Pyrosequencing for rapid detection of extensively drug-resistant Mycobacterium tuberculosis in clinical isolates and clinical specimens - PubMed (original) (raw)

Pyrosequencing for rapid detection of extensively drug-resistant Mycobacterium tuberculosis in clinical isolates and clinical specimens

S-Y Grace Lin et al. J Clin Microbiol. 2014 Feb.

Abstract

Treating extensively drug-resistant (XDR) tuberculosis (TB) is a serious challenge. Culture-based drug susceptibility testing (DST) may take 4 weeks or longer from specimen collection to the availability of results. We developed a pyrosequencing (PSQ) assay including eight subassays for the rapid identification of Mycobacterium tuberculosis complex (MTBC) and concurrent detection of mutations associated with resistance to drugs defining XDR TB. The entire procedure, from DNA extraction to the availability of results, was accomplished within 6 h. The assay was validated for testing clinical isolates and clinical specimens, which improves the turnaround time for molecular DST and maximizes the benefit of using molecular testing. A total of 130 clinical isolates and 129 clinical specimens were studied. The correlations between the PSQ results and the phenotypic DST results were 94.3% for isoniazid, 98.7% for rifampin, 97.6% for quinolones (ofloxacin, levofloxacin, or moxifloxacin), 99.2% for amikacin, 99.2% for capreomycin, and 96.4% for kanamycin. For testing clinical specimens, the PSQ assay yielded a 98.4% sensitivity for detecting MTBC and a 95.8% sensitivity for generating complete sequencing results from all subassays. The PSQ assay was able to rapidly and accurately detect drug resistance mutations with the sequence information provided, which allows further study of the association of drug resistance or susceptibility with each mutation and the accumulation of such knowledge for future interpretation of results. Thus, reporting of false resistance for mutations known not to confer resistance can be prevented, which is a significant benefit of the assay over existing molecular diagnostic methods endorsed by the World Health Organization.

PubMed Disclaimer

Cited by

Pyrosequencing for diagnosis of multidrug and extensively drug-resistant tuberculosis: A systemic review and meta-analysis.
Getachew E, Adebeta T, Gebrie D, Charlie L, Said B, Assefa DG, Wanjiru CL, Zeleke ED, Tesfahunei HA, Abebe M, Joseph M, Manyazewal T. Getachew E, et al. J Clin Tuberc Other Mycobact Dis. 2021 Jun 29;24:100254. doi: 10.1016/j.jctube.2021.100254. eCollection 2021 Aug. J Clin Tuberc Other Mycobact Dis. 2021. PMID: 34278006 Free PMC article. Review.
Performance of a pyrosequencing platform in diagnosing drug-resistant extra-pulmonary tuberculosis in India.
Georghiou SB, Ajbani K, Rodrigues C, Rodwell TC. Georghiou SB, et al. Int J Tuberc Lung Dis. 2016 Feb;20(2):160-5. doi: 10.5588/ijtld.15.0459. Int J Tuberc Lung Dis. 2016. PMID: 26792466 Free PMC article.
Novel katG mutations causing isoniazid resistance in clinical M. tuberculosis isolates.
Torres JN, Paul LV, Rodwell TC, Victor TC, Amallraja AM, Elghraoui A, Goodmanson AP, Ramirez-Busby SM, Chawla A, Zadorozhny V, Streicher EM, Sirgel FA, Catanzaro D, Rodrigues C, Gler MT, Crudu V, Catanzaro A, Valafar F. Torres JN, et al. Emerg Microbes Infect. 2015 Jul;4(7):e42. doi: 10.1038/emi.2015.42. Epub 2015 Jul 15. Emerg Microbes Infect. 2015. PMID: 26251830 Free PMC article.
Frequency and Distribution of Tuberculosis Resistance-Associated Mutations between Mumbai, Moldova, and Eastern Cape.
Georghiou SB, Seifert M, Catanzaro D, Garfein RS, Valafar F, Crudu V, Rodrigues C, Victor TC, Catanzaro A, Rodwell TC. Georghiou SB, et al. Antimicrob Agents Chemother. 2016 Jun 20;60(7):3994-4004. doi: 10.1128/AAC.00222-16. Print 2016 Jul. Antimicrob Agents Chemother. 2016. PMID: 27090176 Free PMC article.
Predicting extensively drug-resistant Mycobacterium tuberculosis phenotypes with genetic mutations.
Rodwell TC, Valafar F, Douglas J, Qian L, Garfein RS, Chawla A, Torres J, Zadorozhny V, Kim MS, Hoshide M, Catanzaro D, Jackson L, Lin G, Desmond E, Rodrigues C, Eisenach K, Victor TC, Ismail N, Crudu V, Gler MT, Catanzaro A. Rodwell TC, et al. J Clin Microbiol. 2014 Mar;52(3):781-9. doi: 10.1128/JCM.02701-13. Epub 2013 Dec 18. J Clin Microbiol. 2014. PMID: 24353002 Free PMC article.

References

1. Hoffner S. 2012. Unexpected high levels of multidrug-resistant tuberculosis present new challenges for tuberculosis control. Lancet 380:1367–1369. 10.1016/S0140-6736(12)61069-1 - DOI - PubMed
1. WHO 2012. Global tuberculosis report 2012. World Health Organization, Geneva, Switzerland
1. Bravo LTC, Tuohy MJ, Ang C, Destura RV, Mendoza M, Procop GW, Gordon SM, Hall GS, Shrestha NK. 2009. Pyrosequencing for rapid detection of Mycobacterium tuberculosis resistance to rifampin, isoniazid, and fluoroquinolones. J. Clin. Microbiol. 47:3985–3990. 10.1128/JCM.01229-09 - DOI - PMC - PubMed
1. Boehme CC, Nabeta P, Hillemann D, Nicol MP, Shenai S, Krapp F, Allen J, Tahirli R, Blakemore R, Rustomjee R, Milovic A, Jones M, O'Brien SM, Persing DH, Ruesch-Gerdes S, Gotuzzo E, Rodrigues C, Alland D, Perkins MD. 2010. Rapid molecular detection of tuberculosis and rifampin resistance. N. Engl. J. Med. 363:1005–1015. 10.1056/NEJMoa0907847 - DOI - PMC - PubMed
1. WHO 2013. The use of molecular line probe assay for the detection of resistance to second-line anti-tuberculosis drugs. World Health Organization, Geneva, Switzerland

Publication types

MeSH terms

Substances

LinkOut - more resources

Full Text Sources
Other Literature Sources
- The Lens - Patent Citations Database
- scite Smart Citations

Pyrosequencing for rapid detection of extensively drug-resistant Mycobacterium tuberculosis in clinical isolates and clinical specimens - PubMed (original) (raw)