Removing the bottleneck in whole genome sequencing of M. tuberculosis for rapid drug resistance analysis: a call to action.


McNerney, R; Clark, TG; Campino, S; Rodrigues, C; Dolinger, D; Smith, L; Cabibbe, AM; Dheda, K; Schito, M; (2016) Removing the bottleneck in whole genome sequencing of M. tuberculosis for rapid drug resistance analysis: a call to action. International journal of infectious diseases . ISSN 1201-9712 DOI: 10.1016/j.ijid.2016.11.422

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Abstract

Whole genome sequencing (WGS) can provide comprehensive analysis of Mycobacterium tuberculosis (Mtb) mutations that cause resistance to anti-tuberculosis drugs. With the deployment of benchtop sequencers and rapid analytical software WGS is poised to become a useful tool to guide treatment. However, direct sequencing from clinical specimens to provide a full drug resistance profile remains a serious challenge. This article reviews current practices for extracting Mtb DNA and possible solutions for sampling sputum. Techniques under consideration include enzymatic digestion, physical disruption, chemical degradation, detergent solubilisation, solvent extraction, ligand coated magnetic beads, silica columns and oligonucleotide pull-down baits. Selective amplification of genomic bacterial DNA in sputum prior to whole genome sequencing may provide a solution and differential lysis, to reduce the levels of contaminating human DNA is also being explored. To remove this bottleneck and accelerate access to WGS for patients with suspected drug resistant tuberculosis we suggest a coordinated and collaborative approach be taken to more rapidly optimise, compare and validate methodologies for sequencing from patient samples.

Item Type: Article
Faculty and Department: Faculty of Epidemiology and Population Health > Dept of Infectious Disease Epidemiology
Faculty of Infectious and Tropical Diseases > Dept of Pathogen Molecular Biology
Research Centre: Antimicrobial Resistance Centre (AMR)
TB Centre
PubMed ID: 27986491
Web of Science ID: 397946200024
URI: http://researchonline.lshtm.ac.uk/id/eprint/3234035

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