{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,26]],"date-time":"2026-10-26T13:16:10Z","timestamp":1793020570547,"version":"4.5.0"},"reference-count":260,"publisher":"Oxford University Press (OUP)","license":[{"start":{"date-parts":[[2025,4,27]],"date-time":"2025-04-27T00:00:00Z","timestamp":1745712000000},"content-version":"vor","delay-in-days":116,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100004442","name":"National Science Centre, Poland","doi-asserted-by":"publisher","award":["2017\/27\/L\/NZ6\/03279"],"award-info":[{"award-number":["2017\/27\/L\/NZ6\/03279"]}],"id":[{"id":"10.13039\/501100004442","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2025,1,14]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Studies on the epidemiology and clinical relevance of Mycobacterium tuberculosis complex (MTBC) have immensely benefited from molecular typing methods, associated software applications, and bioinformatics tools. Over the last two decades, the Pasteur Institute of Guadeloupe has developed a range of bioinformatic resources, including databases and software, to advance understanding of TB epidemiology. Traditional methods, such as IS6110-RFLP, MIRU-VNTR typing, and spoligotyping, have been instrumental but are increasingly supplanted by more precise and high-throughput techniques. These typing methods offer relatively good discrimination and reproducibility, making them popular choices for epidemiological studies. However, the advent of whole-genome sequencing (WGS) has revolutionized Mycobacterium tuberculosis complex (MTBC) typing, providing unparalleled resolution and data analysis depth. WGS enables the identification of single nucleotide polymorphisms and other genetic variations, facilitating robust phylogenetic reconstructions, and detailed outbreak investigations. This review summarizes current molecular typing methods, as well as databases and software tools used for MTBC data analysis. A comprehensive comparison of available tools and databases is provided to guide future research on the epidemiology of TB and pathogen-associated variables (drug resistance or virulence) and public health initiatives.<\/jats:p>","DOI":"10.1093\/femsre\/fuaf017","type":"journal-article","created":{"date-parts":[[2025,4,27]],"date-time":"2025-04-27T02:13:05Z","timestamp":1745719985000},"source":"Crossref","is-referenced-by-count":18,"title":["Molecular typing of <i>Mycobacterium tuberculosis<\/i>: a review of current methods, databases, softwares, and analytical tools"],"prefix":"10.1093","volume":"49","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-7897-9023","authenticated-orcid":false,"given":"David","family":"Couvin","sequence":"first","affiliation":[{"name":"WHO Supranational TB Reference Laboratory\u2014TB and Mycobacteria Unit, Institut Pasteur de la Guadeloupe , F-97139, Les Abymes, Guadeloupe ,","place":["France"]},{"name":"Laboratoire de Math\u00e9matiques Informatique et Applications (LAMIA), Universit\u00e9 des Antilles , F-97154, Pointe-\u00e0-Pitre, Guadeloupe ,","place":["France"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Anne-Sophie","family":"Allaguy","sequence":"additional","affiliation":[{"name":"Laboratoire de Math\u00e9matiques Informatique et Applications (LAMIA), Universit\u00e9 des Antilles , F-97154, Pointe-\u00e0-Pitre, Guadeloupe ,","place":["France"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ayoub","family":"Ez-zari","sequence":"additional","affiliation":[{"name":"Abdelmalek Essa\u00e2di University Laboratory of Biology and Health (UAE\/U06FS), Department of Biology, Faculty of Science, , BP 2121, 93002 Tetouan ,","place":["Morocco"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9553-5742","authenticated-orcid":false,"given":"Tomasz","family":"Jagielski","sequence":"additional","affiliation":[{"name":"University of Warsaw Department of Medical Microbiology, Institute of Microbiology, Faculty of Biology, , I. 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