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131 results for “Campylobacter jejuni”
Genome assemblies and respective wg/cgMLST profiles of a diverse dataset comprising 3,076 Campylobacter jejuni isolates
<p><strong>Dataset</strong></p> <p>This dataset comprises the genome assemblies and respective 2,794-loci whole-genome (wg) Multiple Locus Sequence Type (MLST) profiles [INNUENDO schema (<a href="https://efsa.onlinelibrary.wiley.com/doi/epdf/10.2903/sp.efsa.2018.EN-1498">Llarena et al. 2018</a>) available in <a href="https://chewbbaca.online/species/4/schemas/1">chewie-NS</a> (<a href="https://academic.oup.com/nar/article/49/D1/D660/5929238">Mamede et al. 2022</a>)] of a final set of 3,076 <em>Campylobacter jejuni </em>samples selected among the Whole-Genome Sequencing (WGS) data publicly available in the European Nucleotide Archive (ENA) or in the <a href="https://www.ncbi.nlm.nih.gov/">National Center for Biotechnology Information</a> (NCBI) Sequence Read Archive (SRA) at the beginning of the analysis (November 2021). This set of samples was carefully selected to cover a wide genetic diversity (assessed in terms of Sequence Type [ST]). In total, 476 different STs are represented in this dataset, with ST21, ST50, ST48, ST45 and ST257 being the most represented ones and, together, corresponding to 29.1% of the dataset.</p> <p>File “Cj_metadata.xlsx” contains metadata information for each isolate, including ENA/SRA accession number, BioProject and in-silico MLST ST.</p> <p>The directory “assemblies/” contains all the genome assemblies (.fasta format) of each isolate presented in the metadata file. </p> <p>The file “profiles/Cj_profiles_wgMLST.tsv” corresponds to a tab separated file with the 2,794-loci wgMLST profiles of each solate presented in the metadata file. The files “profiles/Cj_profiles_cgMLST_95.tsv”, “profiles/Cj_profiles_cgMLST_98.tsv” and “profiles/Cj_profiles_cgMLST_100.tsv” correspond to a 1,012-loci, 987-loci and 29-loci cgMLST profiles of each isolate presented in the metadata file, respectively. These profiles were determined as explained below.</p> <p> </p> <p><strong>Dataset selection and curation</strong></p> <p>With the objective of creating a diverse dataset of <em>C. jejuni</em> genome assemblies, we collected information about the genetic diversity (serotype) of the isolates available at <a href="https://pubmlst.org/organisms/campylobacter-jejunicoli">PubMLST</a> database in the beginning of this analysis (November 2021) and in other previous works. Based on this information, we selected an initial dataset comprising 3,539 samples. The majority of them are associated with the INNUENDO project (<a href="https://efsa.onlinelibrary.wiley.com/doi/epdf/10.2903/sp.efsa.2018.EN-1498">Llarena et al. 2018</a>). The remaining ones are associated with five BioProjects (<a href="https://www.ncbi.nlm.nih.gov/bioproject/PRJEB31119">PRJEB31119</a>, <a href="https://www.ncbi.nlm.nih.gov/bioproject/PRJEB38253">PRJEB38253</a>, <a href="https://www.ncbi.nlm.nih.gov/bioproject/?term=PRJEB40238">PRJEB40238</a>, <a href="https://www.ncbi.nlm.nih.gov/bioproject/?term=PRJEB4165">PRJEB4165</a> and <a href="https://www.ncbi.nlm.nih.gov/bioproject/?term=PRJNA350537">PRJNA350537</a>). Their WGS data was downloaded from ENA/SRA with <a href="https://github.com/rpetit3/fastq-dl">fastq-dl</a> v1.0.6. Read quality control, trimming and assembly were performed with the Aquamis v1.3.9 (<a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8145556/">Deneke et al. 2021</a>) using default parameters. Assembly quality control (QC), including contamination assessment, as well as MLST ST determination were performed with the same pipeline. All genome assemblies passing the QC were included in the final dataset. Among the others, we noticed that a considerable proportion of assemblies was flagged as “QC fail” exclusively due to the “NumContamSNVs” parameter, suggesting that this setting might have been too strict. After manual inspection of a random subset, assemblies for which the percentage of reads corresponding to the correct species was >98% were recovered and integrated in the final dataset (those