Role and value of whole genome sequencing in studying tuberculosis transmission

Vladyslav Nikolayevskyy*, S. Niemann, R. Anthony, D. van Soolingen, E. Tagliani, C. Ködmön, M. J. van der Werf, D. M. Cirillo

*Corresponding author for this work

Research output: Contribution to journalReview articlepeer-review

15 Citations (Scopus)

Abstract

Background: Tuberculosis (TB) remains a serious public health threat worldwide. Theoretically ultimate resolution of whole genome sequencing (WGS) for Mycobacterium tuberculosis complex (MTBC) strain classification makes this technology very attractive for epidemiological investigations. Objectives: To summarize the evidence available in peer-reviewed publications on the role and place of WGS in detection of TB transmission. Sources: A total of 69 peer-reviewed publications identified in Pubmed database. Content: Evidence from >30 publications suggests that a cut-off value of fewer than six single nucleotide polymorphisms between strains efficiently excludes cases that are not the result of recent transmission and could be used for the identification of drug-sensitive isolates involved in direct human-to-human TB transmission. Sensitivity of WGS to identify epidemiologically linked isolates is high, reaching 100% in eight studies with specificity (17%–95%) highly dependent on the settings. Drug resistance and specific phylogenetic lineages may be associated with accelerated mutation rates affecting genetic distances. WGS can be potentially used to distinguish between true relapses and re-infections but in high-incidence low-diversity settings this would require consideration of epidemiological links and minority alleles. Data from four studies looking into within-host diversity highlight a need for developing criteria for acceptance or rejection of WGS relatedness results depending on the proportion of minority alleles. Implications: WGS will potentially allow for more targeted public health actions preventing unnecessary investigations of false clusters. Consensus on standardization of raw data quality control processing criteria, analytical pipelines and reporting language is yet to be reached.

Original languageEnglish
Pages (from-to)1377-1382
Number of pages6
JournalClinical Microbiology and Infection
Volume25
Issue number11
DOIs
Publication statusPublished - Nov 2019

Bibliographical note

Funding Information:
The authors declare no conflicts of interests related to this study. This study has received funding from European Centre for Disease Control within EUSeqMyTB project. Stefan Niemann received funding from the German Centre for Infection Research, Deutsche Forschungsgemeinschaft (German Research Foundation) under Germany's Excellence Strategy (Grant EXC 22167-390884018) and from Leibniz Science Campus EvoLUNG (Evolutionary medicine of the lung).

Funding Information:
The authors declare no conflicts of interests related to this study. This study has received funding from European Centre for Disease Control within EUSeqMyTB project. Stefan Niemann received funding from the German Centre for Infection Research , Deutsche Forschungsgemeinschaft (German Research Foundation) under Germany's Excellence Strategy (Grant EXC 22167-390884018 ) and from Leibniz Science Campus EvoLUNG (Evolutionary medicine of the lung).

Publisher Copyright:
© 2019

Copyright:
Copyright 2019 Elsevier B.V., All rights reserved.

Keywords

  • Outbreak
  • Standardization
  • Transmission
  • Tuberculosis
  • Whole genome sequencing

Fingerprint

Dive into the research topics of 'Role and value of whole genome sequencing in studying tuberculosis transmission'. Together they form a unique fingerprint.

Cite this