To facilitate the management of multidrug-resistant (MDR) tuberculosis, two nucleic acid sequence-based methods, the GenoType MTBDRplus test and DNA sequencing, were assessed for the rapid detection of drug-resistant Mycobacterium tuberculosis for the first time in the Asia-Pacific region. The performances of these two assays in detecting the presence of rifampin (rifampicin) (RIF) and isoniazid (INH) resistanceassociated mutations in the rpoB, katG, inhA regulatory region, inhA, and oxyR-ahpC genes were compared to that of a conventional agar proportion drug susceptibility test. A total of 242 MDR and 30 pansusceptible M. tuberculosis isolates were evaluated in this study. The sensitivities obtained for RIF-resistant detection by the GenoType MTBDRplus test and by resistance gene sequencing were 95.5% and 97.9%, respectively. The sensitivities for INH resistance detection by the GenoType MTBDRplus test and by resistance gene sequencing were 81.8% and 93.4%, respectively. Together, the sensitivity for MDR tuberculosis detection was 78.5% with the GenoType MTBDRplus test and 91.3% by resistance gene sequencing. The specificity for RIF resistance, INH resistance, and MDR detection was 100% by both methods. The GenoType MTBDRplus test has the advantage of a short turnaround time for drug-resistant M. tuberculosis detection. Overall, the two assays performed equally well in detecting RIF resistance (P ‫؍‬ 0.13). However, DNA sequencing demonstrated superior performance in detecting INH resistance (P < 0.001) and MDR tuberculosis (P < 0.001). We suggest that new alleles of INH resistance genes should be evaluated to improve the sensitivity of the GenoType MTBDRplus test, especially for different geographic areas with genetically diverse M. tuberculosis strains.

Mycobacterium tuberculosis isolates with a region of difference 105 (RD105) deletion, mainly Beijing family spoligotypes, were phylogenetically grouped into the East Asia lineage. We identified a single nucleotide polymorphism in codon 507, ATC to ATT, of the fadD28 gene as a robust marker and developed a rapid assay for East Asia lineage M. tuberculosis.Beijing family Mycobacterium tuberculosis has successfully disseminated worldwide (8). The Beijing family isolates were reported to be associated with drug-resistant tuberculosis and disease manifestations (14). In Taiwan, the Beijing family was the most prevalent (44.4%) spoligotype determined by spacer oligonucleotide typing (11) and was associated with isoniazid and ethambutol resistance (10). Furthermore, approximately 3% of our isolates (mostly shared type [ST] no. 523, 246, and 955) could not be classified into any spoligotype families (R. Jou et al., unpublished data). Both single nucleotide polymorphisms (SNPs) and large sequence polymorphisms, with deletions in regions of difference (RD) identified by comparative genomics (16), were robust phylogenetic markers of M. tuberculosis complex. We identified nine SNPs to classify the main lineages of M. tuberculosis and proved that spoligotype ST no. 523 (carrying all 43 spacers) might share the same common ancestor with the Beijing family (4). Analyses of SNPs and deletion of RD105 (including Rv0071, Rv0072, Rv0073, and partial Rv0074 genes of the H37Rv reference strain) provided evidence that not only the Beijing family but also several nonBeijing isolates-ST no. 523 (strain 94_M4241A), 955 (strain 98_1663), and 623 (strain 96_1548)-belonged to the East Asia lineage (lineage 2) (7, 9). The results inferred they should be genetically more similar than other lineages. The aim of this study is to identify a marker for rapid screening of East Asia lineage M. tuberculosis in regions of tuberculosis endemicity, especially if genotyping is not readily accessible, and to facilitate case treatment and public health management.The mycobacterial cell wall is the site of action of some first-line antimycobacterial agents, such as isoniazid, by inhibiting the biosynthesis of mycolic acids (12). We investigated several genes that mediated cell envelope processing of M. tuberculosis. In particular, we focused on one protein of the fatty-acyl AMP ligase (FAAL) family, FadD28. It is responsible for the attachment of mycocerosic acids to phthiocerol in the phthiocerol dimycocerosate (PDIM) synthesis pathway.PDIM is found only in the cell wall of pathogenic mycobacteria (1, 13, 15). We conducted analyses to explore unique SNP of the fadD28 gene in M. tuberculosis lineages.Initially, we interrogated a set of 95 representative and genetic diversified isolates with 95 different IS6110 restriction fragment length polymorphism (RFLP) profiles containing 28 distinct spoligotypes. These 95 isolates included 42 Beijing family isolates, 6 East-African-Indian (EAI) isolates, 30 Haarlem and Haarlem-like isolates (defined in our previous...