Insights into RpoB clinical mutants in mediating rifampicin resistance in Mycobacterium tuberculosis

Unissa, Ameeruddin Nusrath; Hassan, Sameer; Kumari, V. Indira; Revathy, Ravi; Hanna, Luke Elizabeth

doi:10.1016/j.jmgm.2016.04.005

Cited by 14 publications

(9 citation statements)

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“…Even though species identification showed very few hits for Mycobacterium abscessus , which is an NTM, the functional analysis showed higher numbers of reads for Mycobacterium virulence operon involved in DNA transcription. Most of the BLAST hits under this category were identified as a DNA-directed RNA polymerase beta subunit (EC 2.7.7.6), which has undergone specific mutation rendering them resistant to antibiotics [ 95 ] via a common variation (Gln ➔ His) at codon 513 [ 96 ]. The SEED database does not specifically identify the mutation but provides collective information about the various Mycobacterium virulence operons.…”

Section: Discussionmentioning

confidence: 99%

Succession and persistence of microbial communities and antimicrobial resistance genes associated with International Space Station environmental surfaces

et al. 2018

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BackgroundThe International Space Station (ISS) is an ideal test bed for studying the effects of microbial persistence and succession on a closed system during long space flight. Culture-based analyses, targeted gene-based amplicon sequencing (bacteriome, mycobiome, and resistome), and shotgun metagenomics approaches have previously been performed on ISS environmental sample sets using whole genome amplification (WGA). However, this is the first study reporting on the metagenomes sampled from ISS environmental surfaces without the use of WGA. Metagenome sequences generated from eight defined ISS environmental locations in three consecutive flights were analyzed to assess the succession and persistence of microbial communities, their antimicrobial resistance (AMR) profiles, and virulence properties. Metagenomic sequences were produced from the samples treated with propidium monoazide (PMA) to measure intact microorganisms.ResultsThe intact microbial communities detected in Flight 1 and Flight 2 samples were significantly more similar to each other than to Flight 3 samples. Among 318 microbial species detected, 46 species constituting 18 genera were common in all flight samples. Risk group or biosafety level 2 microorganisms that persisted among all three flights were Acinetobacter baumannii, Haemophilus influenzae, Klebsiella pneumoniae, Salmonella enterica, Shigella sonnei, Staphylococcus aureus, Yersinia frederiksenii, and Aspergillus lentulus. Even though Rhodotorula and Pantoea dominated the ISS microbiome, Pantoea exhibited succession and persistence. K. pneumoniae persisted in one location (US Node 1) of all three flights and might have spread to six out of the eight locations sampled on Flight 3. The AMR signatures associated with β-lactam, cationic antimicrobial peptide, and vancomycin were detected. Prominent virulence factors were cobalt-zinc-cadmium resistance and multidrug-resistance efflux pumps.ConclusionsThere was an increase in AMR and virulence gene factors detected over the period sampled, and metagenome sequences of human pathogens persisted over time. Comparative analysis of the microbial compositions of ISS with Earth analogs revealed that the ISS environmental surfaces were different in microbial composition. Metagenomics coupled with PMA treatment would help future space missions to estimate problematic risk group microbial pathogens. Cataloging AMR/virulence characteristics, succession, accumulation, and persistence of microorganisms would facilitate the development of suitable countermeasures to reduce their presence in the closed built environment.Electronic supplementary materialThe online version of this article (10.1186/s40168-018-0585-2) contains supplementary material, which is available to authorized users.

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Section: Discussionmentioning

confidence: 99%

Succession and persistence of microbial communities and antimicrobial resistance genes associated with International Space Station environmental surfaces

et al. 2018

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“…Kumar and Sobhia (2015) demonstrated that inhA mutants reduced the interaction between NADH and binding site residues, causing isoniazid resistance in Mtb 27 . Similarly, various studies reported that mutation in rpoB gene leads to rifampicin resistance in Mtb 28–30 . Likewise, the mechanism of pyrazinamide resistance in the pncA gene mutants has been studied using a computational approach 31 .…”

Section: Discussionmentioning

confidence: 90%

Analysis of mutations leading to para-aminosalicylic acid resistance in Mycobacterium tuberculosis

