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Delbeau M, Froom R, Landick R, Darst SA, Campbell EA. The yin and yang of the universal transcription factor NusG. Curr Opin Microbiol 2024; 81:102540. [PMID: 39226817 DOI: 10.1016/j.mib.2024.102540] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2024] [Revised: 08/19/2024] [Accepted: 08/20/2024] [Indexed: 09/05/2024]
Abstract
RNA polymerase (RNAP), the central enzyme of transcription, intermittently pauses during the elongation stage of RNA synthesis. Pausing provides an opportunity for regulatory events such as nascent RNA folding or the recruitment of transregulators. NusG (Spt5 in eukaryotes and archaea) regulates RNAP pausing and is the only transcription factor conserved across all cellular life. NusG is a multifunctional protein: its N-terminal domain (NGN) binds to RNAP, and its C-terminal KOW domain in bacteria interacts with transcription regulators such as ribosomes and termination factors. In Escherichia coli, NusG acts as an antipausing factor. However, recent studies have revealed that NusG has distinct transcriptional regulatory roles specific to bacterial clades with clinical implications. Here, we focus on NusG's dual roles in the regulation of pausing.
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Affiliation(s)
- Madeleine Delbeau
- Laboratory of Molecular Pathogenesis, The Rockefeller University, New York, NY 10065, USA
| | - Ruby Froom
- Laboratory of Molecular Pathogenesis, The Rockefeller University, New York, NY 10065, USA
| | - Robert Landick
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA; Department of Bacteriology, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Seth A Darst
- Laboratory of Molecular Biophysics, The Rockefeller University, New York, NY 10065, USA
| | - Elizabeth A Campbell
- Laboratory of Molecular Pathogenesis, The Rockefeller University, New York, NY 10065, USA.
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2
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Billows N, Phelan J, Xia D, Peng Y, Clark TG, Chang YM. Large-scale statistical analysis of Mycobacterium tuberculosis genome sequences identifies compensatory mutations associated with multi-drug resistance. Sci Rep 2024; 14:12312. [PMID: 38811658 PMCID: PMC11137121 DOI: 10.1038/s41598-024-62946-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2024] [Accepted: 05/22/2024] [Indexed: 05/31/2024] Open
Abstract
Tuberculosis (TB), caused by Mycobacterium tuberculosis, has a significant impact on global health worldwide. The development of multi-drug resistant strains that are resistant to the first-line drugs isoniazid and rifampicin threatens public health security. Rifampicin and isoniazid resistance are largely underpinned by mutations in rpoB and katG respectively and are associated with fitness costs. Compensatory mutations are considered to alleviate these fitness costs and have been observed in rpoC/rpoA (rifampicin) and oxyR'-ahpC (isoniazid). We developed a framework (CompMut-TB) to detect compensatory mutations from whole genome sequences from a large dataset comprised of 18,396 M. tuberculosis samples. We performed association analysis (Fisher's exact tests) to identify pairs of mutations that are associated with drug-resistance, followed by mediation analysis to identify complementary or full mediators of drug-resistance. The analyses revealed several potential mutations in rpoC (N = 47), rpoA (N = 4), and oxyR'-ahpC (N = 7) that were considered either 'highly likely' or 'likely' to confer compensatory effects on drug-resistance, including mutations that have previously been reported and validated. Overall, we have developed the CompMut-TB framework which can assist with identifying compensatory mutations which is important for more precise genome-based profiling of drug-resistant TB strains and to further understanding of the evolutionary mechanisms that underpin drug-resistance.
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Affiliation(s)
- Nina Billows
- Royal Veterinary College, University of London, London, UK.
