Whole-Genome Sequences of Two Clinical Isolates of Mycobacterium tuberculosis from Kerala, South India

Abstract

bWe report the annotated genome sequence of two clinical isolates of Mycobacterium tuberculosis isolated from Kerala, India.

Unraveling Mycobacterium tuberculosis genomic diversity and evolution in Lisbon, Portugal, a highly drug resistant setting

“…No RD region was found to be absent in RGTB423 and only RD RIO deletion was detected in RGTB327. Strain RGTB423 has been found to belong to SCG 1 and PGG 1 [ 25 ], but in-silico PCR analysis showed that the strain had the pks15/1 7 bp frameshift deletion and the TbD1 deletion indicative of a modern Euro-American strain [ 23 ]. Nevertheless, this classification is incongruent with the SCG and PGG classification [ 11 ].…”

A glimpse into the past and predictions for the future: the molecular evolution of the tuberculosis agent

“…S1, some genome sequences, e.g. Mtb_CAS_NITR204, Mtb_Haarlem3_NITR202, Beijing/ NITR203, Mtb_EAI5_NITR206, RGTB423, RGTB327 or Mtb_EAI5 (Madhavilatha et al, 2012;Narayanan and Deshpande, 2013;Al Rashdi et al, 2014) indicate much greater diversity than other related MTBC strains and/or show characteristics that do not match with the phylogenetic groupings suggested by their names and the clustering obtained. The genome sequences of Mtb_EAI5, Mtb_EAI5_NITR206 and RGTB423, for example, cluster with well characterized TbD1-intact L1 M. tuberculosis strains (Fig.…”

“…As shown in http://onlinelibrary.wiley.com/10.1111/mmi.12720/suppinfo, some genome sequences, e.g. Mtb_CAS_NITR204, Mtb_Haarlem3_NITR202, Beijing/NITR203, Mtb_EAI5_NITR206, RGTB423, RGTB327 or Mtb_EAI5 (Madhavilatha et al ., ; Narayanan and Deshpande, ; Al Rashdi et al ., ) indicate much greater diversity than other related MTBC strains and/or show characteristics that do not match with the phylogenetic groupings suggested by their names and the clustering obtained. The genome sequences of Mtb_EAI5, Mtb_EAI5_NITR206 and RGTB423, for example, cluster with well characterized TbD1‐intact L1 M. tuberculosis strains (http://onlinelibrary.wiley.com/doi/10.1111/mmi.12720/suppinfo), but whole genome BLAST searches in GenBank show a TbD1‐deleted locus and several other specific sequence characteristics of the H37Rv M. tuberculosis strain [e.g.…”

“…the truncation of gene rv2024c , also known as chromosomal deletion RvD1 (GenBank: Y18605.1) that is intact in all other MTBC strains (Gordon et al ., )] in these sequences. As in the corresponding publications it is mentioned that the H37Rv reference sequence was used for read‐alignment during genome assembly (Madhavilatha et al ., ; Narayanan and Deshpande, ; Al Rashdi et al ., ), these findings point to artefacts caused by the reference‐directed genome assembly method used in these studies that essentially reproduced an H37Rv genome sequence backbone with the SNP profiles of the endemic isolates, thereby ignoring the larger sequence polymorphisms, such as the TbD1, RvD1 or other strain‐specific regions. Sequence submissions such as these will confuse data analysis and they emphasize the need for de novo assembly and appropriate peer review, quality control and curation of genome data submitted to public databases.…”

Whole-Genome Sequences of Four Clinical Isolates of Mycobacterium tuberculosis from Tamil Nadu, South India

“…The prevalence of ancestral strains of Mycobacterium tuberculosis in India has been reported using various genotyping methods (1–5). The current genotyping methods have low discriminatory power, and whole-genome sequencing of clinical isolates of M. tuberculosis has now become the preferred approach for genotyping these clinical isolates.…”