samples are labeled in the Metadata file). In total, 3,076 isolates passed this curation step and were included in the final dataset. wgMLST profiles of each of these isolates were determined with chewBBACA v2.8.5 (<a href="https://pubmed.ncbi.nlm.nih.gov/29543149/">Silva et al. 2018</a>), using the 2,794-loci INNUENDO schema available in <a href="https://chewbbaca.online/species/4">chewie-NS</a> (<a href="https://efsa.onlinelibrary.wiley.com/doi/epdf/10.2903/sp.efsa.2018.EN-1498">Llarena et al. 2018</a>; <a href="https://academic.oup.com/nar/article/49/D1/D660/5929238">Mamede et al. 2022</a>) and downloaded on May 31st, 2022. Three cgMLST schemas were obtained with <a href="https://github.com/insapathogenomics/ReporTree">ReporTree</a> v1.0.0 (<a href="https://www.researchsquare.com/article/rs-1404655/v1">Mixão et al. 2022</a>) using the 2,794-loci wgMLST profiles of the 3,076 isolates as input and setting distinct “--site-inclusion” thresholds: 0.95, 0.98 and 1.0 (i.e., keep schema loci called in at least 95%, 98% and 100% of the samples, resulting in a 1,012-loci, 987-loci and 29-loci allelic matrices, respectively).</p> <p> </p> <p><strong>Acknowledgements</strong></p> <p>We thank the National Distributed Computing Infrastructure of Portugal (INCD) for providing the necessary resources to run the genome assemblies. INCD was funded by FCT and FEDER under the project 22153-01/SAICT/2016.</p>
Supplementary dataset to publication: "Genomic insight into Campylobacter jejuni isolated from commercial turkey flocks in Germany using whole-genome sequencing analysis"
<p><em>Campylobacter jejuni </em>is a zoonotic bacterium of public health significance. The present investigation was designed to assess the epidemiology and genetic heterogeneity of <em>Campylobacter jejuni</em> recovered from commercial turkey farms in Germany using whole-genome sequencing. The Illumina MiSeq<sup>®</sup> technology was used to sequence 66 <em>Campylobacter jejuni </em>isolates obtained between 2010 and 2011 from commercial meat turkey flocks located in ten German federal states. Phenotypic antimicrobial resistance was determined. Phylogeny, resistome, plasmidome and virulome profiles were analyzed using whole-genome sequencing data. Genetic resistancemarkers were identified with bioinformatics tools (AMRFinder, ResFinder, NCBI and ABRicate) and compared with the phenotypic antimicrobial resistance.</p>
The OHEJP BeONE Project – Campylobacter jejuni genome assembly dataset
<p><strong>Dataset</strong></p> <p>This dataset comprises the genome assemblies of 610 <em>Campylobacter jejuni </em>samples collected by the BeONE Consortium on behalf of the One Health European Joint Programme “BeONE: Building Integrative Tools for One Health Surveillance” (<a href="https://onehealthejp.eu/jrp-beone/">https://onehealthejp.eu/jrp-beone/</a>). Additionally, a complementary dataset is also made available (<a href="https://zenodo.org/record/7120166">https://zenodo.org/record/7120166</a>), comprising genome assemblies of 3,076 <em>C. jejuni</em> samples selected among the Whole-Genome Sequencing (WGS) data publicly available in the European Nucleotide Archive (ENA) or in the National Center for Biotechnology Information (NCBI) Sequence Read Archive (SRA).</p> <p>File “<strong>BeONE_Cj_metadata.xlsx</strong>” contains the genome assembly statistics for each isolate, including European Nucleotide Archive accession numbers and <em>in-silico</em> Multi Locus Sequence Type, and information regarding year of sampling, country and source.</p> <p>The archive “<strong>BeONE_Cj_assemblies.zip</strong>” contains all the genome assemblies (.fasta format) of each isolate presented in the metadata file.