{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,29]],"date-time":"2026-03-29T08:04:57Z","timestamp":1774771497553,"version":"3.50.1"},"reference-count":103,"publisher":"Frontiers Media SA","license":[{"start":{"date-parts":[[2023,7,13]],"date-time":"2023-07-13T00:00:00Z","timestamp":1689206400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100020884","name":"Agencia Nacional de Investigaci\u00f3n y Desarrollo","doi-asserted-by":"publisher","award":["1221209, 1191074, 1201805, ECOS200037"],"award-info":[{"award-number":["1221209, 1191074, 1201805, ECOS200037"]}],"id":[{"id":"10.13039\/501100020884","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100002941","name":"Departamento de Investigaciones Cient\u00edficas y Tecnol\u00f3gicas, Universidad de Santiago de Chile","doi-asserted-by":"publisher","award":["022001BZ"],"award-info":[{"award-number":["022001BZ"]}],"id":[{"id":"10.13039\/501100002941","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000011","name":"Howard Hughes Medical Institute","doi-asserted-by":"publisher","award":["55008749"],"award-info":[{"award-number":["55008749"]}],"id":[{"id":"10.13039\/100000011","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["frontiersin.org"],"crossmark-restriction":true},"short-container-title":["Front. Cell. Infect. Microbiol."],"abstract":"<jats:p><jats:italic>Campylobacter<\/jats:italic> is the leading cause of bacterial gastroenteritis worldwide and an emerging and neglected pathogen in South America. This zoonotic pathogen colonizes the gastrointestinal tract of a wide range of mammals and birds, with poultry as the most important reservoir for human infections. Apart from its high morbidity rates, the emergence of resistant strains is of global concern. The aims of this work were to determine genetic diversity, presence of antimicrobial resistance determinants and virulence potential of <jats:italic>Campylobacter<\/jats:italic> spp. isolated from patients with acute gastrointestinal disease at \u2018Clinica Alemana\u2019, Santiago de Chile. The study considered the isolation of <jats:italic>Campylobacter<\/jats:italic> spp., from stool samples during a 20-month period (January 2020 to September 2021). We sequenced (NextSeq, Illumina) and performed an in-depth analysis of the genome sequences of 88 <jats:italic>Campylobacter jejuni<\/jats:italic> and 2 <jats:italic>Campylobacter<\/jats:italic> coli strains isolated from clinical samples in Chile. We identified a high genetic diversity among C. je<jats:italic>juni<\/jats:italic> strains and the emergence of prevalent clonal complexes, which were not identified in our previous reports. While ~40% of strains harbored a mutation in the gyrA gene associated with fluoroquinolone resistance, no macrolide-resistance determinants were detected. Interestingly, gene clusters encoding virulence factors such as the T6SS or genes associated with long-term sequelae such as Guillain-Barr\u00e9 syndrome showed lineage-relatedness. In addition, our analysis revealed a high degree of variability regarding the presence of fT3SS and T6SS effector proteins in comparison to type strains 81-176, F38011, and NCTC 11168 and 488. Our study provides important insights into the molecular epidemiology of this emerging foodborne pathogen. In addition, the differences observed regarding the repertoire of fT3SS and T6SS effector proteins could have an impact on the pathogenic potential and transmissibility of these Latin American isolates, posing another challenge in characterizing the infection dynamics of this emergent and neglected bacterial pathogen.<\/jats:p>","DOI":"10.3389\/fcimb.2023.1208825","type":"journal-article","created":{"date-parts":[[2023,7,13]],"date-time":"2023-07-13T19:51:26Z","timestamp":1689277886000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":10,"title":["Whole-genome sequencing reveals changes in genomic diversity and distinctive repertoires of T3SS and T6SS effector candidates in Chilean clinical Campylobacter strains"],"prefix":"10.3389","volume":"13","author":[{"given":"Assaf","family":"Katz","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Lorena","family":"Porte","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Thomas","family":"Weitzel","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Carmen","family":"Varela","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Cristina","family":"Mu\u00f1oz-Rehbein","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Juan