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