{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,5]],"date-time":"2026-09-05T01:07:36Z","timestamp":1788570456230,"version":"build-2803163510"},"reference-count":110,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2024,2,8]],"date-time":"2024-02-08T00:00:00Z","timestamp":1707350400000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"},{"start":{"date-parts":[[2024,2,8]],"date-time":"2024-02-08T00:00:00Z","timestamp":1707350400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"}],"funder":[{"name":"Bundesinstitut f\u00fcr Risikobewertung (BfR)"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Genomics"],"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Background<\/jats:title>\n                    <jats:p>\n                      <jats:italic>Campylobacter<\/jats:italic>\n                      spp. is the most frequent cause of bacterial food-borne gastroenteritis and a high priority antibiotic resistant bacterium according to the World Health Organization (WHO). European monitoring of thermotolerant\n                      <jats:italic>Campylobacter<\/jats:italic>\n                      spp. does not reflect the global burden of resistances already circulating within the bacterial population worldwide.\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Methods<\/jats:title>\n                    <jats:p>\n                      We systematically compared whole genome sequencing with comprehensive phenotypic antimicrobial susceptibility, analyzing 494 thermotolerant\n                      <jats:italic>Campylobacter<\/jats:italic>\n                      poultry isolates from Vietnam and Germany. Any discrepancy was checked by repeating the wet lab and improving the dry lab part. Selected isolates were additionally analyzed via long-read Oxford Nanopore technology, leading to closed chromosomes and plasmids.\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>\n                      Overall, 22 different resistance genes and gene variants (e. g.\n                      <jats:italic>erm<\/jats:italic>\n                      (B),\n                      <jats:italic>aph(3\u2019)-IIIa<\/jats:italic>\n                      ,\n                      <jats:italic>aph(2\u2019\u2019)-If<\/jats:italic>\n                      ,\n                      <jats:italic>catA<\/jats:italic>\n                      ,\n                      <jats:italic>lnu<\/jats:italic>\n                      (C),\n                      <jats:italic>bla<\/jats:italic>\n                      <jats:sub>OXA<\/jats:sub>\n                      ,\n                      <jats:italic>sat4<\/jats:italic>\n                      ) and point mutations in three distinct genes (\n                      <jats:italic>gyrA<\/jats:italic>\n                      , 23S rRNA,\n                      <jats:italic>rpsL<\/jats:italic>\n                      ) associated with AMR were present in the\n                      <jats:italic>Campylobacter<\/jats:italic>\n                      isolates. Two AMR genes were missing in the database and one falsely associated with resistance. Bioinformatic analysis based on short-read data partly failed to identify\n                      <jats:italic>tet<\/jats:italic>\n                      (O) and\n                      <jats:italic>aadE<\/jats:italic>\n                      , when the genes were present as duplicate or homologous gene variants. Intriguingly, isolates also contained different determinants, redundantly conferring resistance to chloramphenicol, gentamicin, kanamycin, lincomycin and streptomycin. We found a novel\n                      <jats:italic>tet<\/jats:italic>\n                      (W) in tetracycline sensitive strains, harboring point mutations. Furthermore, analysis based on assemblies from short-read data was impaired to identify full length phase variable\n                      <jats:italic>aad9<\/jats:italic>\n                      , due to variations of the poly-C tract within the gene. The genetic determinant responsible for gentamicin resistance of one isolate from Germany could not be identified. GyrT86I, presenting the main determinant for (fluoro-)quinolone resistance led to a rare atypical phenotype of ciprofloxacin resistance but nalidixic acid sensitivity. Long-read sequencing predicted AMR genes were mainly located on the chromosome, and rarely on plasmids. Predictions from long- and short-read sequencing, respectively, often differed. AMR genes were often organized in multidrug resistance islands (MDRI) and partially located in proximity to transposase genes, suggesting main mobilization of resistance determinants is via natural transformation and transposition in\n                      <jats:italic>Campylobacter<\/jats:italic>\n                      .\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Conclusions<\/jats:title>\n                    <jats:p>\n                      The results of this study suggest that there is frequent resistance gene duplication, mosaicism, and mutation leading to gene variation and truncation in\n                      <jats:italic>Campylobacter<\/jats:italic>\n                      strains that have not been reported in previous studies and are missing from databases. Furthermore, there is a need for deciphering yet unknown resistance mechanisms and resistance spread in thermotolerant\n                      <jats:italic>Campylobacter<\/jats:italic>\n                      spp. that may pose a challenge to global food safety.\n                    <\/jats:p>\n                  <\/jats:sec>","DOI":"10.1186\/s12864-024-10014-w","type":"journal-article","created":{"date-parts":[[2024,2,8]],"date-time":"2024-02-08T03:05:10Z","timestamp":1707361510000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":16,"title":["Identification of knowledge gaps in whole-genome sequence analysis of multi-resistant thermotolerant Campylobacter spp."],"prefix":"10.1186","volume":"25","author":[{"given":"Michael","family":"Zarske","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Huong Quynh","family":"Luu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Carlus","family":"Deneke","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Marie-Theres","family":"Kn\u00fcver","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Maja","family":"Thieck","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ha Thi Thu","family":"Hoang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nancy","family":"Bretschneider","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ngoc Thi","family":"Pham","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ingrid","family":"Huber","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kerstin","family":"Stingl","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2024,2,8]]},"reference":[{"key":"10014_CR1","doi-asserted-by":"publisher","unstructured":"ECDC, WHO. Antimicrobial resistance surveillance in Europe: 2022: 2020 data: Publications Office of the European Union; 2022. https:\/\/doi.org\/10.2900\/112339","DOI":"10.2900\/112339"},{"key":"10014_CR2","doi-asserted-by":"publisher","unstructured":"EFSA ECDC. The European Union One Health 2019 Zoonoses Report. EFSA J. 2021;19(2). https:\/\/doi.org\/10.2903\/j.efsa.2021.6406","DOI":"10.2903\/j.efsa.2021.6406"},{"issue":"2","key":"10014_CR3","doi-asserted-by":"publisher","first-page":"293","DOI":"10.1017\/S0950268812000568","volume":"141","author":"AH Havelaar","year":"2013","unstructured":"Havelaar AH, Ivarsson S, L\u00f6fdahl M, Nauta MJ. Estimating the true incidence of campylobacteriosis and salmonellosis in the European Union, 2009. Epidemiol Infect. 