</p> <p> </p> <p><strong>Dataset selection and curation</strong></p> <p>This anonymized dataset of <em>C. jejuni</em> genome assemblies was generated using Next Generation Sequencing data collected within the BeONE Consortium available at the European Nucleotide Archive under BioProject Accession Number <a href="https://www.ebi.ac.uk/ena/browser/view/PRJEB57119">PRJEB57119</a>. Read quality control, trimming and assembly were performed with Aquamis v1.3.9 (<a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8145556/">Deneke et al. 2021</a>) using default parameters. Assembly quality control (QC), including contamination assessment, as well as MLST ST determination were performed with the same pipeline. All genome assemblies passing the QC were included in the final dataset. Among the others, we noticed that a considerable proportion of assemblies was flagged as “QC fail” exclusively due to the “NumContamSNVs” parameter, suggesting that this setting might have been too strict. After manual inspection of a random subset, assemblies for which the percentage of reads corresponding to the correct species was >98% were recovered and integrated in the final dataset (those samples are labeled in the Metadata file). In total, 610 isolates passed the dataset curation step and were included in the final dataset.</p> <p> </p> <p><strong>Funding</strong></p> <p>This work was supported by funding from the European Union’s Horizon 2020 Research and Innovation programme under grant agreement No 773830: One Health European Joint Programme. </p> <p> </p> <p><strong>Acknowledgements</strong></p> <p>We thank the National Distributed Computing Infrastructure of Portugal (INCD) for providing the necessary resources to run the genome assemblies. INCD was funded by FCT and FEDER under the project 22153-01/SAICT/2016.</p>
Supporting data for: Persistent contamination of raw milk by Campylobacter jejuni ST-883
<p>Supporting data for the article: "Persistent contamination of raw milk by <em>Campylobacter jejuni</em> ST-883"</p>
INNUENDO whole genome and core genome MLST schemas and datasets for Campylobacter jejuni
<p><strong>Dataset</strong></p> <p>Raw reads deposited in the European Nucleotide Archive (ENA) or in the NCBI Sequence Read Archive (SRA) as <em>C. jejuni</em> were retrieved in April 2017. In total 5,691 genomes passed the INNUca v3.1 pipeline have been selected. Additionally, 566 raw reads previously published in <a href="https://www.ncbi.nlm.nih.gov/pubmed/27041390">Kovanen et al., 2016</a>, <a href="https://www.ncbi.nlm.nih.gov/pubmed/28348829">Llarena et al., 2016</a>, <a href="https://www.ncbi.nlm.nih.gov/pubmed/25232158">Kovanen et al., 2014</a>, <a href="https://www.ncbi.nlm.nih.gov/pubmed/24655229">Kovanen et al., 2014</a> and <a href="http://www.sciencedirect.com/science/article/pii/S0740002016310449?via%3Dihub">Gacia-Sanchez et a., 2017</a> were included. The database also includes 269 <em>C. jejuni</em> belonging to the INNUENDO Sequence Dataset (<a href="https://www.ebi.ac.uk/ena/data/view/PRJEB27020">PRJEB27020</a>). Genomes were assembled using <a href="https://github.com/INNUENDOCON/INNUca">INNUca v3.1 pipeline</a> and passed the QC. </p> <p>File 'Metadata/Cjejuni_metadata.txt' contains metadata information for each strain including country and year of isolation, source classification and taxa of the host, classical pubMLST 7 genes ST and CC classification. </p> <p>The directory 'Genomes' contains all the 6,526 INNUca V3.1 assemblies of the strains listed in 'Metadata/Cjejuni_metadata.txt'.</p> <p><strong>Schema creation and validation</strong></p> <p>Draft genome assemblies were annotated using Prokka and initial pangenome was defined using Roary. The <a href="https://github.com/B-UMMI/chewBBACA/wiki/1.-Schema-Creation"><em>chewBBACA CreateSchema.py</em></a> was used for creating a whole genome schema starting from roary pangenome. The schema was initially composed by 5,447 loci and has been populated with the 6,526 <em>C. jejuni</em> genomes. The quality of the loci has been assessed using <a href="https://github.com/B-UMMI/chewBBACA/wiki/1.-Schema-Creation"><em>chewBBACA Schema Evaluation</em></a>. Loci with single alleles and those with high length variability (i.e. if more than 1 allele is outside the mode +/- 0.05 size) have been removed. The wgMLST schema has been further curated, excluding all those loci detected as “Repeated Loci” and loci annotated as “non-informative paralogous hit (NIPH/ NIPHEM)” or “Allele Larger/ Smaller than length mode (ALM/ ASM)” by the <a href="https://github.com/B-UMMI/chewBBACA/wiki/2.