{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,3]],"date-time":"2026-07-03T01:40:00Z","timestamp":1783042800858,"version":"3.54.6"},"reference-count":35,"publisher":"Frontiers Media SA","license":[{"start":{"date-parts":[[2021,8,18]],"date-time":"2021-08-18T00:00:00Z","timestamp":1629244800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["frontiersin.org"],"crossmark-restriction":true},"short-container-title":["Front. Microbiol."],"abstract":"<jats:p>Turkey is an important stopover site for many migrating birds between Europe, Asia and Africa. <jats:italic>Campylobacter<\/jats:italic> spp. are frequently found in wildlife, in particular waterfowl, and distinct strains are disseminated within this reservoir. In this study, 183 wild birds of hunting areas in Turkey were collected and thermophilic <jats:italic>Campylobacter<\/jats:italic> spp. from cloacal swabs were isolated at a prevalence of 5.2% from song thrushes (6\/116) and 93% from Eurasian coots (41\/44). After PCR species differentiation and <jats:italic>flaA<\/jats:italic> restriction profiles determination, <jats:italic>C. jejuni<\/jats:italic> and <jats:italic>C. coli<\/jats:italic> strains were further investigated by whole genome sequencing. PCR target amplification of the <jats:italic>ceuE<\/jats:italic> gene, commonly used for <jats:italic>C. coli<\/jats:italic> species-identification was inefficient and even hampered in one isolate. A close look on the <jats:italic>ceuE<\/jats:italic> sequence revealed that various mismatches in the <jats:italic>ceuE<\/jats:italic> oligo annealing sites caused less efficient diagnostic detection. All <jats:italic>C. coli<\/jats:italic> isolates belonged to the environmental clade II and clade III, for which thirty-six novel MLST types were identified. Further single nucleotide polymorphism (SNP) analysis showed a high genomic divergence between the <jats:italic>C. coli<\/jats:italic> isolates. High variability was also implicated for putative plasmid-located genes detected in 51% of the <jats:italic>C. coli<\/jats:italic> isolates. Distinct gene variants in clades II and III <jats:italic>C. coli<\/jats:italic> were identified by a <jats:italic>k-mer<\/jats:italic> analysis. After substracting <jats:italic>k-mers<\/jats:italic> in common with <jats:italic>C. coli<\/jats:italic> clade I database, 11 and 35 distinct genes were identified in clades II and III isolates, mainly involved in surface structures and modifications as well as signal transduction, suggesting niche adaptation of <jats:italic>C. coli<\/jats:italic> strains in wild birds. All strains were susceptible against (fluoro-)quinolones, erythromycin, tetracycline, gentamicin and only one isolate was resistant against streptomycin, suggesting that the sensitive phenotype was due to absence of selective pressure and niche separation in wild birds in Turkey. We conclude that <jats:italic>Campylobacter<\/jats:italic> spp. isolates from wildlife and environmental sources are still scarce in the databases and that there is a need for more studies on thermophilic <jats:italic>Campylobacter<\/jats:italic> spp. from different places all over the world in order to complement our understanding on dissemination and adaptation to distinct niches of this global food-borne pathogen.<\/jats:p>","DOI":"10.3389\/fmicb.2021.712106","type":"journal-article","created":{"date-parts":[[2021,8,18]],"date-time":"2021-08-18T13:26:01Z","timestamp":1629293161000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":18,"title":["Characterization of Campylobacter spp. Strains Isolated From Wild Birds in Turkey"],"prefix":"10.3389","volume":"12","author":[{"given":"Cemil","family":"K\u00fcrekci","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Fatih","family":"Sakin","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lennard","family":"Epping","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Marie-Theres","family":"Kn\u00fcver","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Torsten","family":"Semmler","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kerstin","family":"Stingl","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1965","published-online":{"date-parts":[[2021,8,18]]},"reference":[{"key":"B1","doi-asserted-by":"publisher","first-page":"688","DOI":"10.1002\/ece3.974","article-title":"Extraordinary MHC class II B diversity in a non-passerine, wild bird: the Eurasian Coot Fulica atra (Aves: rallidae).","volume":"4","author":"Alcaide","year":"2014","journal-title":"Ecol. Evol."},{"key":"B2","doi-asserted-by":"publisher","first-page":"516","DOI":"10.1111\/tbed.12169","article-title":"Free-living waterfowl as a source of zoonotic bacteria in a dense wild bird population area in northeastern Spain.","volume":"62","author":"Antilles","year":"2015","journal-title":"Transbound. Emerg. Dis."