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Mokrousov I. Origin and dispersal of the Mycobacterium tuberculosis Haarlem genotype: Clues from its phylogeographic landscape and human migration. Mol Phylogenet Evol 2024; 195:108045. [PMID: 38447923 DOI: 10.1016/j.ympev.2024.108045] [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: 07/11/2023] [Revised: 01/04/2024] [Accepted: 02/27/2024] [Indexed: 03/08/2024]
Abstract
The Haarlem family belongs to the Euro-American phylogenetic lineage of Mycobacterium tuberculosis and is one of the globally spread genotypes of this important human pathogen. In spite of the sporadic observations on drug resistance and peculiar virulence profile, Haarlem remains in the shade of other M. tuberculosis genotypes. I analyzed genotyping data of the Haarlem genotype in light of its pathogenic properties and relevant human migration, to gain insight into its origin, evolutionary history, and current spread. Central Europe is marked with a very high prevalence of both major Haarlem subclades ancestral H3/SIT50 and derived H1, jointly making 33-41% in Czechia, Austria, and Hungary. There is a declining gradient of Haarlem beyond central Europe with 10-18% in Italy, France, Belgium, 10-13% in the Balkan countries and Turkey. Placing the available genetic diversity and ancient DNA data within the historical context, I hypothesize that M. tuberculosis Haarlem genotype likely originated in Central Europe and its primary long-term circulation occurred within the area of the former Austria/Austria-Hungary Empire in the 14th-19th centuries. The genotype is not highly transmissible and its spread was driven by long-term human migration. The European colonial expansion (when accompanied by a sufficient volume of migration) was a vehicle of its secondary dissemination. I conclude that human migration and its lack thereof (but not strain pathobiology) was a major driving force that shaped the population structure of this global lineage of M. tuberculosis. At the same time, Haarlem strains appear over-represented in some ethnic groups which warrants in-depth experimental research.
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Affiliation(s)
- Igor Mokrousov
- Laboratory of Molecular Epidemiology and Evolutionary Genetics, St. Petersburg Pasteur Institute, St. Petersburg 197101, Russia; Henan International Joint Laboratory of Children's Infectious Diseases, Henan Children's Hospital, Children's Hospital, Zhengzhou University, Zhengzhou Children's Hospital, Zhengzhou, China.
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2
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Tomasiunaite U, Kielkowski P, Krafczyk R, Forné I, Imhof A, Jung K. Decrypting the functional design of unmodified translation elongation factor P. Cell Rep 2024; 43:114063. [PMID: 38635400 DOI: 10.1016/j.celrep.2024.114063] [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: 09/20/2023] [Revised: 01/17/2024] [Accepted: 03/21/2024] [Indexed: 04/20/2024] Open
Abstract
Bacteria overcome ribosome stalling by employing translation elongation factor P (EF-P), which requires post-translational modification (PTM) for its full activity. However, EF-Ps of the PGKGP subfamily are unmodified. The mechanism behind the ability to avoid PTM while retaining active EF-P requires further examination. Here, we investigate the design principles governing the functionality of unmodified EF-Ps in Escherichia coli. We screen for naturally unmodified EF-Ps with activity in E. coli and discover that the EF-P from Rhodomicrobium vannielii rescues growth defects of a mutant lacking the modification enzyme EF-P-(R)-β-lysine ligase. We identify amino acids in unmodified EF-P that modulate its activity. Ultimately, we find that substitution of these amino acids in other marginally active EF-Ps of the PGKGP subfamily leads to fully functional variants in E. coli. These results provide strategies to improve heterologous expression of proteins with polyproline motifs in E. coli and give insights into cellular adaptations to optimize protein synthesis.
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Affiliation(s)
- Urte Tomasiunaite
- Faculty of Biology, Microbiology, Ludwig-Maximilians-Universität München, 82152 Martinsried, Germany
| | - Pavel Kielkowski
- Department of Chemistry, Institut für Chemische Epigenetik (ICEM), Ludwig-Maximilians-Universität München, 81375 Munich, Germany
| | - Ralph Krafczyk
- Faculty of Biology, Microbiology, Ludwig-Maximilians-Universität München, 82152 Martinsried, Germany
| | - Ignasi Forné
- Zentrallabor für Proteinanalytik, Biomedical Center Munich, Ludwig-Maximilians-Universität München, 82152 Martinsried, Germany
| | - Axel Imhof
- Zentrallabor für Proteinanalytik, Biomedical Center Munich, Ludwig-Maximilians-Universität München, 82152 Martinsried, Germany
| | - Kirsten Jung
- Faculty of Biology, Microbiology, Ludwig-Maximilians-Universität München, 82152 Martinsried, Germany.
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Painter H, Willcocks S, Zelmer A, Reljic R, Tanner R, Fletcher H. Demonstrating the utility of the ex vivo murine mycobacterial growth inhibition assay (MGIA) for high-throughput screening of tuberculosis vaccine candidates against multiple Mycobacterium tuberculosis complex strains. Tuberculosis (Edinb) 2024; 146:102494. [PMID: 38367368 DOI: 10.1016/j.tube.2024.102494] [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: 12/06/2023] [Revised: 02/05/2024] [Accepted: 02/11/2024] [Indexed: 02/19/2024]
Abstract
Human tuberculosis (TB) is caused by various members of the Mycobacterium tuberculosis (Mtb) complex. Differences in host response to infection have been reported, illustrative of a need to evaluate efficacy of novel vaccine candidates against multiple strains in preclinical studies. We previously showed that the murine lung and spleen direct mycobacterial growth inhibition assay (MGIA) can be used to assess control of ex vivo mycobacterial growth by host cells. The number of mice required for the assay is significantly lower than in vivo studies, facilitating testing of multiple strains and/or the incorporation of other cellular analyses. Here, we provide proof-of-concept that the murine MGIA can be applied to evaluate vaccine-induced protection against multiple Mtb clinical isolates. Using an ancient and modern strain of the Mtb complex, we demonstrate that ex vivo bacillus Calmette-Guérin (BCG)-mediated mycobacterial growth inhibition recapitulates protection observed in the lung and spleen following in vivo infection of mice. Further, we provide the first report of cellular and transcriptional correlates of BCG-induced growth inhibition in the lung MGIA. The ex vivo MGIA represents a promising platform to gain early insight into vaccine performance against a collection of Mtb strains and improve preclinical evaluation of TB vaccine candidates.
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Affiliation(s)
- Hannah Painter
- Department of Infection Biology, London School of Hygiene and Tropical Medicine, Keppel Street, London, WC1E 7HT, UK.
| | - Sam Willcocks
- Department of Infection Biology, London School of Hygiene and Tropical Medicine, Keppel Street, London, WC1E 7HT, UK
| | - Andrea Zelmer
- Department of Infection Biology, London School of Hygiene and Tropical Medicine, Keppel Street, London, WC1E 7HT, UK
| | - Rajko Reljic
- Institute of Infection and Immunity, St George's University of London, Cranmer Terrrace, London, SW17 0RE, UK
| | - Rachel Tanner
- Department of Biology, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford, OX3 7DQ, UK
| | - Helen Fletcher
- Department of Infection Biology, London School of Hygiene and Tropical Medicine, Keppel Street, London, WC1E 7HT, UK
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4
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Hiza H, Zwyer M, Hella J, Arbués A, Sasamalo M, Borrell S, Xu ZM, Ross A, Brites D, Fellay J, Reither K, Gagneux S, Portevin D. Bacterial diversity dominates variable macrophage responses of tuberculosis patients in Tanzania. Sci Rep 2024; 14:9287. [PMID: 38653771 DOI: 10.1038/s41598-024-60001-0] [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: 02/07/2024] [Accepted: 04/17/2024] [Indexed: 04/25/2024] Open
Abstract
The Mycobacterium tuberculosis complex (MTBC) comprises nine human-adapted lineages that differ in their geographical distribution. Local adaptation of specific MTBC genotypes to the respective human host population has been invoked in this context. We aimed to assess if bacterial genetics governs MTBC pathogenesis or if local co-adaptation translates into differential susceptibility of human macrophages to infection by different MTBC genotypes. We generated macrophages from cryopreserved blood mononuclear cells of Tanzanian tuberculosis patients, from which the infecting MTBC strains had previously been phylogenetically characterized. We infected these macrophages ex vivo with a phylogenetically similar MTBC strain ("matched infection") or with strains representative of other MTBC lineages ("mismatched infection"). We found that L1 infections resulted in a significantly lower bacterial burden and that the intra-cellular replication rate of L2 strains was significantly higher compared the other MTBC lineages, irrespective of the MTBC lineage originally infecting the patients. Moreover, L4-infected macrophages released significantly greater amounts of TNF-α, IL-6, IL-10, MIP-1β, and IL-1β compared to macrophages infected by all other strains. While our results revealed no measurable effect of local adaptation, they further highlight the strong impact of MTBC phylogenetic diversity on the variable outcome of the host-pathogen interaction in human tuberculosis.
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Affiliation(s)
- Hellen Hiza
- Swiss Tropical and Public Health Institute, Allschwil, Basel, Switzerland
- University of Basel, Basel, Switzerland
- Ifakara Health Institute, Bagamoyo, Tanzania
| | - Michaela Zwyer
- Swiss Tropical and Public Health Institute, Allschwil, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Jerry Hella
- Swiss Tropical and Public Health Institute, Allschwil, Basel, Switzerland
- University of Basel, Basel, Switzerland
- Ifakara Health Institute, Bagamoyo, Tanzania
| | - Ainhoa Arbués
- Swiss Tropical and Public Health Institute, Allschwil, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Mohamed Sasamalo
- Swiss Tropical and Public Health Institute, Allschwil, Basel, Switzerland
- University of Basel, Basel, Switzerland
- Ifakara Health Institute, Bagamoyo, Tanzania
| | - Sonia Borrell
- Swiss Tropical and Public Health Institute, Allschwil, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Zhi Ming Xu
- School of Life Sciences, Ecole Polytechnique Federale de Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
- Precision Medicine Unit, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Amanda Ross
- Swiss Tropical and Public Health Institute, Allschwil, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Daniela Brites
- Swiss Tropical and Public Health Institute, Allschwil, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Jacques Fellay
- School of Life Sciences, Ecole Polytechnique Federale de Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
- Precision Medicine Unit, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Klaus Reither
- Swiss Tropical and Public Health Institute, Allschwil, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Sébastien Gagneux
- Swiss Tropical and Public Health Institute, Allschwil, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Damien Portevin
- Swiss Tropical and Public Health Institute, Allschwil, Basel, Switzerland.
- University of Basel, Basel, Switzerland.
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Deng L, Wang Q, Liu H, Jiang Y, Xu M, Xiang Y, Yang T, Yang S, Yan D, Li M, Zhao L, Zhao X, Wan K, He G, Mijiti X, Li G. Identification of positively selected genes in Mycobacterium tuberculosis from southern Xinjiang Uygur autonomous region of China. Front Microbiol 2024; 15:1290227. [PMID: 38686109 PMCID: PMC11056549 DOI: 10.3389/fmicb.2024.1290227] [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: 09/07/2023] [Accepted: 03/28/2024] [Indexed: 05/02/2024] Open
Abstract
Background Tuberculosis (TB), mainly caused by Mycobacterium tuberculosis (Mtb), remains a serious public health problem. Increasing evidence supports that selective evolution is an important force affecting genomic determinants of Mtb phenotypes. It is necessary to further understand the Mtb selective evolution and identify the positively selected genes that probably drive the phenotype of Mtb. Methods This study mainly focused on the positive selection of 807 Mtb strains from Southern Xinjiang of China using whole genome sequencing (WGS). PAML software was used for identifying the genes and sites under positive selection in 807 Mtb strains. Results Lineage 2 (62.70%) strains were the dominant strains in this area, followed by lineage 3 (19.45%) and lineage 4 (17.84%) strains. There were 239 codons in 47 genes under positive selection, and the genes were majorly associated with the functions of transcription, defense mechanisms, and cell wall/membrane/envelope biogenesis. There were 28 codons (43 mutations) in eight genes (gyrA, rpoB, rpoC, katG, pncA, embB, gid, and cut1) under positive selection in multi-drug resistance (MDR) strains but not in drug-susceptible (DS) strains, in which 27 mutations were drug-resistant loci, 9 mutations were non-drug-resistant loci but were in drug-resistant genes, 2 mutations were compensatory mutations, and 5 mutations were in unknown drug-resistant gene of cut1. There was a codon in Rv0336 under positive selection in L3 strains but not in L2 and L4 strains. The epitopes of T and B cells were both hyper-conserved, particularly in the T-cell epitopes. Conclusion This study revealed the ongoing selective evolution of Mtb. We found some special genes and sites under positive selection which may contribute to the advantage of MDR and L3 strains. It is necessary to further study these mutations to understand their impact on phenotypes for providing more useful information to develop new TB interventions.
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Affiliation(s)
- Lele Deng
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Quan Wang
- Eighth Affiliated Hospital of Xinjiang Medical University, Urumqi, China
| | - Haican Liu
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Yi Jiang
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Miao Xu
- Eighth Affiliated Hospital of Xinjiang Medical University, Urumqi, China
| | - Yu Xiang
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
- School of Public Health, University of South China, Hengyang, China
| | - Ting Yang
- Eighth Affiliated Hospital of Xinjiang Medical University, Urumqi, China
| | - Shuliu Yang
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
- School of Public Health, University of South China, Hengyang, China
| | - Di Yan
- Eighth Affiliated Hospital of Xinjiang Medical University, Urumqi, China
| | - Machao Li
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Lili Zhao
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Xiuqin Zhao
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Kanglin Wan
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Guangxue He
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Xiaokaiti Mijiti
- Eighth Affiliated Hospital of Xinjiang Medical University, Urumqi, China
| | - Guilian Li
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
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Mvubu NE, Jacoby K. Mycobacterium tuberculosis complex molecular networks and their regulation: Implications of strain heterogeneity on epigenetic diversity and transcriptome regulation. Heliyon 2023; 9:e22611. [PMID: 38046135 PMCID: PMC10686871 DOI: 10.1016/j.heliyon.2023.e22611] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2023] [Revised: 11/13/2023] [Accepted: 11/15/2023] [Indexed: 12/05/2023] Open
Abstract
Tuberculosis has been a public health crisis since the 1900, which has caused the highest mortalities due to a single bacterial infection worldwide, that was recently further complicated by the Coronavirus disease 2019 pandemic. The causative agent of Tuberculosis, Mycobacterium tuberculosis, belongs to a genetically well-characterized family of strains known as the Mycobacterium tuberculosis complex, which has complicated progress made towards eradicating Tuberculosis due to pathogen-specific phenotypic differences in the members of this complex. Mycobacterium tuberculosis complex strains are genetically diverse human- and animal-adapted pathogens belonging to 7 lineages (Indo-Oceanic, East-Asian, East-African Indian, Euro-American, M. africanum West Africa 1, M. africanum West Africa 2 and Ethopia), respectively and the recently identified Lineage 8 and M. africanum Lineage 9. Genomic studies have revealed that Mycobacterium tuberculosis complex members are ∼99 % similar, however, due to selective pressure and adaptation to human host, they are prone to mutations that have resulted in development of drug resistance and phenotypic heterogeneity that impact strain virulence. Furthermore, members of the Mycobacterium tuberculosis complex have preferred geographic locations and possess unique phenotypic characteristics that is linked to their pathogenicity. Due to the recent advances in development next generation sequencing platforms, several studies have revealed epigenetic changes in genomic regions combined with "unique" gene regulatory mechanisms through non-coding RNAs that are responsible for strain-specific behaviour on in vitro and in vivo infection models. The current review provides up to date epigenetic patterns, gene regulation through non-coding RNAs, together with implications of these mechanisms in down-stream proteome and metabolome, which may be responsible for "unique" responses to infection by members of the Mycobacterium tuberculosis complex. Understanding lineage-specific molecular mechanisms during infection may provide novel drug targets and disease control measures towards World Health organization END-TB strategy.
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Affiliation(s)
- Nontobeko Eunice Mvubu
- Medical Microbiology, School of Laboratory Medicine and Medical Sciences, College of Health Sciences, University of KwaZulu-Natal, Durban, 4000, South Africa
| | - Kieran Jacoby
- Medical Microbiology, School of Laboratory Medicine and Medical Sciences, College of Health Sciences, University of KwaZulu-Natal, Durban, 4000, South Africa
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Koleske BN, Jacobs WR, Bishai WR. The Mycobacterium tuberculosis genome at 25 years: lessons and lingering questions. J Clin Invest 2023; 133:e173156. [PMID: 37781921 PMCID: PMC10541200 DOI: 10.1172/jci173156] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/03/2023] Open
Abstract
First achieved in 1998 by Cole et al., the complete genome sequence of Mycobacterium tuberculosis continues to provide an invaluable resource to understand tuberculosis (TB), the leading cause of global infectious disease mortality. At the 25-year anniversary of this accomplishment, we describe how insights gleaned from the M. tuberculosis genome have led to vital tools for TB research, epidemiology, and clinical practice. The increasing accessibility of whole-genome sequencing across research and clinical settings has improved our ability to predict antibacterial susceptibility, to track epidemics at the level of individual outbreaks and wider historical trends, to query the efficacy of the bacille Calmette-Guérin (BCG) vaccine, and to uncover targets for novel antitubercular therapeutics. Likewise, we discuss several recent efforts to extract further discoveries from this powerful resource.
