 2, 3, and 4 fall into lineage I. Additionally, unique markers were found in rhsA and rhsJ that might be used to define clade 8 and clade 6. Therefore, rhs genes may be useful markers for phylogenetic analysis of E. coli O157:H7.Keywords
This publication has 41 references indexed in Scilit:
- A precise reconstruction of the emergence and constrained radiations of Escherichia coli O157 portrayed by backbone concatenomic analysisProceedings of the National Academy of Sciences, 2009
- Phylogenetic classification of Escherichia coli O157:H7 strains of human and bovine origin using a novel set of nucleotide polymorphismsGenome Biology, 2009
- Rapid Determination ofEscherichia coliO157:H7 Lineage Types and Molecular Subtypes by Using Comparative Genomic FingerprintingApplied and Environmental Microbiology, 2008
- Genotypic Characterization and Prevalence of Virulence Factors among Canadian Escherichia coli O157:H7 StrainsApplied and Environmental Microbiology, 2008
- Genetic Differentiation of Escherichia coli O157:H7 Clades Associated with Human Disease by Real-Time PCRJournal of Clinical Microbiology, 2008
- Variation in virulence among clades of Escherichia coli O157:H7 associated with disease outbreaksProceedings of the National Academy of Sciences, 2008
- Genes under positive selection in Escherichia coliGenome Research, 2007
- Genome evolution in major Escherichia coli O157:H7 lineagesBMC Genomics, 2007
- Probing genomic diversity and evolution of Escherichia coli O157 by single nucleotide polymorphismsGenome Research, 2006
- Gapped BLAST and PSI-BLAST: a new generation of protein database search programsNucleic Acids Research, 1997