Insight into the biology of Mycobacterium mucogenicum and Mycobacterium neoaurum clade members

Behra, Phani Rama Krishna; Pettersson, B. M. Fredrik; Ramesh, Malavika; Dasgupta, Santanu; Kirsebom, Leif A.

doi:10.1038/s41598-019-55464-5

Cited by 13 publications

(14 citation statements)

References 94 publications

(125 reference statements)

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“…The numbers and types of IS elements, and the presence of phage sequences and plasmids vary among mycobacteria. These and other factors all possibly contribute to the evolution of the genus and bacteria in general (see also Refs [ 6 , 24 , 26 , 27 , 57 ]), e.g., the presence of HNH endonucleases, transposases, RNA elements such as ALIL pseudoknots (required to induce transposition [ 46 , 55 ]), presence/absence of ncRNAs, numbers of tRNA genes, and horizontally transferred genes all possibly contribute to the evolution of the genus and bacteria in general.…”

Section: Discussionmentioning

confidence: 99%

Comparative genome analysis of mycobacteria focusing on tRNA and non-coding RNA

et al. 2022

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Background The Mycobacterium genus encompasses at least 192 named species, many of which cause severe diseases such as tuberculosis. Non-tuberculosis mycobacteria (NTM) can also infect humans and animals. Some are of emerging concern because they show high resistance to commonly used antibiotics while others are used and evaluated in bioremediation or included in anticancer vaccines. Results We provide the genome sequences for 114 mycobacterial type strains and together with 130 available mycobacterial genomes we generated a phylogenetic tree based on 387 core genes and supported by average nucleotide identity (ANI) data. The 244 genome sequences cover most of the species constituting the Mycobacterium genus. The genome sizes ranged from 3.2 to 8.1 Mb with an average of 5.7 Mb, and we identified 14 new plasmids. Moreover, mycobacterial genomes consisted of phage-like sequences ranging between 0 and 4.64% dependent on mycobacteria while the number of IS elements varied between 1 and 290. Our data also revealed that, depending on the mycobacteria, the number of tRNA and non-coding (nc) RNA genes differ and that their positions on the chromosome varied. We identified a conserved core set of 12 ncRNAs, 43 tRNAs and 18 aminoacyl-tRNA synthetases among mycobacteria. Conclusions Phages, IS elements, tRNA and ncRNAs appear to have contributed to the evolution of the Mycobacterium genus where several tRNA and ncRNA genes have been horizontally transferred. On the basis of our phylogenetic analysis, we identified several isolates of unnamed species as new mycobacterial species or strains of known mycobacteria. The predicted number of coding sequences correlates with genome size while the number of tRNA, rRNA and ncRNA genes does not. Together these findings expand our insight into the evolution of the Mycobacterium genus and as such they establish a platform to understand mycobacterial pathogenicity, their evolution, antibiotic resistance/tolerance as well as the function and evolution of ncRNA among mycobacteria.

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Section: Discussionmentioning

confidence: 99%

Comparative genome analysis of mycobacteria focusing on tRNA and non-coding RNA

et al. 2022

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“…1 ). In the non-tuberculous mycobacteria, the subsystem classification suggested that 18% of the gene ontologies belong to amino acids and its derivatives category, 12% to Cofactors, vitamins, prosthetic groups and pigments [ 33 ]. The biosynthesis of amino acids and their derivatives greatly determines the survival of bacteria.…”

Section: Discussionmentioning

confidence: 99%

The whole-genome sequencing in predicting Mycobacterium tuberculosis drug susceptibility and resistance in Papua, Indonesia

