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Xia X. Horizontal Gene Transfer and Drug Resistance Involving Mycobacterium tuberculosis. Antibiotics (Basel) 2023; 12:1367. [PMID: 37760664 PMCID: PMC10526031 DOI: 10.3390/antibiotics12091367] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Revised: 08/13/2023] [Accepted: 08/21/2023] [Indexed: 09/29/2023] Open
Abstract
Mycobacterium tuberculosis (Mtb) acquires drug resistance at a rate comparable to that of bacterial pathogens that replicate much faster and have a higher mutation rate. One explanation for this rapid acquisition of drug resistance in Mtb is that drug resistance may evolve in other fast-replicating mycobacteria and then be transferred to Mtb through horizontal gene transfer (HGT). This paper aims to address three questions. First, does HGT occur between Mtb and other mycobacterial species? Second, what genes after HGT tend to survive in the recipient genome? Third, does HGT contribute to antibiotic resistance in Mtb? I present a conceptual framework for detecting HGT and analyze 39 ribosomal protein genes, 23S and 16S ribosomal RNA genes, as well as several genes targeted by antibiotics against Mtb, from 43 genomes representing all major groups within Mycobacterium. I also included mgtC and the insertion sequence IS6110 that were previously reported to be involved in HGT. The insertion sequence IS6110 shows clearly that the Mtb complex participates in HGT. However, the horizontal transferability of genes depends on gene function, as was previously hypothesized. HGT is not observed in functionally important genes such as ribosomal protein genes, rRNA genes, and other genes chosen as drug targets. This pattern can be explained by differential selection against functionally important and unimportant genes after HGT. Functionally unimportant genes such as IS6110 are not strongly selected against, so HGT events involving such genes are visible. For functionally important genes, a horizontally transferred diverged homologue from a different species may not work as well as the native counterpart, so the HGT event involving such genes is strongly selected against and eliminated, rendering them invisible to us. In short, while HGT involving the Mtb complex occurs, antibiotic resistance in the Mtb complex arose from mutations in those drug-targeted genes within the Mtb complex and was not gained through HGT.
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Affiliation(s)
- Xuhua Xia
- Department of Biology, University of Ottawa, Ottawa, ON K1N 9A7, Canada; ; Tel.: +1-613-562-5718
- Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, ON K1H 8M5, Canada
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Renau-Mínguez C, Herrero-Abadía P, Ruiz-Rodriguez P, Sentandreu V, Torrents E, Chiner-Oms Á, Torres-Puente M, Comas I, Julián E, Coscolla M. Genomic analysis of Mycobacterium brumae sustains its nonpathogenic and immunogenic phenotype. Front Microbiol 2023; 13:982679. [PMID: 36687580 PMCID: PMC9850167 DOI: 10.3389/fmicb.2022.982679] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Accepted: 12/06/2022] [Indexed: 01/07/2023] Open
Abstract
Mycobacterium brumae is a rapid-growing, non-pathogenic Mycobacterium species, originally isolated from environmental and human samples in Barcelona, Spain. Mycobacterium brumae is not pathogenic and it's in vitro phenotype and immunogenic properties have been well characterized. However, the knowledge of its underlying genetic composition is still incomplete. In this study, we first describe the 4 Mb genome of the M. brumae type strain ATCC 51384T assembling PacBio reads, and second, we assess the low intraspecies variability by comparing the type strain with Illumina reads from three additional strains. Mycobacterium brumae genome is composed of a circular chromosome with a high GC content of 69.2% and containing 3,791 CDSs, 97 pseudogenes, one prophage and no CRISPR loci. Mycobacterium brumae has shown no pathogenic potential in in vivo experiments, and our genomic analysis confirms its phylogenetic position with other non-pathogenic and rapid growing mycobacteria. Accordingly, we determined the absence of virulence-related genes, such as ESX-1 locus and most PE/PPE genes, among others. Although the immunogenic potential of M. brumae was proved to be as high as Mycobacterium bovis BCG, the only mycobacteria licensed to treat cancer, the genomic content of M. tuberculosis T cell and B cell antigens in M. brumae genome is considerably lower than those antigens present in M. bovis BCG genome. Overall, this work provides relevant genomic data on one of the species of the mycobacterial genus with high therapeutic potential.