-Allele-Calling"><em>chewBBACA Allele Calling</em></a> engine in more than 1% of the <em>C. jejuni</em> genomes dataset.</p> <p>File 'Schema/Cjejuni_wgMLST_2795_schema.tar.gz' contains the wgMLST schema formatted for chewBBACA and includes a total of 2,795 loci.</p> <p>File 'Schema/Cjejuni_cgMLST_678_listGenes.txt' contains the list of genes from the wgMLST schema which defines the cgMLST schema. The cgMLST schema consists of 678 loci and has been defined as the loci present in at least the 99.9% of the 6,526 <em>C. jejuni</em> genomes. Genomes have no more than 2% of missing loci.</p> <p>File 'Allele_Profles/Cjejuni_wgMLST_alleleProfiles.tsv' contains the wgMLST allelic profile of the 6,526 <em>C. jejuni</em> genomes of the dataset. Please note that missing loci follow the annotation of chewBBACA Allele Calling software.</p> <p>File 'Allele_Profles/Cjejuni_cgMLST_alleleProfiles.tsv' contains the cgMLST allelic profile of the 6,526 <em>C. jejuni</em> genomes of the dataset. Please note that missing loci are indicated with a zero.</p> <p><strong>Additional citations</strong></p> <p>The schema are prepared to be used with <a href="https://github.com/B-UMMI/chewBBACA/wiki"><strong>chewBBACA</strong></a>. When using the schema in this repository please cite also</p> <blockquote> <p>Silva M, Machado M, Silva D, Rossi M, Moran-Gilad J, Santos S, Ramirez M, Carriço J. chewBBACA: A complete suite for gene-by-gene schema creation and strain identification. 15/03/2018. M Gen 4(3): doi:10.1099/mgen.0.000166 <a href="http://mgen.microbiologyresearch.org/content/journal/mgen/10.1099/mgen.0.000166">http://mgen.microbiologyresearch.org/content/journal/mgen/10.1099/mgen.0.000166</a></p> </blockquote>
Supporting data and code for: Longitudinal Study on Shiga Toxin–producing Escherichia coli and Campylobacter jejuni on Finnish Dairy Farms and in Raw Milk
<p>Supporting data and code for the article: "Longitudinal Study on Shiga Toxin–producing <em>Escherichia coli</em> and <em>Campylobacter jejuni</em> on Finnish Dairy Farms and in Raw Milk".</p>
Metadata: In-ovo stimulation trains innate immunity to mitigate Campylobacter jejuni in broiler chickens
<p><span><span>Metadata of the paper investigating the physiological and genomic responses of these <em>in-ovo </em>stimulated chickens to <em>Campylobacter jejuni </em>infection. </span> </span></p>
In-vitro selection of lactic acid bacteria to combat Salmonella enterica and Campylobacter jejuni in broiler chickens
<p><em><span>In-vitro</span></em><span> selection of LAB strains for antimicrobial applications in livestock production required specific focus on certain LAB strains. Accordingly, six commercial LAB strains (homofermentative, obligatory heterofermentative and facultative heterofermentative) belonging to different genera, were chosen for screening against strains of <em>Salmonella </em>and <em>Campylobacter jejuni </em>under <em>in-vitro </em>conditions.</span></p> <p> </p>
Recurrent Campylobacter jejuni infections with in vivo selection of resistance to macrolides and carbapenems – assembly dataset
<p><strong>Dataset</strong></p> <p>This dataset comprises the genome assemblies of the first isolate collected from each clinical case (A1 and B1), together with the respective annotation.</p> <p>File “Cje_metadata.xlsx” contains the genome assembly statistics for each isolate, including the European Nucleotide Archive (ENA) accession numbers, genotyping and antibiotic resistance profiles.</p> <p>The directory “Assemblies/” contains the genome assembly (.fasta and .gbk formats) of each isolate presented in the metadata file.</p> <p> </p> <p><strong>Genome assembly and annotation</strong></p> <p>Reads quality control and improvement, species confirmation (using the 8GB database available at https://ccb.jhu.edu/software/kraken/) and <em>de novo</em> assembly were performed using the INNUca v4.2.2 pipeline (https://github.com/B-UMMI/INNUca). Briefly, after reads’ quality analysis using FastQC v0.11.5 (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) and cleaning with Trimmomatic v0.38 (http://www.usadellab.org/cms/?page=trimmomatic), genomes were <em>de novo</em> assembled with SPAdes 3.14.0 (http://bioinf.spbau.ru/spades) with a mean depth of coverage above 160x, and subsequently improved using Pilon v1.23. Multi-Locus Sequence Typing (MLST) was performed using mlst v2.18.1 software (https://github.com/tseemann/mlst). Genome annotation was performed with RAST server v2.0 (http://rast.nmpdr.org/).</p> <p>The raw sequence reads of each isolate were deposited at ENA under the study accession numbers PRJEB42628 and PRJNA505131.</p> <p> </p> <p><strong>Funding</strong></p> <p>This work was supported by GenomePT (ref. POCI-01-0145-FEDER-022184) from Fundação para a Ciência e Tecnologia, Portugal.</p>
