Evidence map›Paper›PMID 41736736›Full record

ArticleERJ open research2026

Targeted and whole-genome sequencing for drug resistance and genetic relatedness inference of rifampicin-resistant

Miguel de Diego Fuertes, Emilyn Costa Conceição, Felicia Wells, Vincent Rennie, Tim Heupink, Gavin Churchyard, Felix Ndebele, Anneke Van der Spoel Van Dijk, Boitumelo Fanampe, Salome Charalombous and 5 more

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Article in ERJ open research, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 3 papers.

0numbers the graph read from it
0cells of the map it votes in
3citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

3 citing papers in PubMed.

  1. Article
  2. Article
  3. Heteroresistance inFrontiers in cellular and infection microbiology · 2026
    Review
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

15 authors.

Miguel de Diego FuertesDepartment of Family Medicine and Population Health, Global Health Institute, Faculty of Medicine and Health Sciences, University of Antwerp, Antwerp, Belgium.ORCID https://orcid.org/0009-0001-1909-7397
Emilyn Costa ConceiçãoSouth African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa.
Felicia WellsSouth African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa.
Vincent RennieDepartment of Family Medicine and Population Health, Global Health Institute, Faculty of Medicine and Health Sciences, University of Antwerp, Antwerp, Belgium.
Tim HeupinkDepartment of Family Medicine and Population Health, Global Health Institute, Faculty of Medicine and Health Sciences, University of Antwerp, Antwerp, Belgium.ORCID https://orcid.org/0000-0001-6237-3898
Gavin ChurchyardThe Aurum Institute, Parktown, South Africa.
Felix NdebeleThe Aurum Institute, Parktown, South Africa.ORCID https://orcid.org/0000-0002-7499-7486
Anneke Van der Spoel Van DijkThe Aurum Institute, Parktown, South Africa.
Boitumelo FanampeThe Aurum Institute, Parktown, South Africa.
Salome CharalombousThe Aurum Institute, Parktown, South Africa.
Emmanuel Ayodeji OgunbayoThe Aurum Institute, Parktown, South Africa.
Wilma Quispe RojasDepartment of Family Medicine and Population Health, Global Health Institute, Faculty of Medicine and Health Sciences, University of Antwerp, Antwerp, Belgium.
Rob M WarrenSouth African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa.
Annelies Van RieDepartment of Family Medicine and Population Health, Global Health Institute, Faculty of Medicine and Health Sciences, University of Antwerp, Antwerp, Belgium.ORCID https://orcid.org/0000-0001-7666-3263
Anzaan DippenaarDepartment of Family Medicine and Population Health, Global Health Institute, Faculty of Medicine and Health Sciences, University of Antwerp, Antwerp, Belgium.

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

Background: Challenges in tuberculosis (TB) control have fuelled interest in routine next generation sequencing (NGS). However, the comparative performance of targeted NGS (tNGS) and whole genome sequencing (WGS) for drug resistance and genetic relatedness inference remains unclear. Methods: In this cross-sectional study, we compared WGS (MICK-MAGMA platform) and the Deeplex MycTB tNGS assay in 90 patients with rifampicin-resistant TB in South Africa. A pairwise analysis was conducted for a total of 60 isolates, for which tNGS was conducted directly on DNA from sputum, and WGS on cultured isolates from the same samples. Results: Drug resistance inference was highly concordant (≥92%) for most drugs, but lower for isoniazid (82%) and ethionamide (78%). Mixed infections were more commonly detected in tNGS (6.7%) than WGS (1.7%), though likely due to analytical errors. tNGS detected more minor variants (allelic frequency <25%) than WGS (76 Conclusion: In this cohort, drug resistance inference was largely concordant between tNGS and WGS. WGS offered higher resolution for genetic relatedness, while tNGS showed greater sensitivity for minor variants. Further research is needed to clarify the clinical relevance of minor variants and assess the utility of WGS for transmission control.

Identifiers

PMID41736736
PMCPMC12926815

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