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Publication Details
AFRICAN RESEARCH NEXUS
SHINING A SPOTLIGHT ON AFRICAN RESEARCH
immunology and microbiology
Evaluation of a gene-by-gene approach for prospective whole-genome sequencing-based surveillance of multidrug resistant Mycobacterium tuberculosis
Tuberculosis, Volume 115, Year 2019
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Description
Whole-genome sequencing (WGS) offers unprecedented resolution for tracking Mycobacterium tuberculosis transmission and antibiotic-resistance spread. Still, the establishment of standardized WGS-based pipelines and the definition of epidemiological clusters based on genetic relatedness are under discussion. We aimed to implement a dynamic gene-by-gene approach, fully relying on freely available software, for prospective WGS-based tuberculosis surveillance, demonstrating its application for detecting transmission chains by retrospectively analysing all M/XDR strains isolated in 2013–2017 in Portugal. We observed a good correlation between genetic relatedness and epidemiological links, with strongly epilinked clusters displaying mean pairwise allele differences (AD) always below 0.3% (ratio of mean AD over the total number of shared loci between same-cluster strains). This data parallels the genetic distances acquired by the core-SNV analysis, while providing higher resolution and epidemiological concordance than MIRU-VNTR genotyping. The dynamic analysis of strain sub-sets (i.e., increasing the number of shared loci within each sub-set) also strengthens the confidence in detecting epilinked clusters. This gene-by-gene strategy also offers several practical benefits (e.g., reliance on freely-available software, scalability and low computational requirements) that further consolidated its suitability for a timely and robust prospective WGS-based laboratory surveillance of M/XDR-TB cases. © 2019
Authors & Co-Authors
MacEdo, Rita
Portugal, Lisbon
Instituto Nacional de Saúde Dr. Ricardo Jorge
Pinto, Miguel Ferreira
Portugal, Lisbon
Instituto Nacional de Saúde Dr. Ricardo Jorge
Borges, Vítor
Portugal, Lisbon
Instituto Nacional de Saúde Dr. Ricardo Jorge
Oliveira, Olena
Portugal, Braga
Universidade do Minho
Portugal, Porto
Universidade do Porto
Portugal, Isabel
Portugal, Lisbon
Universidade de Lisboa
Duarte, R. A.B.
Portugal, Porto
Universidade do Porto
Portugal, Vila Nova de Gaia
Centro Hospitalar de Vila Nova de Gaia
Gomes, João Paulo
Portugal, Lisbon
Instituto Nacional de Saúde Dr. Ricardo Jorge
Statistics
Citations: 10
Authors: 7
Affiliations: 5
Identifiers
Doi:
10.1016/j.tube.2019.02.006
ISSN:
14729792
Research Areas
Genetics And Genomics
Infectious Diseases
Study Design
Cohort Study