Whole-genome sequencing of Mycobacterium tuberculosis directly from clinical samples for high-resolution genomic epidemiology and drug resistance surveillance: an observational study
The Lancet Microbe·
- DOI
- 10.1016/s2666-5247(20)30060-4
- PMID
- 35544271
- PMCID
- —
- OpenAlex
- W3047564893
- Study type
- Genomic study
- Publisher
- Elsevier BV
- Article type
- journal-article
- Integrity
- current
Why this research matters now
Direct whole-genome sequencing may enable culture-independent, real-time genomic epidemiology and drug resistance surveillance, which could be particularly valuable in settings lacking culture and phenotypic drug susceptibility testing capacity.
Structured evidence summary
Research question
The study examined whether direct whole-genome sequencing of Mycobacterium tuberculosis from clinical specimens can support high-resolution genomic epidemiology and drug resistance surveillance.
Study design
An observational genomic study using direct whole-genome sequencing on 37 clinical specimens from 23 tuberculosis patients, with nine non-tuberculous mycobacteria/negative sputum controls and 780 clinical isolates from Comunidad Valenciana, Spain (Jan 1, 2014–Dec 31, 2016).
Population and setting
Clinical specimens and isolates from tuberculosis patients in the Comunidad Valenciana region of Spain, sequenced between 2014 and 2016.
Main findings
Of 37 clinical specimens, 28 (76%) met quality criteria for downstream analysis, including 85% of smear-positive and 55% of smear-negative specimens. All 28 matched their corresponding culture isolates with a median distance of 0 SNPs. Sixteen specimens (57%) were assigned to ten regional transmission clusters and twelve (43%) were unique cases. Transmission inferences and drug-susceptibility predictions were concordant with culture-based sequencing and phenotypic testing. Complete analysis was achievable within a week of specimen receipt at €217 per sample.
Public-health relevance
Direct whole-genome sequencing may enable culture-independent, real-time genomic epidemiology and drug resistance surveillance, which could be particularly valuable in settings lacking culture and phenotypic drug susceptibility testing capacity.
Important limitations
The summary is limited to the supplied single-article abstract/metadata and requires the original paper for decision-grade interpretation. The abstract does not explicitly state study limitations; the reported sample size of 37 clinical specimens and the regional focus on Comunidad Valenciana may constrain generalisability, but these are not limitations explicitly declared by the authors.
GIDS interpretation
This paper is discoverable in the GIDS evidence base as a Spanish genomic epidemiology study on tuberculosis transmission and surveillance. It does not in itself confirm or refute any live surveillance signal and should be consulted at the abstract level for contextual awareness only.
Related GIDS surveillance
Literature context does not validate, explain, or change a surveillance signal. Exact and contextual relationships are shown separately.
Evidence relationships
This article has 6 auditable classifier relationships to diseases, places, topics, and study design.