A.","family":"Ugalde","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Christopher","family":"Grim","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Narjol","family":"Gonz\u00e1lez-Escalona","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Carlos J.","family":"Blondel","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ver\u00f3nica","family":"Bravo","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"1965","published-online":{"date-parts":[[2023,7,13]]},"reference":[{"key":"B1","doi-asserted-by":"publisher","first-page":"1201","DOI":"10.1086\/319760","article-title":"Campylobacter jejuni infections: update on emerging issues and trends","volume":"32","author":"Acheson","year":"2001","journal-title":"Clin. Infect. Diseases"},{"key":"B2","doi-asserted-by":"publisher","first-page":"237","DOI":"10.1186\/s12879-019-3858-x","article-title":"Clinical impact of the type VI secretion system on virulence of campylobacter species during infection","volume":"19","author":"Agnetti","year":"2019","journal-title":"BMC Infect. Dis."},{"key":"B3","doi-asserted-by":"publisher","first-page":"D690","DOI":"10.1093\/nar\/gkac920","article-title":"CARD 2023: expanded curation, support for machine learning, and resistome prediction at the comprehensive antibiotic resistance database","volume":"51","author":"Alcock","year":"2022","journal-title":"Nucleic Acids Res."},{"key":"B4","doi-asserted-by":"publisher","first-page":"1742","DOI":"10.1111\/cmi.12532","article-title":"Molecular weaponry: diverse effectors delivered by the type VI secretion system","volume":"17","author":"Alcoforado Diniz","year":"2015","journal-title":"Cell. Microbiol."},{"key":"B5","doi-asserted-by":"publisher","DOI":"10.1111\/cmi.13153","article-title":"Causalities of war: the connection between type VI secretion system and microbiota","volume":"22","author":"Allsopp","year":"2020","journal-title":"Cell. Microbiol."},{"key":"B6","doi-asserted-by":"publisher","DOI":"10.1101\/2021.02.23.432443","article-title":"Machine learning to predict the source of campylobacteriosis using whole genome data","volume":"17","author":"Arning","year":"2021","journal-title":"Bioinformatics"},{"key":"B7","doi-asserted-by":"publisher","first-page":"4384","DOI":"10.1128\/IAI.68.8.4384-4390.2000","article-title":"Involvement of a plasmid in virulence of Campylobacter jejuni 81-176","volume":"68","author":"Bacon","year":"2000","journal-title":"Infect. Immun."},{"key":"B8","doi-asserted-by":"publisher","first-page":"352","DOI":"10.1111\/j.1365-2958.2012.08027.x","article-title":"Identification and analysis of flagellar coexpressed determinants (Feds) of Campylobacter jejuni involved in colonization: flagellar coexpressed determinants of C. jejuni","volume":"84","author":"Barrero-Tobon","year":"2012","journal-title":"Mol. Microbiol."},{"key":"B9","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1111\/1462-2920.13956","article-title":"Type VI secretion systems in plant-associated bacteria","volume":"20","author":"Bernal","year":"2018","journal-title":"Environ. Microbiol."},{"key":"B10","doi-asserted-by":"publisher","first-page":"8098","DOI":"10.1038\/s41598-019-44454-2","article-title":"Source attribution of Campylobacter jejuni shows variable importance of chicken and ruminants reservoirs in non-invasive and invasive French clinical isolates","volume":"9","author":"Berthenet","year":"2019","journal-title":"Sci. Rep."},{"key":"B11","doi-asserted-by":"publisher","DOI":"10.1371\/journal.ppat.1003393","article-title":"Identification of a functional type VI secretion system in Campylobacter jejuni conferring capsule polysaccharide sensitive cytotoxicity","volume":"9","author":"Bleumink-Pluym","year":"2013","journal-title":"PLoS Pathog."},{"key":"B12","doi-asserted-by":"publisher","first-page":"3491","DOI":"10.1093\/jac\/dkaa345","article-title":"ResFinder 4.0 for predictions of phenotypes from genotypes","volume":"75","author":"Bortolaia","year":"2020","journal-title":"J. Antimicrob. Chemother."},{"key":"B13","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pntd.0009207","article-title":"Genomic analysis of the diversity, antimicrobial resistance and virulence potential of clinical Campylobacter jejuni and campylobacter coli strains from Chile","volume":"15","author":"Bravo","year":"2021","journal-title":"PLoS Negl. Trop. Dis."