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Affiliation(s)
- Benjamin N. Koleske
- Center for Tuberculosis Research, Department of Medicine, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
| | - William R. Jacobs
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, New York, USA
| | - William R. Bishai
- Center for Tuberculosis Research, Department of Medicine, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
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8
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Mokrousov I, Vinogradova T, Dogonadze M, Zabolotnykh N, Vyazovaya A, Vitovskaya M, Solovieva N, Ariel B. A multifaceted interplay between virulence, drug resistance, and the phylogeographic landscape of Mycobacterium tuberculosis. Microbiol Spectr 2023; 11:e0139223. [PMID: 37768091 PMCID: PMC10581221 DOI: 10.1128/spectrum.01392-23] [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: 03/31/2023] [Accepted: 08/06/2023] [Indexed: 09/29/2023] Open
Abstract
Latin-American Mediterranean (LAM) family is one of the most significant and global genotypes of Mycobacterium tuberculosis. Here, we used the murine model to study the virulence and lethality of the genetically and epidemiologically distinct LAM strains. The pathobiological characteristics of the four LAM strains (three drug resistant and one drug susceptible) and the susceptible reference strain H37Rv were studied in the C57BL/6 mouse model. The whole-genome sequencing was performed using the HiSeq Illumina platform, followed by bioinformatics and phylogenetic analysis. The susceptible strain H37Rv showed the highest virulence. Drug-susceptible LAM strain (spoligotype SIT264) was more virulent than three multidrug-resistant (MDR) strains (SIT252, SIT254, and SIT266). All three MDR isolates were low lethal, while the susceptible isolate and H37Rv were moderately/highly lethal. Putting the genomic, phenotypic, and virulence features of the LAM strains/spoligotypes in the context of their dynamic phylogeography over 20 years reveals three types of relationships between virulence, resistance, and transmission. First, the most virulent and more lethal drug-susceptible SIT264 increased its circulation in parts of Russia. Second, moderately virulent and pre-XDR SIT266 was prevalent in Belarus and continues to be visible in North-West Russia. Third, the low virulent and MDR strain SIT252 previously considered as emerging has disappeared from the population. These findings suggest that strain virulence impacts the transmission, irrespective of drug resistance properties. The increasing circulation of susceptible but more virulent and lethal strains implies that personalized TB treatment should consider not only resistance but also the virulence of the infecting M. tuberculosis strains. IMPORTANCE The study is multidisciplinary and investigates the epidemically/clinically important and global lineage of Mycobacterium tuberculosis, named Latin-American-Mediterranean (LAM), yet insufficiently studied with regard to its pathobiology. We studied different LAM strains (epidemic vs endemic and resistant vs susceptible) in the murine model and using whole-genome analysis. We also collected long-term, 20-year data on their prevalence in Eurasia. The findings are both expected and unexpected. (i) We observe that a drug-susceptible but highly virulent strain increased its prevalence. (ii) By contrast, the multidrug-resistant (MDR) but low-virulent, low-lethal strain (that we considered as emerging 15 years ago) has almost disappeared. (iii) Finally, an intermediate case is the MDR strain with moderate virulence that continues to circulate. We conclude that (i) the former and latter strains are the most hazardous and require close epidemiological monitoring, and (ii) personalized TB treatment should consider not only drug resistance but also the virulence of the infecting strains and development of anti-virulence drugs is warranted.
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Affiliation(s)
- Igor Mokrousov
- St. Petersburg Pasteur Institute, St. Petersburg, Russia
| | - Tatiana Vinogradova
- St. Petersburg Pasteur Institute, St. Petersburg, Russia
- St. Petersburg Research Institute of Phthisiopulmonology, St. Petersburg, Russia
| | - Marine Dogonadze
- St. Petersburg Research Institute of Phthisiopulmonology, St. Petersburg, Russia
| | - Natalia Zabolotnykh
- St. Petersburg Research Institute of Phthisiopulmonology, St. Petersburg, Russia
| | - Anna Vyazovaya
- St. Petersburg Pasteur Institute, St. Petersburg, Russia
| | - Maria Vitovskaya
- St. Petersburg Research Institute of Phthisiopulmonology, St. Petersburg, Russia
| | - Natalia Solovieva
- St. Petersburg Research Institute of Phthisiopulmonology, St. Petersburg, Russia
| | - Boris Ariel
- St. Petersburg Research Institute of Phthisiopulmonology, St. Petersburg, Russia
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9
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Du X, Sonawane V, Zhang B, Wang C, de Ruijter B, Dömling ASS, Reiling N, Groves MR. Inhibitors of Aspartate Transcarbamoylase Inhibit Mycobacterium tuberculosis Growth. ChemMedChem 2023; 18:e202300279. [PMID: 37294060 DOI: 10.1002/cmdc.202300279] [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: 05/24/2023] [Revised: 06/07/2023] [Accepted: 06/07/2023] [Indexed: 06/10/2023]
Abstract
Aspartate transcarbamoylase (ATCase) plays a key role in the second step of de novo pyrimidine biosynthesis in eukaryotes and has been proposed to be a target to suppress cell proliferation in E. coli, human cells and the malarial parasite. We hypothesized that a library of ATCase inhibitors developed for malarial ATCase (PfATCase) may also contain inhibitors of the tubercular ATCase and provide a similar inhibition of cellular proliferation. Of the 70 compounds screened, 10 showed single-digit micromolar inhibition in an in vitro activity assay and were tested for their effect on M. tuberculosis cell growth in culture. The most promising compound demonstrated a MIC90 of 4 μM. A model of MtbATCase was generated using the experimental coordinates of PfATCase. In silico docking experiments showed this compound can occupy a similar allosteric pocket on MtbATCase to that seen on PfATCase, explaining the observed species selectivity seen for this compound series.
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Affiliation(s)
- Xiaochen Du
- XB20 Drug Design, Groningen Research Institute of Pharmacy, University of Groningen, A. Deusinglaan 1, Groningen, 9700AV (The, Netherlands
| | - Vidhisha Sonawane
- CATRIN, Department of Innovative Chemistry, PalackȳUniversity, 779 00, Olomouc - Holice, Czech Republic
| | - Bidong Zhang
- XB20 Drug Design, Groningen Research Institute of Pharmacy, University of Groningen, A. Deusinglaan 1, Groningen, 9700AV (The, Netherlands
| | - Chao Wang
- XB20 Drug Design, Groningen Research Institute of Pharmacy, University of Groningen, A. Deusinglaan 1, Groningen, 9700AV (The, Netherlands
| | - Bram de Ruijter
- XB20 Drug Design, Groningen Research Institute of Pharmacy, University of Groningen, A. Deusinglaan 1, Groningen, 9700AV (The, Netherlands
| | - Alexander S S Dömling
- XB20 Drug Design, Groningen Research Institute of Pharmacy, University of Groningen, A. Deusinglaan 1, Groningen, 9700AV (The, Netherlands
- CATRIN, Department of Innovative Chemistry, PalackȳUniversity, 779 00, Olomouc - Holice, Czech Republic
| | - Norbert Reiling
- RG Microbial Interface Biology, Research Center Borstel Leibniz Lung Center, Parkallee 1-40, Borstel, 23845, Sülfeld, Germany
- German Center for Infection Research (DZIF), Partner Site Hamburg-Lübeck-Borstel-Riems Borstel, 23845, Greifswald, Germany
| | - Matthew R Groves
- XB20 Drug Design, Groningen Research Institute of Pharmacy, University of Groningen, A. Deusinglaan 1, Groningen, 9700AV (The, Netherlands
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10
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Rollo RF, Mori G, Hill TA, Hillemann D, Niemann S, Homolka S, Fairlie DP, Blumenthal A. Wollamide Cyclic Hexapeptides Synergize with Established and New Tuberculosis Antibiotics in Targeting Mycobacterium tuberculosis. Microbiol Spectr 2023; 11:e0046523. [PMID: 37289062 PMCID: PMC10433873 DOI: 10.1128/spectrum.00465-23] [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: 02/01/2023] [Accepted: 05/11/2023] [Indexed: 06/09/2023] Open
Abstract
Shorter and more effective treatment regimens as well as new drugs are urgent priorities for reducing the immense global burden of tuberculosis (TB). As treatment of TB currently requires multiple antibiotics with diverse mechanisms of action, any new drug lead requires assessment of potential interactions with existing TB antibiotics. We previously described the discovery of wollamides, a new class of Streptomyces-derived cyclic hexapeptides with antimycobacterial activity. To further assess the value of the wollamide pharmacophore as an antimycobacterial lead, we determined wollamide interactions with first- and second-line TB antibiotics by determining fractional inhibitory combination index and zero interaction potency scores. In vitro two-way and multiway interaction analyses revealed that wollamide B1 synergizes with ethambutol, pretomanid, delamanid, and para-aminosalicylic acid in inhibiting the replication and promoting the killing of phylogenetically diverse clinical and reference strains of the Mycobacterium tuberculosis complex (MTBC). Wollamide B1 antimycobacterial activity was not compromised in multi- and extensively drug-resistant MTBC strains. Moreover, growth-inhibitory antimycobacterial activity of the combination of bedaquiline/pretomanid/linezolid was further enhanced by wollamide B1, and wollamide B1 did not compromise the antimycobacterial activity of the isoniazid/rifampicin/ethambutol combination. Collectively, these findings add new dimensions to the desirable characteristics of the wollamide pharmacophore as an antimycobacterial lead compound. IMPORTANCE Tuberculosis (TB) is an infectious disease that affects millions of people globally, with 1.6 million deaths annually. TB treatment requires combinations of multiple different antibiotics for many months, and toxic side effects can occur. Therefore, shorter, safer, more effective TB therapies are required, and these should ideally also be effective against drug-resistant strains of the bacteria that cause TB. This study shows that wollamide B1, a chemically optimized member of a new class of antibacterial compounds, inhibits the growth of drug-sensitive as well as multidrug-resistant Mycobacterium tuberculosis isolated from TB patients. In combination with TB antibiotics, wollamide B1 synergistically enhances the activity of several antibiotics, including complex drug combinations that are currently used for TB treatment. These new insights expand the catalogue of the desirable characteristics of wollamide B1 as an antimycobacterial lead compound that might inspire the development of improved TB treatments.
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Affiliation(s)
- Rachel F. Rollo
- Frazer Institute, The University of Queensland, Brisbane, Queensland, Australia
| | - Giorgia Mori
- Frazer Institute, The University of Queensland, Brisbane, Queensland, Australia
| | - Timothy A. Hill
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia
| | - Doris Hillemann
- National and WHO Supranational Reference Center for Mycobacteria, Research Center Borstel, Leibniz Lung Center, Borstel, Germany
| | - Stefan Niemann
- Molecular and Experimental Mycobacteriology, Priority Area Infections, Research Center Borstel, Leibniz Lung Center, Borstel, Germany
- German Center for Infection Research (DZIF), Partner Site Hamburg-Lübeck-Borstel-Riems, Borstel, Germany
| | - Susanne Homolka
- Molecular and Experimental Mycobacteriology, Priority Area Infections, Research Center Borstel, Leibniz Lung Center, Borstel, Germany
| | - David P. Fairlie
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia
| | - Antje Blumenthal
- Frazer Institute, The University of Queensland, Brisbane, Queensland, Australia
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Bakuła Z, Marczak M, Bluszcz A, Proboszcz M, Kościuch J, Krenke R, Stakėnas P, Mokrousov I, Jagielski T. Phylogenetic relationships of Mycobacterium tuberculosis isolates in Poland: The emergence of Beijing genotype among multidrug-resistant cases. Front Cell Infect Microbiol 2023; 13:1161905. [PMID: 37009494 PMCID: PMC10061152 DOI: 10.3389/fcimb.2023.1161905] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Accepted: 02/28/2023] [Indexed: 03/18/2023] Open
Abstract
IntroductionThe epidemiological situation of tuberculosis (TB) in Poland urges for its continuous and scrupulous monitoring. The objective of this study was to explore the genetic diversity of multidrug-resistant (MDR) and drug-susceptible (DS) Mycobacterium tuberculosis isolates from Poland with a combination of spoligotyping and high-resolution mycobacterial interspersed repetitive unit-variable number tandem repeat (MIRU-VNTR) analysis. The results were placed in the Northern and Eastern Europe context.MethodsThe study included 89 (39 MDR and 50 DS) M. tuberculosis isolates collected from as many patients between 2018 and 2021 in Poland. The analysis was done using spoligotyping, and MIRU-VNTR typing at 24 standard loci. The data were compared to those available on Poland and neighbors and global M. tuberculosis datasets.ResultsThe main identified families were Beijing (28.1%) and Haarlem (16.8%) while 34.8% of isolates were in the heterogeneous L4-unclassified group. Although the Beijing family was the most prevalent (61.5%) among MDR-TB cases, it accounted for only 2% of DS isolates. Among foreign-born patients, a higher ratio of MDR isolates were observed when compared with those who Poland-born (64.3% vs. 40%). Furthermore, all patients from the Former Soviet Union (FSU) countries were infected with MDR-TB.DiscussionWhereas DS M. tuberculosis population in Poland is dominated by L4 isolates, MDR isolates are mostly of the Beijing genotype. The rise in the prevalence of the Beijing isolates in Poland, coupled with high proportion of the Beijing genotype among foreign-born TB patients may reflect an ongoing transmission of this family, imported to Poland mainly from FSU countries.
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Affiliation(s)
- Zofia Bakuła
- Department of Medical Microbiology, Institute of Microbiology, University of Warsaw, Faculty of Biology, Warsaw, Poland
| | - Mateusz Marczak
- Department of Medical Microbiology, Institute of Microbiology, University of Warsaw, Faculty of Biology, Warsaw, Poland
| | - Agata Bluszcz
- Department of Medical Microbiology, Institute of Microbiology, University of Warsaw, Faculty of Biology, Warsaw, Poland
| | - Małgorzata Proboszcz
- Department of Internal Medicine, Pulmonary Diseases & Allergy, Medical University of Warsaw, Warsaw, Poland
| | - Justyna Kościuch
- Department of Internal Medicine, Pulmonary Diseases & Allergy, Medical University of Warsaw, Warsaw, Poland
| | - Rafał Krenke
- Department of Internal Medicine, Pulmonary Diseases & Allergy, Medical University of Warsaw, Warsaw, Poland
| | - Petras Stakėnas
- Department of Immunology and Cell Biology, Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Igor Mokrousov
- Laboratory of Molecular Epidemiology and Evolutionary Genetics, St. Petersburg Pasteur Institute, St. Petersburg, Russia
- Henan International Joint Laboratory of Children’s Infectious Diseases, Henan Children’s Hospital, Zhengzhou Children’s Hospital, Zhengzhou, China
- *Correspondence: Tomasz Jagielski, ; Igor Mokrousov,
| | - Tomasz Jagielski
- Department of Medical Microbiology, Institute of Microbiology, University of Warsaw, Faculty of Biology, Warsaw, Poland
- *Correspondence: Tomasz Jagielski, ; Igor Mokrousov,
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Omics analysis of Mycobacterium tuberculosis isolates uncovers Rv3094c, an ethionamide metabolism-associated gene. Commun Biol 2023; 6:156. [PMID: 36750726 PMCID: PMC9904262 DOI: 10.1038/s42003-023-04433-w] [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: 06/09/2021] [Accepted: 01/05/2023] [Indexed: 02/09/2023] Open
Abstract
Global control of the tuberculosis epidemic is threatened by increasing prevalence of drug resistant M. tuberculosis isolates. Many genome-wide studies focus on SNP-associated drug resistance mechanisms, but drug resistance in 5-30% of M. tuberculosis isolates (varying with antibiotic) appears unrelated to reported SNPs, and alternative drug resistance mechanisms involving variation in gene/protein expression are not well-studied. Here, using an omics approach, we identify 388 genes with lineage-related differential expression and 68 candidate drug resistance-associated gene pairs/clusters in 11 M. tuberculosis isolates (variable lineage/drug resistance profiles). Structural, mutagenesis, biochemical and bioinformatic studies on Rv3094c from the Rv3093c-Rv3095 gene cluster, a gene cluster selected for further investigation as it contains a putative monooxygenase/repressor pair and is associated with ethionamide resistance, provide insights on its involvement in ethionamide sulfoxidation, the initial step in its activation. Analysis of the structure of Rv3094c and its complex with ethionamide and flavin mononucleotide, to the best of our knowledge the first structures of an enzyme involved in ethionamide activation, identify key residues in the flavin mononucleotide and ethionamide binding pockets of Rv3094c, and F221, a gate between flavin mononucleotide and ethionamide allowing their interaction to complete the sulfoxidation reaction. Our work broadens understanding of both lineage- and drug resistance-associated gene/protein expression perturbations and identifies another player in mycobacterial ethionamide metabolism.
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Farzand R, Haigh RD, Monk P, Haldar P, Patel H, Pareek M, Verma R, Barer MR, Woltmann G, Ahyow L, Jagatia H, Decker J, Mukamolova GV, Cooper AM, Garton NJ, O’Hare HM. A Persistent Tuberculosis Outbreak in the UK Is Characterized by Hydrophobic fadB4-Deficient Mycobacterium tuberculosis That Replicates Rapidly in Macrophages. mBio 2022; 13:e0265622. [PMID: 36374090 PMCID: PMC9765663 DOI: 10.1128/mbio.02656-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
The genetic diversity of Mycobacterium tuberculosis can influence disease severity and transmissibility. To better understand how this diversity influences individuals and communities, we phenotyped M. tuberculosis that was causing a persistent outbreak in the East Midlands, United Kingdom. Compared to nonoutbreak isolates, bacilli had higher lipid contents and more hydrophobic cell surfaces. In macrophage infection models, the bacteria increased more rapidly, provoked the enhanced accumulation of macrophage lipid droplets and enhanced the secretion of IL-1β. Natural deletions in fadB4, nrdB, and plcC distinguished the outbreak isolates from other lineage 3 isolates in the region. fadB4 is annotated with a putative role in cell envelope biosynthesis, so the loss of this gene has the potential to alter the interactions of bacteria with immune cells. Reintroduction of fadB4 to the outbreak strain led to a phenotype that more closely resembled those of nonoutbreak strains. The improved understanding of the microbiological characteristics and the corresponding genetic polymorphisms that associate with outbreaks have the potential to inform tuberculosis control. IMPORTANCE Tuberculosis (TB) killed 1.5 million people in 2020 and affects every country. The extent to which the natural genetic diversity of Mycobacterium tuberculosis influences disease manifestation at both the individual and epidemiological levels remains poorly understood. Insights into how pathogen polymorphisms affect patterns of TB have the potential to translate into clinical and public health practice. Two distinct lineage 3 strains isolated from local TB outbreaks, one of which (CH) was rapidly terminated and the other of which (Lro) persistently transmitted for over a decade, provided us with an opportunity to study these issues. We compared genome sequences, microbiological characteristics, and early immune responses that were evoked upon infection. Our results indicate that the natural lack of fadB4 in the Lro strain contributes to its unique features.
