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Mycobacterium tuberculosis
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===Strain variation=== Typing of strains is useful in the investigation of tuberculosis outbreaks, because it gives the investigator evidence for or against transmission from person to person. Consider the situation where person A has tuberculosis and believes he acquired it from person B. If the bacteria isolated from each person belong to different types, then transmission from B to A is definitively disproven; however, if the bacteria are the same strain, then this supports (but does not definitively prove) the hypothesis that B infected A.{{citation needed|date=May 2024}} Until the early 2000s, ''M. tuberculosis'' strains were typed by [[pulsed field gel electrophoresis]].<ref>{{cite journal | vauthors = Zhang Y, Mazurek GH, Cave MD, Eisenach KD, Pang Y, Murphy DT, Wallace RJ | title = DNA polymorphisms in strains of Mycobacterium tuberculosis analyzed by pulsed-field gel electrophoresis: a tool for epidemiology | journal = Journal of Clinical Microbiology | volume = 30 | issue = 6 | pages = 1551โ56 | date = June 1992 | doi = 10.1128/JCM.30.6.1551-1556.1992 | pmid = 1352518 | pmc = 265327 | url =}}</ref> This has now been superseded by [[variable number tandem repeat|variable numbers of tandem repeats]] (VNTR), which is technically easier to perform and allows better discrimination between strains. This method makes use of the presence of repeated [[DNA]] sequences within the ''M. tuberculosis'' genome.{{citation needed|date=May 2024}} Three generations of VNTR typing for ''M. tuberculosis'' are noted. The first scheme, called exact tandem repeat, used only five loci,<ref>{{cite journal | vauthors = Frothingham R, Meeker-O'Connell WA | title = Genetic diversity in the ''Mycobacterium tuberculosis'' complex based on variable numbers of tandem DNA repeats | journal = Microbiology | volume = 144 | issue = Pt 5 | pages = 1189โ96 | date = May 1998 | pmid = 9611793 | doi = 10.1099/00221287-144-5-1189 | doi-access = free}}</ref> but the resolution afforded by these five loci was not as good as PFGE. The second scheme, called mycobacterial interspersed repetitive unit, had discrimination as good as PFGE.<ref>{{cite journal | vauthors = Mazars E, Lesjean S, Banuls AL, Gilbert M, Vincent V, Gicquel B, Tibayrenc M, Locht C, Supply P | title = High-resolution minisatellite-based typing as a portable approach to global analysis of Mycobacterium tuberculosis molecular epidemiology | journal = Proceedings of the National Academy of Sciences of the United States of America | volume = 98 | issue = 4 | pages = 1901โ06 | date = February 2001 | pmid = 11172048 | pmc = 29354 | doi = 10.1073/pnas.98.4.1901 | bibcode = 2001PNAS...98.1901M | doi-access = free}}</ref><ref>{{cite journal | vauthors = Hawkey PM, Smith EG, Evans JT, Monk P, Bryan G, Mohamed HH, Bardhan M, Pugh RN | title = Mycobacterial interspersed repetitive unit typing of Mycobacterium tuberculosis compared to IS6110-based restriction fragment length polymorphism analysis for investigation of apparently clustered cases of tuberculosis | journal = Journal of Clinical Microbiology | volume = 41 | issue = 8 | pages = 3514โ20 | date = August 2003 | pmid = 12904348 | pmc = 179797 | doi = 10.1128/JCM.41.8.3514-3520.2003}}</ref> The third generation (mycobacterial interspersed repetitive unit โ 2) added a further nine loci to bring the total to 24. This provides a degree of resolution greater than PFGE and is currently the standard for typing ''M. tuberculosis''.<ref>{{cite journal | vauthors = Supply P, Allix C, Lesjean S, Cardoso-Oelemann M, Rรผsch-Gerdes S, Willery E, Savine E, de Haas P, van Deutekom H, Roring S, Bifani P, Kurepina N, Kreiswirth B, Sola C, Rastogi N, Vatin V, Gutierrez MC, Fauville M, Niemann S, Skuce R, Kremer K, Locht C, van Soolingen D | title = Proposal for standardization of optimized mycobacterial interspersed repetitive unit-variable-number tandem repeat typing of Mycobacterium tuberculosis | journal = Journal of Clinical Microbiology | volume = 44 | issue = 12 | pages = 4498โ510 | date = December 2006 | pmid = 17005759 | pmc = 1698431 | doi = 10.1128/JCM.01392-06}}</ref> However, with regard to archaeological remains, additional evidence may be required because of possible contamination from related soil bacteria.<ref>{{Cite journal| vauthors = Mรผller R, Roberts CA, Brown TA |year=2015|title=Complications in the study of ancient tuberculosis: non-specificity of IS6110 PCRs|journal=Science and Technology of Archaeological Research|volume=1|issue=1|doi=10.1179/2054892314Y.0000000002|pages=1โ8|bibcode=2015STAR....1....1M |doi-access=free}}</ref> Antibiotic resistance in ''M. tuberculosis'' typically occurs due to either the accumulation of mutations in the genes targeted by the antibiotic or a change in titration of the drug.<ref>{{cite journal | vauthors = Rattan A, Kalia A, Ahmad N | title = Multidrug-resistant Mycobacterium tuberculosis: molecular perspectives | journal = Emerging Infectious Diseases | volume = 4 | issue = 2 | pages = 195โ209 | date = June 1998 | pmid = 9621190 | pmc = 2640153 | doi = 10.3201/eid0402.980207}}</ref> ''M. tuberculosis'' is considered to be multidrug-resistant (MDR TB) if it has developed drug resistance to both rifampicin and isoniazid, which are the most important antibiotics used in treatment. Additionally, extensively drug-resistant ''M. tuberculosis'' (XDR TB) is characterized by resistance to both isoniazid and rifampin, plus any [[fluoroquinolone]] and at least one of three injectable second-line drugs (i.e., [[amikacin]], [[kanamycin]], or [[capreomycin]]).<ref>{{cite web | publisher = Center for Disease Control | title = Drug-resistant TB | date = April 2014 | url = https://www.cdc.gov/tb/topic/drtb/ | access-date = 10 September 2017 | archive-date = 6 October 2022 | archive-url = https://web.archive.org/web/20221006054241/https://www.cdc.gov/TB/Topic/DRTB/ | url-status = live}}</ref> [[File:Mycobacterium tuberculosis Ziehl-Neelsen stain 640.jpg|thumb|right|''M. tuberculosis'' (stained red) in tissue (blue)]] [[File:Chording mycobacterium tuberculesis culture.jpg|thumb|Cording ''M. tuberculosis'' (H37Rv strain) culture on the luminescent microscopy]]
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