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Affiliation(s)
| | - Paula Herrero-Abadía
- Genetics and Microbiology Department, Faculty of Biosciences, Autonomous University of Barcelona, Barcelona, Spain
| | | | - Vicente Sentandreu
- Genomics Unit, Central Service for Experimental Research (SCSIE), University of Valencia, Burjassot, Spain
| | - Eduard Torrents
- Bacterial Infections and Antimicrobial Therapies Group, Institute for Bioengineering of Catalonia (IBEC), Barcelona, Spain,Microbiology Section, Department of Genetics, Microbiology, and Statistics, Biology Faculty, Universitat de Barcelona, Barcelona, Spain
| | | | | | - Iñaki Comas
- Instituto de Biomedicina de Valencia (IBV), CSIC, Valencia, Spain
| | - Esther Julián
- Genetics and Microbiology Department, Faculty of Biosciences, Autonomous University of Barcelona, Barcelona, Spain,Esther Julián, ✉
| | - Mireia Coscolla
- I2SysBio, University of Valencia-FISABIO Joint Unit, Paterna, Spain,*Correspondence: Mireia Coscolla, ✉
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Nair RR, Sharan D, Srinivasan V, Mukkayyan N, Jakkala K, Ajitkumar P. The H2O2 inherently released by the mycobacterial minor subpopulation enhances the survival of the major kin subpopulation against rifampicin. CURRENT RESEARCH IN MICROBIAL SCIENCES 2022; 3:100148. [PMID: 35909613 PMCID: PMC9325904 DOI: 10.1016/j.crmicr.2022.100148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Revised: 06/04/2022] [Accepted: 06/15/2022] [Indexed: 11/30/2022] Open
Abstract
Stress survival of mycobacterial minor (SCs) and major (NCs) subpopulations. The SCs enhance survival of the NCs against rifampicin. H2O2 released by the SCs increased KatG levels in the NCs. Increased KatG levels neutralised the H2O2 formed during rifampicin exposure. The enhanced survival was not observed in the furA-katG/katG knockout mutants.
Exposure to antibiotics most often generates oxidative stress in bacteria. Oxidative stress survival mechanisms would facilitate the evolution of antibiotic resistance. As part of an effort to understand oxidative stress survival mechanisms in mycobacteria, here we show that the minor subpopulation (SCs; short-sized cells constituting 10% of the population) of Mycobacterium smegmatis significantly increased the survival of its major kin subpopulation (NCs; normal/long-sized cells constituting 90% of the population) in the mid-log-phase (MLP) cultures against the oxidative stress induced by rifampicin and exogenously added H2O2 (positive control). We had earlier shown that the SCs in the MLP cultures inherently and naturally release significantly high levels of H2O2 into the medium. Addition of the SCs’ culture supernatant, unlike the supernatant of the dimethylthiourea (H2O2 scavenger) exposed SCs, enhanced the survival of NCs. It indicated that NCs’ survival required the H2O2 present in the SCs’ supernatant. This H2O2 transcriptionally induced high levels of catalase-peroxidase (KatG) in the NCs. The naturally high KatG levels in the NCs significantly neutralised the endogenous H2O2 formed upon exposure to rifampicin or H2O2, thereby enhancing the survival of NCs against oxidative stress. The absence of such enhanced survival in the furA-katG and katG knockout (KO) mutants of NCs in the presence of wild-type SCs, confirmed the requirement of the H2O2 present in the SCs’ supernatant and NCs’ KatG for enhanced oxidative stress survival. The presence of SCs:NCs at 1:9 in the pulmonary tuberculosis patients’ sputum alludes to the clinical significance of the finding.
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Affiliation(s)
- Rashmi Ravindran Nair
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore 560012, Karnataka, India
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Deepti Sharan
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore 560012, Karnataka, India
- Department of Microbiology, University of Chicago, Chicago, IL 60637, USA
| | - Vijay Srinivasan
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore 560012, Karnataka, India
- School of Physics and Astronomy, University of Edinburgh, Edinburgh, UK
| | - Nagaraja Mukkayyan
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore 560012, Karnataka, India
- Department of Microbial Pathogenesis, University of Maryland, Baltimore 21201, Maryland, USA
| | - Kishor Jakkala
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore 560012, Karnataka, India
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Parthasarathi Ajitkumar
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore 560012, Karnataka, India
- Corresponding author.
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