{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,18]],"date-time":"2026-08-18T04:33:25Z","timestamp":1787027605921,"version":"build-2736575974"},"reference-count":46,"publisher":"MDPI AG","issue":"9","license":[{"start":{"date-parts":[[2025,9,18]],"date-time":"2025-09-18T00:00:00Z","timestamp":1758153600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100010804","name":"Faculty of Medicine, Prince of Songkla University","doi-asserted-by":"publisher","award":["65-071-3"],"award-info":[{"award-number":["65-071-3"]}],"id":[{"id":"10.13039\/501100010804","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Antibiotics"],"abstract":"<jats:p>Background: Helicobacter pylori is associated with a wide range of gastroduodenal diseases, including chronic gastritis, peptic ulcer disease, and gastric cancer. Eradication efforts are challenged by increasing antimicrobial resistance rates, particularly in Southeast Asia. We sequenced the whole genomes of clinical H. pylori isolates from Southern Thailand to elucidate their resistance profiles, virulence determinants, and evolutionary relationships. Methods: Three clinical H. pylori isolates (004, 117, and 189) were subjected to whole-genome sequencing, phenotypic antimicrobial susceptibility testing, and comparative genomic analyses. Results: All strains exhibited high-level resistance to metronidazole. Additionally, H. pylori 117 was resistant to both amoxicillin and levofloxacin, classifying it as multidrug-resistant. Genomic analysis revealed mutations in rdxA, frxA, and rpoB, as well as in penicillin-binding protein genes (pbp2 and pbp3), supporting the phenotypic findings. While all isolates harboured clarithromycin resistance mutations (A2142G and A2143G in the 23S rRNA gene), they were phenotypically susceptible, highlighting a potential discordance that requires further investigation. Virulence gene profiling identified 115\u2013118 conserved genes per strain, including cagA, vacA, oipA, babA, and flagellar, urease, and lipopolysaccharide biosynthesis genes. Phylogenetic analysis using core-genome single-nucleotide polymorphisms demonstrated that these strains formed a distinct Southern Thai monophyletic clade, suggesting localised clonal expansion driven by regional selective pressures. Conclusions: Region-specific surveillance strategies and treatment guidelines are urgently needed in Thailand. The combination of high-risk virulence genes and rising antimicrobial resistance in H. pylori strains necessitates tailored therapeutic approaches, the integration of genomic surveillance into clinical diagnostics, and expanded studies linking genotype to clinical outcomes in diverse populations.<\/jats:p>","DOI":"10.3390\/antibiotics14090944","type":"journal-article","created":{"date-parts":[[2025,9,18]],"date-time":"2025-09-18T14:45:46Z","timestamp":1758206746000},"page":"944","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":1,"title":["Whole-Genome Sequencing and Antibiotic Resistance Profiling of Helicobacter pylori Isolates from a Tertiary Hospital in Southern Thailand"],"prefix":"10.3390","volume":"14","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-1403-1628","authenticated-orcid":false,"given":"Chonticha","family":"Romyasamit","sequence":"first","affiliation":[{"name":"Department of Medical Technology, School of Allied Health Sciences, Walailak University, Nakhon Si Thammarat 80160, Thailand"},{"name":"Research Center in Tropical Pathobiology, Walailak University, Thasala District, Nakhon Si Thammarat 80160, Thailand"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4058-5977","authenticated-orcid":false,"given":"Apichat","family":"Kaewdech","sequence":"additional","affiliation":[{"name":"Gastroenterology and Hepatology Unit, Division of Internal Medicine, Faculty of Medicine, Prince of Songkla University, Hat Yai, Songkhla 