},{"key":"B14","doi-asserted-by":"publisher","first-page":"e00535","DOI":"10.1128\/MRA.00535-20","article-title":"Complete genome sequences of 17 clinical Campylobacter jejuni strains from Chile","volume":"9","author":"Bravo","year":"2020","journal-title":"Microbiol. Resour. Announc."},{"key":"B15","doi-asserted-by":"publisher","DOI":"10.1128\/MRA.00072-20","article-title":"Whole-genome sequences of 51 Campylobacter jejuni and 12 campylobacter coli clinical isolates from Chile","volume":"9","author":"Bravo","year":"2020","journal-title":"Microbiol. Resour. Announc."},{"key":"B16","doi-asserted-by":"publisher","first-page":"551","DOI":"10.1038\/s41579-018-0037-9","article-title":"Campylobacter jejuni: collective components promoting a successful enteric lifestyle","volume":"16","author":"Burnham","year":"2018","journal-title":"Nat. Rev. Microbiol."},{"key":"B17","doi-asserted-by":"publisher","first-page":"868","DOI":"10.1111\/j.1469-0691.2004.00983.x","article-title":"Campylobacter, from obscurity to celebrity","volume":"10","author":"Butzler","year":"2004","journal-title":"Clin. Microbiol. Infection"},{"key":"B18","doi-asserted-by":"publisher","first-page":"421","DOI":"10.1186\/1471-2105-10-421","article-title":"BLAST+: architecture and applications","volume":"10","author":"Camacho","year":"2009","journal-title":"BMC Bioinf."},{"key":"B19","doi-asserted-by":"publisher","first-page":"464","DOI":"10.1093\/bioinformatics\/btr703","article-title":"Artemis: An integrated platform for visualization and analysis of high-throughput sequence-based experimental data","volume":"28","author":"Carver","year":"2012","journal-title":"Bioinformatics."},{"key":"B20","doi-asserted-by":"publisher","first-page":"3422","DOI":"10.1093\/bioinformatics\/bti553","article-title":"ACT: the Artemis comparison tool","volume":"21","author":"Carver","year":"2005","journal-title":"Bioinformatics."},{"key":"B21","doi-asserted-by":"publisher","first-page":"329","DOI":"10.1016\/j.tim.2018.01.006","article-title":"Antibacterial weapons: targeted destruction in the microbiota","volume":"26","author":"Chassaing","year":"2018","journal-title":"Trends Microbiol."},{"key":"B22","doi-asserted-by":"publisher","DOI":"10.3389\/fmicb.2021.662144","article-title":"Whole resistome analysis in Campylobacter jejuni and c. coli genomes available in public repositories","volume":"12","author":"Cobo-D\u00edaz","year":"2021","journal-title":"Front. Microbiol."},{"key":"B23","doi-asserted-by":"publisher","first-page":"2086","DOI":"10.1128\/JCM.00080-17","article-title":"Core genome multilocus sequence typing scheme for stable, comparative analyses of Campylobacter jejuni and c. coli human disease isolates","volume":"55","author":"Cody","year":"2017","journal-title":"J. Clin. Microbiol."},{"key":"B24","unstructured":"A systematic review of source attribution of human campylobacteriosis using multilocus sequence typing\n            CodyA. J.\n            MaidenM. C.\n            StrachanN. J.\n            McCarthyN. D.\n          10.2807\/1560-7917.ES.2019.24.43.1800696Euro Surveill.242019"},{"key":"B25","doi-asserted-by":"publisher","first-page":"3193","DOI":"10.1128\/JCM.01086-12","article-title":"A longitudinal 6-year study of the molecular epidemiology of clinical campylobacter isolates in Oxfordshire, united kingdom","volume":"50","author":"Cody","year":"2012","journal-title":"J. Clin. Microbiol."},{"key":"B26","doi-asserted-by":"publisher","DOI":"10.4067\/s0716-10182020000300244","article-title":"Diagn\u00f3stico microbiol\u00f3gico y vigilancia epidemiol\u00f3gica de la campilobacteriosis en Chile: situaci\u00f3n actual y desaf\u00edos futuros","volume":"37","author":"Collado","year":"2020","journal-title":"Rev. Chil Infectol"},{"key":"B27","doi-asserted-by":"publisher","first-page":"290","DOI":"10.1016\/j.meegid.2017.12.026","article-title":"Genetic diversity and clonal characteristics of ciprofloxacin-resistant Campylobacter jejuni isolated from Chilean patients with gastroenteritis","volume":"58","author":"Collado","year":"2018","journal-title":"Infection Genet. Evolution"},{"key":"B28","doi-asserted-by":"publisher","first-page":"e00072","DOI":"10.1128\/CMR.00072-18","article-title":"Pathogenomics of emerging Campylobacter species","volume":"32","author":"Costa","year":"2019","journal-title":"Clin. Microbiol. Rev."