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK.
| | - Jody Phelan
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
| | - Dong Xia
- Royal Veterinary College, University of London, London, UK
| | | | - Taane G Clark
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
- Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, London, UK
| | - Yu-Mei Chang
- Royal Veterinary College, University of London, London, UK
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Windels EM, Wampande EM, Joloba ML, Boom WH, Goig GA, Cox H, Hella J, Borrell S, Gagneux S, Brites D, Stadler T. HIV co-infection is associated with reduced Mycobacterium tuberculosis transmissibility in sub-Saharan Africa. PLoS Pathog 2024; 20:e1011675. [PMID: 38696531 DOI: 10.1371/journal.ppat.1011675] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Revised: 05/14/2024] [Accepted: 04/10/2024] [Indexed: 05/04/2024] Open
Abstract
Persons living with HIV are known to be at increased risk of developing tuberculosis (TB) disease upon infection with Mycobacterium tuberculosis (Mtb). However, it has remained unclear how HIV co-infection affects subsequent Mtb transmission from these patients. Here, we customized a Bayesian phylodynamic framework to estimate the effects of HIV co-infection on the Mtb transmission dynamics from sequence data. We applied our model to four Mtb genomic datasets collected in sub-Saharan African countries with a generalized HIV epidemic. Our results confirm that HIV co-infection is a strong risk factor for developing active TB. Additionally, we demonstrate that HIV co-infection is associated with a reduced effective reproductive number for TB. Stratifying the population by CD4+ T-cell count yielded similar results, suggesting that, in this context, CD4+ T-cell count is not a better predictor of Mtb transmissibility than HIV infection status alone. Together, our genome-based analyses complement observational household contact studies, and more firmly establish the negative association between HIV co-infection and Mtb transmissibility.
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Affiliation(s)
- Etthel M Windels
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
- Swiss Tropical and Public Health Institute, Allschwil, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | | | | | - W Henry Boom
- Case Western Reserve University and University Hospitals Cleveland Medical Center, Cleveland, Ohio, United States of America
| | - Galo A Goig
- Swiss Tropical and Public Health Institute, Allschwil, Switzerland
- University of Basel, Basel, Switzerland
| | - Helen Cox
- University of Cape Town, Cape Town, South Africa
| | - Jerry Hella
- Ifakara Health Institute, Dar es Salaam, Tanzania
| | - Sonia Borrell
- Swiss Tropical and Public Health Institute, Allschwil, Switzerland
- University of Basel, Basel, Switzerland
| | - Sebastien Gagneux
- Swiss Tropical and Public Health Institute, Allschwil, Switzerland
- University of Basel, Basel, Switzerland
| | - Daniela Brites
- Swiss Tropical and Public Health Institute, Allschwil, Switzerland
- University of Basel, Basel, Switzerland
| | - Tanja Stadler
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
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Eckartt KA, Delbeau M, Munsamy-Govender V, DeJesus MA, Azadian ZA, Reddy AK, Chandanani J, Poulton NC, Quiñones-Garcia S, Bosch B, Landick R, Campbell EA, Rock JM. Compensatory evolution in NusG improves fitness of drug-resistant M. tuberculosis. Nature 2024; 628:186-194. [PMID: 38509362 PMCID: PMC10990936 DOI: 10.1038/s41586-024-07206-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2023] [Accepted: 02/19/2024] [Indexed: 03/22/2024]
Abstract
Drug-resistant bacteria are emerging as a global threat, despite frequently being less fit than their drug-susceptible ancestors1-8. Here we sought to define the mechanisms that drive or buffer the fitness cost of rifampicin resistance (RifR) in the bacterial pathogen Mycobacterium tuberculosis (Mtb). Rifampicin inhibits RNA polymerase (RNAP) and is a cornerstone of modern short-course tuberculosis therapy9,10. However, RifR Mtb accounts for one-quarter of all deaths due to drug-resistant bacteria11,12. We took a comparative functional genomics approach to define processes that are differentially vulnerable to CRISPR interference (CRISPRi) inhibition in RifR Mtb. Among other hits, we found that the universally conserved transcription factor NusG is crucial for the fitness of RifR Mtb. In contrast to its role in Escherichia coli, Mtb NusG has an essential RNAP pro-pausing function mediated by distinct contacts with RNAP and the DNA13. We find this pro-pausing NusG-RNAP interface to be under positive selection in clinical RifR Mtb isolates. Mutations in the NusG-RNAP interface reduce pro-pausing activity and increase fitness of RifR Mtb. Collectively, these results define excessive RNAP pausing as a molecular mechanism that drives the fitness cost of RifR in Mtb, identify a new mechanism of compensation to overcome this cost, suggest rational approaches to exacerbate the fitness cost, and, more broadly, could inform new therapeutic approaches to develop drug combinations to slow the evolution of RifR in Mtb.