},{"key":"B3","doi-asserted-by":"publisher","first-page":"3380","DOI":"10.1093\/bioinformatics\/btw493","article-title":"PlasmidSPAdes: assembling plasmids from whole genome sequencing data.","volume":"32","author":"Antipov","year":"2016","journal-title":"Bioinformatics"},{"key":"B4","doi-asserted-by":"publisher","first-page":"455","DOI":"10.1089\/cmb.2012.0021","article-title":"SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing.","volume":"19","author":"Bankevich","year":"2012","journal-title":"J. Comput. Biol."},{"key":"B5","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":"B6","doi-asserted-by":"publisher","first-page":"53","DOI":"10.1080\/09674845.2017.1291205","article-title":"Towards understanding clinical Campylobacter infection and its transmission: time for a different approach?","volume":"74","author":"Casey","year":"2017","journal-title":"Br. J. Biomed. Sci."},{"key":"B7","volume-title":"Methods for Antimicrobial Dilution and Disk Susceptibility Testing of Infrequently Isolated or Fastidious Bacteria.","year":"2015"},{"key":"B8","volume-title":"Methods for Antimicrobial Dilution and Disk Susceptibility Testing of Infrequently Isolated or Fastidious Bacteria Isolated From Animals.","year":"2017"},{"key":"B9","doi-asserted-by":"publisher","first-page":"782","DOI":"10.1111\/1758-2229.12314","article-title":"Wild bird-associated Campylobacter jejuni isolates are a consistent source of human disease, in Oxfordshire, United Kingdom.","volume":"7","author":"Cody","year":"2015","journal-title":"Environ. Microbiol. Rep."},{"key":"B10","doi-asserted-by":"publisher","first-page":"3686","DOI":"10.1038\/s41598-020-60320-y","article-title":"Whole genome sequencing reveals extended natural transformation in Campylobacter impacting diagnostics and the pathogens adaptive potential.","volume":"10","author":"Golz","year":"2020","journal-title":"Sci. Rep."},{"key":"B11","doi-asserted-by":"publisher","first-page":"292","DOI":"10.1093\/bioinformatics\/btx610","article-title":"Phandango: an interactive viewer for bacterial population genomics.","volume":"34","author":"Hadfield","year":"2018","journal-title":"Bioinformatics"},{"key":"B12","doi-asserted-by":"publisher","first-page":"2115","DOI":"10.1093\/molbev\/msx148","article-title":"Fast genome-wide functional annotation through orthology assignment by eggNOG-mapper.","volume":"34","author":"Huerta-Cepas","year":"2017","journal-title":"Mol. Biol. Evol."},{"key":"B13","doi-asserted-by":"publisher","first-page":"D309","DOI":"10.1093\/nar\/gky1085","article-title":"EggNOG 5.0: a hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 viruses.","volume":"8","author":"Huerta-Cepas","year":"2019","journal-title":"Nucleic Acids Res."},{"key":"B14","doi-asserted-by":"publisher","first-page":"e0246571","DOI":"10.1371\/journal.pone.0246571","article-title":"Antimicrobial resistance and interspecies gene transfer in Campylobacter coli and Campylobacter jejuni isolated from food animals, poultry processing, and retail meat in North Carolina, 2018\u20132019.","volume":"16","author":"Hull","year":"2021","journal-title":"PLoS One"},{"key":"B15","doi-asserted-by":"publisher","first-page":"e1001940","DOI":"10.1371\/journal.pmed.1001940","article-title":"World Health Organization estimates of the global and regional disease burden of 22 foodborne bacterial, protozoal, and viral diseases, 2010: a data synthesis.","volume":"12","author":"Kirk","year":"2015","journal-title":"PLoS Med."},{"key":"B16","doi-asserted-by":"publisher","first-page":"4453","DOI":"10.1093\/bioinformatics\/btz305","article-title":"RAxML-NG: a fast, scalable and user-friendly tool for maximum likelihood phylogenetic inference.","volume":"35","author":"Kozlov","year":"2019","journal-title":"Bioinformatics"},{"key":"B17","doi-asserted-by":"publisher","first-page":"241","DOI":"10.4315\/0362-028x-73.2.241","article-title":"Rapid detection and differentiation of Campylobacter jejuni, Campylobacter coli, and Campylobacter lari in food, using multiplex real-time PCR.","volume":"73","author":"Mayr","year":"2010","journal-title":"J. Food Prot."},{"key":"B18","doi-asserted-by":"publisher","first-page":"1531","DOI":"10.1128\/jcm.31.6.1531-1536.1993","article-title":"Flagellin gene typing of Campylobacter jejuni by restriction-fragment-length-polymorphism analysis.","volume":"31","author":"Nachamkin","year":"1993","journal-title":"J. Clin. Microbiol."