},{"key":"B29","doi-asserted-by":"publisher","first-page":"503","DOI":"10.1099\/mic.0.000789","article-title":"The type VI secretion system: a versatile bacterial weapon","volume":"165","author":"Coulthurst","year":"2019","journal-title":"Microbiology."},{"key":"B30","doi-asserted-by":"publisher","first-page":"7","DOI":"10.1128\/9781683670285.ch27","article-title":"Type VI secretion systems and the gut microbiota","volume":"7","author":"Coyne","year":"2019","journal-title":"Microbiol. Spectr."},{"key":"B31","doi-asserted-by":"publisher","first-page":"3028","DOI":"10.1038\/s41598-018-21438-2","article-title":"Origin, evolution, and distribution of the molecular machinery for biosynthesis of sialylated lipooligosaccharide structures in campylobacter coli","volume":"8","author":"Culebro","year":"2018","journal-title":"Sci. Rep."},{"key":"B32","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0011147","article-title":"progressiveMauve: multiple genome alignment with gene gain, loss and rearrangement","volume":"5","author":"Darling","year":"2010","journal-title":"PLoS ONE"},{"key":"B33","doi-asserted-by":"publisher","first-page":"721","DOI":"10.1038\/ismej.2015.149","article-title":"Rapid host switching in generalist campylobacter strains erodes the signal for tracing human infections","volume":"10","author":"Dearlove","year":"2016","journal-title":"ISME J."},{"key":"B34","doi-asserted-by":"publisher","first-page":"498","DOI":"10.1016\/j.tim.2014.06.004","article-title":"VgrG, tae, tle, and beyond: the versatile arsenal of type VI secretion effectors","volume":"22","author":"Durand","year":"2014","journal-title":"Trends Microbiol."},{"key":"B35","doi-asserted-by":"publisher","DOI":"10.2903\/j.efsa.2019.5926","article-title":"The European union one health 2018 zoonoses report","volume":"17","year":"2019","journal-title":"EFSA J."},{"key":"B36","doi-asserted-by":"publisher","DOI":"10.3389\/fcimb.2020.607704","article-title":"Revisiting Campylobacter jejuni virulence and fitness factors: role in sensing, adapting, and competing","volume":"10","author":"Elmi","year":"2021","journal-title":"Front. Cell Infect. Microbiol."},{"key":"B37","doi-asserted-by":"publisher","first-page":"10358","DOI":"10.1038\/s41598-021-89683-6","article-title":"Genome-wide insights into population structure and host specificity of Campylobacter jejuni","volume":"11","author":"Epping","year":"2021","journal-title":"Sci. Rep."},{"key":"B38","doi-asserted-by":"publisher","first-page":"e00483","DOI":"10.1128\/AAC.00483-19","article-title":"Validating the AMRFinder tool and resistance gene database by using antimicrobial resistance genotype-phenotype correlations in a collection of isolates","volume":"63","author":"Feldgarden","year":"2019","journal-title":"Antimicrob. Agents Chemother."},{"key":"B39","doi-asserted-by":"publisher","first-page":"D222","DOI":"10.1093\/nar\/gkt1223","article-title":"Pfam: the protein families database","volume":"42","author":"Finn","year":"2014","journal-title":"Nucl. Acids Res."},{"key":"B40","doi-asserted-by":"publisher","first-page":"14222","DOI":"10.3390\/ijms232214222","article-title":"Triggers of Guillain\u2013Barr\u00e9 syndrome: Campylobacter jejuni predominates","volume":"23","author":"Finsterer","year":"2022","journal-title":"IJMS."},{"key":"B41","doi-asserted-by":"publisher","first-page":"000748","DOI":"10.1099\/mgen.0.000748","article-title":"ResFinder \u2013 an open online resource for identification of antimicrobial resistance genes in next-generation sequencing data and prediction of phenotypes from genotypes","volume":"8","author":"Florensa","year":"2022","journal-title":"Microb. Genom."},{"key":"B42","doi-asserted-by":"publisher","first-page":"135","DOI":"10.3390\/biom13010135","article-title":"The missing pieces: the role of secretion systems in Campylobacter jejuni virulence","volume":"13","author":"Gabbert","year":"2023","journal-title":"Biomolecules."},{"key":"B43","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pntd.0010869","article-title":"Candidatus campylobacter infans\u201d detection is not associated with diarrhea in children under the age of 2 in Peru","volume":"16","author":"Garcia Bardales","year":"2022","journal-title":"PLoS Negl. Trop. Dis."