Pandey

Grover

Kaur

et al. 2019

Sci Rep

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Thymidylate synthase A (ThyA) is the key enzyme involved in the folate pathway in Mycobacterium tuberculosis. Mutation of key residues of ThyA enzyme which are involved in interaction with substrate 2′-deoxyuridine-5′-monophosphate (dUMP), cofactor 5,10-methylenetetrahydrofolate (MTHF), and catalytic site have caused para-aminosalicylic acid (PAS) resistance in TB patients. Focusing on R127L, L143P, C146R, L172P, A182P, and V261G mutations, including wild-type, we performed long molecular dynamics (MD) simulations in explicit solvent to investigate the molecular principles underlying PAS resistance due to missense mutations. We found that these mutations lead to (i) extensive changes in the dUMP and MTHF binding sites, (ii) weak interaction of ThyA enzyme with dUMP and MTHF by inducing conformational changes in the structure, (iii) loss of the hydrogen bond and other atomic interactions and (iv) enhanced movement of protein atoms indicated by principal component analysis (PCA). In this study, MD simulations framework has provided considerable insight into mutation induced conformational changes in the ThyA enzyme of Mycobacterium.

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“…RIF interacts with the β-subunit of RpoB, and most RIF resistance in M. tuberculosis is caused by mutations in the RRDR of RpoB (Tupin et al, 2010). The domain structure of RpoB was previously deduced by analyzing the crystal structure, which showed that RpoB directly interacts with RIF via 12 hydrogen bonds (Nusrath Unissa et al, 2016). Molecular docking experiments showed stronger RIF binding by wild-type RpoB than by mutant RpoB proteins (Nusrath Unissa et al, 2016).…”

Section: Discussionmentioning

confidence: 99%

“…The domain structure of RpoB was previously deduced by analyzing the crystal structure, which showed that RpoB directly interacts with RIF via 12 hydrogen bonds (Nusrath Unissa et al, 2016). Molecular docking experiments showed stronger RIF binding by wild-type RpoB than by mutant RpoB proteins (Nusrath Unissa et al, 2016). Q432 is an energetically favorable binding site and is considered part of the active site that is involved in ligand binding (Campbell et al, 2001;Nusrath Unissa et al, 2016).…”

Section: Discussionmentioning

confidence: 99%

“…Molecular docking experiments showed stronger RIF binding by wild-type RpoB than by mutant RpoB proteins (Nusrath Unissa et al, 2016). Q432 is an energetically favorable binding site and is considered part of the active site that is involved in ligand binding (Campbell et al, 2001;Nusrath Unissa et al, 2016). RpoB Q 432 insQ might influence the binding enthalpy to weaken the molecular interaction between RpoB and RIF, which could result in RIF resistance.…”

Section: Discussionmentioning

confidence: 99%

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A Glutamine Insertion at Codon 432 of RpoB Confers Rifampicin Resistance in Mycobacterium tuberculosis

et al. 2020

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Tuberculosis (TB) is an infectious respiratory disease caused by Mycobacterium tuberculosis and one of the top 10 causes of death worldwide. Treating TB is challenging; successful treatment requires a long course of multiple antibiotics. Rifampicin (RIF) is a first-line drug for treating TB, and the development of RIF-resistant M. tuberculosis makes treatment even more difficult. To determine the mechanism of RIF resistance in these strains, we searched for novel mutations by sequencing. Four isolates, CDC-1, CDC-2, CDC-3, and CDC-4, had high-level RIF resistance and unique mutations encoding RpoB G 158 R, RpoB V 168 A, RpoB S 188 P, and RpoB Q 432 insQ, respectively. To evaluate their correlation with RIF resistance, plasmids carrying rpoB genes encoding these mutant proteins were transfected into the H 37 Rv reference strain. The plasmid complementation of RpoB indicated that G 158 R, V 168 A, and S 188 P did not affect the MIC of RIF. However, the MIC of RIF was increased in H 37 Rv carrying RpoB Q 432 insQ. To confirm the correlation between RIF resistance and Q 432 insQ, we cloned an rpoB fragment carrying the insertion (encoding RpoB Q 432 insQ) into H 37 Rv by homologous recombination using a suicide vector. All replacement mutants expressing RpoB Q 432 insQ were resistant to RIF (MIC > 1 mg/L). These results indicate that RpoB Q 432 insQ causes RIF resistance in M. tuberculosis.

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Insights into RpoB clinical mutants in mediating rifampicin resistance in Mycobacterium tuberculosis

Cited by 14 publications

References 36 publications

Succession and persistence of microbial communities and antimicrobial resistance genes associated with International Space Station environmental surfaces

Succession and persistence of microbial communities and antimicrobial resistance genes associated with International Space Station environmental surfaces

Analysis of mutations leading to para-aminosalicylic acid resistance in Mycobacterium tuberculosis

A Glutamine Insertion at Codon 432 of RpoB Confers Rifampicin Resistance in Mycobacterium tuberculosis

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