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Affiliation(s)
- Robeena Farzand
- Leicester TB Research Group, Department of Respiratory Sciences, University of Leicestergrid.9918.9, Leicester, UK
| | - Richard D. Haigh
- Leicester TB Research Group, Department of Respiratory Sciences, University of Leicestergrid.9918.9, Leicester, UK
| | - Philip Monk
- Public Health England, Department of Health and Social Care in England, Government Agency, East Midlands, UK
| | - Pranabashis Haldar
- Leicester TB Research Group, Department of Respiratory Sciences, University of Leicestergrid.9918.9, Leicester, UK
| | - Hemu Patel
- Leicester TB Research Group, Department of Respiratory Sciences, University of Leicestergrid.9918.9, Leicester, UK
- University Hospitals Leicester NHS Trust, University of Leicestergrid.9918.9, Leicester, UK
| | - Manish Pareek
- Leicester TB Research Group, Department of Respiratory Sciences, University of Leicestergrid.9918.9, Leicester, UK
- University Hospitals Leicester NHS Trust, University of Leicestergrid.9918.9, Leicester, UK
| | - Raman Verma
- Leicester TB Research Group, Department of Respiratory Sciences, University of Leicestergrid.9918.9, Leicester, UK
- University Hospitals Leicester NHS Trust, University of Leicestergrid.9918.9, Leicester, UK
| | - Michael R. Barer
- Leicester TB Research Group, Department of Respiratory Sciences, University of Leicestergrid.9918.9, Leicester, UK
| | - Gerrit Woltmann
- Leicester TB Research Group, Department of Respiratory Sciences, University of Leicestergrid.9918.9, Leicester, UK
- University Hospitals Leicester NHS Trust, University of Leicestergrid.9918.9, Leicester, UK
| | - Lauren Ahyow
- National TB Unit, UK Health Security Agency, Government Agency, London, UK
| | - Heena Jagatia
- Leicester TB Research Group, Department of Respiratory Sciences, University of Leicestergrid.9918.9, Leicester, UK
| | - Jonathan Decker
- Leicester TB Research Group, Department of Respiratory Sciences, University of Leicestergrid.9918.9, Leicester, UK
| | - Galina V. Mukamolova
- Leicester TB Research Group, Department of Respiratory Sciences, University of Leicestergrid.9918.9, Leicester, UK
| | - Andrea M. Cooper
- Leicester TB Research Group, Department of Respiratory Sciences, University of Leicestergrid.9918.9, Leicester, UK
| | - Natalie J. Garton
- Leicester TB Research Group, Department of Respiratory Sciences, University of Leicestergrid.9918.9, Leicester, UK
| | - Helen M. O’Hare
- Leicester TB Research Group, Department of Respiratory Sciences, University of Leicestergrid.9918.9, Leicester, UK
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Liang C, Li X, Li Q, Zhang X, Ren W, Yao C, Pang Y, Liu Y, Li C, Tang S. Clinical isolates of Mycobacterium tuberculosis with different genotypes exhibit distinct host macrophage responses in vitro. J Med Microbiol 2022; 71. [PMID: 36748527 DOI: 10.1099/jmm.0.001604] [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] [Indexed: 11/29/2022] Open
Abstract
Introduction. Mycobacterium tuberculosis (M.tb), the causative agent of tuberculosis, can survive as an intracellular parasite after entering macrophages via phagocytosis. M.tb strains are genotypically distinct and engage in diverse pathogen-host interactions, with different host immune responses triggered by different M.tb strains. Importantly, differences in intracellular accumulation and triggering of host macrophage responses during early infection stages are key determinants that shape the final outcomes of host innate immune responses to different M.tb strains.Hypothesis/Gap Statement. Clinical M.tb strains with different genotypes elicit different host innate immune responses in vitro.Aim. This work aimed to compare host innate immune responses elicited by genotypically diverse, clinically derived M.tb strains in vitro.Methodology. RAW264.7 cells were infected with three lineage 2 and lineage 4 clinically derived M.tb strains and strain H37Rv. Strains were evaluated for differences in intracellular growth, induction of macrophage apoptosis, and induction of expression of proinflammatory cytokines and associated pattern recognition receptors.Results. Highly variable cytokine profiles were observed subsequent to RAW264.7 cell infection with the different strains. The Beijing genotype strain, a modern Beijing strain belonging to lineage 2, induced milder host proinflammatory responses and less apoptosis and exhibited greater intracellular growth as compared to the other strains. Moreover, mRNA expression levels of iNOS in Beijing and MANU2 genotype strains exceeded corresponding levels obtained for the T1 genotype strain. Meanwhile, mRNA expression levels of toll-like receptor (TLR)-encoding genes TLR2 and TLR7 in macrophages infected with the Beijing genotype strain were higher than corresponding levels observed in MANU2 genotype strain-infected macrophages.Conclusion. The higher intracellular survival rate and lower level of host cell apoptosis associated with macrophage infection with the Beijing genotype strain indicated greater virulence of this strain relative to that of the other strains. Furthermore, in vitro immune responses induced by the Beijing genotype strain were unique in that this strain induced a weaker inflammatory response than was induced by T1 or MANU2 genotype strains. Nevertheless, additional evidence is needed to confirm that Beijing genotype strains possess greater virulence than strains with other genotypes.
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Affiliation(s)
- Chen Liang
- Department of Bacteriology and Immunology, Beijing Key Laboratory on Drug-Resistant Tuberculosis Research, Beijing Chest Hospital, Capital Medical University & Beijing Tuberculosis and Thoracic Tumor Research Institute, Tongzhou District, Beijing, 101149, PR China
| | - Xiaomeng Li
- Department of Bacteriology and Immunology, Beijing Key Laboratory on Drug-Resistant Tuberculosis Research, Beijing Chest Hospital, Capital Medical University & Beijing Tuberculosis and Thoracic Tumor Research Institute, Tongzhou District, Beijing, 101149, PR China
| | - Qiao Li
- Department of Bacteriology and Immunology, Beijing Key Laboratory on Drug-Resistant Tuberculosis Research, Beijing Chest Hospital, Capital Medical University & Beijing Tuberculosis and Thoracic Tumor Research Institute, Tongzhou District, Beijing, 101149, PR China
| | - Xuxia Zhang
- Department of Bacteriology and Immunology, Beijing Key Laboratory on Drug-Resistant Tuberculosis Research, Beijing Chest Hospital, Capital Medical University & Beijing Tuberculosis and Thoracic Tumor Research Institute, Tongzhou District, Beijing, 101149, PR China
| | - Weicong Ren
- Department of Bacteriology and Immunology, Beijing Key Laboratory on Drug-Resistant Tuberculosis Research, Beijing Chest Hospital, Capital Medical University & Beijing Tuberculosis and Thoracic Tumor Research Institute, Tongzhou District, Beijing, 101149, PR China
| | - Cong Yao
- Department of Bacteriology and Immunology, Beijing Key Laboratory on Drug-Resistant Tuberculosis Research, Beijing Chest Hospital, Capital Medical University & Beijing Tuberculosis and Thoracic Tumor Research Institute, Tongzhou District, Beijing, 101149, PR China
| | - Yu Pang
- Department of Bacteriology and Immunology, Beijing Key Laboratory on Drug-Resistant Tuberculosis Research, Beijing Chest Hospital, Capital Medical University & Beijing Tuberculosis and Thoracic Tumor Research Institute, Tongzhou District, Beijing, 101149, PR China
| | - Yi Liu
- Department of Bacteriology and Immunology, Beijing Key Laboratory on Drug-Resistant Tuberculosis Research, Beijing Chest Hospital, Capital Medical University & Beijing Tuberculosis and Thoracic Tumor Research Institute, Tongzhou District, Beijing, 101149, PR China
| | - Chuanyou Li
- Department of Bacteriology and Immunology, Beijing Key Laboratory on Drug-Resistant Tuberculosis Research, Beijing Chest Hospital, Capital Medical University & Beijing Tuberculosis and Thoracic Tumor Research Institute, Tongzhou District, Beijing, 101149, PR China
- Department of Tuberculosis, Beijing Center for Tuberculosis Research and Control, Beijing Center for Disease Prevention and Control, Xicheng District, Beijing 100035, PR China
| | - Shenjie Tang
- Tuberculosis Clinical Medical Center, Beijing Chest Hospital, Capital Medical University & Beijing Tuberculosis and Thoracic Tumor Research Institute, Tongzhou District, Beijing, 101149, PR China
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Rapid Identification of Drug Resistance and Phylogeny in M. tuberculosis, Directly from Sputum Samples. Microbiol Spectr 2022; 10:e0125222. [PMID: 36102651 PMCID: PMC9602270 DOI: 10.1128/spectrum.01252-22] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Tuberculosis (TB) remains one of the most important infectious diseases globally. Establishing a resistance profile from the initial TB diagnosis is a priority. Rapid molecular tests evaluate only the most common genetic variants responsible for resistance to certain drugs, and Whole Genome Sequencing (WGS) needs culture prior to next-generation sequencing (NGS), limiting their clinical value. Targeted sequencing (TS) from clinical samples avoids these drawbacks, providing a signature of genetic markers that can be associated with drug resistance and phylogeny. In this study, a proof-of-concept protocol was developed for detecting genomic variants associated with drug resistance and for the phylogenetic classification of Mycobacterium Tuberculosis (Mtb) in sputum samples. Initially, a set of Mtb reference strains from the WHO were sequenced (WGS and TS). The results from the protocol agreed >95% with WHO reported data and phenotypic drug susceptibility testing (pDST). Lineage genetics results were 100% concordant with those derived from WGS. After that, the TS protocol was applied to sputum samples from TB patients to detect resistance to first- and second-line drugs and derive phylogeny. The accuracy was >90% for all evaluated drugs, except Eto/Pto (77.8%), and 100% were phylogenetically classified. The results indicate that the described protocol, which affords the complete drug resistance profile and phylogeny of Mtb from sputum, could be useful in the clinical area, advancing toward more personalized and more effective treatments in the near future. IMPORTANCE The COVID-19 pandemic negatively affected the progress in accessing essential Tuberculosis (TB) services and reducing the burden of TB disease, resulting in a decreased detection of new cases and increased deaths. Generating molecular diagnostic tests with faster results without losing reliability is considered a priority. Specifically, developing an antimicrobial resistance profile from the initial stages of TB diagnosis is essential to ensure appropriate treatment. Currently available rapid molecular tests evaluate only the most common genetic variants responsible for resistance to certain drugs, limiting their clinical value. In this work, targeted sequencing on sputum samples from TB patients was used to identify Mycobacterium tuberculosis mutations in genes associated with drug resistance and to derive a phylogeny of the infecting strain. This protocol constitutes a proof-of-concept toward the goal of helping clinicians select a timely and appropriate treatment by providing them with actionable information beyond current molecular approaches.
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Quantitative Systems Pharmacology Modeling Framework of Autophagy in Tuberculosis: Application to Adjunctive Metformin Host-Directed Therapy. Antimicrob Agents Chemother 2022; 66:e0036622. [PMID: 35862740 PMCID: PMC9380544 DOI: 10.1128/aac.00366-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
Quantitative systems pharmacology (QSP) modeling of the host immune response against Mycobacterium tuberculosis can inform the rational design of host-directed therapies (HDTs). We aimed to develop a QSP framework to evaluate the effects of metformin-associated autophagy induction in combination with antibiotics. A QSP framework for autophagy was developed by extending a model for host immune response to include adenosine monophosphate-activated protein kinase (AMPK)-mTOR-autophagy signaling. This model was combined with pharmacokinetic-pharmacodynamic models for metformin and antibiotics against M. tuberculosis. We compared the model predictions to mice infection experiments and derived predictions for the pathogen- and host-associated dynamics in humans treated with metformin in combination with antibiotics. The model adequately captured the observed bacterial load dynamics in mice M. tuberculosis infection models treated with metformin. Simulations for adjunctive metformin therapy in newly diagnosed patients suggested a limited yet dose-dependent effect of metformin on reduction of the intracellular bacterial load when the overall bacterial load is low, late during antibiotic treatment. We present the first QSP framework for HDTs against M. tuberculosis, linking cellular-level autophagy effects to disease progression and adjunctive HDT treatment response. This framework may be extended to guide the design of HDTs against M. tuberculosis.
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Gómez-González PJ, Campino S, Phelan JE, Clark TG. Portable sequencing of Mycobacterium tuberculosis for clinical and epidemiological applications. Brief Bioinform 2022; 23:6650479. [PMID: 35894606 PMCID: PMC9487601 DOI: 10.1093/bib/bbac256] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Revised: 05/23/2022] [Accepted: 06/01/2022] [Indexed: 11/14/2022] Open
Abstract
With >1 million associated deaths in 2020, human tuberculosis (TB) caused by the bacteria Mycobacterium tuberculosis remains one of the deadliest infectious diseases. A plethora of genomic tools and bioinformatics pipelines have become available in recent years to assist the whole genome sequencing of M. tuberculosis. The Oxford Nanopore Technologies (ONT) portable sequencer is a promising platform for cost-effective application in clinics, including personalizing treatment through detection of drug resistance-associated mutations, or in the field, to assist epidemiological and transmission investigations. In this study, we performed a comparison of 10 clinical isolates with DNA sequenced on both long-read ONT and (gold standard) short-read Illumina HiSeq platforms. Our analysis demonstrates the robustness of the ONT variant calling for single nucleotide polymorphisms, despite the high error rate. Moreover, because of improved coverage in repetitive regions where short sequencing reads fail to align accurately, ONT data analysis can incorporate additional regions of the genome usually excluded (e.g. pe/ppe genes). The resulting extra resolution can improve the characterization of transmission clusters and dynamics based on inferring closely related isolates. High concordance in variants in loci associated with drug resistance supports its use for the rapid detection of resistant mutations. Overall, ONT sequencing is a promising tool for TB genomic investigations, particularly to inform clinical and surveillance decision-making to reduce the disease burden.
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Affiliation(s)
- Paula J Gómez-González
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, WC1E 7HT London, UK
| | - Susana Campino
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, WC1E 7HT London, UK
| | - Jody E Phelan
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, WC1E 7HT London, UK
| | - Taane G Clark
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, WC1E 7HT London, UK.,Faculty of Epidemiology and Population Health, London School of Hygiene & Tropical Medicine, WC1E 7HT London, UK
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18
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Lipobiotin-capture magnetic bead assay for isolation, enrichment and detection of Mycobacterium tuberculosis from saliva. PLoS One 2022; 17:e0265554. [PMID: 35839162 PMCID: PMC9286268 DOI: 10.1371/journal.pone.0265554] [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: 03/02/2022] [Accepted: 05/01/2022] [Indexed: 11/19/2022] Open
Abstract
Background
Pulmonary Tuberculosis (TB) is diagnosed through sputum samples. As sputum sampling is challenging in children and cachexic patients, the development of diagnostic tests using saliva appears promising but has been discouraged due to low bacterial load and poor sensitivity. Here, we present a novel and rapid method to enrich Mycobacterium tuberculosis (Mtb) from saliva, which may serve as a basis for a diagnostic saliva test.
Methods
Lipobiotin-functionalized magnetic beads (LMBs) were incubated with Mtb-spiked PBS and saliva from healthy donors as well as with saliva from TB patients. Flow cytometry was used to evaluate the capacity of the beads to bind Mtb, while real-time quantitative polymerase chain reaction (qPCR) was utilized to detect Mtb and determine the amount of mycobacterial DNA in different sample types.
Results
We found that LMBs bind Mtb efficiently when compared to non-functionalized beads. The development of an qPCR assay based on the use of LMBs (LMB assay) allowed us to enrich mycobacterial DNA in spiked sample types, including PBS and saliva from healthy donors (enrichment of up to ~8.7 fold). In Mtb-spiked saliva samples, we found that the LMB assay improved the detection rate of 102 bacteria in a volume of 5 ml from 0 out of 15 (0%) to 6 out of 15 (40%). Consistent with that, the LMB assay increased the rate of correctly identified saliva samples from TB patients in two independent cohorts.
Conclusions
Implementation of the principle of the LMB-based assay may improve the sensitivity of existing diagnostic techniques, e.g. by functionalizing materials that facilitate Mtb sampling from the oral cavity.
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Molina-Torres CA, Quinn FD, Castro-Garza J, Gómez-Velasco A, Ocampo-Candiani J, Bencomo-Alerm A, Sánchez-Pérez HJ, Muñoz-Jiménez S, Rendón A, Ansari A, Sharma M, Singh P, Vera-Cabrera L. Genetic Diversity of Mycobacterium tuberculosis Isolates From an Amerindian Population in Chiapas, México. Front Cell Infect Microbiol 2022; 12:875909. [PMID: 35909960 PMCID: PMC9326120 DOI: 10.3389/fcimb.2022.875909] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Accepted: 06/13/2022] [Indexed: 11/13/2022] Open
Abstract
This is the first report of the genetic diversity of the Mycobacterium tuberculosis complex isolates found in a Mexican-Amerindian setting. In this study, we analyzed isolates collected from the Highlands region of Chiapas, Mexico, by using spoligotyping and whole-genome sequencing analyses. Seventy-three M. tuberculosis isolates were analyzed initially by spoligotyping; no new spoligotypes were identified. Nineteen percent of the isolates were identified as SIT53 (T1) (n = 14), followed by SIT42 (14%, n = 10, LAM9) and SIT119 (11%; n = 8, X1). SIT53, SIT42, and orphan isolates (16.4%, n = 12) constituted about 50% of the isolates studied and were subjected to whole-genome sequencing (WGS) analysis. Most SIT53 (10/12) isolates belonged to the Euro-American sub-lineage 4.8. Most SIT42 isolates (4/7) as .well as most orphan isolates (5/8) belonged to the lineage 4.3.3 LAM group. By comparing the single-nucleotide polymorphism (SNP) patterns of the SIT53 isolates, we found one clone (<7 SNPs) and four clustered isolates (<15 SNPs). In isolates from the SIT42 and orphan groups, we did not find any clones or clusters. This work demonstrates the success of sub-lineage 4.8 to predominate in Mexico and confirms the dominion of sub-lineage 4.3.3 in Central and South America.