2013;141(2):293\u2013302. https:\/\/doi.org\/10.1017\/S0950268812000568","journal-title":"Epidemiol Infect"},{"issue":"12","key":"10014_CR4","doi-asserted-by":"publisher","first-page":"e06971","DOI":"10.2903\/j.efsa.2021.6971","volume":"19","author":"ECDC EFSA","year":"2021","unstructured":"EFSA ECDC. The European Union One Health 2020 Zoonoses Report. EFSA J. 2021;19(12):e06971. https:\/\/doi.org\/10.2903\/j.efsa.2021.6971","journal-title":"EFSA J"},{"issue":"2","key":"10014_CR5","doi-asserted-by":"publisher","first-page":"229","DOI":"10.1017\/s0950268801005933","volume":"127","author":"DW Isenbarger","year":"2001","unstructured":"Isenbarger DW, Hien BT, Ha HT, Ha TT, Bodhidatta L, Pang LW, et al. Prospective study of the incidence of diarrhoea and prevalence of bacterial pathogens in a cohort of Vietnamese children along the Red River. Epidemiol Infect. 2001;127(2):229\u201336. https:\/\/doi.org\/10.1017\/s0950268801005933","journal-title":"Epidemiol Infect"},{"key":"10014_CR6","doi-asserted-by":"publisher","first-page":"3","DOI":"10.1016\/j.ijid.2015.03.013","volume":"35","author":"KL Anders","year":"2015","unstructured":"Anders KL, Thompson CN, Thuy NT, Nguyet NM, Tu le TP, Dung TT, et al. The epidemiology and aetiology of diarrhoeal disease in infancy in southern Vietnam: a birth cohort study. Int J Infect Dis. 2015;35:3\u201310. https:\/\/doi.org\/10.1016\/j.ijid.2015.03.013","journal-title":"Int J Infect Dis"},{"issue":"3","key":"10014_CR7","doi-asserted-by":"publisher","first-page":"687","DOI":"10.1128\/CMR.00006-15","volume":"28","author":"NO Kaakoush","year":"2015","unstructured":"Kaakoush NO, Casta\u00f1o-Rodr\u00edguez N, Mitchell HM, Man SM. Global Epidemiology of Campylobacter Infection. Clin Microbiol Rev. 2015;28(3):687\u2013720. https:\/\/doi.org\/10.1128\/CMR.00006-15","journal-title":"Clin Microbiol Rev"},{"key":"10014_CR8","doi-asserted-by":"publisher","first-page":"1203","DOI":"10.1186\/1471-2458-14-1203","volume":"14","author":"J Keithlin","year":"2014","unstructured":"Keithlin J, Sargeant J, Thomas MK, Fazil A. Systematic review and meta-analysis of the proportion of Campylobacter cases that develop chronic sequelae. BMC Public Health. 2014;14:1203. https:\/\/doi.org\/10.1186\/1471-2458-14-1203","journal-title":"BMC Public Health"},{"issue":"1","key":"10014_CR9","doi-asserted-by":"publisher","first-page":"5139","DOI":"10.1038\/s41598-017-05227-x","volume":"7","author":"BM Rosner","year":"2017","unstructured":"Rosner BM, Schielke A, Didelot X, Kops F, Breidenbach J, Willrich N, et al. A combined case-control and molecular source attribution study of human Campylobacter infections in Germany, 2011\u20132014. Sci Rep. 2017;7(1):5139. https:\/\/doi.org\/10.1038\/s41598-017-05227-x","journal-title":"Sci Rep"},{"key":"10014_CR10","unstructured":"WHO. Global priority list of antibiotic-resistant bacteria to guide research, discovery, and development of new antibiotics, World Health Organization. 2017. Available from: last accessed on 01\/05\/2024. http:\/\/remed.org\/wp-content\/uploads\/2017\/03\/lobal-priority-list-of-antibiotic-resistant-bacteria-2017.pdf"},{"issue":"6","key":"10014_CR11","doi-asserted-by":"publisher","first-page":"562","DOI":"10.1111\/zph.12611","volume":"66","author":"E Rukambile","year":"2019","unstructured":"Rukambile E, Sintchenko V, Muscatello G, Kock R, Alders R. Infection, colonization and shedding of Campylobacter and Salmonella in animals and their contribution to human disease: a review. Zoonoses Public Health. 2019;66(6):562\u201378. https:\/\/doi.org\/10.1111\/zph.12611","journal-title":"Zoonoses Public Health"},{"key":"10014_CR12","unstructured":"BVL. BVL-Reports 16.1 Reports on food safety - zoonoses monitoring 2020 [in German]. German Federal Office of Consumer Protection and Food Safety (BVL). 2021. Available from: &v=4, last accessed on 01\/05\/2024.https:\/\/www.bvl.bund.de\/SharedDocs\/Downloads\/01_Lebensmittel\/04_Zoonosen_Monitoring\/Zoonosen_Monitoring_Bericht_2020.pdf?__blob=publicationFile"},{"key":"10014_CR13","doi-asserted-by":"publisher","first-page":"273","DOI":"10.1196\/annals.1373.036","volume":"1081","author":"HQ Luu","year":"2006","unstructured":"Luu HQ, Tran TH, Phung DC, Nguyen TB. Study on the prevalence of Campylobacter spp. from chicken meat in Hanoi, Vietnam. Ann N Y Acad Sci. 2006;1081:273\u20135. https:\/\/doi.org\/10.1196\/annals.1373.036","journal-title":"Ann N Y Acad Sci"},{"issue":"1","key":"10014_CR14","doi-asserted-by":"publisher","first-page":"102","DOI":"10.1016\/j.ijfoodmicro.2012.04.020","volume":"157","author":"B Garin","year":"2012","unstructured":"Garin B, Gouali M, Wouafo M, Perchec AM, Pham MT, Ravaonindrina N, et al. Prevalence, quantification and antimicrobial resistance of Campylobacter spp. on chicken neck-skins at points of slaughter in 5 major cities located on 4 continents. Int J Food Microbiol. 2012;157(1):102\u20137. https:\/\/doi.org\/10.1016\/j.ijfoodmicro.2012.04.020","journal-title":"Int J Food Microbiol"},{"key":"10014_CR15","doi-asserted-by":"publisher","first-page":"19","DOI":"10.1186\/s13099-016-0100-x","volume":"8","author":"TN Nguyen","year":"2016","unstructured":"Nguyen TN, Hotzel H, El-Adawy H, Tran HT, Le MT, Tomaso H, et al. Genotyping and antibiotic resistance of thermophilic Campylobacter isolated from chicken and pig meat in Vietnam. Gut Pathog. 2016;8:19. https:\/\/doi.org\/10.1186\/s13099-016-0100-x","journal-title":"Gut Pathog"},{"key":"10014_CR16","unstructured":"Schwan P. Prevalence and antibiotic resistance of Campylobacter spp. in poultry and raw meat in the Can Tho Province, Vietnam. Swedish University of Agricultural Sciences Library 2010. Available from: -6-192, last accessed on 01\/05\/2024. https:\/\/stud.epsilon.slu.se\/1066\/1\/Schwan_P_20100419.pdf"},{"key":"10014_CR17","unstructured":"BVL, BVL-Reports. 