90110, Thailand"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0007-8214","authenticated-orcid":false,"given":"Pimsiri","family":"Sripongpun","sequence":"additional","affiliation":[{"name":"Gastroenterology and Hepatology Unit, Division of Internal Medicine, Faculty of Medicine, Prince of Songkla University, Hat Yai, Songkhla 90110, Thailand"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Naichaya","family":"Chamroonkul","sequence":"additional","affiliation":[{"name":"Gastroenterology and Hepatology Unit, Division of Internal Medicine, Faculty of Medicine, Prince of Songkla University, Hat Yai, Songkhla 90110, Thailand"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7793-7561","authenticated-orcid":false,"given":"Komwit","family":"Surachat","sequence":"additional","affiliation":[{"name":"Department of Biomedical Sciences and Biomedical Engineering, Faculty of Medicine, Prince of Songkla University, Hat Yai, Songkhla 90110, Thailand"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0004-9699-8350","authenticated-orcid":false,"given":"Sirikan","family":"Suwannasin","sequence":"additional","affiliation":[{"name":"Department of Biomedical Sciences and Biomedical Engineering, Faculty of Medicine, Prince of Songkla University, Hat Yai, Songkhla 90110, Thailand"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yosita","family":"Leepromma","sequence":"additional","affiliation":[{"name":"Department of Medical Technology, School of Allied Health Sciences, Walailak University, Nakhon Si Thammarat 80160, Thailand"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7419-0116","authenticated-orcid":false,"given":"Morteza","family":"Saki","sequence":"additional","affiliation":[{"name":"Department of Microbiology, Faculty of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Maseetoh","family":"Samaeng","sequence":"additional","affiliation":[{"name":"Division of Internal Medicine, Faculty of Medicine, Prince of Songkla University, Hat Yai, Songkhla 90110, Thailand"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6992-033X","authenticated-orcid":false,"given":"Phoomjai","family":"Sornsenee","sequence":"additional","affiliation":[{"name":"Family Medicine and Preventive Medicine, Faculty of Medicine, Prince of Songkla University, Songkhla 90110, Thailand"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2025,9,18]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"1597","DOI":"10.1056\/NEJMcp1001110","article-title":"Clinical practice. Helicobacter pylori infection","volume":"362","author":"McColl","year":"2010","journal-title":"N. Engl. J. Med."},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1007\/978-1-0716-1302-3_1","article-title":"An overview of Helicobacter pylori infection","volume":"2283","author":"FitzGerald","year":"2021","journal-title":"Methods Mol. Biol."},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"1175","DOI":"10.1056\/NEJMra020542","article-title":"Helicobacter pylori infection","volume":"347","author":"Suerbaum","year":"2002","journal-title":"N. Engl. J. Med."},{"key":"ref_4","doi-asserted-by":"crossref","unstructured":"Ali, A., and AlHussaini, K.I. (2024). Helicobacter pylori: A contemporary perspective on pathogenesis, diagnosis and treatment strategies. Microorganisms, 12.","DOI":"10.3390\/microorganisms12010222"},{"key":"ref_5","first-page":"587","article-title":"Working group report on schistosomes, liver flukes and Helicobacter pylori","volume":"60","author":"Heseltine","year":"1995","journal-title":"Int. J. Cancer"},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"19","DOI":"10.1038\/s41572-023-00431-8","article-title":"Helicobacter pylori infection","volume":"9","author":"Malfertheiner","year":"2023","journal-title":"Nat. Rev. Dis. Primers"},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"605","DOI":"10.1053\/j.gastro.2023.12.022","article-title":"Global prevalence of Helicobacter pylori infection and incidence of gastric cancer between 1980 and 2022","volume":"166","author":"Chen","year":"2024","journal-title":"Gastroenterology"},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"717","DOI":"10.4269\/ajtmh.15-0449","article-title":"Extremely high prevalence of metronidazole-resistant Helicobacter pylori strains in mountain people (Karen and Hmong) in Thailand","volume":"94","author":"Vilaichone","year":"2016","journal-title":"Am. J. Trop. Med. Hyg."