},{"key":"B44","doi-asserted-by":"publisher","first-page":"1516","DOI":"10.1089\/mdr.2019.0266","article-title":"Molecular epidemiology and resistance profile of Campylobacter jejuni and Campylobacter coli strains isolated from different sources in Brazil","volume":"26","author":"Gomes","year":"2020","journal-title":"Microbial Drug Resistance"},{"key":"B45","doi-asserted-by":"publisher","first-page":"325","DOI":"10.3390\/microorganisms8030325","article-title":"Differential distribution of the wlaN and cgtB genes, associated with Guillain-Barr\u00e9 syndrome, in Campylobacter jejuni isolates from humans, broiler chickens, and wild birds","volume":"8","author":"Guirado","year":"2020","journal-title":"Microorganisms."},{"key":"B46","doi-asserted-by":"publisher","first-page":"212","DOI":"10.1128\/AAC.01310-13","article-title":"ARG-ANNOT, a new bioinformatic tool to discover antibiotic resistance genes in bacterial genomes","volume":"58","author":"Gupta","year":"2014","journal-title":"Antimicrob. Agents Chemother."},{"key":"B47","doi-asserted-by":"publisher","first-page":"81","DOI":"10.1016\/j.mib.2015.11.006","article-title":"Type VI secretion and anti-host effectors","volume":"29","author":"Hachani","year":"2016","journal-title":"Curr. Opin. Microbiol."},{"key":"B48","article-title":"DeepTMHMM predicts alpha and beta transmembrane proteins using deep neural networks","author":"Hallgren","year":"2022","journal-title":"Bioinformatics"},{"key":"B49","doi-asserted-by":"publisher","first-page":"9","DOI":"10.1016\/j.chom.2013.11.008","article-title":"A view to a kill: the bacterial type VI secretion system","volume":"15","author":"Ho","year":"2014","journal-title":"Cell Host Microbe"},{"key":"B50","doi-asserted-by":"publisher","first-page":"237","DOI":"10.1016\/j.ijfoodmicro.2007.01.006","article-title":"Campylobacters as zoonotic pathogens: a food production perspective","volume":"117","author":"Humphrey","year":"2007","journal-title":"Int. J. Food Microbiol."},{"key":"B51","doi-asserted-by":"publisher","first-page":"124","DOI":"10.12688\/wellcomeopenres.14826.1","article-title":"Open-access bacterial population genomics: BIGSdb software, the PubMLST.org website and their applications","volume":"3","author":"Jolley","year":"2018","journal-title":"Wellcome Open Res."},{"key":"B52","doi-asserted-by":"publisher","first-page":"687","DOI":"10.1128\/CMR.00006-15","article-title":"Global epidemiology of campylobacter infection","volume":"28","author":"Kaakoush","year":"2015","journal-title":"Clin. Microbiol. Rev."},{"key":"B53","doi-asserted-by":"publisher","first-page":"42","DOI":"10.1093\/nar\/30.1.42","article-title":"The KEGG databases at GenomeNet","volume":"30","author":"Kanehisa","year":"2002","journal-title":"Nucleic Acids Res."},{"key":"B54","doi-asserted-by":"publisher","first-page":"691","DOI":"10.1046\/j.1365-2958.1999.01376.x","article-title":"Bacterial secreted proteins are required for the internaliztion of Campylobacter jejuni into cultured mammalian cells","volume":"32","author":"Konkel","year":"1999","journal-title":"Mol. Microbiol."},{"key":"B55","doi-asserted-by":"publisher","first-page":"10409","DOI":"10.1007\/s00253-020-10974-5","article-title":"Campylobacter sp.: pathogenicity factors and prevention methods\u2013new molecular targets for innovative antivirulence drugs","volume":"104","author":"Kreling","year":"2020","journal-title":"Appl. Microbiol. Biotechnol."},{"key":"B56","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0042842","article-title":"Campylobacter jejuni type VI secretion system: roles in adaptation to deoxycholic acid, host cell adherence, invasion, and In vivo colonization","volume":"7","author":"Lertpiriyapong","year":"2012","journal-title":"PLoS One"},{"key":"B57","doi-asserted-by":"publisher","first-page":"W256","DOI":"10.1093\/nar\/gkz239","article-title":"Interactive tree of life (iTOL) v4: recent updates and new developments","volume":"47","author":"Letunic","year":"2019","journal-title":"Nucleic Acids Res."},{"key":"B58","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1155\/2019\/1902732","article-title":"Genomic analysis of Chilean strains of Campylobacter jejuni from human faeces","volume":"2019","author":"Levican","year":"2019","journal-title":"BioMed. Res. Int."},{"key":"B59","doi-asserted-by":"publisher","DOI":"10.3389\/fmicb.2019.02864","article-title":"The Campylobacter jejuni type VI secretion system enhances the oxidative stress response and host colonization","volume":"10","author":"Liaw","year":"2019","journal-title":"Front. Microbiol."