Comparative genomic assessment of Multi-Locus Sequence Typing: rapid accumulation of genomic heterogeneity among clonal isolates of Campylobacter jejuni

<p>Abstract</p> <p>Background</p> <p>Multi-Locus Sequence Typing (MLST) has emerged as a leading molecular typing method owing to its high ability to discriminate among bacterial isolates, the relative ease with which data acquisition and analysis can be standardized, and the high portability of the resulting sequence data. While MLST has been successfully applied to the study of the population structure for a number of different bacterial species, it has also provided compelling evidence for high rates of recombination in some species. We have analyzed a set of <it>Campylobacter jejuni </it>strains using MLST and Comparative Genomic Hybridization (CGH) on a full-genome microarray in order to determine whether recombination and high levels of genomic mosaicism adversely affect the inference of strain relationships based on the analysis of a restricted number of genetic loci.</p> <p>Results</p> <p>Our results indicate that, in general, there is significant concordance between strain relationships established by MLST and those based on shared gene content as established by CGH. While MLST has significant predictive power with respect to overall genome similarity of isolates, we also found evidence for significant differences in genomic content among strains that would otherwise appear to be highly related based on their MLST profiles.</p> <p>Conclusion</p> <p>The extensive genomic mosaicism between closely related strains has important implications in the context of establishing strain to strain relationships because it suggests that the exact gene content of strains, and by extension their phenotype, is less likely to be "predicted" based on a small number of typing loci. This in turn suggests that a greater emphasis should be placed on analyzing genes of clinical interest as we forge ahead with the next generation of molecular typing methods.</p

Genome evolution in major Escherichia coli O157:H7 lineages

© 2007 Zhang et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution Licens

In silico genomic analyses reveal three distinct lineages of Escherichia coli O157:H7, one of which is associated with hyper-virulence

<p>Abstract</p> <p>Background</p> <p>Many approaches have been used to study the evolution, population structure and genetic diversity of <it>Escherichia coli </it>O157:H7; however, observations made with different genotyping systems are not easily relatable to each other. Three genetic lineages of <it>E. coli </it>O157:H7 designated I, II and I/II have been identified using octamer-based genome scanning and microarray comparative genomic hybridization (mCGH). Each lineage contains significant phenotypic differences, with lineage I strains being the most commonly associated with human infections. Similarly, a clade of hyper-virulent O157:H7 strains implicated in the 2006 spinach and lettuce outbreaks has been defined using single-nucleotide polymorphism (SNP) typing. In this study an <it>in silico </it>comparison of six different genotyping approaches was performed on 19 <it>E. coli </it>genome sequences from 17 O157:H7 strains and single O145:NM and K12 MG1655 strains to provide an overall picture of diversity of the <it>E. coli </it>O157:H7 population, and to compare genotyping methods for O157:H7 strains.</p> <p>Results</p> <p><it>In silico </it>determination of lineage, Shiga-toxin bacteriophage integration site, comparative genomic fingerprint, mCGH profile, novel region distribution profile, SNP type and multi-locus variable number tandem repeat analysis type was performed and a supernetwork based on the combination of these methods was produced. This supernetwork showed three distinct clusters of strains that were O157:H7 lineage-specific, with the SNP-based hyper-virulent clade 8 synonymous with O157:H7 lineage I/II. Lineage I/II/clade 8 strains clustered closest on the supernetwork to <it>E. coli </it>K12 and <it>E. coli </it>O55:H7, O145:NM and sorbitol-fermenting O157 strains.</p> <p>Conclusion</p> <p>The results of this study highlight the similarities in relationships derived from multi-locus genome sampling methods and suggest a "common genotyping language" may be devised for population genetics and epidemiological studies. Future genotyping methods should provide data that can be stored centrally and accessed locally in an easily transferable, informative and extensible format based on comparative genomic analyses.</p

Pan-genome sequence analysis using Panseq: an online tool for the rapid analysis of core and accessory genomic regions