},{"key":"B19","doi-asserted-by":"publisher","first-page":"e00583","DOI":"10.1002\/mbo3.583","article-title":"Characterization of Swedish Campylobacter coli clade 2 and clade 3 water isolates.","volume":"7","author":"Nilsson","year":"2018","journal-title":"Microbiologyopen"},{"key":"B20","doi-asserted-by":"publisher","first-page":"14","DOI":"10.1097\/MOG.0000000000000329","article-title":"The consequences of Campylobacter infection.","volume":"33","author":"O\u2019Brien","year":"2017","journal-title":"Curr. Opin. Gastroenterol"},{"key":"B21","first-page":"77","article-title":"G\u00f6\u00e7men ku\u015flar\u0131 tehdit eden fakt\u00f6rler.","volume":"2","author":"\u00d6zkazan\u00e7","year":"2019","journal-title":"JONAS"},{"key":"B22","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":"B23","doi-asserted-by":"publisher","first-page":"883","DOI":"10.1093\/jac\/dkz539","article-title":"Comparison of phenotypic and WGS-derived antimicrobial resistance profiles of Campylobacter jejuni and Campylobacter coli isolated from cases of diarrheal disease in England and Wales, 2015\u201316.","volume":"75","author":"Painset","year":"2020","journal-title":"J. Antimicrob. Chemother."},{"key":"B24","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":"B25","doi-asserted-by":"crossref","first-page":"829","DOI":"10.1017\/S0950268815002162","article-title":"Assessing risk factors of sporadic Campylobacter infection: a case\u2013control study in Arizona.","volume":"144","author":"Pogreba-Brown","year":"2016","journal-title":"Epidemiol. Infect."},{"key":"B26","doi-asserted-by":"publisher","first-page":"1072","DOI":"10.1086\/597402","article-title":"Campylobacter genotyping to determine the source of human infection.","volume":"48","author":"Sheppard","year":"2009","journal-title":"Clin. Infect. Dis."},{"key":"B27","doi-asserted-by":"publisher","first-page":"e15708","DOI":"10.1371\/journal.pone.0015708","article-title":"Evolution of an agriculture-associated disease causing Campylobacter coli clade: evidence from national surveillance data in Scotland.","volume":"5","author":"Sheppard","year":"2010","journal-title":"PLoS One"},{"key":"B28","doi-asserted-by":"publisher","first-page":"1051","DOI":"10.1111\/mec.12162","article-title":"Progressive genome-wide introgression in agricultural Campylobacter coli.","volume":"22","author":"Sheppard","year":"2013","journal-title":"Mol. Ecol."},{"key":"B29","doi-asserted-by":"crossref","first-page":"a018119","DOI":"10.1101\/cshperspect.a018119","article-title":"The evolution of Campylobacter jejuni and Campylobacter coli.","volume":"7","author":"Sheppard","year":"2015","journal-title":"Cold Spring Harb. Perspect. Biol."},{"key":"B30","doi-asserted-by":"publisher","first-page":"237","DOI":"10.1126\/science.1155532","article-title":"Convergence of Campylobacter species: implications for bacterial evolution.","volume":"320","author":"Sheppard","year":"2008","journal-title":"Science"},{"key":"B31","doi-asserted-by":"publisher","first-page":"129","DOI":"10.1128\/AEM.00942-09","article-title":"Investigation of food and environmental exposures relating to epidemiology of Campylobacter coli in humans in Northwest England.","volume":"76","author":"Sopwith","year":"2010","journal-title":"Appl. Environ. Microbiol."},{"key":"B32","doi-asserted-by":"publisher","first-page":"9305","DOI":"10.1038\/s41598-018-27558-z","article-title":"Ruminant and chicken: important sources of campylobacteriosis in France despite a variation of source attribution in 2009 and 2015.","volume":"8","author":"Th\u00e9pault","year":"2018","journal-title":"Sci. Rep."},{"key":"B33","doi-asserted-by":"publisher","first-page":"5911","DOI":"10.1128\/AEM.68.12.5911-5917.2002","article-title":"Prevalence of Campylobacter jejuni, Campylobacter lari, and Campylobacter coli in different ecological guilds and taxa of migrating birds.","volume":"68","author":"Waldenstr\u00f6m","year":"2002","journal-title":"Appl. Environ. Microbiol."},{"key":"B34","author":"Winn","year":"2006","journal-title":"Curved Gram-Negative Bacilli and Oxidase-Positive Fermenters: Campylobacteraceae and Vibrionaceae, vol. 6, Konemans\u2019 Color Atlas and Textbook of Diagnostic Microbiology."},{"key":"B35","doi-asserted-by":"publisher","first-page":"1395","DOI":"10.1101\/gr.232397.117","article-title":"Grapetree: visualization of core genomic relationships among 100,000 bacterial pathogens.","volume":"28","author":"Zhou","year":"2018","journal-title":"Genome Res."}],"container-title":["Frontiers in Microbiology"],"original-title":[],"link":[{"URL":"https:\/\/www.frontiersin.org\/articles\/10.3389\/fmicb.2021.712106\/full","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2021,8,18]],"date-time":"2021-08-18T13:26:13Z","timestamp":1629293173000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.frontiersin.org\/articles\/10.3389\/fmicb.2021.712106\/full"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2021,8,18]]},"references-count":35,"alternative-id":["10.3389\/fmicb.2021.712106"],"URL":"https:\/\/doi.org\/10.3389\/fmicb.2021.712106","relation":{},"ISSN":["1664-302X"],"issn-type":[{"value":"1664-302X","type":"electronic"}],"subject":[],"published":{"date-parts":[[2021,8,18]]},"article-number":"712106"}}