12.2 Reports on food safety - zoonoses monitoring 2016 [in German]. German Federal Office of Consumer Protection and Food Safety (BVL). 2017. Available from: &v=5, last accessed on 01\/05\/2024. https:\/\/biosicherheit-bch.de\/SharedDocs\/Downloads\/01_Lebensmittel\/04_Zoonosen_Monitoring\/Zoonosen_Monitoring_Bericht_2016.pdf?__blob=publicationFile&v=5"},{"key":"10014_CR18","unstructured":"BVL. BVL-Reports 14.1 Reports on food safety - zoonoses monitoring 2018 [in German]. German Federal Office of Consumer Protection and Food Safety (BVL). 2019. Available from: last accessed on 01\/05\/2024. https:\/\/www.bvl.bund.de\/SharedDocs\/Downloads\/01_Lebensmittel\/04_Zoonosen_Monitoring\/Zoonosen_Monitoring_Bericht_2018.pdf"},{"key":"10014_CR19","unstructured":"WHO. Antimicrobial resistance and primary health care. Geneva, World Health Organization. 2018. Contract No.: WHO\/HIS\/SDS\/2018.56. Available from: last accessed on 01\/05\/2024. https:\/\/apps.who.int\/iris\/handle\/10665\/326454"},{"issue":"4","key":"10014_CR20","doi-asserted-by":"publisher","first-page":"718","DOI":"10.1128\/CMR.00002-11","volume":"24","author":"BM Marshall","year":"2011","unstructured":"Marshall BM, Levy SB. Food animals and antimicrobials: impacts on human health. Clin Microbiol Rev. 2011;24(4):718\u201333. https:\/\/doi.org\/10.1128\/CMR.00002-11","journal-title":"Clin Microbiol Rev"},{"key":"10014_CR21","unstructured":"O\u2019Neill J. Antimicrobials in agriculture and the environment: reducing unnecessary use and waste. London, UK: Review on Antimicrobial Resistance. 2015. Available from: last accessed on 01\/05\/2024. https:\/\/amr-review.org\/sites\/default\/files\/Antimicrobials%20in%20agriculture%20and%20the%20environment%20-%20Reducing%20unnecessary%20use%20and%20waste.pdf"},{"key":"10014_CR22","unstructured":"BMEL. Report of the Federal Ministry of Food and Agriculture on the Evaluation of the Antibiotics Minimisation Concept introduced with the 16th Act to Amend the Medicinal Products Act (16th AMG Amendment). German Federal Ministry of Food and Agriculture. 2019. Available from: last accessed on 01\/05\/2024. https:\/\/www.bmel.de\/SharedDocs\/Downloads\/EN\/_Animals\/16-AMG-Novelle.pdf"},{"key":"10014_CR23","unstructured":"BfR. Therapieh\u00e4ufigkeit und Antibiotikaverbrauchsmengen 2018\u20132021: Entwicklung in zur Fleischerzeugung gehaltenen Rindern, Schweinen, H\u00fchnern und Puten: Bericht des BfR vom 20. Dezember 2022 [only available in German]. Berlin, Germany: Bundesinstitut f\u00fcr Risikobewertung. 2022. Available from: last accessed on 01\/05\/2024. https:\/\/www.bfr.bund.de\/cm\/343\/therapiehaeufigkeit-und-antibiotikaverbrauchsmengen-2018-2021-bericht.pdf"},{"issue":"1","key":"10014_CR24","doi-asserted-by":"publisher","first-page":"16","DOI":"10.1186\/s13756-019-0671-7","volume":"9","author":"JJ Carrique-Mas","year":"2020","unstructured":"Carrique-Mas JJ, Choisy M, Van Cuong N, Thwaites G, Baker S. An estimation of total antimicrobial usage in humans and animals in Vietnam. Antimicrob Resist Infect Control. 2020;9(1):16. https:\/\/doi.org\/10.1186\/s13756-019-0671-7","journal-title":"Antimicrob Resist Infect Control"},{"key":"10014_CR25","doi-asserted-by":"publisher","first-page":"174","DOI":"10.3389\/fvets.2019.00174","volume":"6","author":"NV Cuong","year":"2019","unstructured":"Cuong NV, Phu DH, Van NTB, Dinh Truong B, Kiet BT, Hien BV, et al. High-resolution monitoring of antimicrobial consumption in Vietnamese small-scale chicken farms highlights discrepancies between Study Metrics. Front Vet Sci. 2019;6:174. https:\/\/doi.org\/10.3389\/fvets.2019.00174","journal-title":"Front Vet Sci"},{"issue":"13","key":"10014_CR26","doi-asserted-by":"publisher","first-page":"3727","DOI":"10.1128\/AEM.00337-16","volume":"82","author":"NT Nguyen","year":"2016","unstructured":"Nguyen NT, Nguyen HM, Nguyen CV, Nguyen TV, Nguyen MT, Thai HQ, et al. Use of Colistin and other critical antimicrobials on Pig and Chicken Farms in Southern Vietnam and its Association with Resistance in Commensal Escherichia coli bacteria. Appl Environ Microbiol. 2016;82(13):3727\u201335. https:\/\/doi.org\/10.1128\/AEM.00337-16","journal-title":"Appl Environ Microbiol"},{"key":"10014_CR27","doi-asserted-by":"publisher","unstructured":"Nhung NT, Cuong NV, Thwaites G, Carrique-Mas J. Antimicrobial usage and Antimicrobial Resistance in Animal Production in Southeast Asia: a review. Antibiot (Basel). 2016;5(4). https:\/\/doi.org\/10.3390\/antibiotics5040037","DOI":"10.3390\/antibiotics5040037"},{"key":"10014_CR28","doi-asserted-by":"publisher","first-page":"84","DOI":"10.3389\/fvets.2019.00084","volume":"6","author":"DB Truong","year":"2019","unstructured":"Truong DB, Doan HP, Doan Tran VK, Nguyen VC, Bach TK, Rueanghiran C, et al. Assessment of Drivers of Antimicrobial Usage in Poultry Farms in the Mekong Delta of Vietnam: a combined participatory epidemiology and Q-Sorting Approach. Front Vet Sci. 2019;6:84. https:\/\/doi.org\/10.3389\/fvets.2019.00084","journal-title":"Front Vet Sci"},{"issue":"4","key":"10014_CR29","doi-asserted-by":"publisher","first-page":"673","DOI":"10.1007\/s10096-020-04043-y","volume":"40","author":"LG Dahl","year":"2021","unstructured":"Dahl LG, Joensen KG, \u00d8sterlund MT, Kiil K, Nielsen EM. Prediction of antimicrobial resistance in clinical Campylobacter jejuni isolates from whole-genome sequencing data. Eur J Clin Microbiol Infect Dis. 2021;40(4):673\u201382. https:\/\/doi.org\/10.1007\/s10096-020-04043-y","journal-title":"Eur J Clin Microbiol Infect Dis"},{"issue":"2","key":"10014_CR30","doi-asserted-by":"publisher","first-page":"e0246571","DOI":"10.1371\/journal.pone.0246571","volume":"16","author":"DM Hull","year":"2021","unstructured":"Hull DM, Harrell E, van Vliet AHM, Correa M, Thakur S. 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. PLoS ONE. 2021;16(2):e0246571. https:\/\/doi.org\/10.1371\/journal.pone.0246571","journal-title":"PLoS ONE"},{"issue":"1","key":"10014_CR31","doi-asserted-by":"publisher","first-page":"e0173621","DOI":"10.1128\/aac.01736-21","volume":"66","author":"YS Liao","year":"2022","unstructured":"Liao YS, Chen BH, Teng RH, Wang YW, Chang JH, Liang SY, et al. Antimicrobial Resistance in Campylobacter coli and Campylobacter jejuni from human campylobacteriosis in Taiwan, 2016 to 2019. Antimicrob Agents Chemother. 