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
Hlavní autoři: Papaventsis, D, Casali, N, Kontsevaya, I, Drobniewski, F, Cirillo, D M, Nikolayevskyy, V
Médium: Journal Article
Jazyk:angličtina
Vydáno: England 01.02.2017
Témata:
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
Performance characteristics
Tuberculosis
Drug resistance
Whole genome sequencing
Genetic polymorphisms
Laboratory diagnostics
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.
AbstractList 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.
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.
Author Casali, N
Kontsevaya, I
Drobniewski, F
Nikolayevskyy, V
Cirillo, D M
Papaventsis, D
Author_xml – sequence: 1
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  surname: Papaventsis
  fullname: Papaventsis, D
  organization: National Reference Laboratory for Mycobacteria, Sotiria Chest Diseases Hospital, Athens, Greece
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  surname: Casali
  fullname: Casali, N
  organization: Department of Medicine, Imperial College London, London, UK
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  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
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  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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Snippet We conducted a systematic review to determine the diagnostic accuracy of whole genome sequencing (WGS) of Mycobacterium tuberculosis for the detection of...
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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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