Whole-Genome Comparison of Two Campylobacter jejuni Isolates of the Same Sequence Type Reveals Multiple Loci of Different Ancestral Lineage

Biggs, Patrick J.; Fearnhead, Paul; Hotter, Grant S.; Mohan, Vathsala; Collins-Emerson, Julie; Kwan, Errol; Besser, Thomas E.; Cookson, Adrian L.; Carter, Philip E.; French, Nigel P.

doi:10.1371/journal.pone.0027121

Cited by 29 publications

(30 citation statements)

References 68 publications

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“…The estimated core genome of C. jejuni was 947 genes in 130 genomes ( Figure 3A ). Our estimates are consistent with previous studies where core genome size of C. jejuni was estimated to range from 847 genes [33] and 1,001 genes [34] to a maximum of 1,295 genes [29]. However, it is interesting to note that the core genome size does not reach a clear plateau, even when about 200 genomes are sampled, which indicates that if more diverse samples were added to this analysis, even fewer genes would be shared, something that has also been shown for Escherichia coli [35].…”

Section: Resultssupporting

confidence: 92%

A Reference Pan-Genome Approach to Comparative Bacterial Genomics: Identification of Novel Epidemiological Markers in Pathogenic Campylobacter

et al. 2014

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The increasing availability of hundreds of whole bacterial genomes provides opportunities for enhanced understanding of the genes and alleles responsible for clinically important phenotypes and how they evolved. However, it is a significant challenge to develop easy-to-use and scalable methods for characterizing these large and complex data and relating it to disease epidemiology. Existing approaches typically focus on either homologous sequence variation in genes that are shared by all isolates, or non-homologous sequence variation - focusing on genes that are differentially present in the population. Here we present a comparative genomics approach that simultaneously approximates core and accessory genome variation in pathogen populations and apply it to pathogenic species in the genus Campylobacter. A total of 7 published Campylobacter jejuni and Campylobacter coli genomes were selected to represent diversity across these species, and a list of all loci that were present at least once was compiled. After filtering duplicates a 7-isolate reference pan-genome, of 3,933 loci, was defined. A core genome of 1,035 genes was ubiquitous in the sample accounting for 59% of the genes in each isolate (average genome size of 1.68 Mb). The accessory genome contained 2,792 genes. A Campylobacter population sample of 192 genomes was screened for the presence of reference pan-genome loci with gene presence defined as a BLAST match of ≥70% identity over ≥50% of the locus length - aligned using MUSCLE on a gene-by-gene basis. A total of 21 genes were present only in C. coli and 27 only in C. jejuni, providing information about functional differences associated with species and novel epidemiological markers for population genomic analyses. Homologs of these genes were found in several of the genomes used to define the pan-genome and, therefore, would not have been identified using a single reference strain approach.

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Section: Resultssupporting

confidence: 92%

A Reference Pan-Genome Approach to Comparative Bacterial Genomics: Identification of Novel Epidemiological Markers in Pathogenic Campylobacter

et al. 2014

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“…Significant genomic differences have been previously observed between strains of the same MLST ST by microarray analysis (Taboada et al, 2008) and more recently by WGS analysis (Biggs et al, 2011). Because genomic differences between clonal strains are likely a reflection of the underlying epidemiology (i.e., separation in time and space), which would allow for the accumulation of such genomic differences, approaches to target such features through laboratory-based assays or to rapidly extract and analyze them from WGS data will become increasingly important in the deployment of genomic-based approaches in an epidemiological context.…”

Section: Resultsmentioning

confidence: 94%

A Framework for Assessing the Concordance of Molecular Typing Methods and the True Strain Phylogeny of Campylobacter jejuni and C. coli Using Draft Genome Sequence Data

Carrillo¹,

Kruczkiewicz²,

Mutschall³

et al. 2012

Front. Cell. Inf. Microbio.