2022;66(1):e0173621. https:\/\/doi.org\/10.1128\/aac.01736-21","journal-title":"Antimicrob Agents Chemother"},{"issue":"1","key":"10014_CR32","doi-asserted-by":"publisher","first-page":"8998","DOI":"10.1038\/s41598-021-88318-0","volume":"11","author":"M Ocejo","year":"2021","unstructured":"Ocejo M, Oporto B, Lav\u00edn JL, Hurtado A. Whole genome-based characterisation of antimicrobial resistance and genetic diversity in Campylobacter jejuni and Campylobacter coli from ruminants. Sci Rep. 2021;11(1):8998. https:\/\/doi.org\/10.1038\/s41598-021-88318-0","journal-title":"Sci Rep"},{"key":"10014_CR33","doi-asserted-by":"publisher","first-page":"365","DOI":"10.3389\/fcimb.2020.00365","volume":"10","author":"A Rokney","year":"2020","unstructured":"Rokney A, Valinsky L, Vranckx K, Feldman N, Agmon V, Moran-Gilad J, et al. WGS-Based prediction and Analysis of Antimicrobial Resistance in Campylobacter jejuni isolates from Israel. Front Cell Infect Microbiol. 2020;10:365. https:\/\/doi.org\/10.3389\/fcimb.2020.00365","journal-title":"Front Cell Infect Microbiol"},{"key":"10014_CR34","doi-asserted-by":"publisher","first-page":"122","DOI":"10.1016\/j.fm.2018.01.018","volume":"73","author":"CA Whitehouse","year":"2018","unstructured":"Whitehouse CA, Young S, Li C, Hsu CH, Martin G, Zhao S. Use of whole-genome sequencing for Campylobacter surveillance from NARMS retail poultry in the United States in 2015. Food Microbiol. 2018;73:122\u20138. https:\/\/doi.org\/10.1016\/j.fm.2018.01.018","journal-title":"Food Microbiol"},{"issue":"2","key":"10014_CR35","doi-asserted-by":"publisher","first-page":"459","DOI":"10.1128\/AEM.02873-15","volume":"82","author":"S Zhao","year":"2016","unstructured":"Zhao S, Tyson GH, Chen Y, Li C, Mukherjee S, Young S, et al. Whole-genome sequencing analysis accurately predicts Antimicrobial Resistance Phenotypes in Campylobacter spp. Appl Environ Microbiol. 2016;82(2):459\u201366. https:\/\/doi.org\/10.1128\/AEM.02873-15","journal-title":"Appl Environ Microbiol"},{"key":"10014_CR36","unstructured":"ISO. 10272-1:2006: Microbiology of the food chain - horizontal method for detection and enumeration of Campylobacter spp. - part 1: detection method. International Organization for Standardization; 2006."},{"key":"10014_CR37","unstructured":"ISO. 10272-1:2017: Microbiology of the food chain - horizontal method for detection and enumeration of Campylobacter spp. - part 1: detection method. International Organization for Standardization; 2017."},{"issue":"2","key":"10014_CR38","doi-asserted-by":"publisher","first-page":"241","DOI":"10.4315\/0362-028x-73.2.241","volume":"73","author":"AM Mayr","year":"2010","unstructured":"Mayr AM, Lick S, Bauer J, Th\u00e4rigen D, Busch U, Huber I. Rapid detection and differentiation of Campylobacter jejuni, Campylobacter coli, and Campylobacter lari in food, using multiplex real-time PCR. J Food Prot. 2010;73(2):241\u201350. https:\/\/doi.org\/10.4315\/0362-028x-73.2.241","journal-title":"J Food Prot"},{"key":"10014_CR39","doi-asserted-by":"publisher","first-page":"110064","DOI":"10.1016\/j.ijfoodmicro.2022.110064","volume":"388","author":"S Ferrari","year":"2023","unstructured":"Ferrari S, Astvaldsson A, Jernberg T, Stingl K, Messelh\u00e4u\u00dfer U, Skarin H. Validation of PCR methods for confirmation and species identification of thermotolerant Campylobacter as part of EN ISO 10272 - Microbiology of the food chain - horizontal method for detection and enumeration of Campylobacter spp. Int J Food Microbiol. 2023;388:110064. https:\/\/doi.org\/10.1016\/j.ijfoodmicro.2022.110064","journal-title":"Int J Food Microbiol"},{"key":"10014_CR40","unstructured":"CLSI. Methods for Antimicrobial Dilution and Disk Susceptibility Testing of Infrequently Isolated or Fastidious Bacteria. 3rd ed. CLSI guideline M45. Wayne, PA, USA: Clinical and Laboratory Standards Institute 2015."},{"key":"10014_CR41","volume-title":"CLSI supplement VET06","author":"CLSI. Methods for Antimicrobial Susceptibility Testing of Infrequently Isolated or Fastidious Bacteria Isolated From Animals","year":"2017","unstructured":"CLSI. Methods for Antimicrobial Susceptibility Testing of Infrequently Isolated or Fastidious Bacteria Isolated From Animals. CLSI supplement VET06. 1st ed. Wayne, PA, USA: Clinical and Laboratory Standards Institute; 2017.","edition":"1"},{"issue":"2","key":"10014_CR42","doi-asserted-by":"publisher","first-page":"e88108","DOI":"10.1371\/journal.pone.0088108","volume":"9","author":"NJ Kruger","year":"2014","unstructured":"Kruger NJ, Buhler C, Iwobi AN, Huber I, Ellerbroek L, Appel B, et al. Limits of control--crucial parameters for a reliable quantification of viable campylobacter by real-time PCR. PLoS ONE. 2014;9(2):e88108. https:\/\/doi.org\/10.1371\/journal.pone.0088108","journal-title":"PLoS ONE"},{"key":"10014_CR43","unstructured":"EUCAST. European Committee on Antimicrobial Susceptibility Testing., Data from the EUCAST MIC distribution website 2023. Available from: last accessed on 01\/05\/2024. https:\/\/mic.eucast.org\/search\/"},{"issue":"2","key":"10014_CR44","doi-asserted-by":"publisher","first-page":"294","DOI":"10.1111\/j.1365-2672.2012.05354.x","volume":"113","author":"AS Obeng","year":"2012","unstructured":"Obeng AS, Rickard H, Sexton M, Pang Y, Peng H, Barton M. Antimicrobial susceptibilities and resistance genes in Campylobacter strains isolated from poultry and pigs in Australia. J Appl Microbiol. 2012;113(2):294\u2013307. https:\/\/doi.org\/10.1111\/j.1365-2672.2012.05354.x","journal-title":"J Appl Microbiol"},{"issue":"1","key":"10014_CR45","doi-asserted-by":"publisher","first-page":"14","DOI":"10.1128\/JCM.39.1.14-23.2001","volume":"39","author":"KE Dingle","year":"2001","unstructured":"Dingle KE, Colles FM, Wareing DR, Ure R, Fox AJ, Bolton FE, et al. Multilocus sequence typing system for Campylobacter jejuni. J Clin Microbiol. 2001;39(1):14\u201323. https:\/\/doi.org\/10.1128\/JCM.39.1.14-23.2001","journal-title":"J Clin Microbiol"},{"key":"10014_CR46","doi-asserted-by":"publisher","unstructured":"Deneke C, Brendebach H, Uelze L, Borowiak M, Malorny B, Tausch SH. Species-specific Quality Control, Assembly and Contamination Detection in Microbial isolate sequences with AQUAMIS. Genes (Basel). 2021;12(5). https:\/\/doi.org\/10.3390\/genes12050644","DOI":"10.3390\/genes12050644"},{"issue":"17","key":"10014_CR47","doi-asserted-by":"publisher","first-page":"i884","DOI":"10.1093\/bioinformatics\/bty560","volume":"34","author":"S Chen","year":"2018","unstructured":"Chen S, Zhou Y, Chen Y, Gu J. Fastp: an ultra-fast all-in-one FASTQ preprocessor. Bioinformatics. 2018;34(17):i884\u2013i90. https:\/\/doi.org\/10.1093\/bioinformatics\/bty560","journal-title":"Bioinformatics"},{"key":"10014_CR48","unstructured":"Seemann T, Shovill. Assemble bacterial isolate genomes from Illumina paired-end reads. 2020. Available from: last accessed on 01\/05\/2024. https:\/\/github.com\/tseemann\/shovill"},{"key":"10014_CR49","unstructured":"Deneke C, Brendebach H, BakCharak. Bakterial Characterization Pipeline. 