<p>Abstract</p> <p>Background</p> <p>The pan-genome of a bacterial species consists of a core and an accessory gene pool. The accessory genome is thought to be an important source of genetic variability in bacterial populations and is gained through lateral gene transfer, allowing subpopulations of bacteria to better adapt to specific niches. Low-cost and high-throughput sequencing platforms have created an exponential increase in genome sequence data and an opportunity to study the pan-genomes of many bacterial species. In this study, we describe a new online pan-genome sequence analysis program, Panseq.</p> <p>Results</p> <p>Panseq was used to identify <it>Escherichia coli </it>O157:H7 and <it>E. coli </it>K-12 genomic islands. Within a population of 60 <it>E. coli </it>O157:H7 strains, the existence of 65 accessory genomic regions identified by Panseq analysis was confirmed by PCR. The accessory genome and binary presence/absence data, and core genome and single nucleotide polymorphisms (SNPs) of six <it>L. monocytogenes </it>strains were extracted with Panseq and hierarchically clustered and visualized. The nucleotide core and binary accessory data were also used to construct maximum parsimony (MP) trees, which were compared to the MP tree generated by multi-locus sequence typing (MLST). The topology of the accessory and core trees was identical but differed from the tree produced using seven MLST loci. The Loci Selector module found the most variable and discriminatory combinations of four loci within a 100 loci set among 10 strains in 1 s, compared to the 449 s required to exhaustively search for all possible combinations; it also found the most discriminatory 20 loci from a 96 loci <it>E. coli </it>O157:H7 SNP dataset.</p> <p>Conclusion</p> <p>Panseq determines the core and accessory regions among a collection of genomic sequences based on user-defined parameters. It readily extracts regions unique to a genome or group of genomes, identifies SNPs within shared core genomic regions, constructs files for use in phylogeny programs based on both the presence/absence of accessory regions and SNPs within core regions and produces a graphical overview of the output. Panseq also includes a loci selector that calculates the most variable and discriminatory loci among sets of accessory loci or core gene SNPs.</p> <p>Availability</p> <p>Panseq is freely available online at <url>http://76.70.11.198/panseq</url>. Panseq is written in Perl.</p

Comparative genomic assessment of Multi-Locus Sequence Typing: rapid accumulation of genomic heterogeneity among clonal isolates of -1

Io data has been colour-coded according to data interpretation thresholds described in Taboada . []. Strains showing discordant clustering results are boxed in green.<p><b>Copyright information:</b></p><p>Taken from "Comparative genomic assessment of Multi-Locus Sequence Typing: rapid accumulation of genomic heterogeneity among clonal isolates of "</p><p>http://www.biomedcentral.com/1471-2148/8/229</p><p>BMC Evolutionary Biology 2008;8():229-229.</p><p>Published online 8 Aug 2008</p><p>PMCID:PMC2527321.</p><p></p

Comparative genomic assessment of Multi-Locus Sequence Typing: rapid accumulation of genomic heterogeneity among clonal isolates of -4

Uption of linkage is apparent among members the same CC that share the same loci.<p><b>Copyright information:</b></p><p>Taken from "Comparative genomic assessment of Multi-Locus Sequence Typing: rapid accumulation of genomic heterogeneity among clonal isolates of "</p><p>http://www.biomedcentral.com/1471-2148/8/229</p><p>BMC Evolutionary Biology 2008;8():229-229.</p><p>Published online 8 Aug 2008</p><p>PMCID:PMC2527321.</p><p></p

Comparative genomic assessment of Multi-Locus Sequence Typing: rapid accumulation of genomic heterogeneity among clonal isolates of -3

hyper-variable loci in the genome (B). Mosaicism observed in the CGH data is consistent with that observed in newly sequenced genomes (C). (note: Log Ratio data in (A) and (B) and sequence identity data in (C) were colour coded using a common scale reflecting the likelihood of gene presence/absence).<p><b>Copyright information:</b></p><p>Taken from "Comparative genomic assessment of Multi-Locus Sequence Typing: rapid accumulation of genomic heterogeneity among clonal isolates of "</p><p>http://www.biomedcentral.com/1471-2148/8/229</p><p>BMC Evolutionary Biology 2008;8():229-229.</p><p>Published online 8 Aug 2008</p><p>PMCID:PMC2527321.</p><p></p

Comparative genomic assessment of Multi-Locus Sequence Typing: rapid accumulation of genomic heterogeneity among clonal isolates of -5

boxed in red. Allelic differences with respect to the central sequence type (ST) of the CC are highlighted in blue.<p><b>Copyright information:</b></p><p>Taken from "Comparative genomic assessment of Multi-Locus Sequence Typing: rapid accumulation of genomic heterogeneity among clonal isolates of "</p><p>http://www.biomedcentral.com/1471-2148/8/229</p><p>BMC Evolutionary Biology 2008;8():229-229.</p><p>Published online 8 Aug 2008</p><p>PMCID:PMC2527321.</p><p></p