2,606
Views
25
CrossRef citations to date
0
Altmetric
Original Articles

Comparative genomics of Campylobacter concisus: Analysis of clinical strains reveals genome diversity and pathogenic potential

, , , ORCID Icon, , , & ORCID Icon show all
Pages 1-17 | Received 08 Dec 2017, Accepted 24 May 2018, Published online: 26 Jun 2018

References

  • TannerACWolinella gen. nov., Wolinella succinogenes (Vibrio succinogenes Wolin et al.) comb. nov., and description of Bacteroides gracilis sp. nov., Wolinella recta sp. nov., Campylobacter concisus sp. nov., and Eikenella corrodens from humans with periodontal diseaseInt. J. Syst. Evol. Microbiol.198131 432 445
  • NielsenHLEjlertsenTEngbergJNielsenHHigh incidence of Campylobacter concisus in gastroenteritis in North Jutland, Denmark: a population‐based studyClin. Microbiol. Infect.20131944545010.1111/j.1469-0691.2012.03852.x
  • ManSMCampylobacter concisus and other Campylobacter species in children with newly diagnosed Crohn’s diseaseInflamm. Bowel Dis.2010161008101610.1002/ibd.21157
  • MukhopadhyaIDetection of Campylobacter concisus and other Campylobacter species in colonic biopsies from adults with ulcerative colitisPLOS ONE20116e2149010.1371/journal.pone.00214903124515
  • ZhangLIsolation and detection of Campylobacter concisus from saliva of healthy individuals and patients with inflammatory bowel diseaseJ. Clin. Microbiol.2010482965296710.1128/JCM.02391-092916630
  • WangYCampylobacter concisus genomospecies 2 is better adapted to the human gastrointestinal tract as compared with campylobacter concisus genomospecies 1Front. Physiol.2017854310.3389/fphys.2017.005435541300
  • LavrencicPKaakoushNOHuinaoKDKainNMitchellHMInvestigation of motility and biofilm formation by intestinal Campylobacter concisus strainsGut Pathog.2012410.1186/1757-4749-4-223548772
  • NielsenHLOral and fecal Campylobacter concisus strains perturb barrier function by apoptosis induction in HT-29/B6 intestinal epithelial cellsPLOS ONE20116e2385810.1371/journal.pone.00238583161070
  • KaakoushNOMitchellHMManSMRole of emerging Campylobacter species in inflammatory bowel diseasesInflamm. Bowel Dis.2014202189219710.1097/MIB.0000000000000074
  • MukhopadhyaIHansenREl-OmarEMHoldGLIBD-what role do Proteobacteria play?Nat. Rev. Gastroenterol. Hepatol.2012921923010.1038/nrgastro.2012.14
  • ChungHKLGenome analysis of Campylobacter concisus strains from patients with inflammatory bowel disease and gastroenteritis provides new insights into pathogenicitySci. Rep.2016610.1038/srep384425133609
  • KaakoushNOComparative analyses of Campylobacter concisus strains reveal the genome of the reference strain BAA-1457 is not representative of the speciesGut Pathogens201131510.1186/1757-4749-3-153219677
  • KaakoushNOThe pathogenic potential of Campylobacter concisus strains associated with chronic intestinal diseasesPLOS ONE20116e2904510.1371/journal.pone.00290453237587
  • CoilDJospinGDarlingAEA5-miseq: an updated pipeline to assemble microbial genomes from Illumina MiSeq dataBioinformatics20143158758910.1093/bioinformatics/btu661
  • ChinCSNonhybrid, finished microbial genome assemblies from long-read SMRT sequencing dataNat. Methods20131056356910.1038/nmeth.2474
  • BoetzerMPirovanoWToward almost closed genomes with GapFillerGenome Biol.20121310.1186/gb-2012-13-6-r563446322
  • SeemannTProkka: rapid prokaryotic genome annotationBioinformatics2014302068206910.1093/bioinformatics/btu153