},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"346","DOI":"10.1016\/j.diagmicrobio.2013.08.010","article-title":"Nationwide survey of Helicobacter pylori antibiotic resistance in Thailand","volume":"77","author":"Vilaichone","year":"2013","journal-title":"Diagn. Microbiol. Infect. Dis."},{"key":"ref_10","doi-asserted-by":"crossref","unstructured":"Yi, M., Chen, S., Yi, X., Zhang, F., Zhou, X., Zeng, M., and Song, H. (2025). Helicobacter pylori infection process: From the molecular world to clinical treatment. Front. Microbiol., 16.","DOI":"10.3389\/fmicb.2025.1541140"},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"5578","DOI":"10.3748\/wjg.v25.i37.5578","article-title":"Pathogenesis and clinical management of Helicobacter pylori gastric infection","volume":"25","author":"Soares","year":"2019","journal-title":"World J. Gastroenterol."},{"key":"ref_12","doi-asserted-by":"crossref","unstructured":"Machlowska, J., Baj, J., Sitarz, M., Maciejewski, R., and Sitarz, R. (2020). Gastric cancer: Epidemiology, risk factors, classification, genomic characteristics and treatment strategies. Int. J. Mol. Sci., 21.","DOI":"10.3390\/ijms21114012"},{"key":"ref_13","doi-asserted-by":"crossref","first-page":"1372","DOI":"10.1053\/j.gastro.2018.07.007","article-title":"Prevalence of antibiotic resistance in Helicobacter pylori: A systematic review and meta-analysis in World Health Organization regions","volume":"155","author":"Savoldi","year":"2018","journal-title":"Gastroenterology"},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"34","DOI":"10.1136\/gutjnl-2012-302254","article-title":"Helicobacter pylori resistance to antibiotics in Europe and its relationship to antibiotic consumption","volume":"62","author":"Megraud","year":"2013","journal-title":"Gut"},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"613","DOI":"10.1038\/s41575-021-00449-x","article-title":"Helicobacter pylori infection and antibiotic resistance\u2014From biology to clinical implications","volume":"18","author":"Yamaoka","year":"2021","journal-title":"Nat. Rev. Gastroenterol. Hepatol."},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"5155","DOI":"10.1128\/JB.183.17.5155-5162.2001","article-title":"Roles of FrxA and RdxA nitroreductases of Helicobacter pylori in susceptibility and resistance to metronidazole","volume":"183","author":"Jeong","year":"2001","journal-title":"J. Bacteriol."},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"2379439","DOI":"10.1080\/19490976.2024.2379439","article-title":"The crosstalk between efflux pump and resistance gene mutation in Helicobacter pylori","volume":"16","author":"Gong","year":"2024","journal-title":"Gut Microbes"},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"995","DOI":"10.1093\/jac\/dkn051","article-title":"Mutations in penicillin-binding proteins 1, 2 and 3 are responsible for amoxicillin resistance in Helicobacter pylori","volume":"61","author":"Rimbara","year":"2008","journal-title":"J. Antimicrob. Chemother."},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"43","DOI":"10.1186\/s13099-021-00438-0","article-title":"The penicillin binding protein 1A of Helicobacter pylori, its amoxicillin binding site and access routes","volume":"13","author":"Attaran","year":"2021","journal-title":"Gut Pathog."