2020. Available from: last accessed on 01\/05\/2024. https:\/\/gitlab.com\/bfr_bioinformatics\/bakcharak"},{"issue":"1","key":"10014_CR50","doi-asserted-by":"publisher","first-page":"12728","DOI":"10.1038\/s41598-021-91456-0","volume":"11","author":"M Feldgarden","year":"2021","unstructured":"Feldgarden M, Brover V, Gonzalez-Escalona N, Frye JG, Haendiges J, Haft DH, et al. AMRFinderPlus and the reference gene catalog facilitate examination of the genomic links among antimicrobial resistance, stress response, and virulence. Sci Rep. 2021;11(1):12728. https:\/\/doi.org\/10.1038\/s41598-021-91456-0","journal-title":"Sci Rep"},{"key":"10014_CR51","unstructured":"Seemann T, ABRicate. 2020. Available from: last accessed on 01\/05\/2024. https:\/\/github.com\/tseemann\/abricate"},{"key":"10014_CR52","doi-asserted-by":"publisher","unstructured":"Schwengers O, Barth P, Falgenhauer L, Hain T, Chakraborty T, Goesmann A. Platon: identification and characterization of bacterial plasmid contigs in short-read draft assemblies exploiting protein sequence-based replicon distribution scores. Microb Genom. 2020;6(10).Available from: https:\/\/github.com\/oschwengers\/platon, last accessed on 01\/05\/2024. https:\/\/doi.org\/10.1099\/mgen.0.000398","DOI":"10.1099\/mgen.0.000398"},{"key":"10014_CR53","doi-asserted-by":"publisher","unstructured":"Bortolaia V, Kaas RS, Ruppe E, Roberts MC, Schwarz S, Cattoir V et al. ResFinder 4.0 for predictions of phenotypes from genotypes. J Antimicrob Chemother. 2020;75(12):3491\u2013\u2009500. Available from: https:\/\/cge.food.dtu.dk\/services\/ResFinder\/, last accessed on 01\/05\/2024. https:\/\/doi.org\/10.1093\/jac\/dkaa345","DOI":"10.1093\/jac\/dkaa345"},{"issue":"3","key":"10014_CR54","doi-asserted-by":"publisher","first-page":"403","DOI":"10.1016\/S0022-2836(05)80360-2","volume":"215","author":"SF Altschul","year":"1990","unstructured":"Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool. J Mol Biol. 1990;215(3):403\u201310. https:\/\/doi.org\/10.1016\/S0022-2836(05)80360-2","journal-title":"J Mol Biol"},{"issue":"1","key":"10014_CR55","doi-asserted-by":"publisher","first-page":"39","DOI":"10.1089\/cmb.1994.1.39","volume":"1","author":"DJ States","year":"1994","unstructured":"States DJ, Gish W. Combined use of sequence similarity and codon bias for coding region identification. J Comput Biol. 1994;1(1):39\u201350. https:\/\/doi.org\/10.1089\/cmb.1994.1.39","journal-title":"J Comput Biol"},{"key":"10014_CR56","doi-asserted-by":"publisher","unstructured":"The UniProt Consortium. UniProt: the Universal Protein Knowledgebase in 2023. Nucleic Acids Res. 2022;51(D1):D523-D31.Available from: https:\/\/www.uniprot.org\/, last accessed on 01\/05\/2024. https:\/\/doi.org\/10.1093\/nar\/gkac1052","DOI":"10.1093\/nar\/gkac1052"},{"issue":"7","key":"10014_CR57","doi-asserted-by":"publisher","first-page":"2086","DOI":"10.1128\/JCM.00080-17","volume":"55","author":"AJ Cody","year":"2017","unstructured":"Cody AJ, Bray JE, Jolley KA, McCarthy ND, Maiden MCJ. Core Genome Multilocus sequence typing Scheme for stable, comparative analyses of Campylobacter jejuni and C. Coli Human Disease isolates. J Clin Microbiol. 2017;55(7):2086\u201397. https:\/\/doi.org\/10.1128\/JCM.00080-17","journal-title":"J Clin Microbiol"},{"key":"10014_CR58","doi-asserted-by":"publisher","unstructured":"Jolley KA, Bray JE, Maiden MCJ. Open-access bacterial population genomics: BIGSdb software, the PubMLST.org website and their applications. Wellcome Open Res. 2018;3:124.Available from: https:\/\/pubmlst.org\/, last accessed on 01\/05\/2024. https:\/\/doi.org\/10.12688\/wellcomeopenres.14826.1","DOI":"10.12688\/wellcomeopenres.14826.1"},{"key":"10014_CR59","unstructured":"Deneke C, Borowiak M, MiLongA:. A snakemake workflow for Long-read assembly. 2020. Available from: last accessed on 01\/05\/2024. https:\/\/gitlab.com\/bfr_bioinformatics\/milonga"},{"key":"10014_CR60","unstructured":"Wick RR. Porechop: adapter trimmer for oxford nanopore reads. 2017. Available from: last accessed on 01\/05\/2024. https:\/\/github.com\/rrwick\/Porechop"},{"issue":"6","key":"10014_CR61","doi-asserted-by":"publisher","first-page":"e1005595","DOI":"10.1371\/journal.pcbi.1005595","volume":"13","author":"RR Wick","year":"2017","unstructured":"Wick RR, Judd LM, Gorrie CL, Holt KE, Unicycler. Resolving bacterial genome assemblies from short and long sequencing reads. PLoS Comput Biol. 2017;13(6):e1005595. https:\/\/doi.org\/10.1371\/journal.pcbi.1005595","journal-title":"PLoS Comput Biol"},{"key":"10014_CR62","doi-asserted-by":"publisher","unstructured":"Schwengers O, Jelonek L, Dieckmann MA, Beyvers S, Blom J, Goesmann A. Bakta: rapid and standardized annotation of bacterial genomes via alignment-free sequence identification. Microb Genom. 2021;7(11).Available from: https:\/\/github.com\/oschwengers\/bakta, last accessed on 01\/05\/2024. https:\/\/doi.org\/10.1099\/mgen.0.000685","DOI":"10.1099\/mgen.0.000685"},{"key":"10014_CR63","doi-asserted-by":"publisher","unstructured":"Altman DG. Practical statistics for medical research. Chapman and Hall; 1991. p. 611. https:\/\/doi.org\/10.1002\/sim.4780101015","DOI":"10.1002\/sim.4780101015"},{"key":"10014_CR64","unstructured":"MedCalc Software Ltd. Odds ratio calculator. Version 22.016. Available from:, last accessed on 11\/28\/2023. https:\/\/www.medcalc.org\/calc\/odds_ratio.php"},{"key":"10014_CR65","unstructured":"BfR. ZooNotify - Web-based query of surveillance data according to RL 99\/2003\/EU (Zoonoses Guideline) 2023. Available from: https:\/\/zoonotify.bfr.berlin\/, last accessed on 11\/29\/2023."},{"issue":"7","key":"10014_CR66","doi-asserted-by":"publisher","first-page":"1967","DOI":"10.1016\/j.micinf.2005.12.032","volume":"8","author":"S Payot","year":"2006","unstructured":"Payot S, Bolla JM, Corcoran D, Fanning S, M\u00e9graud F, Zhang Q. Mechanisms of fluoroquinolone and macrolide resistance in Campylobacter spp. Microbes Infect. 2006;8(7):1967\u201371. https:\/\/doi.org\/10.1016\/j.micinf.2005.12.032","journal-title":"Microbes Infect"},{"key":"10014_CR67","unstructured":"Benchling. [Biology Software]. 2023. Available from: last accessed on 01\/05\/2024. https:\/\/benchling.com"},{"key":"10014_CR68","doi-asserted-by":"publisher","unstructured":"Fabre A, Oleastro M, Nunes A, Santos A, Sifr\u00e9 E, Ducournau A, et al. Whole-genome sequence analysis of Multidrug-Resistant Campylobacter isolates: a focus on Aminoglycoside Resistance determinants. J Clin Microbiol. 2018;56(9). https:\/\/doi.org\/10.1128\/JCM.00390-18","DOI":"10.1128\/JCM.00390-18"},{"issue":"5","key":"10014_CR69","doi-asserted-by":"publisher","first-page":"1215","DOI":"10.1093\/jac\/dkt515","volume":"69","author":"X Zeng","year":"2014","unstructured":"Zeng X, Brown S, Gillespie B, Lin J. A single nucleotide in the promoter region modulates the expression of the beta-lactamase OXA-61 in Campylobacter jejuni. J Antimicrob Chemother. 