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Affiliation(s)
- Kathryn A Eckartt
- Laboratory of Host-Pathogen Biology, The Rockefeller University, New York, NY, USA
| | - Madeleine Delbeau
- Laboratory of Molecular Biophysics, The Rockefeller University, New York, NY, USA
| | | | - Michael A DeJesus
- Laboratory of Host-Pathogen Biology, The Rockefeller University, New York, NY, USA
| | - Zachary A Azadian
- Laboratory of Host-Pathogen Biology, The Rockefeller University, New York, NY, USA
| | - Abhijna K Reddy
- Laboratory of Host-Pathogen Biology, The Rockefeller University, New York, NY, USA
| | - Joshua Chandanani
- Laboratory of Molecular Biophysics, The Rockefeller University, New York, NY, USA
| | - Nicholas C Poulton
- Laboratory of Host-Pathogen Biology, The Rockefeller University, New York, NY, USA
| | | | - Barbara Bosch
- Laboratory of Host-Pathogen Biology, The Rockefeller University, New York, NY, USA
| | - Robert Landick
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, USA
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, USA
| | - Elizabeth A Campbell
- Laboratory of Molecular Biophysics, The Rockefeller University, New York, NY, USA.
| | - Jeremy M Rock
- Laboratory of Host-Pathogen Biology, The Rockefeller University, New York, NY, USA.
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Brunner VM, Fowler PW. Compensatory mutations are associated with increased in vitro growth in resistant clinical samples of Mycobacterium tuberculosis. Microb Genom 2024; 10:001187. [PMID: 38315172 PMCID: PMC10926696 DOI: 10.1099/mgen.0.001187] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2023] [Accepted: 01/11/2024] [Indexed: 02/07/2024] Open
Abstract
Mutations in Mycobacterium tuberculosis associated with resistance to antibiotics often come with a fitness cost for the bacteria. Resistance to the first-line drug rifampicin leads to lower competitive fitness of M. tuberculosis populations when compared to susceptible populations. This fitness cost, introduced by resistance mutations in the RNA polymerase, can be alleviated by compensatory mutations (CMs) in other regions of the affected protein. CMs are of particular interest clinically since they could lock in resistance mutations, encouraging the spread of resistant strains worldwide. Here, we report the statistical inference of a comprehensive set of CMs in the RNA polymerase of M. tuberculosis, using over 70 000 M. tuberculosis genomes that were collated as part of the CRyPTIC project. The unprecedented size of this data set gave the statistical tests more power to investigate the association of putative CMs with resistance-conferring mutations. Overall, we propose 51 high-confidence CMs by means of statistical association testing and suggest hypotheses for how they exert their compensatory mechanism by mapping them onto the protein structure. In addition, we were able to show an association of CMs with higher in vitro growth densities, and hence presumably with higher fitness, in resistant samples in the more virulent M. tuberculosis lineage 2. Our results suggest the association of CM presence with significantly higher in vitro growth than for wild-type samples, although this association is confounded with lineage and sub-lineage affiliation. Our findings emphasize the integral role of CMs and lineage affiliation in resistance spread and increases the urgency of antibiotic stewardship, which implies accurate, cheap and widely accessible diagnostics for M. tuberculosis infections to not only improve patient outcomes but also prevent the spread of resistant strains.