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Affiliation(s)
- Carmen A. Molina-Torres
- Laboratorio Interdisciplinario de Investigación Dermatológica, Servicio de Dermatología, Hospital Universitario, Universidad Autónoma de Nuevo León, Monterrey, Mexico
| | - Frederick D. Quinn
- Department of Infectious Diseases, College of Veterinary Medicine, University of Georgia, Athens, GA, United States
| | - Jorge Castro-Garza
- Centro de Investigación Biomédica del Noreste, Instituto Mexicano del Seguro Social, Monterrey, Mexico
| | - Anaximandro Gómez-Velasco
- Departamento de Ecología Humana, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (Cinvestav), Unidad Mérida, Mérida, Mexico
| | - Jorge Ocampo-Candiani
- Laboratorio Interdisciplinario de Investigación Dermatológica, Servicio de Dermatología, Hospital Universitario, Universidad Autónoma de Nuevo León, Monterrey, Mexico
| | - Alied Bencomo-Alerm
- Laboratorio de Micobacterias, Programa de Prevención y Control de la Tuberculosis, región Altos de Chiapas, Instituto de Salud del Estado de Chiapas, Secretaría de Salud (SSA), San Cristóbal de Las Casas, Mexico
| | | | - Sergio Muñoz-Jiménez
- Laboratorio de Micobacterias, Programa de Prevención y Control de la Tuberculosis, región Altos de Chiapas, Instituto de Salud del Estado de Chiapas, Secretaría de Salud (SSA), San Cristóbal de Las Casas, Mexico
| | - Adrián Rendón
- Centro de Investigación, Prevención y Tratamiento de Infecciones Respiratorias, Hospital Universitario, Universidad Autónoma de Nuevo León, Monterrey, Mexico
| | - Afzal Ansari
- Microbial Pathogenesis and Genomics Lab, ICMR-National Institute of Research in Tribal Health, Jabalpur, India
| | - Mukul Sharma
- Microbial Pathogenesis and Genomics Lab, ICMR-National Institute of Research in Tribal Health, Jabalpur, India
| | - Pushpendra Singh
- Microbial Pathogenesis and Genomics Lab, ICMR-National Institute of Research in Tribal Health, Jabalpur, India
| | - Lucio Vera-Cabrera
- Laboratorio Interdisciplinario de Investigación Dermatológica, Servicio de Dermatología, Hospital Universitario, Universidad Autónoma de Nuevo León, Monterrey, Mexico
- *Correspondence: Lucio Vera-Cabrera,
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20
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Zha BS, Desvignes L, Fergus TJ, Cornelius A, Cheng TY, Moody DB, Ernst JD. Bacterial Strain-Dependent Dissociation of Cell Recruitment and Cell-to-Cell Spread in Early M. tuberculosis Infection. mBio 2022; 13:e0133222. [PMID: 35695454 PMCID: PMC9239178 DOI: 10.1128/mbio.01332-22] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Accepted: 05/16/2022] [Indexed: 11/20/2022] Open
Abstract
In the initial stage of respiratory infection, Mycobacterium tuberculosis traverses from alveolar macrophages to phenotypically diverse monocyte-derived phagocytes and neutrophils in the lung parenchyma. Here, we compare the in vivo kinetics of early bacterial growth and cell-to-cell spread of two strains of M. tuberculosis: a lineage 2 strain, 4334, and the widely studied lineage 4 strain H37Rv. Using flow cytometry, live cell sorting of phenotypic subsets, and quantitation of bacteria in cells of the distinct subsets, we found that 4334 induces less leukocyte influx into the lungs but demonstrates earlier population expansion and cell-to-cell spread. The earlier spread of 4334 to recruited cells, including monocyte-derived dendritic cells, is accompanied by earlier and greater magnitude of CD4+ T cell activation. The results provide evidence that strain-specific differences in interactions with lung leukocytes can shape adaptive immune responses in vivo. IMPORTANCE Tuberculosis is a leading infectious disease killer worldwide and is caused by Mycobacterium tuberculosis. After exposure to M. tuberculosis, outcomes range from apparent elimination to active disease. Early innate immune responses may contribute to differences in outcomes, yet it is not known how bacterial strains alter the early dynamics of innate immune and T cell responses. We infected mice with distinct strains of M. tuberculosis and discovered striking differences in innate cellular recruitment, cell-to-cell spread of bacteria in the lungs, and kinetics of initiation of antigen-specific CD4 T cell responses. We also found that M. tuberculosis can spread beyond alveolar macrophages even before a large influx of inflammatory cells. These results provide evidence that distinct strains of M. tuberculosis can exhibit differential kinetics in cell-to-cell spread which is not directly linked to early recruitment of phagocytes but is subsequently linked to adaptive immune responses.
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Affiliation(s)
- B. Shoshana Zha
- Division of Pulmonary, Critical Care, Allergy and Sleep Medicine, Department of Medicine, University of California, San Francisco, California, USA
- Division of Experimental Medicine, Department of Medicine, University of California, San Francisco, California, USA
| | - Ludovic Desvignes
- Department of Medicine, New York University School of Medicine, New York, New York, USA
| | - Tawania J. Fergus
- Department of Medicine, New York University School of Medicine, New York, New York, USA
| | - Amber Cornelius
- Department of Medicine, New York University School of Medicine, New York, New York, USA
| | - Tan-Yun Cheng
- Division of Rheumatology, Immunity and Inflammation, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - D. Branch Moody
- Division of Rheumatology, Immunity and Inflammation, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Joel D. Ernst
- Division of Experimental Medicine, Department of Medicine, University of California, San Francisco, California, USA
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21
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Silva ML, Cá B, Osório NS, Rodrigues PNS, Maceiras AR, Saraiva M. Tuberculosis caused by Mycobacterium africanum: Knowns and unknowns. PLoS Pathog 2022; 18:e1010490. [PMID: 35617217 PMCID: PMC9135246 DOI: 10.1371/journal.ppat.1010490] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Tuberculosis (TB), one of the deadliest threats to human health, is mainly caused by 2 highly related and human-adapted bacteria broadly known as Mycobacterium tuberculosis and Mycobacterium africanum. Whereas M. tuberculosis is widely spread, M. africanum is restricted to West Africa, where it remains a significant cause of tuberculosis. Although several differences have been identified between these 2 pathogens, M. africanum remains a lot less studied than M. tuberculosis. Here, we discuss the genetic, phenotypic, and clinical similarities and differences between strains of M. tuberculosis and M. africanum. We also discuss our current knowledge on the immune response to M. africanum and how it possibly articulates with distinct disease progression and with the geographical restriction attributed to this pathogen. Understanding the functional impact of the diversity existing in TB-causing bacteria, as well as incorporating this diversity in TB research, will contribute to the development of better, more specific approaches to tackle TB.
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Affiliation(s)
- Marta L. Silva
- i3S - Instituto de Investigação e Inovação em Saúde, University of Porto, Porto, Portugal
- IBMC - Instituto de Biologia Molecular e Celular, University of Porto, Porto, Portugal
- Doctoral Program in Molecular and Cell Biology, ICBAS - Instituto de Ciências Biomédicas Abel Salazar, University of Porto, Porto, Portugal
| | - Baltazar Cá
- INASA - Instituto Nacional de Saúde Pública da Guiné-Bissau, Bissau, Guinea-Bissau
- Bandim Health Project, Indepth Network, Bissau, Guinea-Bissau
| | - Nuno S. Osório
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Campus Gualtar, Braga, Portugal
- ICVS/3B’s - PT Government Associate Laboratory, Braga/Guimarães, Portugal
| | - Pedro N. S. Rodrigues
- i3S - Instituto de Investigação e Inovação em Saúde, University of Porto, Porto, Portugal
- IBMC - Instituto de Biologia Molecular e Celular, University of Porto, Porto, Portugal
| | - Ana Raquel Maceiras
- i3S - Instituto de Investigação e Inovação em Saúde, University of Porto, Porto, Portugal
- IBMC - Instituto de Biologia Molecular e Celular, University of Porto, Porto, Portugal
| | - Margarida Saraiva
- i3S - Instituto de Investigação e Inovação em Saúde, University of Porto, Porto, Portugal
- IBMC - Instituto de Biologia Molecular e Celular, University of Porto, Porto, Portugal
- * E-mail:
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22
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Ma R, Farrell D, Gonzalez G, Browne JA, Nakajima C, Suzuki Y, Gordon SV. The TbD1 Locus Mediates a Hypoxia-Induced Copper Response in Mycobacterium bovis. Front Microbiol 2022; 13:817952. [PMID: 35495699 PMCID: PMC9048740 DOI: 10.3389/fmicb.2022.817952] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Accepted: 02/10/2022] [Indexed: 12/12/2022] Open
Abstract
The Mycobacterium tuberculosis complex (MTBC) contains the causative agents of tuberculosis (TB) in mammals. The archetypal members of the MTBC, Mycobacterium tuberculosis and Mycobacterium bovis, cause human tuberculosis and bovine tuberculosis, respectively. Although M. tuberculosis and M. bovis share over 99.9% genome identity, they show distinct host adaptation for humans and animals; hence, while the molecular basis of host adaptation is encoded in their genomes, the mechanistic basis of host tropism is still unclear. Exploration of the in vitro phenotypic consequences of known genetic difference between M. bovis and M. tuberculosis offers one route to explore genotype–phenotype links that may play a role in host adaptation. The TbD1 (“Mycobacterium tuberculosis deletion 1 region”) locus encompasses the mmpS6 and mmpL6 genes. TbD1 is absent in M. tuberculosis “modern” lineages (Lineages 2, 3, and 4) but present in “ancestral” M. tuberculosis (Lineages 1 and 7), Mycobacterium africanum lineages (Lineages 5 and 6), newly identified M. tuberculosis lineages (Lineages 8 and 9), and animal adapted strains, such as M. bovis. The function of TbD1 has previously been investigated in M. tuberculosis, where conflicting data has emerged on the role of TbD1 in sensitivity to oxidative stress, while the underlying mechanistic basis of such a phenotype is unclear. In this study, we aimed to shed further light on the role of the TbD1 locus by exploring its function in M. bovis. Toward this, we constructed an M. bovis TbD1 knockout (ΔTbD1) strain and conducted comparative transcriptomics to define global gene expression profiles of M. bovis wild-type (WT) and the ΔTbD1 strains under in vitro culture conditions (rolling and standing cultures). This analysis revealed differential induction of a hypoxia-driven copper response in WT and ΔTbD1 strains. In vitro phenotypic assays demonstrated that the deletion of TbD1 sensitized M. bovis to H2O2 and hypoxia-specific copper toxicity. Our study provides new information on the function of the TbD1 locus in M. bovis and its role in stress responses in the MTBC.
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Affiliation(s)
- Ruoyao Ma
- UCD School of Veterinary Medicine, University College Dublin, Dublin, Ireland
| | - Damien Farrell
- UCD School of Veterinary Medicine, University College Dublin, Dublin, Ireland
| | - Gabriel Gonzalez
- Hokkaido University International Institute for Zoonosis Control, Sapporo, Japan
| | - John A. Browne
- UCD School of Agriculture and Food Science, University College Dublin, Dublin, Ireland
| | - Chie Nakajima
- Hokkaido University International Institute for Zoonosis Control, Sapporo, Japan
- Division of Bioresources, Research Center for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Yasuhiko Suzuki
- Hokkaido University International Institute for Zoonosis Control, Sapporo, Japan
- Division of Bioresources, Research Center for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Stephen V. Gordon
- UCD School of Veterinary Medicine, University College Dublin, Dublin, Ireland
- Hokkaido University International Institute for Zoonosis Control, Sapporo, Japan
- UCD Conway Institute, University College Dublin, Dublin, Ireland
- *Correspondence: Stephen V. Gordon,
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23
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Gisch N, Utpatel C, Gronbach LM, Kohl TA, Schombel U, Malm S, Dobos KM, Hesser DC, Diel R, Götsch U, Gerdes S, Shuaib YA, Ntinginya NE, Khosa C, Viegas S, Kerubo G, Ali S, Al-Hajoj SA, Ndung'u PW, Rachow A, Hoelscher M, Maurer FP, Schwudke D, Niemann S, Reiling N, Homolka S. Sub-Lineage Specific Phenolic Glycolipid Patterns in the Mycobacterium tuberculosis Complex Lineage 1. Front Microbiol 2022; 13:832054. [PMID: 35350619 PMCID: PMC8957993 DOI: 10.3389/fmicb.2022.832054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Accepted: 01/20/2022] [Indexed: 12/01/2022] Open
Abstract
“Ancestral” Mycobacterium tuberculosis complex (MTBC) strains of Lineage 1 (L1, East African Indian) are a prominent tuberculosis (TB) cause in countries around the Indian Ocean. However, the pathobiology of L1 strains is insufficiently characterized. Here, we used whole genome sequencing (WGS) of 312 L1 strains from 43 countries to perform a characterization of the global L1 population structure and correlate this to the analysis of the synthesis of phenolic glycolipids (PGL) – known MTBC polyketide-derived virulence factors. Our results reveal the presence of eight major L1 sub-lineages, whose members have specific mutation signatures in PGL biosynthesis genes, e.g., pks15/1 or glycosyltransferases Rv2962c and/or Rv2958c. Sub-lineage specific PGL production was studied by NMR-based lipid profiling and strains with a completely abolished phenolphthiocerol dimycoserosate biosynthesis showed in average a more prominent growth in human macrophages. In conclusion, our results show a diverse population structure of L1 strains that is associated with the presence of specific PGL types. This includes the occurrence of mycoside B in one sub-lineage, representing the first description of a PGL in an M. tuberculosis lineage other than L2. Such differences may be important for the evolution of L1 strains, e.g., allowing adaption to different human populations.
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Affiliation(s)
- Nicolas Gisch
- Bioanalytical Chemistry, Priority Area Infections, Research Center Borstel, Leibniz Lung Center, Borstel, Germany
| | - Christian Utpatel
- Molecular and Experimental Mycobacteriology, Priority Area Infections, Research Center Borstel, Leibniz Lung Center, Borstel, Germany
| | - Lisa M Gronbach
- Bioanalytical Chemistry, Priority Area Infections, Research Center Borstel, Leibniz Lung Center, Borstel, Germany
| | - Thomas A Kohl
- Molecular and Experimental Mycobacteriology, Priority Area Infections, Research Center Borstel, Leibniz Lung Center, Borstel, Germany
| | - Ursula Schombel
- Bioanalytical Chemistry, Priority Area Infections, Research Center Borstel, Leibniz Lung Center, Borstel, Germany
| | - Sven Malm
- Molecular and Experimental Mycobacteriology, Priority Area Infections, Research Center Borstel, Leibniz Lung Center, Borstel, Germany
| | - Karen M Dobos
- Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, CO, United States
| | - Danny C Hesser
- Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, CO, United States
| | - Roland Diel
- Lung Clinic Grosshansdorf, Airway Disease Center North (ARCN), German Center for Lung Research (DZL), Großhansdorf, Germany
| | - Udo Götsch
- Municipal Health Authority Frankfurt am Main, Frankfurt am Main, Germany
| | - Silke Gerdes
- Municipal Health Authority Hannover, Hanover, Germany
| | - Yassir A Shuaib
- College of Veterinary Medicine, Sudan University of Science and Technology, Khartoum, Sudan.,WHO-Supranational Reference Laboratory of Tuberculosis, Institute of Microbiology and Laboratory Medicine (IML Red), Gauting, Germany
| | - Nyanda E Ntinginya
- National Institute for Medical Research Tanzania - Mbeya Medical Research Center, Mbeya, Tanzania
| | - Celso Khosa
- Instituto Nacional de Saúde (INS), Marracuene, Mozambique
| | - Sofia Viegas
- Instituto Nacional de Saúde (INS), Marracuene, Mozambique
| | - Glennah Kerubo
- Department of Medical Microbiology and Parasitology, School of Medicine, Kenyatta University, Nairobi, Kenya
| | - Solomon Ali
- Department of Microbiology, Immunology, and Parasitology, St. Paul's Hospital Millennium Medical College, Addis Ababa, Ethiopia
| | - Sahal A Al-Hajoj
- Mycobacteriology Research Section, Department of Infection and Immunity, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
| | - Perpetual W Ndung'u
- Institute of Tropical Medicine and Infectious Diseases (ITROMID), Jomo Kenyatta University of Agriculture and Technology (JKUAT), Nairobi, Kenya
| | - Andrea Rachow
- Division of Infectious Diseases and Tropical Medicine, University Hospital, LMU Munich, Munich, Germany.,German Centre for Infection Research (DZIF), Partner Site Munich, Munich, Germany
| | - Michael Hoelscher
- Division of Infectious Diseases and Tropical Medicine, University Hospital, LMU Munich, Munich, Germany.,German Centre for Infection Research (DZIF), Partner Site Munich, Munich, Germany
| | - Florian P Maurer
- National and WHO Supranational Reference Centre for Mycobacteria, Research Center Borstel, Leibniz Lung Center, Borstel, Germany.,Institute of Medical Microbiology, Virology, and Hygiene, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Dominik Schwudke
- Bioanalytical Chemistry, Priority Area Infections, Research Center Borstel, Leibniz Lung Center, Borstel, Germany.,German Center for Infection Research (DZIF), Partner Site Hamburg-Lübeck-Borstel-Riems, Borstel, Germany.,Airway Research Center North, Member of the German Center for Lung Research (DZL), Borstel, Germany
| | - Stefan Niemann
- Molecular and Experimental Mycobacteriology, Priority Area Infections, Research Center Borstel, Leibniz Lung Center, Borstel, Germany.,German Center for Infection Research (DZIF), Partner Site Hamburg-Lübeck-Borstel-Riems, Borstel, Germany
| | - Norbert Reiling
- German Center for Infection Research (DZIF), Partner Site Hamburg-Lübeck-Borstel-Riems, Borstel, Germany.,Microbial Interface Biology, Priority Area Infections, Research Center Borstel, Leibniz Lung Center, Borstel, Germany
| | - Susanne Homolka
- Molecular and Experimental Mycobacteriology, Priority Area Infections, Research Center Borstel, Leibniz Lung Center, Borstel, Germany
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24
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Aryal N, Chen J, Bhattarai K, Hennrich O, Handayani I, Kramer M, Straetener J, Wommer T, Berscheid A, Peter S, Reiling N, Brötz-Oesterhelt H, Geibel C, Lämmerhofer M, Mast Y, Gross H. High Plasticity of the Amicetin Biosynthetic Pathway in Streptomyces sp. SHP 22-7 Led to the Discovery of Streptcytosine P and Cytosaminomycins F and G and Facilitated the Production of 12F-Plicacetin. JOURNAL OF NATURAL PRODUCTS 2022; 85:530-539. [PMID: 35263115 DOI: 10.1021/acs.jnatprod.1c01051] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
A chemical reinvestigation of the Indonesian strain Streptomyces sp. SHP 22-7 led to the isolation of three new pyrimidine nucleosides, along with six known analogues and zincphyrin. The structures of the new compounds (6, 7, 10) were elucidated by employing spectroscopic techniques (NMR, MS, CD, and IR) as well as enantioselective analyses of methyl branched side chain configurations. Application of the precursor-directed feeding approach led to the production and partial isolation of nine further pyrimidine analogues. The new compounds 6, 7, and 11 and three of the known compounds (2-4) were found to possess antimycobacterial and cytotoxic properties.