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Tracking of sources of sporadic cases of campylobacteriosis remains challenging, as commonly used molecular typing methods have limited ability to unambiguously link genetically related strains. Genomics has become increasingly prominent in the public health response to enteric pathogens as methods enable characterization of pathogens at an unprecedented level of resolution. However, the cost of sequencing and expertise required for bioinformatic analyses remains prohibitive, and these comprehensive analyses are limited to a few priority strains. Although several molecular typing methods are currently widely used for epidemiological analysis of campylobacters, it is not clear how accurately these methods reflect true strain relationships. To address this, we have developed a framework and associated computational tools to rapidly analyze draft genome sequence data for the assessment of molecular typing methods against a “gold standard” based on the phylogenetic analysis of highly conserved core (HCC) genes with high sequence quality. We analyzed 104 publicly available whole genome sequences (WGS) of C. jejuni and C. coli. In addition to in silico determination of multi-locus sequence typing (MLST), flaA, and porA type, as well as comparative genomic fingerprinting (CGF) type, we inferred a “reference” phylogeny based on 389 HCC genes. Molecular typing data were compared to the reference phylogeny for concordance using the adjusted Wallace coefficient (AWC) with confidence intervals. Although MLST targets the sequence variability in core genes and CGF targets insertions/deletions of accessory genes, both methods are based on multi-locus analysis and provided better estimates of true phylogeny than methods based on single loci (porA, flaA). A more comprehensive WGS dataset including additional genetically related strains, both epidemiologically linked and unlinked, will be necessary to more comprehensively assess the performance of subtyping methods for outbreak investigations and surveillance activities. Analyses of the strengths and weaknesses of widely used typing methodologies in inferring true strain relationships will provide guidance in the interpretation of this data for epidemiological purposes.

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“…Although generally considered to be poor survivors outside of their animal hosts, some C. jejuni appear to be more able to survive and persist in environmental niches (French et al, 2005;Sopwith et al, 2008). For example, a study of C. jejuni in a specific area of cattle farmland in the UK found that environmental water isolates clustered within the ST-45 clonal complex much more frequently than other common clonal complexes (Biggs et al, 2011). The prevalence of specific strain types amongst isolates from multiple sources, including animals and the natural environment, can be compared with similar data from isolates associated with infections in humans.…”

Section: Use Of Genotyping To Attribute Routes Of Infectionmentioning

confidence: 99%

Role of environmental survival in transmission ofCampylobacter jejuni

Bronowski

James

Winstanley

2014

FEMS Microbiol Lett

157

152

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Campylobacter species are the most common cause of bacterial gastroenteritis, with C. jejuni responsible for the majority of these cases. Although it is clear that livestock, and particularly poultry, are the most common source, it is likely that the natural environment (soil and water) plays a key role in transmission, either directly to humans or indirectly via farm animals. It has been shown using multilocus sequence typing that some clonal complexes (such as ST-45) are more frequently isolated from environmental sources such as water, suggesting that strains vary in their ability to survive in the environment. Although C. jejuni are fastidious microaerophiles generally unable to grow in atmospheric levels of oxygen, C. jejuni can adapt to survival in the environment, exhibiting aerotolerance and starvation survival. Biofilm formation, the viable but nonculturable state, and interactions with other microorganisms can all contribute to survival outside the host. By exploiting high-throughput technologies such as genome sequencing and RNA Seq, we are well placed to decipher the mechanisms underlying the variations in survival between strains in environments such as soil and water and to better understand the role of environmental persistence in the transmission of C. jejuni directly or indirectly to humans.

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Whole-Genome Comparison of Two Campylobacter jejuni Isolates of the Same Sequence Type Reveals Multiple Loci of Different Ancestral Lineage

Cited by 29 publications

References 68 publications

A Reference Pan-Genome Approach to Comparative Bacterial Genomics: Identification of Novel Epidemiological Markers in Pathogenic Campylobacter

A Reference Pan-Genome Approach to Comparative Bacterial Genomics: Identification of Novel Epidemiological Markers in Pathogenic Campylobacter

A Framework for Assessing the Concordance of Molecular Typing Methods and the True Strain Phylogeny of Campylobacter jejuni and C. coli Using Draft Genome Sequence Data

Role of environmental survival in transmission ofCampylobacter jejuni

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