et al. 2021

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Background Tuberculosis is one of the deadliest disease caused by Mycobacterium tuberculosis. Its treatment still becomes a burden for many countries including Indonesia. Drug resistance is one of the problems in TB treatment. However, a development in the molecular field through Whole-genome sequencing (WGS) can be used as a solution in detecting mutations associated with TB- drugs. This investigation intended to implement this data for supporting the scientific community in deeply understanding any TB epidemiology and evolution in Papua along with detecting any mutations in genes associated with TB-Drugs. Result A whole-genome sequencing was performed on the random samples from TB Referral Laboratory in Papua utilizing MiSeq 600 cycle Reagent Kit (V3). Furthermore, TBProfiler was used for genome analysis, RAST Server was employed for annotation, while Gview server was applied for BLAST genome mapping and a Microscope server was implemented for Regions of Genomic Plasticity (RGP). The largest genome of M. tuberculosis obtained was at the size of 4,396,040 bp with subsystems number at 309 and the number of coding sequences at 4326. One sample (TB751) contained one RGP. The drug resistance analysis revealed that several mutations associated with TB-drug resistance existed. In details, mutations of rpoB gene which were identified as S450L, D435Y, H445Y, L430P, and Q432K had caused the reduced effectiveness of rifampicin; while the mutases in katG (S315T), kasA (312S), inhA (I21V), and Rv1482c-fabG1 (C-15 T) genes had contributed to the resistance in isoniazid. In streptomycin, the resistance was triggered by the mutations in rpsL (K43R) and rrs (A514C, A514T) genes, and, in Amikacin, its resistance was led by mutations in rrs (A514C) gene. Additionally, in Ethambutol and Pyrazinamide, their reduced effectiveness was provoked by embB gene mutases (M306L, M306V, D1024N) and pncA (W119R). Conclusions The results from whole-genome sequencing of TB clinical sample in Papua, Indonesia could contribute to the surveillance of TB-drug resistance. In the drug resistance profile, there were 15 Multi Drugs Resistance (MDR) samples. However, Extensively Drug-resistant (XDR) samples have not been found, but samples were resistant to only Amikacin, a second-line drug.

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“…This information was gathered for CFP‐10 from M. ulcerans (WP_012392185.1), M. scrofulaceum (ORB70459.1), and M. mucogenicum (WP_061000007.1). To confirm gene duplication events detected in several species, literature reviews were conducted to identify articles that examined gene duplications for the affected species: M. xenopi , [ 27 ] M. kansasii, M. szulgai , and M. marinum , [ 28 ] M. mucogenicum , [ 29 ] M. chelonae , and M. fortuitum . [ 30 ]…”

Section: Methodsmentioning

confidence: 99%

Peptidomic analysis of mycobacterial secreted proteins enables species identification

Shu

Rajagopal

Fan

et al. 2022

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Pulmonary disease arising from slow‐growing mycobacterial infections has emerged as an increasingly prevalent clinical concern over the past two to three decades. Proteins belonging to the family of ESAT‐6 secretion (Esx) systems play critical roles in the virulence of most pathogenic mycobacterial species and are associated with drug resistance. However, no clinical applications can detect and discriminate the expression of species‐specific variants of these proteins in clinical samples, such as early growth cultures, for rapid diagnosis of specific mycobacterial infections, which may require distinct interventions. Conventional immunoassay approaches are not suitable for this purpose due to the significant degree of conservation of Esx proteins among species. Herein we describe the development of a novel immunoprecipitation‐coupled mass spectrometry assay that can distinguish Esx proteins that are expressed by slow‐growing mycobacterial species commonly detected in clinical isolates. This approach uses custom antibodies raised against single semi‐conserved peptide regions in M. tuberculosis (Mtb) EsxB and EsxN to capture corresponding peptides from protein orthologs of mycobacteria associated with human respiratory infections, including Mtb, M. avium, M. intracellulare, M. kansasii, M. gordonae, and M. marinum, to detect these species in standard clinical cultures at the first sign mycobacterial growth to allow rapid disease diagnosis.

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Insight into the biology of Mycobacterium mucogenicum and Mycobacterium neoaurum clade members

Cited by 13 publications

References 94 publications

Comparative genome analysis of mycobacteria focusing on tRNA and non-coding RNA

Comparative genome analysis of mycobacteria focusing on tRNA and non-coding RNA

The whole-genome sequencing in predicting Mycobacterium tuberculosis drug susceptibility and resistance in Papua, Indonesia

Peptidomic analysis of mycobacterial secreted proteins enables species identification

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