1. Additional file 2 of Evolution and spread of a highly drug resistant strain of Mycobacterium tuberculosis in Papua New Guinea
- Author
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Bainomugisa, Arnold, Lavu, Evelyn, Pandey, Sushil, Majumdar, Suman, Banamu, Jennifer, Coulter, Chris, Marais, Ben, Coin, Lachlan, Graham, Stephen M., and du Cros, Philipp
- Abstract
Additional file 2: Table S2. M. tuberculosis genes associated with resistance or compensatory mutation. Table S3. Phylogenetic markers in known drug resistance genes as per Merker et al 2020. Figure S1. Phylogeny of 194 isolates collected from Daru (blue tip labels) and CPHL, Papua New Guinea. Figure S2. Phylogeny of 176 lineage 2 PNG isolates (purple - monophyletic clade) with a global collection of 110 Beijing genomes. Figure S3. Linear regression analysis showing correlation between root-to-tip distance and sampling years (R2 = 0.384) of an extended collection of 176 PNG Beijing datasets covering the period 2012 to 2019. Table S4. Bayesian evaluation of temporal signal (BETS) results for strict and relaxed molecular clock analysis of Beijing isolates. Table S5. Path and stepping stone sampling results of relaxed clock model selection based on marginal likelihood considering 100 steps and 10 million chain length. Figure S4. Evolutionary history of drug resistance among the Beijing strains of PNG forming two clades. Figure S5. Concordance of phenotypic and genotypic drug resistance among Beijing strains from CPHL (Green—bars) and Daru (Red—bars). Figure S6. Number of unique mutations within some of the common genes known to confer resistance to First-line drugs (embB—Ethambutol; fabG1, fabG1-inhA, inhA, katG—Isoniazid; pncA—Pyrazinamide; rpoB—Rifampicin) and Fluoroquinolone (gyrA). Figure S7. Genomic clusters created by Transcluster software (transmission threshold—21 and transmission rate—2) among Beijing strains, stratified by identified PNG provinces. Table S6. Association of genomic clustering among Beijing strains and two genomic features thought to be risk factors of transmission.
- Published
- 2022
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