  • LaslettDCanbackBARAGORN, a program to detect tRNA genes and tmRNA genes in nucleotide sequencesNucleic Acids Res.200432111610.1093/nar/gkh152373265
  • FinnRDClementsJEddySRHMMER web server: interactive sequence similarity searchingNucleic Acids Res.201139W29W3710.1093/nar/gkr3673125773
  • KolbeDLEddySRFast filtering for RNA homology searchBioinformatics2011273102310910.1093/bioinformatics/btr5453208395
  • LagesenKRNAmmer: consistent and rapid annotation of ribosomal RNA genesNucleic Acids Res.2007353100310810.1093/nar/gkm1601888812
  • PetersenTNBrunakSvon HeijneGNielsenHSignalP 4.0: discriminating signal peptides from transmembrane regionsNat. Methods2011878578610.1038/nmeth.1701
  • GurevichASavelievVVyahhiNTeslerGQUAST: quality assessment tool for genome assembliesBioinformatics2013291072107510.1093/bioinformatics/btt0863624806
  • SimãoFAWaterhouseRMIoannidisPKriventsevaEVZdobnovEMBUSCO: assessing genome assembly and annotation completeness with single-copy orthologsBioinformatics2015313210321210.1093/bioinformatics/btv351
  • HuntMREAPR: a universal tool for genome assembly evaluationGenome Biol.20131410.1186/gb-2013-14-5-r473798757
  • LiHDurbinRFast and accurate short read alignment with Burrows–Wheeler transformBioinformatics2009251754176010.1093/bioinformatics/btp3242705234
  • LaetschDBlaxterMBlobTools: interrogation of genome assemblies [version 1; referees: 2 approved with reservations]F1000Res.20176128710.12688/f1000research.12232.1
  • AntipovDplasmidSPAdes: assembling plasmids from whole genome sequencing dataBioinformatics2016323380338710.1093/bioinformatics/btv688
  • QuinlanARBEDTools: the Swiss‐army tool for genome feature analysisCurr. Protoc. Bioinforma.20144713410.1002/0471250953.bi1112s47
  • TamuraKStecherGPetersonDFilipskiAKumarSMEGA6: molecular evolutionary genetics analysis version 6.0Mol. Biol. Evol.2013302725272910.1093/molbev/mst1973840312
  • EdgarRCMUSCLE: multiple sequence alignment with high accuracy and high throughputNucleic Acids Res.2004321792179710.1093/nar/gkh340390337
  • BertelsFSilanderOKPachkovMRaineyPBvan NimwegenEAutomated reconstruction of whole-genome phylogenies from short-sequence readsMol. Biol. Evol.2014311077108810.1093/molbev/msu0883995342
  • StamatakisARAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed modelsBioinformatics2006222688269010.1093/bioinformatics/btl446
  • LangmeadBTrapnellCPopMSalzbergSLUltrafast and memory-efficient alignment of short DNA sequences to the human genomeGenome Biol.20091010.1186/gb-2009-10-3-r252690996
  • McArthurAGThe comprehensive antibiotic resistance databaseAntimicrob. Agents Chemother.2013573348335710.1128/AAC.00419-133697360
  • ChenLZhengDLiuBYangJJinQVFDB 2016: hierarchical and refined dataset for big data analysis – 10 years onNucleic Acids Res.201644D694D69710.1093/nar/gkv1239
  • PageAJRoary: rapid large-scale prokaryote pan genome analysisBioinformatics2015313691369310.1093/bioinformatics/btv4214817141
  • KanehisaMSatoYMorishimaKBlastKOALA and GhostKOALA: KEGG tools for functional characterization of genome and metagenome sequencesJ. Mol. Biol.201642872673110.1016/j.jmb.2015.11.006
  • LetunicIBorkPInteractive tree of life (iTOL)v3: an online tool for the display and annotation of phylogenetic and other treesNucleic Acids Res.201644W242W24510.1093/nar/gkw2904987883
  • MahendranVDelineation of genetic relatedness and population structure of oral and enteric Campylobacter concisus strains by analysis of housekeeping genesMicrobiology20151611600161210.1099/mic.0.000112