Genomic analysis of the diversity, antimicrobial resistance and virulence potential of Campylobacter jejuni and Campylobacter coli strains from a private health care center in Central Chile
<p>Supplementary Dataset for the work entitled "Genomic analysis of the diversity, antimicrobial resistance and virulence potential of Campylobacter jejuni and Campylobacter coli strains from a private health care center in Central Chile".</p> <p>This dataset includes bacterial draft genome sequence reannotations of 69 C. jejuni and 12 C. coli strains, the fasta file containing the nucleotide sequence of <em>Campylobacter</em> pathogenicity genes screened for the virulome analysis and the fasta file for the in-house database for plasmid screening analysis in <em>Campylobacter </em>genomes.</p>
Data from: Campylobacter jejuni infection associated with relatively poor condition and low survival in a wild bird
Campylobacter jejuni is the most common foodborne pathogen in industrialized countries. Most human infections come from contaminated poultry, but wild birds are also known to harbor C. jejuni. Wild birds are often described as asymptomatic carriers, but this assumption is based on domestic poultry research. We studied the effects of C. jejuni infection on body condition and survival of adult and nestling American crows Corvus brachyrhynchos in Davis, California. Previous work demonstrated that more than half of the crows in this population are infected with C. jejuni and that at least some of the isolates carried by crows are similar to those found in domestic animals and humans. In this study, we compared the body condition of infected and uninfected individuals at the time of capture among adults (n = 44; 52% infected) and nestlings (n = 97; 77% infected). We subsequently monitored these banded individuals for up to 3 yr and used mark–recapture survival analysis to estimate relationships between infection status and later survival. We found that adult crows infected with C. jejuni were in poor condition relative to uninfected adults: average body mass of infected birds was 12% lower, whereas average body size did not differ between the two groups. Likewise, apparent survival probability was lower for infected adults. In contrast, nestling body condition, fledging success, and survival did not differ by infection status. This is the first study to document adverse effects of C. jejuni infection in a free-living, wild bird. If these effects are widespread, C. jejuni exposure may be a cause of conservation concern for some species, especially when human activities increase exposure to infections or introduce novel strains to wild bird populations. Our results add to the growing body of work demonstrating hidden long-term costs of seemingly mild infections in wild populations.
Atomistic modelling of lysophospholipids from the Campylobacter jejuni lipidome
<p>Input files for and trajectory files from the modelling and simulation of lysophospholipids from the C. jejuni lipidome. </p>
Campylobacter Jejuni Challenge Model Development: Assessment of Homologous Protection
ClinicalTrials.gov study NCT01048112. IPD Sharing: Not stated. Countries: 1. Publications: 1.
Data from: Campylobacter jejuni infection associated with relatively poor condition and low survival in a wild bird
Open the record for dataset details and reuse information.
Data from: Marked host specificity and lack of phylogeographic population structure of Campylobacter jejuni in wild birds
Open the record for dataset details and reuse information.
