ArticleBMC genomics2013
Genetic heterogeneity revealed by sequence analysis of Mycobacterium tuberculosis isolates from extra-pulmonary tuberculosis patients.
Article in BMC genomics, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
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12 citing papers in PubMed, 16 citations in OpenAlex.
- Whole Genome Sequencing of Mycobacterium tuberculosis Isolates From Extrapulmonary Sites.Omics : a journal of integrative biology · 2017Article
- Mycobacterium tuberculosis Whole Genome Sequences From Southern India Suggest Novel Resistance Mechanisms and the Need for Region-Specific Diagnostics.Clinical infectious diseases : an official publication of the Infectious Diseases Society of America · 2017Article
- Next-generation sequencing of tissue: A logical extension.Neurology(R) neuroimmunology & neuroinflammation · 2016Article
- Clinical Features and Drug-Resistance Profile of Urinary Tuberculosis in South-Western China: A Cross-sectional Study.Medicine · 2016Article
- Analysis of IS6110 insertion sites provide a glimpse into genome evolution of Mycobacterium tuberculosis.Scientific reports · 2015Article
- Genetic markers, genotyping methods & next generation sequencing in Mycobacterium tuberculosis.The Indian journal of medical research · 2015Article
- High Genotypic Discordance of Concurrent Mycobacterium tuberculosis Isolates from Sputum and Blood of HIV-Infected Individuals.PloS one · 2015Article
- Next-generation sequencing in veterinary medicine: how can the massive amount of information arising from high-throughput technologies improve diagnosis, control, and management of infectious diseases?Methods in molecular biology (Clifton, N.J.) · 2015Review
- Genome-wide Mycobacterium tuberculosis variation (GMTV) database: a new tool for integrating sequence variations and epidemiology.BMC genomics · 2014Article
- A phylogeny-based sampling strategy and power calculator informs genome-wide associations study design for microbial pathogens.Genome medicine · 2014Article
- Emerging rapid resistance testing methods for clinical microbiology laboratories and their potential impact on patient management.BioMed research international · 2014Review
- Next-Generation Anchor Based Phylogeny (NexABP): constructing phylogeny from next-generation sequencing data.Scientific reports · 2013Article
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Authors and funding
9 authors at 3 institutions in 1 country.
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No grant is acknowledged in the PubMed record.
Abstract
backgroundTuberculosis remains a major public health problem. Clinical tuberculosis manifests often as pulmonary and occasionally as extra-pulmonary tuberculosis. The emergence of drug resistant tubercle bacilli and its association with HIV is a formidable challenge to curb the spread of tuberculosis. There have been concerted efforts by whole genome sequencing and bioinformatics analysis to identify genomic patterns and to establish a relationship between the genotype of the organism and clinical manifestation of tuberculosis. Extra-pulmonary TB constitutes 15-20 percent of the total clinical cases of tuberculosis reported among immunocompetent patients, whereas among HIV patients the incidence is more than 50 percent. Genomic analysis of M. tuberculosis isolates from extra pulmonary patients has not been explored.
resultsThe genomic DNA of 5 extra-pulmonary clinical isolates of M. tuberculosis derived from cerebrospinal fluid, lymph node fine needle aspirates (FNAC) / biopsies, were sequenced. Next generation sequencing approach (NGS) was employed to identify Single Nucleotide Variations (SNVs) and computational methods used to predict their consequence on functional genes. Analysis of distribution of SNVs led to the finding that there are mixed genotypes in patient isolates and that many SNVs are likely to influence either gene function or their expression. Phylogenetic relationship between the isolates correlated with the origin of the isolates. In addition, insertion sites of IS elements were identified and their distribution revealed a variation in number and position of the element in the 5 extra-pulmonary isolates compared to the reference M. tuberculosis H37Rv strain.
conclusionsThe results suggest that NGS sequencing is able to identify small variations in genomes of M. tuberculosis isolates including changes in IS element insertion sites. Moreover, variations in isolates of M. tuberculosis from non-pulmonary sites were documented. The analysis of our results indicates genomic heterogeneity in the clinical isolates.
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