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Table 2 Literature search results

From: A phylogeny-based sampling strategy and power calculator informs genome-wide associations study design for microbial pathogens

Author Reference Year Strains sequenced (n) Stated study purposea Clinical strains? Time series? Method Report specific genotypic association?
Zhang et al. [26] 2013 161 Identify drug resistance genes Yes No Phylogenetics and comparison of rates with poisson distribution Yes; list of genes provided
Farhat et al. [15] 2013 124 Identify drug resistance genes Yes No Phylogenetics and convergence analysis Yes; list of genes provided
Lin et al. [27] 2013 2 Identify drug resistance genes Yes No Comparison with reference mycobacterial strains No
Wu et al. [28] 2013 4 Identify Beijing associated pathways Yes No COG enrichment of genes with snps General pathways rather than individual genes
Das et al. [29] 2013 5 Identify genes related to extrapulmonary TB Yes No COG enrichment of genes with snps General pathways rather than individual genes
Ilina et al. [30] 2013 4 Identify drug resistance genes Yes No Comparison with reference mycobacterial strains No
Abrahams et al. [31] 2013 - Identify resistance targets(s) for novel imidazole No Yes: spontaneous mutants resistant to drug and their sensitive ancestor Identification of all mutations Yes qcrb
Supply et al. [32] 2013 5 Identify genes associated with smooth TB phenotype Yes No Comparison with reference mycobacterial strains General pathways rather than individual genes
Hartkoorn et al. [33] 2012 - Identify resistance targets(s) for pyridomycin No Yes: spontaneous mutants resistant to drug and their sensitive ancestor Identification of all mutations Yes acyl-carrier-protein inha
G. Sun et al. [34] 2012 7 Identify drug resistance genes Yes Yes: serial samples from same patient Identification of all mutations No; but list of potential candidates with new fixed mutations provided
Grzegorzewicz et al. [35] 2012 - Identify resistance targets(s) for novel compound Adamantyl Urea Yes Yes: serial samples from the same patient Identification of all mutations Yes mmpl3
Casali et al. [36] 2012 59 Identify drug resistance genes Yes No Phylogenetic tree and parallel evolution and convergence Yes rpoc
Tahlan et al. [37] 2012 - Identify resistance targets(s) for novel compound SQ109 No Yes: spontaneous mutants resistant to drug and their sensitive ancestor Identification of all mutations Yes mmpl3
La Rosa et al. [38] 2012 - Identify resistance target(s) for 1,5-diarylpyrrole derivative BM212 No Yes: spontaneous mutants resistant to drug and their sensitive ancestor Identification of all mutations Yes mmpl3
Comas et al. [39] 2011 10 Identify drug resistance genes Yes Yes: serial samples from the same patient Identification of all mutations in rpoc. Assessment of convergence across different strain pairs Yes confirmed rpoc
Manjunatha et al. [40] 2006 - Identify resistance targets(s) for PA-824 No Yes: spontaneous mutants resistant to drug and their sensitive ancestor Identification of all mutations Yes Rv3547
  1. aThe term `phenotype related genes is used loosely here to describe genes that are associated with but not necessarily causative of the phenotype.