Evidence map›Paper›PMID 35194683›Full record

ArticleArchives of microbiology2022

Optimized analysis parameters of variant calling for whole genome-based phylogeny of Mycobacteroides abscessus.

Orawee Kaewprasert, Sissades Tongsima, Rick Twee-Hee Ong, Kiatichai Faksri

Abstract read
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In one paragraph

Article in Archives of microbiology, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 2 papers.

0numbers the graph read from it
0cells of the map it votes in
2citing papers in PubMed
0.3field-weighted citation impact, top 44% of its field
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

2 citing papers in PubMed, 2 citations in OpenAlex.

  1. Article
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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

4 authors at 3 institutions in 2 countries.

Orawee KaewprasertDepartment of Microbiology, Faculty of Medicine, Khon Kaen University, Khon Kaen, 40002, Thailand.
Sissades TongsimaNational Biobank of Thailand, National Science and Technology Development Agency, Khlong Luang, Pathum Thani, Thailand.
Rick Twee-Hee OngSaw Swee Hock School of Public Health, National University of Singapore, Singapore, Singapore.
Kiatichai FaksriDepartment of Microbiology, Faculty of Medicine, Khon Kaen University, Khon Kaen, 40002, Thailand. kiatichai@kku.ac.th.ORCID http://orcid.org/0000-0001-5022-4182
Khon Kaen University · THNational Science and Technology Development Agency · THNational University of Singapore · SG

Funding

Thailand and General Supportive Grant, Khon Kaen University, Thailand 2019 KKU 6200039The National University of Singapore Start-Up Grant to RTHOthe Royal Golden Jubilee (RGJ)-Ph.D. program Grant of the Thailand Research Fund (TRF) PHD/0115/2559
6 · The paper itself

Abstract

Whole-genome sequence (WGS) analysis provides the best resolution for reconstructing bacterial phylogeny. However, the resulting tree could vary according to parameters used in the WGS pipeline, making it difficult to compare results across multiple studies. This study compares effects on phylogenies when applying different parameter stringencies. We used as the study model to optimize parameters strains of Mycobacteroides abscessus serially isolated at various intervals, isolates known to represent persistent infection (PI) cases or re-infection (RI) cases and isolates from different subspecies. Un-optimized parameters with low stringency provided an excessive number of SNPs (823) compared to the optimized setting (3 SNPs) between paired strains isolated 1 day apart from PI cases, discordant tree topology and misclassification of subspecies and of instances of RI. We demonstrated that using high-quality variants provides more accuracy for recognizing serial isolates of the same clone versus different clones and for phylogenetic analysis of M. abscessus. Our approach might be used as a model for analyses requiring phylogenetic reconstruction of other bacteria.

Indexed as

Mycobacterium abscessusPhylogenyGenome, BacterialWhole Genome SequencingAnalysis parametersMycobacteroides abscessusPhylogenetic treeWhole genome sequence

Identifiers

PMID35194683
OpenAlexW4213456598

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.