2014;69(5):1215\u201323. https:\/\/doi.org\/10.1093\/jac\/dkt515","journal-title":"J Antimicrob Chemother"},{"issue":"1","key":"10014_CR70","doi-asserted-by":"publisher","first-page":"65","DOI":"10.4315\/0362-028X.JFP-14-109","volume":"78","author":"MI Khalid","year":"2015","unstructured":"Khalid MI, Tang JY, Baharuddin NH, Rahman NS, Rahimi NF, Radu S. Prevalence, antibiogram, and cdt genes of toxigenic Campylobacter jejuni in salad style vegetables (ulam) at farms and retail outlets in Terengganu. J Food Prot. 2015;78(1):65\u201371. https:\/\/doi.org\/10.4315\/0362-028X.JFP-14-109","journal-title":"J Food Prot"},{"issue":"2","key":"10014_CR71","doi-asserted-by":"publisher","first-page":"96","DOI":"10.1089\/fpd.2016.2186","volume":"14","author":"B Li","year":"2017","unstructured":"Li B, Ma L, Li Y, Jia H, Wei J, Shao D, et al. Antimicrobial Resistance of Campylobacter species isolated from broilers in Live Bird markets in Shanghai, China. Foodborne Pathog Dis. 2017;14(2):96\u2013102. https:\/\/doi.org\/10.1089\/fpd.2016.2186","journal-title":"Foodborne Pathog Dis"},{"issue":"3","key":"10014_CR72","doi-asserted-by":"publisher","first-page":"311","DOI":"10.7883\/yoken.JJID.2016.309","volume":"70","author":"PW Lim","year":"2017","unstructured":"Lim PW, Tiam-Lee DC, Paclibare PA, Subejano MS, Cabero-Palma JA, Penuliar GM. High rates of contamination of Poultry Meat products with Drug-Resistant Campylobacter in Metro Manila, Philippines. Jpn J Infect Dis. 2017;70(3):311\u20133. https:\/\/doi.org\/10.7883\/yoken.JJID.2016.309","journal-title":"Jpn J Infect Dis"},{"key":"10014_CR73","doi-asserted-by":"publisher","unstructured":"Tenhagen BA, Flor M, Alt K, Kn\u00fcver MT, Buhler C, K\u00e4sbohrer A, et al. Association of Antimicrobial Resistance in Campylobacter spp. in broilers and turkeys with Antimicrobial Use. Antibiot (Basel). 2021;10(6). https:\/\/doi.org\/10.3390\/antibiotics10060673","DOI":"10.3390\/antibiotics10060673"},{"issue":"2","key":"10014_CR74","doi-asserted-by":"publisher","first-page":"98","DOI":"10.1089\/1076629041310127","volume":"10","author":"A Gibreel","year":"2004","unstructured":"Gibreel A, Sk\u00f6ld O, Taylor DE. Characterization of plasmid-mediated aphA-3 kanamycin resistance in Campylobacter jejuni. Microb Drug Resist. 2004;10(2):98\u2013105. https:\/\/doi.org\/10.1089\/1076629041310127","journal-title":"Microb Drug Resist"},{"issue":"1","key":"10014_CR75","doi-asserted-by":"publisher","first-page":"40","DOI":"10.1016\/j.ijantimicag.2005.08.019","volume":"27","author":"D Corcoran","year":"2006","unstructured":"Corcoran D, Quinn T, Cotter L, Fanning S. An investigation of the molecular mechanisms contributing to high-level erythromycin resistance in Campylobacter. Int J Antimicrob Agents. 2006;27(1):40\u20135. https:\/\/doi.org\/10.1016\/j.ijantimicag.2005.08.019","journal-title":"Int J Antimicrob Agents"},{"key":"10014_CR76","doi-asserted-by":"publisher","unstructured":"Juraschek K, Borowiak M, Tausch SH, Malorny B, K\u00e4sbohrer A, Otani S, et al. Outcome of different sequencing and Assembly approaches on the detection of plasmids and localization of Antimicrobial Resistance genes in Commensal Escherichia coli. Microorganisms. 2021;9(3). https:\/\/doi.org\/10.3390\/microorganisms9030598","DOI":"10.3390\/microorganisms9030598"},{"key":"10014_CR77","doi-asserted-by":"publisher","unstructured":"Horme\u00f1o L, Campos MJ, Vadillo S, Quesada A. Occurrence of tet(O\/M\/O) Mosaic Gene in Tetracycline-Resistant Campylobacter. Microorganisms. 2020;8(11). https:\/\/doi.org\/10.3390\/microorganisms8111710","DOI":"10.3390\/microorganisms8111710"},{"issue":"12","key":"10014_CR78","doi-asserted-by":"publisher","first-page":"3333","DOI":"10.1093\/jac\/dkw304","volume":"71","author":"PJ Warburton","year":"2016","unstructured":"Warburton PJ, Amodeo N, Roberts AP. Mosaic tetracycline resistance genes encoding ribosomal protection proteins. J Antimicrob Chemother. 2016;71(12):3333\u20139. https:\/\/doi.org\/10.1093\/jac\/dkw304","journal-title":"J Antimicrob Chemother"},{"issue":"6","key":"10014_CR79","doi-asserted-by":"publisher","first-page":"1646","DOI":"10.1111\/j.1365-2958.2006.05336.x","volume":"61","author":"DR Hendrixson","year":"2006","unstructured":"Hendrixson DR. A phase-variable mechanism controlling the Campylobacter jejuni FlgR response regulator influences commensalism. Mol Microbiol. 2006;61(6):1646\u201359. https:\/\/doi.org\/10.1111\/j.1365-2958.2006.05336.x","journal-title":"Mol Microbiol"},{"issue":"2","key":"10014_CR80","doi-asserted-by":"publisher","first-page":"519","DOI":"10.1111\/j.1365-2958.2008.06428.x","volume":"70","author":"DR Hendrixson","year":"2008","unstructured":"Hendrixson DR. Restoration of flagellar biosynthesis by varied mutational events in Campylobacter jejuni. Mol Microbiol. 2008;70(2):519\u201336. https:\/\/doi.org\/10.1111\/j.1365-2958.2008.06428.x","journal-title":"Mol Microbiol"},{"issue":"3","key":"10014_CR81","doi-asserted-by":"publisher","first-page":"297","DOI":"10.1128\/AAC.33.3.297","volume":"33","author":"WJ Page","year":"1989","unstructured":"Page WJ, Huyer G, Huyer M, Worobec EA. Characterization of the porins of Campylobacter jejuni and Campylobacter coli and implications for antibiotic susceptibility. Antimicrob Agents Chemother. 1989;33(3):297\u2013303. https:\/\/doi.org\/10.1128\/AAC.33.3.297","journal-title":"Antimicrob Agents Chemother"},{"issue":"2","key":"10014_CR82","doi-asserted-by":"publisher","first-page":"341","DOI":"10.1093\/jac\/dkh331","volume":"54","author":"L Pumbwe","year":"2004","unstructured":"Pumbwe L, Randall LP, Woodward MJ, Piddock LJ. Expression of the efflux pump genes cmeB, cmeF and the porin gene porA in multiple-antibiotic-resistant Campylobacter jejuni. J Antimicrob Chemother. 2004;54(2):341\u20137. https:\/\/doi.org\/10.1093\/jac\/dkh331","journal-title":"J Antimicrob Chemother"},{"issue":"3","key":"10014_CR83","doi-asserted-by":"publisher","first-page":"1067","DOI":"10.1128\/AAC.49.3.1067-1075.2005","volume":"49","author":"J Lin","year":"2005","unstructured":"Lin J, Akiba M, Sahin O, Zhang Q. CmeR functions as a transcriptional repressor for the multidrug efflux pump CmeABC in Campylobacter jejuni. Antimicrob Agents Chemother. 2005;49(3):1067\u201375. https:\/\/doi.org\/10.1128\/AAC.49.3.1067-1075.2005","journal-title":"Antimicrob Agents Chemother"},{"issue":"7","key":"10014_CR84","doi-asserted-by":"publisher","first-page":"2124","DOI":"10.1128\/AAC.46.7.2124-2131.2002","volume":"46","author":"J Lin","year":"2002","unstructured":"Lin J, Michel LO, Zhang Q. CmeABC functions as a multidrug efflux system in Campylobacter jejuni. Antimicrob Agents Chemother. 