Elsevier

Tuberculosis

Volume 98, May 2016, Pages 77-85
Tuberculosis

Review
Whole genome sequencing of Mycobacterium tuberculosis for detection of recent transmission and tracing outbreaks: A systematic review

https://doi.org/10.1016/j.tube.2016.02.009Get rights and content

Summary

Contact tracing complemented with genotyping is considered an important means of understanding person-to-person transmission of tuberculosis (TB). It still remains unclear whether Whole Genome Sequencing (WGS) of Mycobacterium tuberculosis can rule in transmission and how it performs in different human populations, risk groups and across TB lineages. This systematic review aimed to determine the sensitivity and specificity of WGS for detection of recent transmission using conventional epidemiology as the gold standard and investigate if WGS identifies previously undetected transmission events.

Systematic review was conducted according to the criteria of the Preferred Reporting Items for Systematic Reviews and Meta-Analyses group. A compound search strategy was developed to identify all relevant studies published between 01/01/2005 and 30/11/2014 using three online databases. Publications satisfying specific criteria have been identified and data extracted.

A total of 12 publications were included. We established that WGS has a higher discriminatory power compared to conventional genotyping and detects transmission events missed by epidemiological investigations. A cut-off value of <6 SNPs between isolates may predict recent transmission. None of the studies performed a head-to-head comparison between WGS and conventional genotyping using unselected prospectively collected isolates. Minimum reporting criteria for WGS studies have been proposed and quality control parameters considered.

Section snippets

Background

Tuberculosis (TB) remains a serious public health problem killing more than 1.7 million people annually [1]. The varying impact of control measures in different settings highlights the need for better diagnostics, treatment, preventive strategies and improved understanding of transmission at the population level.

Since the 1990s molecular epidemiological studies have provided valuable insights into the phylogeography of Mycobacterium tuberculosis complex (MTBC), its evolutionary pathways and

Methods

This systematic review was conducted according to the criteria of the Preferred Reporting Items for Systematic Reviews and Meta-Analyses group [26]. The protocol was registered with PROSPERO (registration number CRD42015023675).

Study selection

A total of 2085 publications were identified; 59 studies were selected for full text review, 47 of those were excluded leaving 12 studies being included in the current systematic review [16], [22], [23], [24], [28], [29], [30], [31], [32], [33], [34], [35]. PRISMA diagram is depicted on Figure 1.

General characteristics of included studies

The characteristics of included studies and relevant outcome data are summarised in Table 1, Table 2. WGS data was available for 1088 MTBC isolates. The number of isolates included in each study varied

Discussion

Previous studies indicated that WGS sequencing provides a higher discrimination of clinical MTBC isolates compared to classical genotyping e.g. based on MIRU-VNTR typing but this has not been investigated systematically to date. By performing a systematic analysis of 12 studies, this review confirms the notion that WGS has a higher discriminatory power and is able to subdivide clusters defined by classical genotyping. Studies included in this review have shown that the proposed cut-off value of

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    These authors contributed equally to the study.

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