Evidence map›Paper›PMID 38949712›Full record

ArticleMethods in molecular biology (Clifton, N.J.)2024

Use of Whole Genome Sequencing for Mycobacterium tuberculosis Complex Antimicrobial Susceptibility Testing: From Sequence Data to Resistance Profiles.

Viola Dreyer, Lindsay Sonnenkalb, Margo Diricks, Christian Utpatel, Ivan Barilar, Vanessa Mohr, Stefan Niemann, Thomas A Kohl, Matthias Merker

Abstract read
PubMed Publisher
In one paragraph

Article in Methods in molecular biology (Clifton, N.J.), 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

0numbers the graph read from it
0cells of the map it votes in
0citing 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

0 citing papers in PubMed.

No citing paper in PubMed yet.

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

9 authors.

Viola DreyerMolecular and Experimental Mycobacteriology, Research Center Borstel - Leibniz Lung Center, Borstel, Germany.
Lindsay SonnenkalbMolecular and Experimental Mycobacteriology, Research Center Borstel - Leibniz Lung Center, Borstel, Germany.
Margo DiricksMolecular and Experimental Mycobacteriology, Research Center Borstel - Leibniz Lung Center, Borstel, Germany.
Christian UtpatelMolecular and Experimental Mycobacteriology, Research Center Borstel - Leibniz Lung Center, Borstel, Germany.
Ivan BarilarMolecular and Experimental Mycobacteriology, Research Center Borstel - Leibniz Lung Center, Borstel, Germany.
Vanessa MohrMolecular and Experimental Mycobacteriology, Research Center Borstel - Leibniz Lung Center, Borstel, Germany.
Stefan NiemannMolecular and Experimental Mycobacteriology, Research Center Borstel - Leibniz Lung Center, Borstel, Germany.
Thomas A KohlMolecular and Experimental Mycobacteriology, Research Center Borstel - Leibniz Lung Center, Borstel, Germany.
Matthias MerkerEvolution of the Resistome, Research Center Borstel - Leibniz Lung Center, Borstel, Germany. mmerker@fz-borstel.de.

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

Whole genome sequencing of Mycobacterium tuberculosis complex (MTBC) isolates has been shown to provide accurate predictions for resistance and susceptibility for many first- and second-line anti-tuberculosis drugs. However, bioinformatic pipelines and mutation catalogs to predict antimicrobial resistances in MTBC isolates are often customized and detailed protocols are difficult to access. Here, we provide a step-by-step workflow for the processing and interpretation of short-read sequencing data and give an overview of available analysis pipelines.

Indexed as

Antitubercular AgentsComputational BiologyMicrobial Sensitivity TestsMycobacterium tuberculosisWhole Genome SequencingDrug Resistance, BacterialGenome, BacterialHumansMutationTuberculosisAntitubercular AgentsBioinformaticsBioinformatics pipelineMutationMutations catalogMycobacterium tuberculosisMycobacterium tuberculosis (M. tuberculosis) complexResistance prediction

Identifiers

PMID38949712

What OpenQuestion holds

Textmetadata
Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.