  • DeshpandeNPKaakoushNOWilkinsMRMitchellHMComparative genomics of Campylobacter concisus isolates reveals genetic diversity and provides insights into disease associationBMC Genom.20131410.1186/1471-2164-14-585
  • MahendranVThe prevalence and polymorphisms of zonula occluden toxin gene in multiple Campylobacter concisus strains isolated from saliva of patients with inflammatory bowel disease and controlsPLoS One20138e7552510.1371/journal.pone.00755253781098
  • GundogduORe-annotation and re-analysis of the Campylobacter jejuni NCTC11168 genome sequenceBMC Genom.2007810.1186/1471-2164-8-162
  • WatanabeYCuiLKatayamaYKozueKHiramatsuKImpact of rpoB mutations on reduced vancomycin susceptibility in Staphylococcus aureusJ. Clin. Microbiol.2011492680268410.1128/JCM.02144-103147882
  • CorneliusAJComplete genome Sequence of Campylobacter concisus ATCC 33237T and draft genome sequences for an additional eight well-characterized C. concisus StrainsGenome Announc.20175e00711e0071710.1128/genomeA.00711-175522948
  • ManSMKaakoushNOOctaviaSMitchellHThe internal transcribed spacer region, a new tool for use in species differentiation and delineation of systematic relationships within the Campylobacter genusAppl. Environ. Microbiol.2010763071308110.1128/AEM.02551-092869123
  • FasanoAVibrio cholerae produces a second enterotoxin, which affects intestinal tight junctionsProc. Natl Acad. Sci. USA1991885242524610.1073/pnas.88.12.524251848
  • WarrenRLCo-occurrence of anaerobic bacteria in colorectal carcinomasMicrobiome2013110.1186/2049-2618-1-163971631
  • MacIntyreDLMiyataSTKitaokaMPukatzkiSThe Vibrio cholerae type VI secretion system displays antimicrobial propertiesProc. Natl Acad. Sci. USA2010107195201952410.1073/pnas.10129311072984155
  • ChowJMazmanianSKA pathobiont of the microbiota balances host colonization and intestinal inflammationCell Host Microbe2010726527610.1016/j.chom.2010.03.0042859213
  • SanaTGThe second type VI secretion system of Pseudomonas aeruginosa strain PAO1 is regulated by quorum sensing and Fur and modulates internalization in epithelial cellsJ. Biol. Chem.2012287270952710510.1074/jbc.M112.3763683411052
  • LuduJSThe Francisella pathogenicity island protein PdpD is required for full virulence and associates with homologues of the type VI secretion systemJ. Bacteriol.20081904584459510.1128/JB.00198-082446798
  • RussellABMougousJDPetersonSBType VI secretion system effectors: poisons with a purposeNat. Rev. Microbiol.20141213710.1038/nrmicro31854256078
  • StecherBMaierLHardtWD‘Blooming’in the gut: how dysbiosis might contribute to pathogen evolutionNat. Rev. Microbiol.20131127728410.1038/nrmicro2989
  • ChandranSPDetection of virulence genes in ESBL producing, quinolone resistant commensal Escherichia coli from rural Indian childrenJ. Infect. Dev. Ctries.20171138739210.3855/jidc.8574
  • MacuchPTannerACampylobacter species in health, gingivitis, and periodontitisJ. Dent. Res.20007978579210.1177/00220345000790021301
  • RoundJLMazmanianSKThe gut microbiota shapes intestinal immune responses during health and diseaseNat. Rev. Immunol.2009931332310.1038/nri25154095778
  • AchermannYGoldsteinEJCoenyeTShirtliffMEPropionibacterium acnes: from commensal to opportunistic biofilm-associated implant pathogenClin. Microbiol. Rev.20142741944010.1128/CMR.00092-134135900
  • HubeBFrom commensal to pathogen: stage-and tissue-specific gene expression of Candida albicansCurr. Opin. Microbiol.2004733634110.1016/j.mib.2004.06.003