Enriched whole genome sequencing identified compensatory mutations in the RNA polymerase gene of rifampicin-resistant <em>Mycobacterium leprae</em> strains

ABSTRACT A case of Mycobacterium leprae rifampin resistance after irregular antileprosy treatments since 1971 is reported. Whole-genome sequencing from four longitudinal samples indicated relapse due to acquired rifampin resistance and not to reinfection with another strain. A putative compensatory mutation in rpoC was also detected. Clinical improvement was achieved using an alternative therapy.

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Single nucleotide polymorphism in the rpoB gene Mycobacterium tuberculosis from Papua-Indonesia and its impact on rifampicin resistance: A whole genome sequencing analysis

Microbiology Indonesia ◽

10.5454/mi.15.2.1 ◽

2021 ◽

Vol 15 (2) ◽

pp. 1

Author(s):

Yustinus Maladan ◽

Tri Wahyuni ◽

Hana Krismawati

Keyword(s):

Single Nucleotide Polymorphism ◽

Mycobacterium Tuberculosis ◽

Single Nucleotide Polymorphisms ◽

Rna Polymerase ◽

Whole Genome Sequencing ◽

Genome Sequencing ◽

Whole Genome ◽

Nucleotide Polymorphisms ◽

Nucleotide Polymorphism ◽

Single Nucleotide

In the antibiotic era, Tuberculosis (TB) drugs resistance especially Rifampicin (RIF) is highly reported around the world. Resistance of RIF is caused by the mutation of genes that associated with RIF receptor. The aims of this study are detecting the Single Nucleotide Polymorphism of Rifampicin resistant genes using Whole Genome Sequencing (WGS) and analysing the profile of protein changing caused by SNP. Twenty Mycobacterium tuberculosis culture samples were passed on WGS procedure and 19 samples were adequate to further bioinformatics analysis. Single Nucleotide Polymorphisms Analysis was done using TBprofiler. Based on TBProfiler, seventeen samples were resistant to rifampicin. The mutations that cause the resistance are S450L, D435Y, H445Y, 430P, Q432K. Other Single Nucleotide Polymorphisms H835R, V534M and R224C were also found. The H835R mutants are present together with the S450L, V534M with S450L mutants, and R224C with Q432K mutants. Native protein for RNA Polymerase Subunit β used was the result of separation from the crystal structure of Mycobacterium tuberculosis H37Rv RNA polymerase (PDB: 5UHB). Binding affinity RIF to RNA Polymerase Subunit β calculated using AutoDock vina. Construction of mutant 3D structures using FoldX5. From the analysis, it was found that seventeen samples were resistant to rifampicin and two samples did not contain SNP which could cause resistance to rifampicin.

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Mutation of RNA Polymerase β-Subunit Gene Promotes Heterogeneous-to-Homogeneous Conversion of β-Lactam Resistance in Methicillin-Resistant Staphylococcus aureus

Antimicrobial Agents and Chemotherapy ◽

10.1128/aac.00720-13 ◽

2013 ◽

Vol 57 (10) ◽

pp. 4861-4871 ◽

Cited By ~ 21

Author(s):

Yoshifumi Aiba ◽

Yuki Katayama ◽

Tomomi Hishinuma ◽

Hiroko Murakami-Kuroda ◽

Longzhu Cui ◽

...

Keyword(s):

Staphylococcus Aureus ◽

Rna Polymerase ◽

Whole Genome Sequencing ◽

Genome Sequencing ◽

Phenotypic Expression ◽

Amino Acid Replacement ◽

Whole Genome ◽

Β Subunit ◽

Methicillin Resistant ◽

Content Type

ABSTRACTThree types of phenotypic expression of β-lactam resistance have been reported in methicillin-resistantStaphylococcus aureus(MRSA): heterogeneous, homogeneous, and Eagle-type resistance. Heterogeneous-to-homogeneous conversion of β-lactam resistance is postulated to be caused by a chromosomal mutation (chr*) in addition to the expression of themecAgene. Eagle-type resistance is a unique phenotype ofchr*occurring in pre-MRSA strain N315 whosemecAgene expression is strongly repressed by an intactmecIgene. We here report that certain mutations of therpoBgene, encoding the RNA polymerase β subunit, belong tochr*. We studied homogeneous MRSA (homo-MRSA) strain N315ΔIP-H5 (abbreviated as ΔIP-H5), which was obtained from hetero-MRSA strain N315ΔIP by selection with 8 mg/liter imipenem. Whole-genome sequencing of ΔIP-H5 revealed the presence of a unique mutation in therpoBgene,rpoB(N967I), causing the amino acid replacement of Asn by Ile at position 967 of RpoB. The effect of therpoB(N967I) mutation was confirmed by constructing a revertant H5rpoB(I967N) strain as well as an N315-derived mutant, N315rpoB(N967I). H5rpoB(I967N) regained the hetero-resistance phenotype, and the N315rpoB(N967I) strain showed an Eagle-type phenotype similar to that of the typical Eagle-type MRSA strain N315h4. Furthermore, subsequent whole-genome sequencing revealed that N315h4 also had a missense mutation ofrpoB(R644H). Introduction of therpoB(N967I) mutation was accompanied by decreased autolysis, prolonged doubling time, and tolerance to bactericidal concentrations of methicillin. We consider thatrpoBmutations are the major cause for heterogeneous-to-homogeneous phenotypic conversion of β-lactam resistance in MRSA strain N315 and its derived strains.

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