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Affiliation(s)
- Niraj Aryal
- Pharmaceutical Institute, Department of Pharmaceutical Biology, University of Tübingen, 72076 Tübingen, Germany
| | - Junhong Chen
- Pharmaceutical Institute, Department of Pharmaceutical Biology, University of Tübingen, 72076 Tübingen, Germany
| | - Keshab Bhattarai
- Pharmaceutical Institute, Department of Pharmaceutical Biology, University of Tübingen, 72076 Tübingen, Germany
| | - Oliver Hennrich
- Department of Microbial Bioactive Compounds, Interfaculty Institute of Microbiology and Infection Medicine, Tübingen (IMIT), Cluster of Excellence 'Controlling Microbes to Fight Infections', University of Tübingen, 72076 Tübingen, Germany
| | - Ira Handayani
- Research Center for Biotechnology, National Research and Innovation Agency of Indonesia (RC Biotechnology BRIN), Jl.Raya Bogor Km.46, Cibinong, 16911, Bogor, West Java, Indonesia
| | - Markus Kramer
- Institute of Organic Chemistry, University of Tübingen, 72076 Tübingen, Germany
| | - Jan Straetener
- Department of Microbial Bioactive Compounds, Interfaculty Institute of Microbiology and Infection Medicine, Tübingen (IMIT), Cluster of Excellence 'Controlling Microbes to Fight Infections', University of Tübingen, 72076 Tübingen, Germany
| | - Tatjana Wommer
- Department of Microbial Bioactive Compounds, Interfaculty Institute of Microbiology and Infection Medicine, Tübingen (IMIT), Cluster of Excellence 'Controlling Microbes to Fight Infections', University of Tübingen, 72076 Tübingen, Germany
| | - Anne Berscheid
- Department of Microbial Bioactive Compounds, Interfaculty Institute of Microbiology and Infection Medicine, Tübingen (IMIT), Cluster of Excellence 'Controlling Microbes to Fight Infections', University of Tübingen, 72076 Tübingen, Germany
| | - Silke Peter
- Institute of Medical Microbiology and Hygiene, University of Tübingen, 72076 Tübingen, Germany
- German Center for Infection Research (DZIF), partner site Tübingen, 72076 Tübingen, Germany
| | - Norbert Reiling
- Microbial Interface Biology, Research Center Borstel, Leibniz Lung Center, Parkallee 22, 23845 Borstel, Germany
- German Center for Infection Research (DZIF), partner site Hamburg-Lübeck-Borstel-Riems, 20095 Hamburg, Germany
| | - Heike Brötz-Oesterhelt
- Department of Microbial Bioactive Compounds, Interfaculty Institute of Microbiology and Infection Medicine, Tübingen (IMIT), Cluster of Excellence 'Controlling Microbes to Fight Infections', University of Tübingen, 72076 Tübingen, Germany
- German Center for Infection Research (DZIF), partner site Tübingen, 72076 Tübingen, Germany
| | - Christian Geibel
- Pharmaceutical Institute, Department of Pharmaceutical Analysis and Bioanalysis, University of Tübingen, 72076 Tübingen, Germany
| | - Michael Lämmerhofer
- Pharmaceutical Institute, Department of Pharmaceutical Analysis and Bioanalysis, University of Tübingen, 72076 Tübingen, Germany
| | - Yvonne Mast
- German Center for Infection Research (DZIF), partner site Tübingen, 72076 Tübingen, Germany
- Department of Bioresources for Bioeconomy and Health Research, Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, 38124 Braunschweig, Germany
| | - Harald Gross
- Pharmaceutical Institute, Department of Pharmaceutical Biology, University of Tübingen, 72076 Tübingen, Germany
- German Center for Infection Research (DZIF), partner site Tübingen, 72076 Tübingen, Germany
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25
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Early alveolar macrophage response and IL-1R-dependent T cell priming determine transmissibility of Mycobacterium tuberculosis strains. Nat Commun 2022; 13:884. [PMID: 35173157 PMCID: PMC8850437 DOI: 10.1038/s41467-022-28506-2] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Accepted: 01/28/2022] [Indexed: 12/15/2022] Open
Abstract
Mechanisms underlying variability in transmission of Mycobacterium tuberculosis strains remain undefined. By characterizing high and low transmission strains of M.tuberculosis in mice, we show here that high transmission M.tuberculosis strain induce rapid IL-1R-dependent alveolar macrophage migration from the alveolar space into the interstitium and that this action is key to subsequent temporal events of early dissemination of bacteria to the lymph nodes, Th1 priming, granulomatous response and bacterial control. In contrast, IL-1R-dependent alveolar macrophage migration and early dissemination of bacteria to lymph nodes is significantly impeded in infection with low transmission M.tuberculosis strain; these events promote the development of Th17 immunity, fostering neutrophilic inflammation and increased bacterial replication. Our results suggest that by inducing granulomas with the potential to develop into cavitary lesions that aids bacterial escape into the airways, high transmission M.tuberculosis strain is poised for greater transmissibility. These findings implicate bacterial heterogeneity as an important modifier of TB disease manifestations and transmission.
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26
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Asante-Poku A, Morgan P, Osei-Wusu S, Aboagye SY, Asare P, Otchere ID, Adadey SM, Mnika K, Esoh K, Mawuta KH, Arthur N, Forson A, Mazandu GK, Wonkam A, Yeboah-Manu D. Genetic Analysis of TB Susceptibility Variants in Ghana Reveals Candidate Protective Loci in SORBS2 and SCL11A1 Genes. Front Genet 2022; 12:729737. [PMID: 35242163 PMCID: PMC8886735 DOI: 10.3389/fgene.2021.729737] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Accepted: 12/08/2021] [Indexed: 12/31/2022] Open
Abstract
Despite advancements made toward diagnostics, tuberculosis caused by Mycobacterium africanum (Maf) and Mycobacterium tuberculosis sensu stricto (Mtbss) remains a major public health issue. Human host factors are key players in tuberculosis (TB) outcomes and treatment. Research is required to probe the interplay between host and bacterial genomes. Here, we explored the association between selected human/host genomic variants and TB disease in Ghana. Paired host genotype datum and infecting bacterial isolate information were analyzed for associations using a multinomial logistic regression. Mycobacterium tuberculosis complex (MTBC) isolates were obtained from 191 TB patients and genotyped into different phylogenetic lineages by standard methods. Two hundred and thirty-five (235) nondisease participants were used as healthy controls. A selection of 29 SNPs from TB disease-associated genes with high frequency among African populations was assayed using a TaqMan® SNP Genotyping Assay and iPLEX Gold Sequenom Mass Genotyping Array. Using 26 high-quality SNPs across 326 case-control samples in an association analysis, we found a protective variant, rs955263, in the SORBS2 gene against both Maf and Mtb infections (PBH = 0.05; OR = 0.33; 95% CI = 0.32–0.34). A relatively uncommon variant, rs17235409 in the SLC11A1 gene was observed with an even stronger protective effect against Mtb infection (MAF = 0.06; PBH = 0.04; OR = 0.05; 95% CI = 0.04–0.05). These findings suggest SLC11A1 and SORBS2 as a potential protective gene of substantial interest for TB, which is an important pathogen in West Africa, and highlight the need for in-depth host-pathogen studies in West Africa.
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Affiliation(s)
- Adwoa Asante-Poku
- Noguchi Memorial Institute for Medical Research, University of Ghana, Accra, Ghana
- West African Centre for Cell Biology of Infectious Pathogens, University of Ghana, Accra, Ghana
- Department of Biochemistry, Cell, and Molecular Biology, University of Ghana, Accra, Ghana
- *Correspondence: Adwoa Asante-Poku,
| | - Portia Morgan
- Noguchi Memorial Institute for Medical Research, University of Ghana, Accra, Ghana
- West African Centre for Cell Biology of Infectious Pathogens, University of Ghana, Accra, Ghana
- Department of Biochemistry, Cell, and Molecular Biology, University of Ghana, Accra, Ghana
| | - Stephen Osei-Wusu
- Noguchi Memorial Institute for Medical Research, University of Ghana, Accra, Ghana
- West African Centre for Cell Biology of Infectious Pathogens, University of Ghana, Accra, Ghana
- Department of Biochemistry, Cell, and Molecular Biology, University of Ghana, Accra, Ghana
| | - Samuel Yaw Aboagye
- Noguchi Memorial Institute for Medical Research, University of Ghana, Accra, Ghana
| | - Prince Asare
- Noguchi Memorial Institute for Medical Research, University of Ghana, Accra, Ghana
- West African Centre for Cell Biology of Infectious Pathogens, University of Ghana, Accra, Ghana
- Department of Biochemistry, Cell, and Molecular Biology, University of Ghana, Accra, Ghana
| | - Isaac Darko Otchere
- Noguchi Memorial Institute for Medical Research, University of Ghana, Accra, Ghana
- West African Centre for Cell Biology of Infectious Pathogens, University of Ghana, Accra, Ghana
- Department of Biochemistry, Cell, and Molecular Biology, University of Ghana, Accra, Ghana
| | - Samuel Mawuli Adadey
- Division of Human Genetics, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Khuthala Mnika
- Division of Human Genetics, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Kevin Esoh
- Division of Human Genetics, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Kenneth Hayibor Mawuta
- Noguchi Memorial Institute for Medical Research, University of Ghana, Accra, Ghana
- West African Centre for Cell Biology of Infectious Pathogens, University of Ghana, Accra, Ghana
| | - Nelly Arthur
- Department of Chest Diseases, Korle-Bu Teaching Hospital Korle-Bu, Accra, Ghana
| | - Audrey Forson
- Department of Chest Diseases, Korle-Bu Teaching Hospital Korle-Bu, Accra, Ghana
| | - Gaston Kuzamunu Mazandu
- Division of Human Genetics, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Ambroise Wonkam
- Division of Human Genetics, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Dorothy Yeboah-Manu
- Noguchi Memorial Institute for Medical Research, University of Ghana, Accra, Ghana
- West African Centre for Cell Biology of Infectious Pathogens, University of Ghana, Accra, Ghana
- Department of Biochemistry, Cell, and Molecular Biology, University of Ghana, Accra, Ghana
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27
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Tong J, Meng L, Bei C, Liu Q, Wang M, Yang T, Takiff HE, Zhang S, Gao Q, Wang C, Yan B. Modern Beijing sublineage of Mycobacterium tuberculosis shift macrophage into a hyperinflammatory status. Emerg Microbes Infect 2022; 11:715-724. [PMID: 35125072 PMCID: PMC8890550 DOI: 10.1080/22221751.2022.2037395] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
The high prevalence of the modern Beijing sublineage of Mycobacterium tuberculosis may be related to increased virulence, although the responsible mechanisms remain poorly understood. We previously described enhanced triacylglycerol accumulation in modern Beijing strains. Here we show that modern Beijing strains grow faster in vitro and trigger a vigorous immune response and pronounced macrophage infiltration. Transcriptomic analysis of bone marrow derived macrophages infected with modern Beijing lineage strains revealed a significant enrichment of infection, cholesterol homeostasis and amino acid metabolic pathways. The upregulation of proinflammatory / bactericidal cytokines was confirmed by RT–PCR analysis, which is also in consistent with the reduced bacterial burden in modern strains infected macrophages. These results suggest that modern Beijing strains elicit a hyperinflammatory response which might indicate a stronger virulence and contribute to their extensive global prevalence.
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Affiliation(s)
- Jingfeng Tong
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences, Shanghai Medical College and Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
| | - Lu Meng
- The Center for Microbes, Development and Health, Key Laboratory of Molecular Virology & Immunology, Institut Pasteur of Shanghai, Chinese Academy of Sciences/University of Chinese Academy of Sciences, Shanghai, China
| | - Cheng Bei
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences, Shanghai Medical College and Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
| | - Qingyun Liu
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences, Shanghai Medical College and Shanghai Public Health Clinical Center, Fudan University, Shanghai, China.,Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, MA 02115, USA
| | - Min Wang
- Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
| | - TingTing Yang
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences, Shanghai Medical College and Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
| | - Howard E Takiff
- Department of Tuberculosis Control and Prevention, Shenzhen Nanshan Centre for Chronic Disease Control, Shenzhen, China.,Instituto Venezolano de Investigaciones Cientificas, Caracas, Venezuela
| | - Shuye Zhang
- Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
| | - Qian Gao
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences, Shanghai Medical College and Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
| | - Chuan Wang
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences, Shanghai Medical College and Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
| | - Bo Yan
- Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
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28
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Tang P, Liang E, Zhang X, Feng Y, Song H, Xu J, Wu M, Pang Y. Prevalence and Risk Factors of Subclinical Tuberculosis in a Low-Incidence Setting in China. Front Microbiol 2022; 12:731532. [PMID: 35087480 PMCID: PMC8787132 DOI: 10.3389/fmicb.2021.731532] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2021] [Accepted: 12/06/2021] [Indexed: 12/11/2022] Open
Abstract
Objectives: Subclinical tuberculosis (TB) represents a substantial proportion of individuals with TB disease, although limited evidence is available to understand the epidemiological characteristics of these cases. We aimed to explore the prevalence of subclinical patients with TB and identify the underlying association between the subclinical TB cases in the study setting and the Beijing genotype. Methods: A retrospective study was conducted among patients with incident TB at the Fifth People’s Hospital of Suzhou between January and December 2018. A total of 380 patients with TB were included in our analysis. Results: Of the 380 patients, 81.8% were active TB cases, whereas the other 18.2% were subclinical TB cases. Compared with patients aged 65 years and older, the risk of having subclinical TB is higher among younger patients. The use of smear, culture, and Xpert identified 3, 16, and 13 subclinical TB cases, respectively. When using a combination of positive culture and Xpert results, the sensitivity improved to 33.3%. In addition, the neutrophil-to-lymphocyte ratio was significantly elevated in the active TB group compared with that in the subclinical TB group. We also observed that the proportion of the Beijing genotype in the subclinical TB group was significantly lower than that in the active TB group. Conclusion: To conclude, our data demonstrate that approximately one-fifth of patients with TB were subclinical in Suzhou. Mycobacterium tuberculosis could be detected by the existing microbiologic diagnostics in one-third of patients with subclinical TB. The patients with subclinical TB are more prone to having low neutrophil-to-lymphocyte ratio values than those with active TB. Additionally, non-Beijing genotype strains are associated with subclinical TB.
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Affiliation(s)
- Peijun Tang
- Department of Tuberculosis, The Fifth People's Hospital of Suzhou, The Affiliated Infectious Diseases Hospital of Soochow University, Suzhou, China
| | - Ermin Liang
- Department of Tuberculosis, The Fifth People's Hospital of Suzhou, The Affiliated Infectious Diseases Hospital of Soochow University, Suzhou, China
| | - Xuxia Zhang
- Department of Bacteriology and Immunology, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing Chest Hospital Affiliated to Capital Medical University, Beijing, China
| | - Yanjun Feng
- Department of Tuberculosis, The Fifth People's Hospital of Suzhou, The Affiliated Infectious Diseases Hospital of Soochow University, Suzhou, China
| | - Huafeng Song
- Department of Clinical Laboratory, The Fifth People's Hospital of Suzhou, The Affiliated Infectious Diseases Hospital of Soochow University, Suzhou, China
| | - Junchi Xu
- Department of Clinical Laboratory, The Fifth People's Hospital of Suzhou, The Affiliated Infectious Diseases Hospital of Soochow University, Suzhou, China
| | - Meiying Wu
- Department of Tuberculosis, The Fifth People's Hospital of Suzhou, The Affiliated Infectious Diseases Hospital of Soochow University, Suzhou, China
| | - Yu Pang
- Department of Bacteriology and Immunology, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing Chest Hospital Affiliated to Capital Medical University, Beijing, China
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29
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Dohál M, Dvořáková V, Šperková M, Porvazník I, Cabibbe AM, Trovato A, Spitaleri A, Rasmussen EM, Pršo K, Škereňová M, Cirillo DM, Solovič I, Mokrý J. Anti-tuberculosis drug resistance in Slovakia, 2018-2019: The first whole-genome epidemiological study. J Clin Tuberc Other Mycobact Dis 2022; 26:100292. [PMID: 35005254 PMCID: PMC8717600 DOI: 10.1016/j.jctube.2021.100292] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
The Euro-American lineage 4.7 was the most represented among the XDR-TB/MDR-TB resistant strains. Seven of 12 isolates (58%) belonged to the same recent transmission chain. Strains originally from Eastern European countries were diagnosed in patients without any epidemiological links with these countries. Incidence of resistant XDR-TB/MDR-TB in Slovakia, while low, still should be taken to monitor.