},{"key":"B60","doi-asserted-by":"publisher","first-page":"501","DOI":"10.1046\/j.1365-2958.2000.02020.x","article-title":"Phase variation of a \u03b2-1,3 galactosyltransferase involved in generation of the ganglioside GM1-like lipo-oligosaccharide of Campylobacter jejuni: c. jejuni LOS phase variation","volume":"37","author":"Linton","year":"2002","journal-title":"Mol. Microbiol."},{"key":"B61","doi-asserted-by":"publisher","first-page":"1120","DOI":"10.1046\/j.1365-2958.2000.01780.x","article-title":"Multiple n-acetyl neuraminic acid synthetase (neuB) genes in Campylobacter jejuni: identification and characterization of the gene involved in sialylation of lipo-oligosaccharide","volume":"35","author":"Linton","year":"2000","journal-title":"Mol. Microbiol."},{"key":"B62","doi-asserted-by":"publisher","first-page":"D687","DOI":"10.1093\/nar\/gky1080","article-title":"VFDB 2019: a comparative pathogenomic platform with an interactive web interface","volume":"47","author":"Liu","year":"2019","journal-title":"Nucleic Acids Res."},{"key":"B63","doi-asserted-by":"publisher","first-page":"D265","DOI":"10.1093\/nar\/gkz991","article-title":"CDD\/SPARCLE: the conserved domain database in 2020","volume":"48","author":"Lu","year":"2020","journal-title":"Nucleic Acids Res."},{"key":"B64","doi-asserted-by":"publisher","first-page":"e01465","DOI":"10.1128\/MRA.01465-20","article-title":"Closed genome sequence of a salmonella enterica serotype senftenberg strain carrying the mcr-9 gene isolated from broken chicken eggshells in Trinidad and Tobago","volume":"10","author":"Maguire","year":"2021","journal-title":"Microbiol. Resour. Announc."},{"key":"B65","doi-asserted-by":"publisher","DOI":"10.3389\/fmicb.2018.02167","article-title":"Phylogenetic relatedness among plasmids harbored by Campylobacter jejuni and campylobacter coli isolated from retail meats","volume":"9","author":"Marasini","year":"2018","journal-title":"Front. Microbiol."},{"key":"B66","doi-asserted-by":"publisher","first-page":"763","DOI":"10.1093\/gbe\/evy026","article-title":"Convergent amino acid signatures in polyphyletic Campylobacter jejuni subpopulations suggest human niche tropism","volume":"10","author":"M\u00e9ric","year":"2018","journal-title":"Genome Biol. Evolution"},{"key":"B67","doi-asserted-by":"publisher","first-page":"383","DOI":"10.1017\/S0950268802006830","article-title":"The seasonal distribution of campylobacter infection in nine European countries and new Zealand","volume":"128","author":"Nylen","year":"2002","journal-title":"Epidemiol. Infect."},{"key":"B68","doi-asserted-by":"publisher","first-page":"3691","DOI":"10.1093\/bioinformatics\/btv421","article-title":"Roary: rapid large-scale prokaryote pan genome analysis","volume":"31","author":"Page","year":"2015","journal-title":"Bioinformatics."},{"key":"B69","doi-asserted-by":"publisher","first-page":"1538","DOI":"10.3390\/genes12101538","article-title":"The distribution of Campylobacter jejuni virulence genes in genomes worldwide derived from the NCBI pathogen detection database","volume":"12","author":"Panzenhagen","year":"2021","journal-title":"Genes."},{"key":"B70","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pntd.0010815","article-title":"Shotgun metagenomics of fecal samples from children in Peru reveals frequent complex co-infections with multiple campylobacter species","volume":"16","author":"Parker","year":"2022","journal-title":"PloS Negl. Trop. Dis."},{"key":"B71","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pntd.0008533","article-title":"Genomic epidemiology of Campylobacter jejuni associated with asymptomatic paediatric infection in the Peruvian Amazon","volume":"14","author":"Pascoe","year":"2020","journal-title":"PLoS Negl. Trop. Dis."},{"key":"B72","doi-asserted-by":"publisher","first-page":"444","DOI":"10.1097\/QCO.0000000000000091","article-title":"Update on the burden of campylobacter in developing countries","volume":"27","author":"Platts-Mills","year":"2014","journal-title":"Curr. Opin. Infect. Dis."},{"key":"B73","doi-asserted-by":"publisher","first-page":"3859","DOI":"10.1128\/IAI.00159-07","article-title":"Heterogeneity of a Campylobacter jejuni protein that is secreted through the flagellar filament","volume":"75","author":"Poly","year":"2007","journal-title":"Infect. Immun."},{"key":"B74","doi-asserted-by":"publisher","first-page":"504","DOI":"10.3390\/pathogens12030504","article-title":"Campylobacter spp. prevalence in Santiago, Chile: a study based on molecular detection in clinical stool samples from 2014 to 2019","volume":"12","author":"Porte","year":"2023","journal-title":"Pathogens."