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      Common genomic features of Campylobacter jejuni subsp. doylei strains distinguish them from C. jejuni subsp. jejuni

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          Abstract

          Background

          Campylobacter jejuni has been divided into two subspecies: C. jejuni subsp. jejuni ( Cjj) and C. jejuni subsp. doylei ( Cjd). Nearly all of the C. jejuni strains isolated are Cjj; nevertheless, although Cjd strains are isolated infrequently, they differ from Cjj in two key aspects: they are obtained primarily from human clinical samples and are associated often with bacteremia, in addition to gastroenteritis. In this study, we utilized multilocus sequence typing (MLST) and a DNA microarray-based comparative genomic indexing (CGI) approach to examine the genomic diversity and gene content of Cjd strains.

          Results

          A geographically diverse collection of eight Cjd strains was examined by MLST and determined to be phylogenetically distinct from Cjj strains. Microarray-based CGI approach also supported this. We were able to demonstrate that Cjd strains exhibited divergence from Cjj strains NCTC 11168 and RM1221 in many of the intraspecies hypervariable regions. Moreover, multiple metabolic, transport and virulence functions (e.g. cytolethal distending toxin) were shown to be absent in the Cjd strains examined.

          Conclusion

          Our data demonstrate that Cjd are phylogenetically distinct from Cjj strains. Using the CGI approach, we identified subsets of absent genes from amongst the C. jejuni genes that provide clues as to the potential evolutionary origin and unusual pathogenicity of Cjd.

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          MEGA3: Integrated software for Molecular Evolutionary Genetics Analysis and sequence alignment.

          S. KUMAR (2004)
          With its theoretical basis firmly established in molecular evolutionary and population genetics, the comparative DNA and protein sequence analysis plays a central role in reconstructing the evolutionary histories of species and multigene families, estimating rates of molecular evolution, and inferring the nature and extent of selective forces shaping the evolution of genes and genomes. The scope of these investigations has now expanded greatly owing to the development of high-throughput sequencing techniques and novel statistical and computational methods. These methods require easy-to-use computer programs. One such effort has been to produce Molecular Evolutionary Genetics Analysis (MEGA) software, with its focus on facilitating the exploration and analysis of the DNA and protein sequence variation from an evolutionary perspective. Currently in its third major release, MEGA3 contains facilities for automatic and manual sequence alignment, web-based mining of databases, inference of the phylogenetic trees, estimation of evolutionary distances and testing evolutionary hypotheses. This paper provides an overview of the statistical methods, computational tools, and visual exploration modules for data input and the results obtainable in MEGA.
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            The genome sequence of the food-borne pathogen Campylobacter jejuni reveals hypervariable sequences.

            J. Parkhill, B W Wren, K Mungall … (2000)
            Campylobacter jejuni, from the delta-epsilon group of proteobacteria, is a microaerophilic, Gram-negative, flagellate, spiral bacterium-properties it shares with the related gastric pathogen Helicobacter pylori. It is the leading cause of bacterial food-borne diarrhoeal disease throughout the world. In addition, infection with C. jejuni is the most frequent antecedent to a form of neuromuscular paralysis known as Guillain-Barré syndrome. Here we report the genome sequence of C. jejuni NCTC11168. C. jejuni has a circular chromosome of 1,641,481 base pairs (30.6% G+C) which is predicted to encode 1,654 proteins and 54 stable RNA species. The genome is unusual in that there are virtually no insertion sequences or phage-associated sequences and very few repeat sequences. One of the most striking findings in the genome was the presence of hypervariable sequences. These short homopolymeric runs of nucleotides were commonly found in genes encoding the biosynthesis or modification of surface structures, or in closely linked genes of unknown function. The apparently high rate of variation of these homopolymeric tracts may be important in the survival strategy of C. jejuni.
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              Multilocus sequence typing system for Campylobacter jejuni.

              K Dingle, F. Colles, D Wareing … (2001)
              The gram-negative bacterium Campylobacter jejuni has extensive reservoirs in livestock and the environment and is a frequent cause of gastroenteritis in humans. To date, the lack of (i) methods suitable for population genetic analysis and (ii) a universally accepted nomenclature has hindered studies of the epidemiology and population biology of this organism. Here, a multilocus sequence typing (MLST) system for this organism is described, which exploits the genetic variation present in seven housekeeping loci to determine the genetic relationships among isolates. The MLST system was established using 194 C. jejuni isolates of diverse origins, from humans, animals, and the environment. The allelic profiles, or sequence types (STs), of these isolates were deposited on the Internet (http://mlst.zoo.ox.ac.uk), forming a virtual isolate collection which could be continually expanded. These data indicated that C. jejuni is genetically diverse, with a weakly clonal population structure, and that intra- and interspecies horizontal genetic exchange was common. Of the 155 STs observed, 51 (26% of the isolate collection) were unique, with the remainder of the collection being categorized into 11 lineages or clonal complexes of related STs with between 2 and 56 members. In some cases membership in a given lineage or ST correlated with the possession of a particular Penner HS serotype. Application of this approach to further isolate collections will enable an integrated global picture of C. jejuni epidemiology to be established and will permit more detailed studies of the population genetics of this organism.
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                Author and article information

                Journal
                Journal ID (nlm-ta): BMC Microbiol
                Title: BMC Microbiology
                Publisher: BioMed Central (London )
                ISSN (Electronic): 1471-2180
                Publication date Collection: 2007
                Publication date (Electronic): 29 May 2007
                Volume: 7
                Page: 50
                Affiliations
                [1 ]Produce Safety and Microbiology Research Unit, Agricultural Research Service, US. Department of Agriculture, Albany, CA 94710 USA
                [2 ]Department of Biotechnology, University of the Western Cape, Bellville 7535, South Africa
                Article
                Publisher ID: 1471-2180-7-50
                DOI: 10.1186/1471-2180-7-50
                PMC ID: 1892558
                PubMed ID: 17535437
                SO-VID: 31fe030f-4c7a-41b0-ba68-017c70ff9c50
                Copyright © Copyright © 2007 Parker et al; licensee BioMed Central Ltd.
                License:

                This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

                History
                Date received : 22 December 2006
                Date accepted : 29 May 2007
                Categories
                Subject: Research Article

                ScienceOpen disciplines: Microbiology & Virology
                Data availability:
                ScienceOpen disciplines: Microbiology & Virology

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