Objective The resistance of Mycobacterium (M.) tuberculosis to antituberculosis drugs poses a major threat to global public health. Whole genome sequencing (WGS) is an increasingly preferred method in the diagnostics and monitoring of the transmission dynamics of resistant forms of tuberculosis (TB). The aim of the study was to, for the first time, use the sequencing-based analysis to study the transmission and resistance patterns of a systematic and recent collection of extensively drug resistant (XDR) and multidrug resistant tuberculosis (MDR-TB) isolates and to expand our knowledge about drug resistant (DR) TB epidemiological dynamics in Slovakia. Design A total of 495 patients with pulmonary TB, who were referred to National Reference Laboratory for Mycobacteriology (Vyšné Hágy, Slovakia) in the years 2018–2019, were studied. Out of the total of 495 patients, 4 XDR-TB (0.8%) and 8 (1.6%) MDR-TB isolates were identified by conventional drug susceptibility testing on Löwenstein-Jensen solid medium and subjected to whole genome sequencing. Sequencing data were evaluated for molecular-epidemiological analysis and identification of resistance patterns. Results Phylogenetic and cluster analysis showed extensive recent transmission events and the predominance of Euro-American lineage 4.7 in Slovakia. However, phylogenetic analysis revealed the circulation of several lineages that originally occurred in Eastern European countries. Resistance patterns for first- and second-line antituberculosis drugs characterized by whole genome sequencing were in high concordance with the results of phenotypic drug susceptibility testing. Conclusion Forty percent of at least MDR-TB isolates were not genetically linked, indicating that appropriate measures should be taken to monitor and prevent the spread of drug-resistant tuberculosis within the country as well as in other regions.
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Affiliation(s)
- Matúš Dohál
- Department of Pharmacology and Biomedical Center Martin, Jessenius Faculty of Medicine, Comenius University, Slovakia
| | - Věra Dvořáková
- National Reference Laboratory for Mycobacteria, National Institute of Public Health, Praha, Czech Republic
| | - Miluše Šperková
- National Reference Laboratory for Mycobacteria, National Institute of Public Health, Praha, Czech Republic
| | - Igor Porvazník
- National Institute of Tuberculosis, Lung Diseases and Thoracic Surgery, Vyšné Hágy, Slovakia, Faculty of Health, Catholic University, Ružomberok, Slovakia.,Faculty of Health, Catholic University, Ružomberok, Slovakia
| | | | - Alberto Trovato
- Emerging Bacterial Pathogens Unit, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Andrea Spitaleri
- Emerging Bacterial Pathogens Unit, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Erik Michael Rasmussen
- International Reference Laboratory of Mycobacteriology, Statens Serum Institut, Copenhagen, Denmark
| | - Kristián Pršo
- Department of Pharmacology and Biomedical Center Martin, Jessenius Faculty of Medicine, Comenius University, Slovakia
| | - Mária Škereňová
- Biomedical Center Martin, Department of Molecular Medicine, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, Slovakia, Department of Clinical Biochemistry, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, Slovakia
| | - Daniela Maria Cirillo
- Emerging Bacterial Pathogens Unit, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Ivan Solovič
- National Institute of Tuberculosis, Lung Diseases and Thoracic Surgery, Vyšné Hágy, Slovakia, Faculty of Health, Catholic University, Ružomberok, Slovakia
| | - Juraj Mokrý
- Department of Pharmacology and Biomedical Center Martin, Jessenius Faculty of Medicine, Comenius University, Slovakia
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30
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Vinogradova T, Dogonadze M, Zabolotnykh N, Badleeva M, Yarusova I, Vyazovaya A, Gerasimova A, Zhdanova S, Vitovskaya M, Solovieva N, Pasechnik O, Ogarkov O, Mokrousov I. Extremely lethal and hypervirulent Mycobacterium tuberculosis strain cluster emerging in Far East, Russia. Emerg Microbes Infect 2021; 10:1691-1701. [PMID: 34380361 PMCID: PMC8381949 DOI: 10.1080/22221751.2021.1967704] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Mycobacterium tuberculosis strains of the early ancient sublineage of the Beijing genotype are mostly drug susceptible and mainly circulate in East Asia. We have recently discovered two clusters of this sublineage emerging in the Asian part of Russia (VNTR-defined 1071-32 and 14717-15 types) and, to our surprise, both were strongly MDR/XDR-associated. Here, we evaluated their pathogenic features. The clinical isolates and reference laboratory strain H37Rv were investigated in the C57BL/6 mouse model to assess their virulence and lethality properties. The BACTEC MGIT 960 system was used to study the in vitro growth characteristics. In the murine model, strains 396 (14717-15-cluster, from Buryatia, Far East) and 6691 (1071-32-cluster, from Omsk, Siberia) demonstrated contrasting properties. The 396-infected group had significantly higher mortality, more weight loss, higher bacterial burden, and more severe lung pathology. Furthermore, compared to the previously published data on other Russian epidemic Beijing strains (B0/W148, CAO, Central Asian Russian), strain 396 demonstrated the highest mortality. Under the in vitro growth experiment, cluster 14717-15 isolates had significantly shorter lag-phase. To conclude, low-virulent MDR strain 6691 belongs to the Beijing 1071-32-cluster widespread across FSU countries but at low prevalence. This corresponds to common expectation that multiple drug resistance mutations reduce fitness and virulence. In contrast, highly lethal and hypervirulent MDR strain 396 represents an intriguing Beijing 14717-15 cluster predominant only in Buryatia, Far East (16%), sporadically found beyond it, but not forming clusters of transmission. Further in-depth study of this most virulent Russian Beijing cluster is warranted.
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Affiliation(s)
- Tatiana Vinogradova
- Laboratory of Molecular Epidemiology and Evolutionary Genetics, St. Petersburg Pasteur Institute, St. Petersburg, Russia.,Laboratory of Experimental Tuberculosis and New Medical Technologies, St. Petersburg Research Institute of Phthisiopulmonology, St. Petersburg, Russia
| | - Marine Dogonadze
- Bacteriology Laboratory, St. Petersburg Research Institute of Phthisiopulmonology, St. Petersburg, Russia
| | - Natalia Zabolotnykh
- Laboratory of Experimental Tuberculosis and New Medical Technologies, St. Petersburg Research Institute of Phthisiopulmonology, St. Petersburg, Russia
| | - Maria Badleeva
- Department of Infectious Diseases, Buryat State University, Ulan-Ude, Buryatia, Russia
| | - Irina Yarusova
- Laboratory of Molecular Epidemiology and Evolutionary Genetics, St. Petersburg Pasteur Institute, St. Petersburg, Russia.,Bacteriology Laboratory, Clinical Anti-tuberculosis Dispensary, Omsk, Russia
| | - Anna Vyazovaya
- Laboratory of Molecular Epidemiology and Evolutionary Genetics, St. Petersburg Pasteur Institute, St. Petersburg, Russia
| | - Alena Gerasimova
- Laboratory of Molecular Epidemiology and Evolutionary Genetics, St. Petersburg Pasteur Institute, St. Petersburg, Russia
| | - Svetlana Zhdanova
- Department of Epidemiology and Microbiology, Scientific Centre of the Family Health and Human Reproduction Problems, Irkutsk, Russia
| | - Maria Vitovskaya
- Laboratory of Experimental Tuberculosis and New Medical Technologies, St. Petersburg Research Institute of Phthisiopulmonology, St. Petersburg, Russia
| | - Natalia Solovieva
- Bacteriology Laboratory, St. Petersburg Research Institute of Phthisiopulmonology, St. Petersburg, Russia
| | - Oksana Pasechnik
- Department of Public Health, Omsk State Medical University, Omsk, Russia
| | - Oleg Ogarkov
- Department of Epidemiology and Microbiology, Scientific Centre of the Family Health and Human Reproduction Problems, Irkutsk, Russia
| | - Igor Mokrousov
- Laboratory of Molecular Epidemiology and Evolutionary Genetics, St. Petersburg Pasteur Institute, St. Petersburg, Russia
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31
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Brandenburg J, Marwitz S, Tazoll SC, Waldow F, Kalsdorf B, Vierbuchen T, Scholzen T, Gross A, Goldenbaum S, Hölscher A, Hein M, Linnemann L, Reimann M, Kispert A, Leitges M, Rupp J, Lange C, Niemann S, Behrends J, Goldmann T, Heine H, Schaible UE, Hölscher C, Schwudke D, Reiling N. WNT6/ACC2-induced storage of triacylglycerols in macrophages is exploited by Mycobacterium tuberculosis. J Clin Invest 2021; 131:e141833. [PMID: 34255743 DOI: 10.1172/jci141833] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Accepted: 07/06/2021] [Indexed: 11/17/2022] Open
Abstract
In view of emerging drug-resistant tuberculosis (TB), host-directed adjunct therapies are urgently needed to improve treatment outcomes with currently available anti-TB therapies. One approach is to interfere with the formation of lipid-laden "foamy" macrophages in the host, as they provide a nutrient-rich host cell environment for Mycobacterium tuberculosis (Mtb). Here, we provide evidence that Wnt family member 6 (WNT6), a ligand of the evolutionarily conserved Wingless/Integrase 1 (WNT) signaling pathway, promotes foam cell formation by regulating key lipid metabolic genes including acetyl-CoA carboxylase 2 (ACC2) during pulmonary TB. Using genetic and pharmacological approaches, we demonstrated that lack of functional WNT6 or ACC2 significantly reduced intracellular triacylglycerol (TAG) levels and Mtb survival in macrophages. Moreover, treatment of Mtb-infected mice with a combination of a pharmacological ACC2 inhibitor and the anti-TB drug isoniazid (INH) reduced lung TAG and cytokine levels, as well as lung weights, compared with treatment with INH alone. This combination also reduced Mtb bacterial numbers and the size of mononuclear cell infiltrates in livers of infected mice. In summary, our findings demonstrate that Mtb exploits WNT6/ACC2-induced storage of TAGs in macrophages to facilitate its intracellular survival, a finding that opens new perspectives for host-directed adjunctive treatment of pulmonary TB.
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Affiliation(s)
- Julius Brandenburg
- Microbial Interface Biology, Research Center Borstel, Leibniz Lung Center, Borstel, Germany.,German Center for Infection Research (DZIF), Site Hamburg-Lübeck-Borstel-Riems, Hamburg, Germany
| | - Sebastian Marwitz
- Pathology, Research Center Borstel, Borstel, Germany.,Airway Research Center North (ARCN), Member of the German Center for Lung Research (DZL), Grosshansdorf, Germany
| | - Simone C Tazoll
- Microbial Interface Biology, Research Center Borstel, Leibniz Lung Center, Borstel, Germany
| | - Franziska Waldow
- German Center for Infection Research (DZIF), Site Hamburg-Lübeck-Borstel-Riems, Hamburg, Germany.,Bioanalytical Chemistry
| | - Barbara Kalsdorf
- German Center for Infection Research (DZIF), Site Hamburg-Lübeck-Borstel-Riems, Hamburg, Germany.,Clinical Infectious Diseases
| | | | | | - Annette Gross
- Microbial Interface Biology, Research Center Borstel, Leibniz Lung Center, Borstel, Germany
| | - Svenja Goldenbaum
- Microbial Interface Biology, Research Center Borstel, Leibniz Lung Center, Borstel, Germany
| | | | | | - Lara Linnemann
- Cellular Microbiology, Research Center Borstel, Borstel, Germany
| | | | - Andreas Kispert
- Institute for Molecular Biology, Hannover Medical School, Hannover, Germany
| | - Michael Leitges
- Division of BioMedical Sciences/Faculty of Medicine, Memorial University of Newfoundland, St. John's, Newfoundland, Canada
| | - Jan Rupp
- German Center for Infection Research (DZIF), Site Hamburg-Lübeck-Borstel-Riems, Hamburg, Germany.,Department of Infectious Diseases and Microbiology and
| | - Christoph Lange
- German Center for Infection Research (DZIF), Site Hamburg-Lübeck-Borstel-Riems, Hamburg, Germany.,Clinical Infectious Diseases.,Respiratory Medicine & International Health, University of Lübeck, Lübeck, Germany.,Baylor College of Medicine and Texas Children's Hospital, Houston, Texas, USA
| | - Stefan Niemann
- German Center for Infection Research (DZIF), Site Hamburg-Lübeck-Borstel-Riems, Hamburg, Germany.,Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Germany
| | | | - Torsten Goldmann
- Pathology, Research Center Borstel, Borstel, Germany.,Airway Research Center North (ARCN), Member of the German Center for Lung Research (DZL), Grosshansdorf, Germany
| | | | - Ulrich E Schaible
- German Center for Infection Research (DZIF), Site Hamburg-Lübeck-Borstel-Riems, Hamburg, Germany.,Cellular Microbiology, Research Center Borstel, Borstel, Germany
| | - Christoph Hölscher
- German Center for Infection Research (DZIF), Site Hamburg-Lübeck-Borstel-Riems, Hamburg, Germany.,Infection Immunology, and
| | - Dominik Schwudke
- German Center for Infection Research (DZIF), Site Hamburg-Lübeck-Borstel-Riems, Hamburg, Germany.,Airway Research Center North (ARCN), Member of the German Center for Lung Research (DZL), Grosshansdorf, Germany.,Bioanalytical Chemistry
| | - Norbert Reiling
- Microbial Interface Biology, Research Center Borstel, Leibniz Lung Center, Borstel, Germany.,German Center for Infection Research (DZIF), Site Hamburg-Lübeck-Borstel-Riems, Hamburg, Germany
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32
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Tunstall T, Phelan J, Eccleston C, Clark TG, Furnham N. Structural and Genomic Insights Into Pyrazinamide Resistance in Mycobacterium tuberculosis Underlie Differences Between Ancient and Modern Lineages. Front Mol Biosci 2021; 8:619403. [PMID: 34422898 PMCID: PMC8372558 DOI: 10.3389/fmolb.2021.619403] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Accepted: 04/14/2021] [Indexed: 11/30/2022] Open
Abstract
Resistance to drugs used to treat tuberculosis disease (TB) continues to remain a public health burden, with missense point mutations in the underlying Mycobacterium tuberculosis bacteria described for nearly all anti-TB drugs. The post-genomics era along with advances in computational and structural biology provide opportunities to understand the interrelationships between the genetic basis and the structural consequences of M. tuberculosis mutations linked to drug resistance. Pyrazinamide (PZA) is a crucial first line antibiotic currently used in TB treatment regimens. The mutational promiscuity exhibited by the pncA gene (target for PZA) necessitates computational approaches to investigate the genetic and structural basis for PZA resistance development. We analysed 424 missense point mutations linked to PZA resistance derived from ∼35K M. tuberculosis clinical isolates sourced globally, which comprised the four main M. tuberculosis lineages (Lineage 1-4). Mutations were annotated to reflect their association with PZA resistance. Genomic measures (minor allele frequency and odds ratio), structural features (surface area, residue depth and hydrophobicity) and biophysical effects (change in stability and ligand affinity) of point mutations on pncA protein stability and ligand affinity were assessed. Missense point mutations within pncA were distributed throughout the gene, with the majority (>80%) of mutations with a destabilising effect on protomer stability and on ligand affinity. Active site residues involved in PZA binding were associated with multiple point mutations highlighting mutational diversity due to selection pressures at these functionally important sites. There were weak associations between genomic measures and biophysical effect of mutations. However, mutations associated with PZA resistance showed statistically significant differences between structural features (surface area and residue depth), but not hydrophobicity score for mutational sites. Most interestingly M. tuberculosis lineage 1 (ancient lineage) exhibited a distinct protein stability profile for mutations associated with PZA resistance, compared to modern lineages.
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Affiliation(s)
- Tanushree Tunstall
- Department of Infection Biology, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Jody Phelan
- Department of Infection Biology, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Charlotte Eccleston
- Department of Infection Biology, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Taane G. Clark
- Department of Infection Biology, London School of Hygiene and Tropical Medicine, London, United Kingdom
- Department of Infectious Disease Epidemiology, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Nicholas Furnham
- Department of Infection Biology, London School of Hygiene and Tropical Medicine, London, United Kingdom
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Epidemiology of Mycobacterium tuberculosis lineages and strain clustering within urban and peri-urban settings in Ethiopia. PLoS One 2021; 16:e0253480. [PMID: 34252107 PMCID: PMC8274931 DOI: 10.1371/journal.pone.0253480] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Accepted: 06/06/2021] [Indexed: 11/25/2022] Open
Abstract
Background Previous work has shown differential predominance of certain Mycobacterium tuberculosis (M. tb) lineages and sub-lineages among different human populations in diverse geographic regions of Ethiopia. Nevertheless, how strain diversity is evolving under the ongoing rapid socio-economic and environmental changes is poorly understood. The present study investigated factors associated with M. tb lineage predominance and rate of strain clustering within urban and peri-urban settings in Ethiopia. Methods Pulmonary Tuberculosis (PTB) and Cervical tuberculous lymphadenitis (TBLN) patients who visited selected health facilities were recruited in the years of 2016 and 2017. A total of 258 M. tb isolates identified from 163 sputa and 95 fine-needle aspirates (FNA) were characterized by spoligotyping and compared with international M.tb spoligotyping patterns registered at the SITVIT2 databases. The molecular data were linked with clinical and demographic data of the patients for further statistical analysis. Results From a total of 258 M. tb isolates, 84 distinct spoligotype patterns that included 58 known Shared International Type (SIT) patterns and 26 new or orphan patterns were identified. The majority of strains belonged to two major M. tb lineages, L3 (35.7%) and L4 (61.6%). The observed high percentage of isolates with shared patterns (n = 200/258) suggested a substantial rate of overall clustering (77.5%). After adjusting for the effect of geographical variations, clustering rate was significantly lower among individuals co-infected with HIV and other concomitant chronic disease. Compared to L4, the adjusted odds ratio and 95% confidence interval (AOR; 95% CI) indicated that infections with L3 M. tb strains were more likely to be associated with TBLN [3.47 (1.45, 8.29)] and TB-HIV co-infection [2.84 (1.61, 5.55)]. Conclusion Despite the observed difference in strain diversity and geographical distribution of M. tb lineages, compared to earlier studies in Ethiopia, the overall rate of strain clustering suggests higher transmission and warrant more detailed investigations into the molecular epidemiology of TB and related factors.