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Affiliation(s)
| | - Philip W. Fowler
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
- National Institute of Health Research Oxford Biomedical Research Centre, John Radcliffe Hospital, Headley Way, Oxford, UK
- Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, University of Oxford, Oxford, UK
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Dorji T, Horan K, Sherry NL, Tay EL, Globan M, Viberg L, Bond K, Denholm JT, Howden BP, Andersson P. Whole genome sequencing of drug-resistant Mycobacterium tuberculosis isolates in Victoria, Australia. Int J Infect Dis 2024; 138:46-53. [PMID: 37967715 DOI: 10.1016/j.ijid.2023.11.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Revised: 10/31/2023] [Accepted: 11/06/2023] [Indexed: 11/17/2023] Open
Abstract
OBJECTIVES Whole genome sequencing (WGS) can identify clusters, transmission patterns, and drug resistance mutations. This is important in low-burden settings such as Australia, as it can assist in efficient contact tracing and surveillance. METHODS We conducted a retrospective cohort study using WGS from 155 genomically defined drug-resistant Mycobacterium tuberculosis (DR-TB) isolates collected between 2018-2021 in Victoria, Australia. Bioinformatic analysis was performed to identify resistance-conferring mutations, lineages, clusters and understand how local sequences compared with international context. RESULTS Of the 155 sequences, 42% were identified as lineage 2 and 35% as lineage 1; 65.8% (102/155) were isoniazid mono-resistant, 8.4% were multi-drug resistant TB and 5.8% were pre-extensively drug-resistant / extensively drug-resistant TB. The most common mutations were observed in katG and fabG1 genes, especially at Ser315Thr and fabG1 -15 C>T for first-line drugs. Ser450Leu was the most frequent mutation in rpoB gene. Phylogenetic analysis confirmed that Victorian DR-TB were associated with importation events. There was little evidence of local transmission with only five isolate pairs. CONCLUSION Isoniazid-resistant TB is the commonest DR-TB in Victoria, and the mutation profile is similar to global circulating DR-TB. Most cases are diagnosed among migrants with limited transmission. This study highlights the value of WGS in identification of clusters and resistance-conferring mutations. This information is crucial in supporting disease mitigation and treatment strategies.
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Affiliation(s)
- Thinley Dorji
- Department of Microbiology and Immunology at The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Australia
| | - Kristy Horan
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology at The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Australia
| | - Norelle L Sherry
- Department of Microbiology and Immunology at The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Australia; Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology at The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Australia
| | - Ee Laine Tay
- Communicable Disease Epidemiology and Surveillance, Health Protection Branch, Public Health Division, Department of Health, Melbourne, Australia
| | - Maria Globan
- Mycobacterium Reference Laboratory, Victorian Infectious Diseases Reference Laboratory, Royal Melbourne Hospital at The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Australia
| | - Linda Viberg
- Mycobacterium Reference Laboratory, Victorian Infectious Diseases Reference Laboratory, Royal Melbourne Hospital at The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Australia
| | - Katherine Bond
- Mycobacterium Reference Laboratory, Victorian Infectious Diseases Reference Laboratory, Royal Melbourne Hospital at The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Australia; Royal Melbourne Hospital, Melbourne, Australia
| | - Justin T Denholm
- Royal Melbourne Hospital, Melbourne, Australia; Victorian Tuberculosis Program. Melbourne Health at the Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Australia; Department of Infectious Diseases at The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Australia
| | - Benjamin P Howden
- Department of Microbiology and Immunology at The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Australia; Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology at The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Australia; Centre for Pathogen Genomics, University of Melbourne, Australia.
| | - Patiyan Andersson
- Department of Microbiology and Immunology at The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Australia; Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology at The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Australia
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Barton A, Colijn C. Genomic, clinical and immunity data join forces for public health. Nat Rev Microbiol 2023; 21:639. [PMID: 37592055 DOI: 10.1038/s41579-023-00965-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/19/2023]
Affiliation(s)
- Amber Barton
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK.
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