Identification of Immunogenic and Virulence-Associated Campylobacter jejuni Proteins

Nielsen, Lene Nørby; Luijkx, Thomas A.; Vegge, Christina S.; Johnsen, Christina K.; Nuijten, Piet J. M.; Wren, Brendan W.; Ingmer, Hanne; Krogfelt, Karen A.

doi:10.1128/cvi.05161-11

Cited by 18 publications

(21 citation statements)

References 29 publications

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“…Cj0034c was recently reported to be an adhesion and virulence factor in C. jejuni (Nielsen et al 2011). Cj0035c encodes a putative efflux pump (membrane transporter) belonging to the major facilitator family.…”

Section: Resultsmentioning

confidence: 99%

Efficient Inference of Recombination Hot Regions in Bacterial Genomes

Yahara

Didelot

Ansari

et al. 2014

Molecular Biology and Evolution

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In eukaryotes, detailed surveys of recombination rates have shown variation at multiple genomic scales and the presence of “hotspots” of highly elevated recombination. In bacteria, studies of recombination rate variation are less developed, in part because there are few analysis methods that take into account the clonal context within which bacterial evolution occurs. Here, we focus in particular on identifying “hot regions” of the genome where DNA is transferred frequently between isolates. We present a computationally efficient algorithm based on the recently developed “chromosome painting” algorithm, which characterizes patterns of haplotype sharing across a genome. We compare the average genome wide painting, which principally reflects clonal descent, with the painting for each site which additionally reflects the specific deviations at the site due to recombination. Using simulated data, we show that hot regions have consistently higher deviations from the genome wide average than normal regions. We applied our approach to previously analyzed Escherichia coli genomes and revealed that the new method is highly correlated with the number of recombination events affecting each site inferred by ClonalOrigin, a method that is only applicable to small numbers of genomes. Furthermore, we analyzed recombination hot regions in Campylobacter jejuni by using 200 genomes. We identified three recombination hot regions, which are enriched for genes related to membrane proteins. Our approach and its implementation, which is downloadable from https://github.com/bioprojects/orderedPainting, will help to develop a new phase of population genomic studies of recombination in prokaryotes.

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Section: Resultsmentioning

confidence: 99%

Efficient Inference of Recombination Hot Regions in Bacterial Genomes

Yahara

Didelot

Ansari

et al. 2014

Molecular Biology and Evolution

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“…In general, the past decade has provided us with substantial findings, revealing many of the virulence components of C. jejuni [28], however the exact mechanism of its pathology is as yet still unclear [29], [30]. The small, curved shape of this Gram-negative bacterium, coupled with flagella-mediated motility, allow C. jejuni to penetrate intestinal mucus [31], where it can then adhere to epithelial cells via various surface associated adhesions, such as CadF and FlpA, which mediate binding to host tissue fibronectin [32]. Once attached, the bacterium then employs a range of secretion systems including the flagellar type III, the type IV and the recently identified type VI [33], [34], [35], [36], through which it secretes invasion antigens, such as CiaB, which may promote cellular invasion of the intestinal epithelial cells [37] .…”

Section: Introductionmentioning

confidence: 99%

Genomic Investigation into Strain Heterogeneity and Pathogenic Potential of the Emerging Gastrointestinal Pathogen Campylobacter ureolyticus

et al. 2013

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The recent detection and isolation of C. ureolyticus from patients with diarrhoeal illness and inflammatory bowel diseases warrants further investigation into its role as an emerging pathogen of the human gastrointestinal tract. Regarding the pathogenic mechanisms employed by this species we provide the first whole genome analysis of two C. ureolyticus isolates including the type strain. Comparative analysis, subtractive hybridisation and gene ontology searches against other Campylobacter species identifies the high degree of heterogenicity between C. ureolyticus isolates, in addition to the identification of 106 putative virulence associated factors, 52 of which are predicted to be secreted. Such factors encompass each of the known virulence tactics of pathogenic Campylobacter spp. including adhesion and colonisation (CadF, PEB1, IcmF and FlpA), invasion (ciaB and 16 virB-virD4 genes) and toxin production (S-layer RTX and ZOT). Herein, we provide the first virulence catalogue for C. ureolyticus, the components of which theoretically provide this emerging species with sufficient arsenal to establish pathology.

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“…Furthermore, insights into virulence traits including strategies to sequester the iron required for infection were detailed using NCTC 11168 [39–41]. Vaccine targets have been identified [42–44] and the mechanisms of core metabolic processes [45, 46], biofilm production [47–51], capsule production [52] and resistance to oxidative stress have been elucidated [53, 54]. Accidental passage through a laboratory worker also identified putative human host adaptations in vivo [55].…”

Section: Introductionmentioning

confidence: 99%

Domestication ofCampylobacter jejuniNCTC 11168

Pascoe

Williams

Calland

et al. 2019

Preprint

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Reference and type strains of well-known bacteria have been a cornerstone of microbiology research for decades. The sharing of well-characterised isolates among laboratories has parallelised research efforts and enhanced the reproducibility of experiments, leading to a wealth of knowledge about trait variation in different species and the underlying genetics. Campylobacter jejuni strain NCTC 11168, deposited at the National Collection of Type Cultures in 1977, has been adopted widely as a reference strain by researchers worldwide and was the first Campylobacter for which the complete genome was published (in 2000). In this study, we collected 23 C. jejuni NCTC 11168 reference isolates from laboratories across the UK and compared variation in simple laboratory phenotypes with genetic variation in sequenced genomes. Putatively identical isolates identified previously to have aberrant phenotypes varied by up to 281 SNPs (in 15 genes) compared to the most recent reference strain. Isolates also display considerable phenotype variation in motility, morphology, growth at 37°C, invasion of chicken and human cell lines and susceptibility to ampicillin. This study provides evidence of ongoing evolutionary change among C. jejuni isolates as they are cultured in different laboratories and highlights the need for careful consideration of genetic variation within laboratory reference strains.Impact statementIn this paper, we comment on the changing role of laboratory reference strains. While the model organism allows basic comparison within and among laboratories, it is important to remember the effect even small differences in isolate genomes can have on the validity and reproducibility of experimental work. We quantify differences in 23 reference Campylobacter genomes and compare them with observable differences in common laboratory phenotypes.Data summaryShort read data are archived on the NCBI SRA associated with BioProject accession PRJNA517467 (https://www.ncbi.nlm.nih.gov/bioproject/PRJNA517467).All assembled genomes are also available on FigShare (doi: 10.6084/m9.figshare.7849268). Phylogeny visualised on microreact: https://microreact.org/project/NCTC11168.RepositoriesShort read data are archived on the NCBI SRA repository, associated with BioProject accession PRJNA517467 (https://www.ncbi.nlm.nih.gov/bioproject/PRJNA517467; Table S1).The authors confirm all supporting data, code and protocols have been provided within the article or through supplementary data files.

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Identification of Immunogenic and Virulence-Associated Campylobacter jejuni Proteins

Cited by 18 publications

References 29 publications

Efficient Inference of Recombination Hot Regions in Bacterial Genomes

Efficient Inference of Recombination Hot Regions in Bacterial Genomes

Genomic Investigation into Strain Heterogeneity and Pathogenic Potential of the Emerging Gastrointestinal Pathogen Campylobacter ureolyticus

Domestication ofCampylobacter jejuniNCTC 11168

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