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34
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Sanoussi CN, Coscolla M, Ofori-Anyinam B, Otchere ID, Antonio M, Niemann S, Parkhill J, Harris S, Yeboah-Manu D, Gagneux S, Rigouts L, Affolabi D, de Jong BC, Meehan CJ. Mycobacterium tuberculosis complex lineage 5 exhibits high levels of within-lineage genomic diversity and differing gene content compared to the type strain H37Rv. Microb Genom 2021; 7:000437. [PMID: 34241588 PMCID: PMC8477398 DOI: 10.1099/mgen.0.000437] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Accepted: 04/22/2021] [Indexed: 12/27/2022] Open
Abstract
Pathogens of the Mycobacterium tuberculosis complex (MTBC) are considered to be monomorphic, with little gene content variation between strains. Nevertheless, several genotypic and phenotypic factors separate strains of the different MTBC lineages (L), especially L5 and L6 (traditionally termed Mycobacterium africanum) strains, from each other. However, this genome variability and gene content, especially of L5 strains, has not been fully explored and may be important for pathobiology and current approaches for genomic analysis of MTBC strains, including transmission studies. By comparing the genomes of 355 L5 clinical strains (including 3 complete genomes and 352 Illumina whole-genome sequenced isolates) to each other and to H37Rv, we identified multiple genes that were differentially present or absent between H37Rv and L5 strains. Additionally, considerable gene content variability was found across L5 strains, including a split in the L5.3 sub-lineage into L5.3.1 and L5.3.2. These gene content differences had a small knock-on effect on transmission cluster estimation, with clustering rates influenced by the selected reference genome, and with potential overestimation of recent transmission when using H37Rv as the reference genome. We conclude that full capture of the gene diversity, especially high-resolution outbreak analysis, requires a variation of the single H37Rv-centric reference genome mapping approach currently used in most whole-genome sequencing data analysis pipelines. Moreover, the high within-lineage gene content variability suggests that the pan-genome of M. tuberculosis is at least several kilobases larger than previously thought, implying that a concatenated or reference-free genome assembly (de novo) approach may be needed for particular questions.
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Affiliation(s)
- C. N'Dira Sanoussi
- Laboratoire de Référence des Mycobactéries, Cotonou, Benin
- Mycobacteriology Unit, Institute of Tropical Medicine, Antwerp, Belgium
- Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
| | - Mireia Coscolla
- I2SysBio, University of Valencia-FISABIO Joint Unit, Valencia, Spain
| | - Boatema Ofori-Anyinam
- Food and Drugs Authority, Accra, Ghana
- Rutgers New Jersey Medical School, Rutgers University, New Jersey, USA
| | - Isaac Darko Otchere
- Noguchi Memorial Institute for Medical Research, University of Ghana, Legon, Accra, Ghana
| | - Martin Antonio
- Medical Research Council Unit in The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, The Gambia
| | - Stefan Niemann
- German Center for Infection Research, partner site Borstel-Hamburg-Lübeck-Riems, Borstel, Germany
- Research Center Borstel, Molecular and Experimental Mycobacteriology, Borstel, Germany
| | - Julian Parkhill
- Wellcome Sanger Institute, Hinxton, UK
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | | | - Dorothy Yeboah-Manu
- Noguchi Memorial Institute for Medical Research, University of Ghana, Legon, Accra, Ghana
| | - Sebastien Gagneux
- Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Leen Rigouts
- Mycobacteriology Unit, Institute of Tropical Medicine, Antwerp, Belgium
- Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
| | | | - Bouke C. de Jong
- Mycobacteriology Unit, Institute of Tropical Medicine, Antwerp, Belgium
| | - Conor J. Meehan
- Mycobacteriology Unit, Institute of Tropical Medicine, Antwerp, Belgium
- School of Chemistry and Biosciences, University of Bradford, Bradford, UK
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Tafess K, Beyen TK, Girma S, Girma A, Siu G. Spatial clustering and genetic diversity of Mycobacterium tuberculosis isolate among pulmonary tuberculosis suspected patients, Arsi Zone, Ethiopia. BMC Pulm Med 2021; 21:206. [PMID: 34193091 PMCID: PMC8244181 DOI: 10.1186/s12890-021-01567-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2020] [Accepted: 06/10/2021] [Indexed: 11/20/2022] Open
Abstract
BACKGROUND Tuberculosis remains a serious public health concern globally. The enormous social, economic, and health impacts of the diseases are attributed to the lack of updated data on the prevalence, geospatial distribution, population structures, and genotypic variants of the circulating M. tuberculosis. METHODS Structured questionnaire, mycobacterial culture, and standard 24-Mycobacterial Interspersed Repeated Units-Variable Number Tandem Repeats (MIRU-VNTR) were employed to collect sociodemographic characters, residence linked information, and genotype the isolates. The retrospective discrete Bernoulli model was used to identify the hot spot districts of sputum smear positivity, and Web-based Miru-VNTRPlus were used for the identification of lineages and sublineages. RESULTS Out of 832 presumptive pulmonary tuberculosis (PTB) suspects, 119 (14.3%) were smear-positive. In the multivariate binary logistic model, PTB suspected patients in the age groups of 7-25 and 25-34 and those from rural residents were 4.53 (AOR = 4.53; 95% CI 2.25-9.13), 3.00 (AOR = 3.00; 95% CI 1.41-6.35) and 1.65 (AOR = 1.65; 95% CI 1.01-2.70) times at higher risk of turning smear-positive. Eleven (47.8%) districts of Arsi Zone were shown to have a high rate of clustering (RR = 2.27; 95% CI 1.62-3.2) of smear-positive PTB. Of 72 isolates queried for the lineage assignment, 59 (81.9%) were classified into the previously known lineages and 13 (18.1%) were not assigned to any known lineages. Overall, 42 (58.3%) belong to M. tuberculosis lineage 4 (Euro-American), 16 (22.2%) M. tuberculosis lineage 3 (Delhi/CAS), and 1 (1.4%) M. tuberculosis Lineage 1 (Indo-Oceanic/ East Africa Indian). Further classification to the sublineage indicates that the predominant lineage was Delhi/CAS comprising 16 (22.2%) isolates followed by 15 (20.8%) isolates belonging to Haarlem. The remaining isolates were distributed as 13 (18.1%) TUR, 6 (8.3%) LAM, 4 (5.5%) URAL, 4 (4.5%) NEW-1 and 1 (1.4%) EAI. CONCLUSION Our study showed higher smear-positive results among PTB suspected patients and remarkable spatial variation across districts of Arsi Zone in smear-positive PTB. This information together with the genotypic features could be used as input for the efforts of designing control strategies.
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Affiliation(s)
- Ketema Tafess
- Institute of Pharmaceutical Science, School of Applied Natural Science, Adama Science and Technology University, Adama, Ethiopia
| | - Teresa Kisi Beyen
- Department of Public Health, College of Health Sciences, Arsi University, Asella, Ethiopia
| | - Sisay Girma
- Department of Clinical Study, College of Veterinary Medicine and Agriculture, Addis Ababa University, P. O. Box 34, Bishoftu, Ethiopia
| | - Asnakech Girma
- Disease Prevention, Training and Research Division, Federal Prison General Hospital, Addis Ababa, Ethiopia
| | - Gilman Siu
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hung Hom, Hong Kong
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Kaewseekhao B, Roytrakul S, Yingchutrakul Y, Laohaviroj M, Salao K, Faksri K. Characterisation of secretome-based immune responses of human leukocytes infected with various Mycobacterium tuberculosis lineages. PeerJ 2021; 9:e11565. [PMID: 34141493 PMCID: PMC8180191 DOI: 10.7717/peerj.11565] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Accepted: 05/14/2021] [Indexed: 11/27/2022] Open
Abstract
Background Differences in immune responses against different lineages of Mycobacterium tuberculosis (Mtb), and by different types of immune cell, are still poorly understood. We aimed to compare the secretome-based immune responses among three Mtb lineages and among immune-cell types. The immune responses were also investigated during infection and when the bacilli had been eliminated from the immune cells. Methods Human primary leukocytes were infected with strains representing three lineages of Mtb (East-Asian, Indo-Oceanic and Euro-American). Label-free GeLC MS/MS proteomic analysis of secretomes was performed. The response of each immune-cell type was compared with the appropriate interactome database for each. Results The expression pattern of proteins secreted by Mtb-infected leukocytes differed among Mtb lineages. The ancestral lineage (IO lineage) had a greater ability to activate MMP14 (associated with leukocyte migration) than did the more recent lineages (EA and EuA). During infection, proteins secreted by macrophages, dendritic cells, neutrophils and B-cells were associated with cell proliferation. Following clearance of Mtb, proteins associated with interferon signaling were found in macrophages, dendritic cells and neutrophils: proteins associated with antigen processing were found in B-cells and regulatory T-cells. Expression of immune response-related proteins from many immune-cell types might be suppressed by Mtb infection. Our study has provided a better insight into the host-pathogen interaction and immune response against different Mtb lineages.
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Affiliation(s)
- Benjawan Kaewseekhao
- Department of Microbiology, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand.,Research and Diagnostic Center for Emerging Infectious Diseases (RCEID), Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
| | - Sittiruk Roytrakul
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Pathumthani, Thailand
| | - Yodying Yingchutrakul
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Pathumthani, Thailand
| | - Marut Laohaviroj
- Department of Microbiology, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
| | - Kanin Salao
- Department of Microbiology, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
| | - Kiatichai Faksri
- Department of Microbiology, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand.,Research and Diagnostic Center for Emerging Infectious Diseases (RCEID), Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
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Pinheiro B, Scheidler CM, Kielkowski P, Schmid M, Forné I, Ye S, Reiling N, Takano E, Imhof A, Sieber SA, Schneider S, Jung K. Structure and Function of an Elongation Factor P Subfamily in Actinobacteria. Cell Rep 2021; 30:4332-4342.e5. [PMID: 32234471 DOI: 10.1016/j.celrep.2020.03.009] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Revised: 02/06/2020] [Accepted: 03/02/2020] [Indexed: 12/28/2022] Open
Abstract
Translation of consecutive proline motifs causes ribosome stalling and requires rescue via the action of a specific translation elongation factor, EF-P in bacteria and archaeal/eukaryotic a/eIF5A. In Eukarya, Archaea, and all bacteria investigated so far, the functionality of this translation elongation factor depends on specific and rather unusual post-translational modifications. The phylum Actinobacteria, which includes the genera Corynebacterium, Mycobacterium, and Streptomyces, is of both medical and economic significance. Here, we report that EF-P is required in these bacteria in particular for the translation of proteins involved in amino acid and secondary metabolite production. Notably, EF-P of Actinobacteria species does not need any post-translational modification for activation. While the function and overall 3D structure of this EF-P type is conserved, the loop containing the conserved lysine is flanked by two essential prolines that rigidify it. Actinobacteria's EF-P represents a unique subfamily that works without any modification.
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Affiliation(s)
- Bruno Pinheiro
- Department of Biology I, Microbiology, Ludwig-Maximilians-Universität München, Martinsried, Germany
| | | | - Pavel Kielkowski
- Department of Chemistry, Technische Universität München, Garching, Germany
| | - Marina Schmid
- Department of Biology I, Microbiology, Ludwig-Maximilians-Universität München, Martinsried, Germany
| | - Ignasi Forné
- Biomedical Center Munich, Ludwig-Maximilians-Universität München, Martinsried, Germany
| | - Suhui Ye
- Manchester Institute of Biotechnology, Department of Chemistry, School of Natural Sciences, Faculty of Science and Engineering, University of Manchester, Manchester, UK
| | - Norbert Reiling
- RG Microbial Interface Biology, Research Center Borstel, Leibniz Lung Center, Borstel, Germany; German Center for Infection Research (DZIF), Partner Site Hamburg-Lübeck-Borstel-Riems, Borstel, Germany
| | - Eriko Takano
- Manchester Institute of Biotechnology, Department of Chemistry, School of Natural Sciences, Faculty of Science and Engineering, University of Manchester, Manchester, UK
| | - Axel Imhof
- Biomedical Center Munich, Ludwig-Maximilians-Universität München, Martinsried, Germany
| | - Stephan A Sieber
- Department of Chemistry, Technische Universität München, Garching, Germany
| | - Sabine Schneider
- Department of Chemistry, Ludwig-Maximilians-Universität München, Munich, Germany.
| | - Kirsten Jung
- Department of Biology I, Microbiology, Ludwig-Maximilians-Universität München, Martinsried, Germany.
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Survival of hypoxia-induced dormancy is not a common feature of all strains of the Mycobacterium tuberculosis complex. Sci Rep 2021; 11:2628. [PMID: 33514768 PMCID: PMC7846770 DOI: 10.1038/s41598-021-81223-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Accepted: 12/29/2020] [Indexed: 11/30/2022] Open
Abstract
While persistence in a dormant state is crucial for the life cycle of Mycobacterium tuberculosis, no investigation regarding dormancy survival of different strains across different lineages was performed so far. We analyzed responses to oxygen starvation and recovery in terms of growth, metabolism, and transcription. All different strains belonging to the Euro-American lineage (L4) showed similar survival and resuscitation characteristics. Different clinical isolates from the Beijing (L2), East African-Indian (L3), and Delhi/Central Asian (L1) lineage did not survive oxygen starvation. We show that dormancy survival is lineage-dependent. Recovery from O2 starvation was only observed in strains belonging to the Euro-American (L4) lineage but not in strains belonging to different lineages (L1, L2, L3). Thus, resuscitation from dormancy after oxygen starvation is not a general feature of all M. tuberculosis strains as thought before. Our findings are of key importance to understand infection dynamics of non-Euro-American vs Euro-American strains and to develop drugs targeting the dormant state.
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Napier G, Campino S, Merid Y, Abebe M, Woldeamanuel Y, Aseffa A, Hibberd ML, Phelan J, Clark TG. Robust barcoding and identification of Mycobacterium tuberculosis lineages for epidemiological and clinical studies. Genome Med 2020; 12:114. [PMID: 33317631 PMCID: PMC7734807 DOI: 10.1186/s13073-020-00817-3] [Citation(s) in RCA: 58] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2020] [Accepted: 12/03/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Tuberculosis, caused by bacteria in the Mycobacterium tuberculosis complex (MTBC), is a major global public health burden. Strain-specific genomic diversity in the known lineages of MTBC is an important factor in pathogenesis that may affect virulence, transmissibility, host response and emergence of drug resistance. Fast and accurate tracking of MTBC strains is therefore crucial for infection control, and our previous work developed a 62-single nucleotide polymorphism (SNP) barcode to inform on the phylogenetic identity of 7 human lineages and 64 sub-lineages. METHODS To update this barcode, we analysed whole genome sequencing data from 35,298 MTBC isolates (~ 1 million SNPs) covering 9 main lineages and 3 similar animal-related species (M. tuberculosis var. bovis, M. tuberculosis var. caprae and M. tuberculosis var. orygis). The data was partitioned into training (N = 17,903, 50.7%) and test (N = 17,395, 49.3%) sets and were analysed using an integrated phylogenetic tree and population differentiation (FST) statistical approach. RESULTS By constructing a phylogenetic tree on the training MTBC isolates, we characterised 90 lineages or sub-lineages or species, of which 30 are new, and identified 421 robust barcoding mutations, of which a minimal set of 90 was selected that included 20 markers from the 62-SNP barcode. The barcoding SNPs (90 and 421) discriminated perfectly the 86 MTBC isolate (sub-)lineages in the test set and could accurately reconstruct the clades across the combined 35k samples. CONCLUSIONS The validated 90 SNPs can be used for the rapid diagnosis and tracking of MTBC strains to assist public health surveillance and control. To facilitate this, the SNP markers have now been incorporated into the TB-Profiler informatics platform ( https://github.com/jodyphelan/TBProfiler ).
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Affiliation(s)
- Gary Napier
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, Keppel Street, London, WC1E 7HT UK
| | - Susana Campino
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, Keppel Street, London, WC1E 7HT UK
| | - Yared Merid
- Armauer Hansen Research Institute, Addis Ababa, Ethiopia
- Department of Microbiology, Immunology and Parasitology, College of Health Sciences, Addis Ababa University, Addis Ababa, Ethiopia
- Hawassa University College of Medicine and Health Sciences, Hawassa, Ethiopia
| | - Markos Abebe
- Armauer Hansen Research Institute, Addis Ababa, Ethiopia
| | - Yimtubezinash Woldeamanuel
- Department of Microbiology, Immunology and Parasitology, College of Health Sciences, Addis Ababa University, Addis Ababa, Ethiopia
| | - Abraham Aseffa
- Armauer Hansen Research Institute, Addis Ababa, Ethiopia
| | - Martin L. Hibberd
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, Keppel Street, London, WC1E 7HT UK
| | - Jody Phelan
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, Keppel Street, London, WC1E 7HT UK
| | - Taane G. Clark
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, Keppel Street, London, WC1E 7HT UK
- Faculty of Epidemiology and Population Health, London School of Hygiene & Tropical Medicine, London, WC1E 7HT UK
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Mokrousov I. Ubiquitous and multifaceted: SIT53 spoligotype does not correlate with any particular family of Mycobacterium tuberculosis. Tuberculosis (Edinb) 2020; 126:102024. [PMID: 33242765 DOI: 10.1016/j.tube.2020.102024] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2020] [Revised: 10/23/2020] [Accepted: 11/15/2020] [Indexed: 01/17/2023]
Abstract
Euro-American lineage (Lineage 4) of Mycobacterium tuberculosis comprises genetically and geographically diverse families that differ in their clinical and/or epidemiological capacities. Due to the characteristic structure of the CRISPR locus (presence of almost all 43 classical spacers except for deleted signals 33-36), spoligotype SIT53 takes the basal position in the evolution of this lineage. In the SITVIT database, it is assigned to the "ill-defined" T family and T1 subfamily. Here, I analyzed the phylogenetic diversity of SIT53 isolates and discussed interconnected terminological issues concerning M. tuberculosis population structure. The 24-MIRU-VNTR profiles of 266 SIT53 isolates from Europe, Asia, Africa, and South America were submitted to the phylogenetic analysis jointly with reference profiles of different families from MIRU-VNTRplus database. Under this analysis, SIT53 isolates were clustered within different and distant families such as Ghana, NEW-1 (L4.5), TUR (L4.2.2.1), etc whereas many remained unclassified within L4. This confirms the evolutionarily basal position of this spoligotype and in its turn, this demonstrates that SIT53 does not correspond to any particular family of M. tuberculosis. Instead, different SIT53 subpopulations with evolutionarily stable and unchanged CRISPR locus gave rise to different and distant families that in many instances evolved through long-term allopatric evolution.