},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"306","DOI":"10.1016\/j.chom.2014.02.008","article-title":"Helicobacter pylori CagA and gastric cancer: A paradigm for hit-and-run carcinogenesis","volume":"15","author":"Hatakeyama","year":"2014","journal-title":"Cell Host Microbe"},{"key":"ref_21","doi-asserted-by":"crossref","unstructured":"Gareayaghi, N., and Kocazeybek, B. (2022). Detection of A2143G, A2142C, and A2142G point mutations with real-time PCR in stool specimens from children infected with Helicobacter pylori. Diagnostics, 12.","DOI":"10.3390\/diagnostics12092119"},{"key":"ref_22","doi-asserted-by":"crossref","unstructured":"Breurec, S., Guillard, B., Hem, S., Brisse, S., Dieye, F.B., Huerre, M., Oung, C., Raymond, J., Tan, T.S., and Thiberge, J.M. (2011). Evolutionary history of Helicobacter pylori sequences reflect past human migrations in Southeast Asia. PLoS ONE, 6.","DOI":"10.1371\/journal.pone.0022058"},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"2273","DOI":"10.1038\/s41467-019-10050-1","article-title":"Within-host evolution of Helicobacter pylori shaped by niche-specific adaptation, intragastric migrations and selective sweeps","volume":"10","author":"Ailloud","year":"2019","journal-title":"Nat. Commun."},{"key":"ref_24","doi-asserted-by":"crossref","unstructured":"Chen, C., Zhang, Y., Wu, H., Qiao, J., and Caiyin, Q. (2025). Advances in diversity, evolutionary dynamics and biotechnological potential of restriction-modification systems. Microorganisms, 13.","DOI":"10.3390\/microorganisms13051126"},{"key":"ref_25","doi-asserted-by":"crossref","unstructured":"Baquero, F., Mart\u00ednez, J.L., F Lanza, V.F., Rodr\u00edguez-Beltr\u00e1n, J., Gal\u00e1n, J.C., San Mill\u00e1n, A., Cant\u00f3n, R., and Coque, T.M. (2021). Evolutionary pathways and trajectories in antibiotic resistance. Clin. Microbiol. Rev., 34.","DOI":"10.1128\/CMR.00050-19"},{"key":"ref_26","doi-asserted-by":"crossref","unstructured":"Barber, M.F., and Fitzgerald, J.R. (2024). Mechanisms of host adaptation by bacterial pathogens. FEMS Microbiol. Rev., 48.","DOI":"10.1093\/femsre\/fuae019"},{"key":"ref_27","doi-asserted-by":"crossref","unstructured":"Emamalipour, M., Seidi, K., Zununi Vahed, S., Jahanban-Esfahlan, A., Jaymand, M., Majdi, H., Amoozgar, Z., Chitkushev, L.T., Javaheri, T., and Jahanban-Esfahlan, R. (2020). Horizontal gene transfer: From evolutionary flexibility to disease progression. Front. Cell Dev. Biol., 8.","DOI":"10.3389\/fcell.2020.00229"},{"key":"ref_28","doi-asserted-by":"crossref","first-page":"64","DOI":"10.1053\/j.gastro.2015.09.004","article-title":"Pathobiology of Helicobacter pylori-induced gastric cancer","volume":"150","author":"Amieva","year":"2016","journal-title":"Gastroenterology"},{"key":"ref_29","doi-asserted-by":"crossref","first-page":"95","DOI":"10.14196\/mjiri.31.95","article-title":"Determination of Helicobacter pylori virulence-associated genes in duodenal ulcer and gastric biopsies","volume":"31","author":"Saeidi","year":"2017","journal-title":"Med. J. Islam. Repub. Iran"},{"key":"ref_30","doi-asserted-by":"crossref","first-page":"341","DOI":"10.1111\/1751-2980.12054","article-title":"The significance of virulence factors in Helicobacter pylori","volume":"14","author":"Shiota","year":"2013","journal-title":"J. Dig. Dis."},{"key":"ref_31","doi-asserted-by":"crossref","first-page":"1037","DOI":"10.1002\/jgh3.12426","article-title":"Helicobacter pylori healthy South Asians","volume":"4","author":"Kharel","year":"2020","journal-title":"JGH Open"},{"key":"ref_32","first-page":"311","article-title":"Helicobacter pylori infection and gastric cancer worldwide: Thailand distribution and burden disease","volume":"24","author":"Tongtawee","year":"2017","journal-title":"Suranaree J. Sci. Technol."},{"key":"ref_33","doi-asserted-by":"crossref","first-page":"1176","DOI":"10.1001\/jama.1907.25320140022001f","article-title":"The nephelometer: An instrument for estimating the number of bacteria in suspensions used for calculating the opsonic index and for vaccines","volume":"49","author":"McFarland","year":"1907","journal-title":"JAMA"},{"key":"ref_34","unstructured":"The European Committee on Antimicrobial Susceptibility Testing (2025, May 27). Breakpoint Tables for Interpretation of MICs and Zone Diameters, Version 14.0, 2024. Available online: https:\/\/www.eucast.org."