2002;46(7):2124\u201331. https:\/\/doi.org\/10.1128\/AAC.46.7.2124-2131.2002","journal-title":"Antimicrob Agents Chemother"},{"issue":"3","key":"10014_CR85","doi-asserted-by":"publisher","first-page":"491","DOI":"10.1093\/jac\/dki253","volume":"56","author":"L Mamelli","year":"2005","unstructured":"Mamelli L, Prouzet-Maul\u00e9on V, Pag\u00e8s JM, M\u00e9graud F, Bolla JM. Molecular basis of macrolide resistance in Campylobacter: role of efflux pumps and target mutations. J Antimicrob Chemother. 2005;56(3):491\u20137. https:\/\/doi.org\/10.1093\/jac\/dki253","journal-title":"J Antimicrob Chemother"},{"issue":"7","key":"10014_CR86","doi-asserted-by":"publisher","first-page":"1320","DOI":"10.3201\/eid2507.181572","volume":"25","author":"BS Lopes","year":"2019","unstructured":"Lopes BS, Strachan NJC, Ramjee M, Thomson A, MacRae M, Shaw S, et al. Nationwide Stepwise Emergence and Evolution of Multidrug-Resistant Campylobacter jejuni sequence type 5136, United Kingdom. Emerg Infect Dis. 2019;25(7):1320\u20139. https:\/\/doi.org\/10.3201\/eid2507.181572","journal-title":"Emerg Infect Dis"},{"issue":"2","key":"10014_CR87","doi-asserted-by":"publisher","first-page":"189","DOI":"10.2217\/17460913.4.2.189","volume":"4","author":"T Luangtongkum","year":"2009","unstructured":"Luangtongkum T, Jeon B, Han J, Plummer P, Logue CM, Zhang Q. Antibiotic resistance in Campylobacter: emergence, transmission and persistence. Future Microbiol. 2009;4(2):189\u2013200. https:\/\/doi.org\/10.2217\/17460913.4.2.189","journal-title":"Future Microbiol"},{"key":"10014_CR88","doi-asserted-by":"publisher","unstructured":"Whitehouse CA, Zhao S, Mukherjee S, Tate H, Bodeis-Jones S, Young S et al. Gyrase A mutations in Campylobacter Associated with decreased susceptibility to different fluoroquinolones. J Food Prot. 2017:1863\u20136. https:\/\/doi.org\/10.4315\/0362-028X.JFP-17-129","DOI":"10.4315\/0362-028X.JFP-17-129"},{"issue":"3","key":"10014_CR89","doi-asserted-by":"publisher","first-page":"541","DOI":"10.1073\/pnas.0408966102","volume":"102","author":"N Luo","year":"2005","unstructured":"Luo N, Pereira S, Sahin O, Lin J, Huang S, Michel L, et al. Enhanced in vivo fitness of fluoroquinolone-resistant Campylobacter jejuni in the absence of antibiotic selection pressure. Proc Natl Acad Sci U S A. 2005;102(3):541\u20136. https:\/\/doi.org\/10.1073\/pnas.0408966102","journal-title":"Proc Natl Acad Sci U S A"},{"issue":"3","key":"10014_CR90","doi-asserted-by":"publisher","first-page":"257","DOI":"10.1089\/10766290152652800","volume":"7","author":"R Bachoual","year":"2001","unstructured":"Bachoual R, Ouabdesselam S, Mory F, Lascols C, Soussy CJ, Tankovic J. Single or double mutational alterations of gyrA associated with fluoroquinolone resistance in Campylobacter jejuni and Campylobacter coli. Microb Drug Resist. 2001;7(3):257\u201361. https:\/\/doi.org\/10.1089\/10766290152652800","journal-title":"Microb Drug Resist"},{"issue":"11","key":"10014_CR91","doi-asserted-by":"publisher","first-page":"5398","DOI":"10.1128\/AAC.00669-13","volume":"57","author":"Y Chen","year":"2013","unstructured":"Chen Y, Mukherjee S, Hoffmann M, Kotewicz ML, Young S, Abbott J, et al. Whole-genome sequencing of gentamicin-resistant Campylobacter coli isolated from U.S. retail meats reveals novel plasmid-mediated aminoglycoside resistance genes. Antimicrob Agents Chemother. 2013;57(11):5398\u2013405. https:\/\/doi.org\/10.1128\/AAC.00669-13","journal-title":"Antimicrob Agents Chemother"},{"issue":"1","key":"10014_CR92","doi-asserted-by":"publisher","first-page":"12529","DOI":"10.1038\/s41598-023-39588-3","volume":"13","author":"M Ocejo","year":"2023","unstructured":"Ocejo M, Oporto B, Lavin JL, Hurtado A. Monitoring within-farm transmission dynamics of antimicrobial-resistant Campylobacter in dairy cattle using broth microdilution and long-read whole genome sequencing. Sci Rep. 2023;13(1):12529. https:\/\/doi.org\/10.1038\/s41598-023-39588-3","journal-title":"Sci Rep"},{"key":"10014_CR93","doi-asserted-by":"publisher","unstructured":"Moser S, Seth-Smith H, Egli A, Kittl S, Overesch G. Campylobacter jejuni from canine and Bovine Cases of Campylobacteriosis Express High Antimicrobial Resistance Rates against (Fluoro)quinolones and tetracyclines. Pathogens. 2020;9(9). https:\/\/doi.org\/10.3390\/pathogens9090691","DOI":"10.3390\/pathogens9090691"},{"issue":"6","key":"10014_CR94","doi-asserted-by":"publisher","first-page":"2454","DOI":"10.1128\/AAC.49.6.2454-2459.2005","volume":"49","author":"W Nirdnoy","year":"2005","unstructured":"Nirdnoy W, Mason CJ, Guerry P. Mosaic structure of a multiple-drug-resistant, conjugative plasmid from Campylobacter jejuni. Antimicrob Agents Chemother. 2005;49(6):2454\u20139. https:\/\/doi.org\/10.1128\/AAC.49.6.2454-2459.2005","journal-title":"Antimicrob Agents Chemother"},{"key":"10014_CR95","doi-asserted-by":"publisher","first-page":"1092179","DOI":"10.3389\/fvets.2023.1092179","volume":"10","author":"H El-Adawy","year":"2023","unstructured":"El-Adawy H, Hotzel H, Garc\u00eda-Soto S, Tomaso H, Hafez HM, Schwarz S, et al. Genomic insight into Campylobacter jejuni isolated from commercial Turkey flocks in Germany using whole-genome sequencing analysis. Front Vet Sci. 2023;10:1092179. https:\/\/doi.org\/10.3389\/fvets.2023.1092179","journal-title":"Front Vet Sci"},{"key":"10014_CR96","doi-asserted-by":"publisher","first-page":"1805","DOI":"10.12688\/f1000research.12777.1","volume":"6","author":"HE Webb","year":"2017","unstructured":"Webb HE, Angulo FJ, Granier SA, Scott HM, Loneragan GH. Illustrative examples of probable transfer of resistance determinants from food animals to humans: streptothricins, glycopeptides, and colistin. F1000Res. 2017;6:1805. https:\/\/doi.org\/10.12688\/f1000research.12777.1","journal-title":"F1000Res"},{"issue":"3","key":"10014_CR97","doi-asserted-by":"publisher","first-page":"1300","DOI":"10.1128\/AAC.05516-11","volume":"56","author":"T Luangtongkum","year":"2012","unstructured":"Luangtongkum T, Shen Z, Seng VW, Sahin O, Jeon B, Liu P, et al. Impaired fitness and transmission of macrolide-resistant Campylobacter jejuni in its natural host. Antimicrob Agents Chemother. 2012;56(3):1300\u20138. https:\/\/doi.org\/10.1128\/AAC.05516-11","journal-title":"Antimicrob Agents Chemother"},{"issue":"9","key":"10014_CR98","doi-asserted-by":"publisher","first-page":"5405","DOI":"10.1128\/AAC.03039-14","volume":"58","author":"Y Wang","year":"2014","unstructured":"Wang Y, Zhang M, Deng F, Shen Z, Wu C, Zhang J, et al. Emergence of multidrug-resistant Campylobacter species isolates with a horizontally acquired rRNA methylase. Antimicrob Agents Chemother. 