},{"key":"B75","doi-asserted-by":"publisher","first-page":"196","DOI":"10.1186\/s12879-016-1546-7","article-title":"Impact of changing from staining to culture techniques on detection rates of campylobacter spp. in routine stool samples in Chile","volume":"16","author":"Porte","year":"2016","journal-title":"BMC Infect. Dis."},{"key":"B76","doi-asserted-by":"publisher","first-page":"e01187","DOI":"10.1128\/spectrum.01187-22","article-title":"Emergence and molecular epidemiology of Campylobacter jejuni ST-2993 associated with a Large outbreak of Guillain-Barr\u00e9 syndrome in Peru","volume":"10","author":"Quino","year":"2022","journal-title":"Microbiol. Spectr."},{"key":"B77","doi-asserted-by":"publisher","DOI":"10.1212\/NXI.0000000000000952","article-title":"Guillain-Barr\u00e9 Syndrome outbreak in Peru 2019 associated with Campylobacter jejuni infection","volume":"8","author":"Ramos","year":"2021","journal-title":"Neurol. Neuroimmunol. Neuroinflamm."},{"key":"B78","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0219088","article-title":"Molecular characterization of campylobacter causing human clinical infection using whole-genome sequencing: virulence, antimicrobial resistance and phylogeny in Ireland","volume":"14","author":"Redondo","year":"2019","journal-title":"PLoS One"},{"key":"B79","first-page":"555","article-title":"[Genotyping and antibacterial resistance of campylobacter spp strains isolated in children and in free range poultry]","volume":"28","author":"Rivera","year":"2011","journal-title":"Rev. Chil. Infectol."},{"key":"B80","doi-asserted-by":"publisher","first-page":"mgen000898","DOI":"10.1099\/mgen.0.000898","article-title":"In silico investigation of the genus campylobacter type VI secretion system reveals genetic diversity in organization and putative effectors: this article is part of the \u201cGenomics, epidemiology and evolution of campylobacter, helicobacter and related organisms\u201d collection","volume":"8","author":"Robinson","year":"2022","journal-title":"Microbial Genomics"},{"key":"B81","doi-asserted-by":"publisher","DOI":"10.3389\/fmicb.2021.694824","article-title":"Bioinformatic analysis of the Campylobacter jejuni type VI secretion system and effector prediction","volume":"12","author":"Robinson","year":"2021","journal-title":"Front. Microbiol."},{"key":"B82","doi-asserted-by":"publisher","DOI":"10.3389\/fmicb.2018.02432","article-title":"Genomic epidemiology of Campylobacter jejuni transmission in Israel","volume":"9","author":"Rokney","year":"2018","journal-title":"Front. Microbiol."},{"key":"B83","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0064504","article-title":"Elucidating the aetiology of human campylobacter coli infections","volume":"8","author":"Roux","year":"2013","journal-title":"PloS One"},{"key":"B84","doi-asserted-by":"publisher","DOI":"10.1371\/journal.ppat.1006325","article-title":"T6SS: the bacterial \u201cfight club\u201d in the host gut","volume":"13","author":"Sana","year":"2017","journal-title":"PloS Pathog."},{"key":"B85","doi-asserted-by":"publisher","first-page":"2068","DOI":"10.1093\/bioinformatics\/btu153","article-title":"Prokka: rapid prokaryotic genome annotation","volume":"30","author":"Seemann","year":"2014","journal-title":"Bioinformatics."},{"key":"B86","unstructured":"SeemannT.\n          Tseemann\/abricate2020"},{"key":"B87","doi-asserted-by":"publisher","first-page":"3484","DOI":"10.1111\/j.1365-294X.2011.05179.x","article-title":"Niche segregation and genetic structure of Campylobacter jejuni populations from wild and agricultural host species","volume":"20","author":"Sheppard","year":"2011","journal-title":"Mol. Ecology"},{"key":"B88","doi-asserted-by":"publisher","first-page":"D344","DOI":"10.1093\/nar\/gks1067","article-title":"New and continuing developments at PROSITE","volume":"41","author":"Sigrist","year":"2012","journal-title":"Nucleic Acids Res."},{"key":"B89","doi-asserted-by":"publisher","DOI":"10.1099\/mgen.0.000166","article-title":"chewBBACA: a complete suite for gene-by-gene schema creation and strain identification","volume":"4","author":"Silva","year":"2018","journal-title":"Microb. Genom."