Journal
ARCHIVES OF MICROBIOLOGY
Volume 204, Issue 3, Pages -Publisher
SPRINGER
DOI: 10.1007/s00203-022-02792-2
Keywords
Phylogenetic tree; Whole genome sequence; Analysis parameters; Mycobacteroides abscessus
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Funding
- Khon Kaen University, Thailand [KKU 6200039]
- National University of Singapore Start-Up Grant
- Royal Golden Jubilee (RGJ)-Ph.D. program Grant of the Thailand Research Fund (TRF) [PHD/0115/2559]
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This study demonstrates the importance of optimizing parameters and using high-quality variants in whole-genome sequence analysis for accurate bacterial phylogeny reconstruction.
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.
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