Data from: Cytokine responses in birds challenged with the human food-borne pathogen Campylobacter jejuni implies a Th17 response
Development of process orientated understanding of cytokine interactions within the gastrointestinal tract during an immune response to pathogens requires experimentation and statistical modelling. The immune response against pathogen challenge depends on the specific threat to the host. Here, we show that broiler chickens mount a breed-dependent immune response to Campylobacter jejuni infection in the caeca by analysing experimental data using frequentist and Bayesian structural equation models (SEM). SEM provides a framework by which cytokine interdependencies, based on prior knowledge, can be tested. In both breeds important cytokines including pro-inflammatory interleukin (IL)-1β, , IL-4, IL-17A, interferon (IFN)-γ and anti-inflammatory IL-10 and transforming growth factor (TGF)-β4 were expressed post-challenge. The SEM revealed a putative regulatory pathway illustrating a T helper (Th)17 response and regulation of IL-10, which is breed-dependent. The prominence of the Th17 pathway indicates the cytokine response aims to limit the invasion or colonization of an extracellular bacterial pathogen but the time-dependent nature of the response differs between breeds.
Data from: High throughput method for analysis of repeat number for 28 phase variable loci of Campylobacter jejuni strain NCTC11168
Mutations in simple sequence repeat tracts are a major mechanism of phase variation in several bacterial species including Campylobacter jejuni. Changes in repeat number of tracts located within the reading frame can produce a high frequency of reversible switches in gene expression between ON and OFF states. The genome of C. jejuni strain NCTC11168 contains 29 loci with polyG/polyC tracts of seven or more repeats. This protocol outlines a method—the 28-locus-CJ11168 PV-analysis assay—for rapidly determining ON/OFF states of 28 of these phase-variable loci in a large number of individual colonies from C. jejuni strain NCTC11168. The method combines a series of multiplex PCR assays with a fragment analysis assay and automated extraction of fragment length, repeat number and expression state. This high throughput, multiplex assay has utility for detecting shifts in phase variation states within and between populations over time and for exploring the effects of phase variation on adaptation to differing selective pressures. Application of this method to analysis of the 28 polyG/polyC tracts in 90 C. jejuni colonies detected a 2.5-fold increase in slippage products as tracts lengthened from G8 to G11 but no difference between tracts of similar length indicating that flanking sequence does not influence slippage rates. Comparison of this observed slippage to previously measured mutation rates for G8 and G11 tracts in C. jejuni indicates that PCR amplification of a DNA sample will over-estimate phase variation frequencies by 20-35-fold. An important output of the 28-locus-CJ11168 PV-analysis assay is combinatorial expression states that cannot be determined by other methods. This method can be adapted to analysis of phase variation in other C. jejuni strains and in a diverse range of bacterial species.
Data from: Cryptic ecology among host generalist Campylobacter jejuni in domestic animals
Homologous recombination between bacterial strains is theoretically capable of preventing the separation of daughter clusters, and producing cohesive clouds of genotypes in sequence space. However, numerous barriers to recombination are known. Barriers may be essential such as adaptive incompatibility, or ecological, which is associated with the opportunities for recombination in the natural habitat. Campylobacter jejuni is a gut colonizer of numerous animal species and a major human enteric pathogen. We demonstrate that the two major generalist lineages of C. jejuni do not show evidence of recombination with each other in nature, despite having a high degree of host niche overlap and recombining extensively with specialist lineages. However, transformation experiments show that the generalist lineages readily recombine with one another in vitro. This suggests ecological rather than essential barriers to recombination, caused by a cryptic niche structure within the hosts.
Figure 4 from: Sundermann EM, Nauta M, Swart A (2021) A ready-to-use dose-response model of Campylobacter jejuni implemented in the FSKX-standard. Food Modelling Journal 2: e63309. https://doi.org/10.3897/fmj.2.63309
Figure 4 The probability of illness and infection for the human population after consumption of Campylobacter jejuni-contaminated food. The probabilities are calculated based on the outbreak dataset with 1000 various mean doses (the so-called OutbreakVarMeanDoses simulation).
Figure 2 from: Sundermann EM, Nauta M, Swart A (2021) A ready-to-use dose-response model of Campylobacter jejuni implemented in the FSKX-standard. Food Modelling Journal 2: e63309. https://doi.org/10.3897/fmj.2.63309
Figure 2 The probability of illness and infection for the human population after consumption of a mean dose of 1 CFU of Campylobacter jejuni-contaminated food. The probabilities are calculated based on the outbreak dataset (the so-called outbreak simulation).
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