Whole genome sequencing of Mycobacterium tuberculosis for detection of drug resistance: a systematic review
We conducted a systematic review to determine the diagnostic accuracy of whole genome sequencing (WGS) of Mycobacterium tuberculosis for the detection of resistance to first- and second-line anti-tuberculosis (TB) drugs. The study was conducted according to the criteria of the Preferred Reporting It...
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| Vydáno v: | Clinical microbiology and infection Ročník 23; číslo 2; s. 61 - 68 |
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| Hlavní autoři: | , , , , , |
| Médium: | Journal Article |
| Jazyk: | angličtina |
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England
01.02.2017
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| ISSN: | 1469-0691 |
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| Abstract | We conducted a systematic review to determine the diagnostic accuracy of whole genome sequencing (WGS) of Mycobacterium tuberculosis for the detection of resistance to first- and second-line anti-tuberculosis (TB) drugs.
The study was conducted according to the criteria of the Preferred Reporting Items for Systematic Reviews group. A total of 20 publications were included. The sensitivity, specificity, positive-predictive value and negative-predictive value of WGS using phenotypic drug susceptibility testing methods as a reference standard were determined.
Anti-TB agents tested included all first-line drugs, a variety of reserve drugs, as well as new drugs. Polymorphisms in a total of 53 genes were tested for associations with drug resistance. Pooled sensitivity and specificity values for detection of resistance to selected first-line drugs were 0.98 (95% CI 0.93-0.98) and 0.98 (95% CI 0.98-1.00) for rifampicin and 0.97 (95% CI 0.94-0.99) and 0.93 (95% CI 0.91-0.96) for isoniazid, respectively. Due to high heterogeneity in study designs, lack of data, knowledge of resistance mechanisms and clarity on exclusion of phylogenetic markers, there was a significant variation in analytical performance of WGS for the remaining first-line, reserved drugs and new drugs.
Whole genome sequencing could be considered a promising alternative to existing phenotypic and molecular drug susceptibility testing methods for rifampicin and isoniazid pending standardization of analytical pipelines. To ensure clinical relevance of WGS for detection of M. tuberculosis complex drug resistance, future studies should include information on clinical outcomes. |
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| AbstractList | We conducted a systematic review to determine the diagnostic accuracy of whole genome sequencing (WGS) of Mycobacterium tuberculosis for the detection of resistance to first- and second-line anti-tuberculosis (TB) drugs.
The study was conducted according to the criteria of the Preferred Reporting Items for Systematic Reviews group. A total of 20 publications were included. The sensitivity, specificity, positive-predictive value and negative-predictive value of WGS using phenotypic drug susceptibility testing methods as a reference standard were determined.
Anti-TB agents tested included all first-line drugs, a variety of reserve drugs, as well as new drugs. Polymorphisms in a total of 53 genes were tested for associations with drug resistance. Pooled sensitivity and specificity values for detection of resistance to selected first-line drugs were 0.98 (95% CI 0.93-0.98) and 0.98 (95% CI 0.98-1.00) for rifampicin and 0.97 (95% CI 0.94-0.99) and 0.93 (95% CI 0.91-0.96) for isoniazid, respectively. Due to high heterogeneity in study designs, lack of data, knowledge of resistance mechanisms and clarity on exclusion of phylogenetic markers, there was a significant variation in analytical performance of WGS for the remaining first-line, reserved drugs and new drugs.
Whole genome sequencing could be considered a promising alternative to existing phenotypic and molecular drug susceptibility testing methods for rifampicin and isoniazid pending standardization of analytical pipelines. To ensure clinical relevance of WGS for detection of M. tuberculosis complex drug resistance, future studies should include information on clinical outcomes. OBJECTIVESWe conducted a systematic review to determine the diagnostic accuracy of whole genome sequencing (WGS) of Mycobacterium tuberculosis for the detection of resistance to first- and second-line anti-tuberculosis (TB) drugs.METHODSThe study was conducted according to the criteria of the Preferred Reporting Items for Systematic Reviews group. A total of 20 publications were included. The sensitivity, specificity, positive-predictive value and negative-predictive value of WGS using phenotypic drug susceptibility testing methods as a reference standard were determined.RESULTSAnti-TB agents tested included all first-line drugs, a variety of reserve drugs, as well as new drugs. Polymorphisms in a total of 53 genes were tested for associations with drug resistance. Pooled sensitivity and specificity values for detection of resistance to selected first-line drugs were 0.98 (95% CI 0.93-0.98) and 0.98 (95% CI 0.98-1.00) for rifampicin and 0.97 (95% CI 0.94-0.99) and 0.93 (95% CI 0.91-0.96) for isoniazid, respectively. Due to high heterogeneity in study designs, lack of data, knowledge of resistance mechanisms and clarity on exclusion of phylogenetic markers, there was a significant variation in analytical performance of WGS for the remaining first-line, reserved drugs and new drugs.CONCLUSIONSWhole genome sequencing could be considered a promising alternative to existing phenotypic and molecular drug susceptibility testing methods for rifampicin and isoniazid pending standardization of analytical pipelines. To ensure clinical relevance of WGS for detection of M. tuberculosis complex drug resistance, future studies should include information on clinical outcomes. |
| Author | Casali, N Kontsevaya, I Drobniewski, F Nikolayevskyy, V Cirillo, D M Papaventsis, D |
| Author_xml | – sequence: 1 givenname: D surname: Papaventsis fullname: Papaventsis, D organization: National Reference Laboratory for Mycobacteria, Sotiria Chest Diseases Hospital, Athens, Greece – sequence: 2 givenname: N surname: Casali fullname: Casali, N organization: Department of Medicine, Imperial College London, London, UK – sequence: 3 givenname: I surname: Kontsevaya fullname: Kontsevaya, I organization: Department of Medicine, Imperial College London, London, UK – sequence: 4 givenname: F surname: Drobniewski fullname: Drobniewski, F organization: Department of Medicine, Imperial College London, London, UK – sequence: 5 givenname: D M surname: Cirillo fullname: Cirillo, D M organization: Division of Immunology, Transplantation and Infectious Diseases, IRCCS San Raffaele Scientific Institute, Milan, Italy – sequence: 6 givenname: V surname: Nikolayevskyy fullname: Nikolayevskyy, V email: vlad.nikolayevskyy@phe.gov.uk organization: Department of Medicine, Imperial College London, London, UK; PHE National Mycobacterium Reference Laboratory, London, UK. Electronic address: vlad.nikolayevskyy@phe.gov.uk |
| BackLink | https://www.ncbi.nlm.nih.gov/pubmed/27665704$$D View this record in MEDLINE/PubMed |
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| Keywords | Performance characteristics Tuberculosis Drug resistance Whole genome sequencing Genetic polymorphisms Laboratory diagnostics |
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| SubjectTerms | Antitubercular Agents - pharmacology Antitubercular Agents - therapeutic use Drug Resistance, Bacterial Genes, Bacterial Genome, Bacterial Genomics - methods Humans Mutation Mycobacterium tuberculosis - drug effects Mycobacterium tuberculosis - genetics Phylogeny Polymorphism, Genetic Tuberculosis - drug therapy Tuberculosis - microbiology |
| Title | Whole genome sequencing of Mycobacterium tuberculosis for detection of drug resistance: a systematic review |
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