2014;58(9):5405\u201312. https:\/\/doi.org\/10.1128\/AAC.03039-14","journal-title":"Antimicrob Agents Chemother"},{"issue":"Suppl 1","key":"10014_CR99","doi-asserted-by":"publisher","first-page":"70","DOI":"10.1111\/zph.12165","volume":"62","author":"JJ Carrique-Mas","year":"2015","unstructured":"Carrique-Mas JJ, Trung NV, Hoa NT, Mai HH, Thanh TH, Campbell JI, et al. Antimicrobial usage in chicken production in the Mekong Delta of Vietnam. Zoonoses Public Health. 2015;62(Suppl 1):70\u20138. https:\/\/doi.org\/10.1111\/zph.12165","journal-title":"Zoonoses Public Health"},{"issue":"4","key":"10014_CR100","doi-asserted-by":"publisher","first-page":"964","DOI":"10.1093\/jac\/dkt492","volume":"69","author":"S Qin","year":"2014","unstructured":"Qin S, Wang Y, Zhang Q, Zhang M, Deng F, Shen Z, et al. Report of ribosomal RNA methylase gene erm(B) in multidrug-resistant Campylobacter coli. J Antimicrob Chemother. 2014;69(4):964\u20138. https:\/\/doi.org\/10.1093\/jac\/dkt492","journal-title":"J Antimicrob Chemother"},{"key":"10014_CR101","doi-asserted-by":"publisher","unstructured":"Chen JC, Tagg KA, Joung YJ, Bennett C, Francois Watkins L, Eikmeier D, et al. Report of erm(B)(+) Campylobacter jejuni in the United States. Antimicrob Agents Chemother. 2018;62(6). https:\/\/doi.org\/10.1128\/AAC.02615-17","DOI":"10.1128\/AAC.02615-17"},{"issue":"3","key":"10014_CR102","doi-asserted-by":"publisher","first-page":"841","DOI":"10.1093\/jac\/dkv383","volume":"71","author":"D Florez-Cuadrado","year":"2016","unstructured":"Florez-Cuadrado D, Ugarte-Ruiz M, Quesada A, Palomo G, Dom\u00ednguez L, Porrero MC. Description of an erm(B)-carrying Campylobacter coli isolate in Europe. J Antimicrob Chemother. 2016;71(3):841\u20133. https:\/\/doi.org\/10.1093\/jac\/dkv383","journal-title":"J Antimicrob Chemother"},{"key":"10014_CR103","doi-asserted-by":"publisher","first-page":"2240","DOI":"10.3389\/fmicb.2017.02240","volume":"8","author":"D Florez-Cuadrado","year":"2017","unstructured":"Florez-Cuadrado D, Ugarte-Ruiz M, Meric G, Quesada A, Porrero MC, Pascoe B, et al. Genome Comparison of Erythromycin Resistant Campylobacter from turkeys identifies hosts and pathways for horizontal spread of erm(B) genes. Front Microbiol. 2017;8:2240. https:\/\/doi.org\/10.3389\/fmicb.2017.02240","journal-title":"Front Microbiol"},{"key":"10014_CR104","doi-asserted-by":"publisher","unstructured":"Golz JC, Stingl K. Take it or leave It-Factors regulating competence development and DNA uptake in Campylobacter jejuni. Int J Mol Sci. 2021;22(18). https:\/\/doi.org\/10.3390\/ijms221810169","DOI":"10.3390\/ijms221810169"},{"key":"10014_CR105","doi-asserted-by":"publisher","unstructured":"Tang B, Wang Y, Luo Y, Zheng X, Qin X, Yang H, et al. Coexistence of optrA and fexA in Campylobacter. mSphere. 2021;6(3). https:\/\/doi.org\/10.1128\/mSphere.00125-21","DOI":"10.1128\/mSphere.00125-21"},{"issue":"3","key":"10014_CR106","doi-asserted-by":"publisher","first-page":"313","DOI":"10.32394\/pe.72.3.8","volume":"72","author":"A Mirecka","year":"2018","unstructured":"Mirecka A. Etiological agents of bacterial meningitis in adults and antibiotic susceptibility of Streptococcus pneumoniae isolated between 2009\u20132016 from patients of Regional specialist hospital of Dr Wl. Bieganski in Lodz. Przegl Epidemiol. 2018;72(3):313\u201324. https:\/\/doi.org\/10.32394\/pe.72.3.8","journal-title":"Przegl Epidemiol"},{"issue":"5","key":"10014_CR107","doi-asserted-by":"publisher","first-page":"433","DOI":"10.1097\/QCO.0000000000000298","volume":"29","author":"DH Paris","year":"2016","unstructured":"Paris DH, Dumler JS. State of the art of diagnosis of rickettsial diseases: the use of blood specimens for diagnosis of scrub typhus, spotted fever group rickettsiosis, and murine typhus. Curr Opin Infect Dis. 2016;29(5):433\u20139. https:\/\/doi.org\/10.1097\/QCO.0000000000000298","journal-title":"Curr Opin Infect Dis"},{"key":"10014_CR108","doi-asserted-by":"publisher","first-page":"3217","DOI":"10.2147\/IDR.S204618","volume":"12","author":"N Patil","year":"2019","unstructured":"Patil N, Mule P. Sensitivity pattern of Salmonella typhi and Paratyphi A isolates to Chloramphenicol and other anti-typhoid drugs: an in Vitro Study. Infect Drug Resist. 2019;12:3217\u201325. https:\/\/doi.org\/10.2147\/IDR.S204618","journal-title":"Infect Drug Resist"},{"key":"10014_CR109","doi-asserted-by":"publisher","first-page":"CD005437","DOI":"10.1002\/14651858.CD005437.pub4","volume":"6","author":"TD Sudarsanam","year":"2017","unstructured":"Sudarsanam TD, Rupali P, Tharyan P, Abraham OC, Thomas K. Pre-admission antibiotics for suspected cases of meningococcal disease. Cochrane Database Syst Rev. 2017;6:CD005437. https:\/\/doi.org\/10.1002\/14651858.CD005437.pub4","journal-title":"Cochrane Database Syst Rev"},{"key":"10014_CR110","unstructured":"WHO. Critically important antimicrobials for human medicine, 6th revision. Geneva: World Health Organization. 2019. Available from:, last accessed on 01\/05\/2024. https:\/\/www.who.int\/publications\/i\/item\/9789241515528"}],"container-title":["BMC Genomics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/s12864-024-10014-w.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/article\/10.1186\/s12864-024-10014-w\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/s12864-024-10014-w.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,2,8]],"date-time":"2024-02-08T03:05:55Z","timestamp":1707361555000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcgenomics.biomedcentral.com\/articles\/10.1186\/s12864-024-10014-w"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2024,2,8]]},"references-count":110,"journal-issue":{"issue":"1","published-online":{"date-parts":[[2024,12]]}},"alternative-id":["10014"],"URL":"https:\/\/doi.org\/10.1186\/s12864-024-10014-w","relation":{"has-preprint":[{"id-type":"doi","id":"10.21203\/rs.3.rs-3465583\/v1","asserted-by":"object"}]},"ISSN":["1471-2164"],"issn-type":[{"value":"1471-2164","type":"electronic"}],"subject":[],"published":{"date-parts":[[2024,2,8]]},"assertion":[{"value":"19 October 2023","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"14 January 2024","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"8 February 2024","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Declarations"}},{"value":"Not applicable.","order":2,"name":"Ethics","group":{"name":"EthicsHeading","label":"Ethics approval and consent to participate"}},{"value":"Not applicable.","order":3,"name":"Ethics","group":{"name":"EthicsHeading","label":"Consent for publication"}},{"value":"The authors declare no competing interests.","order":4,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing interests"}}],"article-number":"156"}}