},{"key":"B90","doi-asserted-by":"publisher","first-page":"1009","DOI":"10.1093\/bioinformatics\/btr039","article-title":"Easyfig: a genome comparison visualizer","volume":"27","author":"Sullivan","year":"2011","journal-title":"Bioinformatics."},{"key":"B91","doi-asserted-by":"publisher","first-page":"87","DOI":"10.1017\/S1466252317000135","article-title":"Antibiotic resistance trends and mechanisms in the foodborne pathogen, campylobacter","volume":"18","author":"Tang","year":"2017","journal-title":"Anim. Health Res. Rev."},{"key":"B92","doi-asserted-by":"publisher","first-page":"839","DOI":"10.3201\/eid1106.041052","article-title":"pVir and bloody diarrhea in Campylobacter jejuni enteritis","volume":"11","author":"Tracz","year":"2005","journal-title":"Emerg. Infect. Dis."},{"key":"B93","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0246843","article-title":"Genetic characterisation of a subset of Campylobacter jejuni isolates from clinical and poultry sources in Ireland","volume":"16","author":"Truccollo","year":"2021","journal-title":"PloS One"},{"key":"B94","doi-asserted-by":"publisher","first-page":"180","DOI":"10.1186\/s13104-019-4201-8","article-title":"Virulence of a T6SS Campylobacter jejuni chicken isolate from north Romania","volume":"12","author":"Ungureanu","year":"2019","journal-title":"BMC Res. Notes"},{"key":"B95","doi-asserted-by":"publisher","first-page":"000729","DOI":"10.1099\/mgen.0.000729","article-title":"A campylobacter integrative and conjugative element with a CRISPR-Cas9 system targeting competing plasmids: a history of plasmid warfare","volume":"7","author":"van Vliet","year":"2021","journal-title":"Microbial Genomics"},{"key":"B96","doi-asserted-by":"publisher","first-page":"2546","DOI":"10.1093\/bioinformatics\/bty155","article-title":"Bastion6: a bioinformatics approach for accurate prediction of type VI secreted effectors","volume":"34","author":"Wang","year":"2018","journal-title":"Bioinformatics."},{"key":"B97","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pcbi.1005595","article-title":"Unicycler: resolving bacterial genome assemblies from short and long sequencing reads","volume":"13","author":"Wick","year":"2017","journal-title":"PLoS Comput. Biol."},{"key":"B98","article-title":"Global priority list of antibiotic-resistant bacteria to guide research, discovery, and development of new antibiotics","year":"2017"},{"key":"B99","volume-title":"The global view of campylobacteriosis: report of an expert consultation","year":"2013"},{"key":"B100","doi-asserted-by":"crossref","first-page":"215","DOI":"10.1007\/82_2018_99","article-title":"The agrobacterium type VI secretion system: a contractile nanomachine for interbacterial competition","volume-title":"Agrobacterium biology","author":"Wu","year":"2018"},{"key":"B101","doi-asserted-by":"publisher","first-page":"2764","DOI":"10.1093\/jac\/dkx217","article-title":"PointFinder: a novel web tool for WGS-based detection of antimicrobial resistance associated with chromosomal point mutations in bacterial pathogens","volume":"72","author":"Zankari","year":"2017","journal-title":"J. Antimicrob. Chemother."},{"key":"B102","doi-asserted-by":"publisher","first-page":"2237","DOI":"10.1016\/j.jmb.2017.12.007","article-title":"A completely reimplemented MPI bioinformatics toolkit with a new HHpred server at its core","volume":"430","author":"Zimmermann","year":"2018","journal-title":"J. Mol. Biol."},{"key":"B103","doi-asserted-by":"publisher","first-page":"1664","DOI":"10.1016\/j.bbamcr.2014.03.018","article-title":"Architecture and assembly of the type VI secretion system","volume":"1843","author":"Zoued","year":"2014","journal-title":"Biochim. Biophys. Acta (BBA) - Mol. Cell Res."}],"container-title":["Frontiers in Cellular and Infection Microbiology"],"original-title":[],"link":[{"URL":"https:\/\/www.frontiersin.org\/articles\/10.3389\/fcimb.2023.1208825\/full","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,7,13]],"date-time":"2023-07-13T19:51:39Z","timestamp":1689277899000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.frontiersin.org\/articles\/10.3389\/fcimb.2023.1208825\/full"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2023,7,13]]},"references-count":103,"alternative-id":["10.3389\/fcimb.2023.1208825"],"URL":"https:\/\/doi.org\/10.3389\/fcimb.2023.1208825","relation":{},"ISSN":["2235-2988"],"issn-type":[{"value":"2235-2988","type":"electronic"}],"subject":[],"published":{"date-parts":[[2023,7,13]]},"article-number":"1208825"}}