},{"key":"ref_35","doi-asserted-by":"crossref","unstructured":"Chukamnerd, A., Jeenkeawpiam, K., Chusri, S., Pomwised, R., Singkhamanan, K., and Surachat, K. (2023). BacSeq: A user-friendly automated pipeline for whole-genome sequence analysis of bacterial genomes. Microorganisms, 11.","DOI":"10.3390\/microorganisms11071769"},{"key":"ref_36","doi-asserted-by":"crossref","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":"ref_37","doi-asserted-by":"crossref","first-page":"1925","DOI":"10.1093\/bioinformatics\/btz848","article-title":"GTDB-Tk: A toolkit to classify genomes with the Genome Taxonomy Database","volume":"36","author":"Chaumeil","year":"2019","journal-title":"Bioinformatics"},{"key":"ref_38","doi-asserted-by":"crossref","first-page":"W484","DOI":"10.1093\/nar\/gkad326","article-title":"Proksee: In-depth characterization and visualization of bacterial genomes","volume":"51","author":"Grant","year":"2023","journal-title":"Nucleic Acids Res."},{"key":"ref_39","doi-asserted-by":"crossref","first-page":"D325","DOI":"10.1093\/nar\/gki008","article-title":"VFDB: A reference database for bacterial virulence factors","volume":"33","author":"Chen","year":"2005","journal-title":"Nucleic Acids Res."},{"key":"ref_40","doi-asserted-by":"crossref","first-page":"3348","DOI":"10.1128\/AAC.00419-13","article-title":"The comprehensive antibiotic resistance database","volume":"57","author":"McArthur","year":"2013","journal-title":"Antimicrob. Agents Chemother."},{"key":"ref_41","doi-asserted-by":"crossref","unstructured":"Brown, C.L., Mullet, J., Hindi, F., Stoll, J.E., Gupta, S., Choi, M., Keenum, I., Vikesland, P., Pruden, A., and Zhang, L. (2022). mobileOG-db: A manually curated database of protein families mediating the life cycle of bacterial mobile genetic elements. Appl. Environ. Microbiol., 88.","DOI":"10.1128\/aem.00991-22"},{"key":"ref_42","doi-asserted-by":"crossref","first-page":"3882","DOI":"10.1093\/bioinformatics\/btaa250","article-title":"Phigaro: High-throughput prophage sequence annotation","volume":"36","author":"Starikova","year":"2020","journal-title":"Bioinformatics"},{"key":"ref_43","doi-asserted-by":"crossref","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":"ref_44","doi-asserted-by":"crossref","unstructured":"Price, M.N., Dehal, P.S., and Arkin, A.P. (2010). FastTree 2\u2014Approximately maximum-likelihood trees for large alignments. PLoS ONE, 5.","DOI":"10.1371\/journal.pone.0009490"},{"key":"ref_45","doi-asserted-by":"crossref","first-page":"W293","DOI":"10.1093\/nar\/gkab301","article-title":"Interactive Tree Of Life (iTOL) v5: An online tool for phylogenetic tree display and annotation","volume":"49","author":"Letunic","year":"2021","journal-title":"Nucleic Acids Res."},{"key":"ref_46","doi-asserted-by":"crossref","unstructured":"Bardou, P., Mariette, J., Escudi\u00e9, F., Djemiel, C., and Klopp, C. (2014). jvenn: An interactive Venn diagram viewer. BMC Bioinform., 15.","DOI":"10.1186\/1471-2105-15-293"}],"container-title":["Antibiotics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/2079-6382\/14\/9\/944\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,9]],"date-time":"2025-10-09T18:48:38Z","timestamp":1760035718000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/2079-6382\/14\/9\/944"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,9,18]]},"references-count":46,"journal-issue":{"issue":"9","published-online":{"date-parts":[[2025,9]]}},"alternative-id":["antibiotics14090944"],"URL":"https:\/\/doi.org\/10.3390\/antibiotics14090944","relation":{},"ISSN":["2079-6382"],"issn-type":[{"value":"2079-6382","type":"electronic"}],"subject":[],"published":{"date-parts":[[2025,9,18]]}}}