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Affiliation(s)
- Igor Mokrousov
- St. Petersburg Pasteur Institute, 14 Mira Street, St. Petersburg, 197101, Russia.
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Sachdeva K, Goel M, Sudhakar M, Mehta M, Raju R, Raman K, Singh A, Sundaramurthy V. Mycobacterium tuberculosis ( Mtb) lipid mediated lysosomal rewiring in infected macrophages modulates intracellular Mtb trafficking and survival. J Biol Chem 2020; 295:9192-9210. [PMID: 32424041 PMCID: PMC7335774 DOI: 10.1074/jbc.ra120.012809] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Revised: 05/14/2020] [Indexed: 12/24/2022] Open
Abstract
Intracellular pathogens commonly manipulate the host lysosomal system for their survival. However, whether this pathogen-induced alteration affects the organization and functioning of the lysosomal system itself is not known. Here, using in vitro and in vivo infections and quantitative image analysis, we show that the lysosomal content and activity are globally elevated in Mycobacterium tuberculosis (Mtb)-infected macrophages. We observed that this enhanced lysosomal state is sustained over time and defines an adaptive homeostasis in the infected macrophage. Lysosomal alterations are caused by mycobacterial surface components, notably the cell wall-associated lipid sulfolipid-1 (SL-1), which functions through the mTOR complex 1 (mTORC1)-transcription factor EB (TFEB) axis in the host cells. An Mtb mutant lacking SL-1, MtbΔpks2, shows attenuated lysosomal rewiring compared with the WT Mtb in both in vitro and in vivo infections. Exposing macrophages to purified SL-1 enhanced the trafficking of phagocytic cargo to lysosomes. Correspondingly, MtbΔpks2 exhibited a further reduction in lysosomal delivery compared with the WT. Reduced trafficking of this mutant Mtb strain to lysosomes correlated with enhanced intracellular bacterial survival. Our results reveal that global alteration of the host lysosomal system is a defining feature of Mtb-infected macrophages and suggest that this altered lysosomal state protects host cell integrity and contributes to the containment of the pathogen.
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Affiliation(s)
- Kuldeep Sachdeva
- National Center for Biological Sciences, Tata Institute of Fundamental Research, Bengaluru, India
| | - Manisha Goel
- National Center for Biological Sciences, Tata Institute of Fundamental Research, Bengaluru, India
| | - Malvika Sudhakar
- Department of Biotechnology, Indian Institute of Technology Madras, Chennai, India; Initiative for Biological Systems Engineering, Robert Bosch Centre for Data Science and Artificial Intelligence (RBC-DSAI), Indian Institute of Technology Madras, Chennai, India
| | - Mansi Mehta
- Center for Infectious Disease Research, Department of Microbiology and Cell Biology, Indian Institute of Science, Bengaluru, India
| | - Rajmani Raju
- Center for Infectious Disease Research, Department of Microbiology and Cell Biology, Indian Institute of Science, Bengaluru, India
| | - Karthik Raman
- Department of Biotechnology, Indian Institute of Technology Madras, Chennai, India; Initiative for Biological Systems Engineering, Robert Bosch Centre for Data Science and Artificial Intelligence (RBC-DSAI), Indian Institute of Technology Madras, Chennai, India
| | - Amit Singh
- Center for Infectious Disease Research, Department of Microbiology and Cell Biology, Indian Institute of Science, Bengaluru, India
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Lin D, Cui Z, Chongsuvivatwong V, Palittapongarnpim P, Chaiprasert A, Ruangchai W, Ou J, Huang L. The geno-spatio analysis of Mycobacterium tuberculosis complex in hot and cold spots of Guangxi, China. BMC Infect Dis 2020; 20:462. [PMID: 32611396 PMCID: PMC7329418 DOI: 10.1186/s12879-020-05189-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Accepted: 06/22/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND At present, there are few studies on polymorphism of Mycobacterium tuberculosis (Mtb) gene and how it affects the TB epidemic. This study aimed to document the differences of polymorphisms between tuberculosis hot and cold spot areas of Guangxi Zhuang Autonomous Region, China. METHODS The cold and hot spot areas, each with 3 counties, had been pre-identified by TB incidence for 5 years from the surveillance database. Whole genome sequencing analysis was performed on all sputum Mtb isolates from the detected cases during January and June 2018. Single nucleotide polymorphism (SNP) of each isolate compared to the H37Rv strain were called and used for lineage and sub-lineage identification. Pairwise SNP differences between every pair of isolates were computed. Analyses of Molecular Variance (AMOVA) across counties of the same hot or cold spot area and between the two areas were performed. RESULTS As a whole, 59.8% (57.7% sub-lineage 2.2 and 2.1% sub-lineage 2.1) and 39.8% (17.8% sub-lineage 4.4, 6.5% sub-lineage 4.2 and 15.5% sub-lineage 4.5) of the Mtb strains were Lineage 2 and Lineage 4 respectively. The percentages of sub-lineage 2.2 (Beijing family strains) are significantly higher in hot spots. Through the MDS dimension reduction, the genomic population structure in the three hot spot counties is significantly different from those three cold spot counties (T-test p = 0.05). The median of SNPs distances among Mtb isolates in cold spots was greater than that in hot spots (897 vs 746, Rank-sum test p < 0.001). Three genomic clusters, each with genomic distance ≤12 SNPs, were identified with 2, 3 and 4 consanguineous strains. Two clusters were from hot spots and one was from cold spots. CONCLUSION Narrower genotype diversity in the hot area may indicate higher transmissibility of the Mtb strains in the area compared to those in the cold spot area.
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Affiliation(s)
- Dingwen Lin
- Department of Tuberculosis Control, Guangxi Zhuang Autonomous Region Center for Disease Control and Prevention, Nanning, 530028 Guangxi China
| | - Zhezhe Cui
- Department of Tuberculosis Control, Guangxi Zhuang Autonomous Region Center for Disease Control and Prevention, Nanning, 530028 Guangxi China
| | | | - Prasit Palittapongarnpim
- Pornchai Matangkasombut Center of Microbial Genomics, Department of Microbiology, Faculty of Science, Mahidol University, Bangkok, 10700 Thailand
| | - Angkana Chaiprasert
- Office for Research and Development, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, 10700 Thailand
| | - Wuthiwat Ruangchai
- Pornchai Matangkasombut Center of Microbial Genomics, Department of Microbiology, Faculty of Science, Mahidol University, Bangkok, 10700 Thailand
| | - Jing Ou
- Department of Tuberculosis Control, Guangxi Zhuang Autonomous Region Center for Disease Control and Prevention, Nanning, 530028 Guangxi China
| | - Liwen Huang
- Department of Tuberculosis Control, Guangxi Zhuang Autonomous Region Center for Disease Control and Prevention, Nanning, 530028 Guangxi China
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Tang J, Liu Z, Shi Y, Zhan L, Qin C. Whole Genome and Transcriptome Sequencing of Two Multi-Drug Resistant Mycobacterium tuberculosis Strains to Facilitate Illustrating Their Virulence in vivo. Front Cell Infect Microbiol 2020; 10:219. [PMID: 32500039 PMCID: PMC7242654 DOI: 10.3389/fcimb.2020.00219] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Accepted: 04/21/2020] [Indexed: 11/29/2022] Open
Abstract
Mycobacterium tuberculosis clinical strains usually possess traits different from the laboratory strains like H37Rv, especially those clinical drug resistant strains. With whole genome and transcriptome sequencing, we depicted the feature of two multi-drug resistant Mtb strains in resistance and virulence. Compared with H37Rv, the differential expressed genes (DEGs) of the MDR strains showed featured enrichment in arginine biosynthesis, fatty acid biosynthesis, and metabolism pathway. In the subset of virulence genes, the overlapping DEGs of the MDR strains exhibited downregulation of the cluster in type VII secretion system. In the mice experiment, the MDR strains showed attenuated but distinct virulence, both in survival rate and pathology. Taken together, the whole genome and transcriptome analysis could help understand the unique feature of the MDR strains both in resistance and virulence.
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Affiliation(s)
- Jun Tang
- Institute of Laboratory Animal Sciences, Chinese Academy of Medical Sciences (CAMS), Comparative Medicine Center, Peking Union Medical College (PUMC), Beijing, China.,NHC Key Laboratory of Human Disease Comparative Medicine, Beijing, China.,Beijing Key Laboratory for Animal Models of Emerging and Reemerging Infectious, Beijing, China.,Beijing Engineering Research Center for Experimental Animal Models of Human Critical Diseases, Beijing, China.,Tuberculosis Center, Chinese Academy of Medical Sciences (CAMS), Beijing, China
| | - Zhihao Liu
- Institute of Laboratory Animal Sciences, Chinese Academy of Medical Sciences (CAMS), Comparative Medicine Center, Peking Union Medical College (PUMC), Beijing, China.,NHC Key Laboratory of Human Disease Comparative Medicine, Beijing, China.,Beijing Key Laboratory for Animal Models of Emerging and Reemerging Infectious, Beijing, China.,Beijing Engineering Research Center for Experimental Animal Models of Human Critical Diseases, Beijing, China.,Tuberculosis Center, Chinese Academy of Medical Sciences (CAMS), Beijing, China
| | - Ya'nan Shi
- Institute of Laboratory Animal Sciences, Chinese Academy of Medical Sciences (CAMS), Comparative Medicine Center, Peking Union Medical College (PUMC), Beijing, China.,NHC Key Laboratory of Human Disease Comparative Medicine, Beijing, China.,Beijing Key Laboratory for Animal Models of Emerging and Reemerging Infectious, Beijing, China.,Beijing Engineering Research Center for Experimental Animal Models of Human Critical Diseases, Beijing, China.,Tuberculosis Center, Chinese Academy of Medical Sciences (CAMS), Beijing, China
| | - Lingjun Zhan
- Institute of Laboratory Animal Sciences, Chinese Academy of Medical Sciences (CAMS), Comparative Medicine Center, Peking Union Medical College (PUMC), Beijing, China.,NHC Key Laboratory of Human Disease Comparative Medicine, Beijing, China.,Beijing Key Laboratory for Animal Models of Emerging and Reemerging Infectious, Beijing, China.,Beijing Engineering Research Center for Experimental Animal Models of Human Critical Diseases, Beijing, China.,Tuberculosis Center, Chinese Academy of Medical Sciences (CAMS), Beijing, China
| | - Chuan Qin
- Institute of Laboratory Animal Sciences, Chinese Academy of Medical Sciences (CAMS), Comparative Medicine Center, Peking Union Medical College (PUMC), Beijing, China.,NHC Key Laboratory of Human Disease Comparative Medicine, Beijing, China.,Beijing Key Laboratory for Animal Models of Emerging and Reemerging Infectious, Beijing, China.,Beijing Engineering Research Center for Experimental Animal Models of Human Critical Diseases, Beijing, China.,Tuberculosis Center, Chinese Academy of Medical Sciences (CAMS), Beijing, China
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Moopanar K, Mvubu NE. Lineage-specific differences in lipid metabolism and its impact on clinical strains of Mycobacterium tuberculosis. Microb Pathog 2020; 146:104250. [PMID: 32407863 DOI: 10.1016/j.micpath.2020.104250] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Revised: 04/01/2020] [Accepted: 05/06/2020] [Indexed: 01/02/2023]
Abstract
Mycobacterium tuberculosis (M. tb) is the causative agent of TB and its incidences has been on the rise since 1993. Lipid metabolism is an imperative metabolic process, which grants M. tb the ability to utilize host-derived lipids as a secondary source of nutrition during infection. In addition to degrading host lipids, M. tb is proficient at using lipids, such as cholesterol, to facilitate its entry into macrophages. Mycolic acids, constituents of the mycobacterial cell wall, offer protection and aid in persistence of the bacterium. These are effectively synthesized using a complex fatty acid synthase system. Many pathogenesis studies have reported differences in lipid-metabolism of clinical strains of M. tb that belongs to diverse lineages of the Mycobacterium tuberculosis complex (MTBC). East-Asian and Euro-American lineages possess "unique" cell wall-associated lipids compared to the less transmissible Ethiopian lineage, which may offer these lineages a competitive advantage. Therefore, it is crucial to comprehend the complexities among the MTBC lineages with lipid metabolism and their impact on virulence, transmissibility and pathogenesis. Thus, this review provides an insight into lipid metabolism in various lineages of the MTBC and their impact on virulence and persistence during infection, as this may provide critical insight into developing novel therapeutics to combat TB.
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Affiliation(s)
- K Moopanar
- School of Life Sciences, College of Agriculture, Engineering and Science, University of KwaZulu-Natal, South Africa.
| | - N E Mvubu
- School of Life Sciences, College of Agriculture, Engineering and Science, University of KwaZulu-Natal, South Africa.
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45
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Aravena P, Pulgar R, Ortiz-Severín J, Maza F, Gaete A, Martínez S, Serón E, González M, Cambiazo V. PCR-RFLP Detection and Genogroup Identification of Piscirickettsia salmonis in Field Samples. Pathogens 2020; 9:pathogens9050358. [PMID: 32397152 PMCID: PMC7281544 DOI: 10.3390/pathogens9050358] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2020] [Revised: 04/28/2020] [Accepted: 04/30/2020] [Indexed: 02/01/2023] Open
Abstract
Piscirickettsia salmons, the causative agent of piscirickettsiosis, is genetically divided into two genomic groups, named after the reference strains as LF-89-like or EM-90-like. Phenotypic differences have been detected between the P. salmonis genogroups, including antibiotic susceptibilities, host specificities and pathogenicity. In this study, we aimed to develop a rapid, sensitive and cost-effective assay for the differentiation of the P. salmonis genogroups. Using an in silico analysis of the P. salmonis 16S rDNA digestion patterns, we have designed a genogroup-specific assay based on PCR-restriction fragment length polymorphism (RFLP). An experimental validation was carried out by comparing the restriction patterns of 13 P. salmonis strains and 57 field samples obtained from the tissues of dead or moribund fish. When the bacterial composition of a set of field samples, for which we detected mixtures of bacterial DNA, was analyzed by a high-throughput sequencing of the 16S rRNA gene amplicons, a diversity of taxa could be identified, including pathogenic and commensal bacteria. Despite the presence of mixtures of bacterial DNA, the characteristic digestion pattern of the P. salmonis genogroups could be detected in the field samples without the need of a microbiological culture and bacterial isolation.
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Affiliation(s)
- Pamela Aravena
- Laboratorio de Bioinformática y Expresión Génica, Instituto de Nutrición y Tecnología de los Alimentos (INTA), Universidad de Chile, Santiago 7830490, Chile; (P.A.); (R.P.); (J.O.-S.); (F.M.); (A.G.); (M.G.)
- FONDAP Center for Genome Regulation, Santiago 8370415, Chile
| | - Rodrigo Pulgar
- Laboratorio de Bioinformática y Expresión Génica, Instituto de Nutrición y Tecnología de los Alimentos (INTA), Universidad de Chile, Santiago 7830490, Chile; (P.A.); (R.P.); (J.O.-S.); (F.M.); (A.G.); (M.G.)
| | - Javiera Ortiz-Severín
- Laboratorio de Bioinformática y Expresión Génica, Instituto de Nutrición y Tecnología de los Alimentos (INTA), Universidad de Chile, Santiago 7830490, Chile; (P.A.); (R.P.); (J.O.-S.); (F.M.); (A.G.); (M.G.)
| | - Felipe Maza
- Laboratorio de Bioinformática y Expresión Génica, Instituto de Nutrición y Tecnología de los Alimentos (INTA), Universidad de Chile, Santiago 7830490, Chile; (P.A.); (R.P.); (J.O.-S.); (F.M.); (A.G.); (M.G.)
- FONDAP Center for Genome Regulation, Santiago 8370415, Chile
| | - Alexis Gaete
- Laboratorio de Bioinformática y Expresión Génica, Instituto de Nutrición y Tecnología de los Alimentos (INTA), Universidad de Chile, Santiago 7830490, Chile; (P.A.); (R.P.); (J.O.-S.); (F.M.); (A.G.); (M.G.)
- FONDAP Center for Genome Regulation, Santiago 8370415, Chile
| | - Sebastián Martínez
- Laboratorio Especialidades Técnicas Marinas (ETECMA), Puerto Montt 5500001, Chile; (S.M.); (E.S.)
| | - Ervin Serón
- Laboratorio Especialidades Técnicas Marinas (ETECMA), Puerto Montt 5500001, Chile; (S.M.); (E.S.)
| | - Mauricio González
- Laboratorio de Bioinformática y Expresión Génica, Instituto de Nutrición y Tecnología de los Alimentos (INTA), Universidad de Chile, Santiago 7830490, Chile; (P.A.); (R.P.); (J.O.-S.); (F.M.); (A.G.); (M.G.)
- FONDAP Center for Genome Regulation, Santiago 8370415, Chile
| | - Verónica Cambiazo
- Laboratorio de Bioinformática y Expresión Génica, Instituto de Nutrición y Tecnología de los Alimentos (INTA), Universidad de Chile, Santiago 7830490, Chile; (P.A.); (R.P.); (J.O.-S.); (F.M.); (A.G.); (M.G.)
- FONDAP Center for Genome Regulation, Santiago 8370415, Chile
- Correspondence:
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46
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Sobkowiak B, Banda L, Mzembe T, Crampin AC, Glynn JR, Clark TG. Bayesian reconstruction of Mycobacterium tuberculosis transmission networks in a high incidence area over two decades in Malawi reveals associated risk factors and genomic variants. Microb Genom 2020; 6:e000361. [PMID: 32234123 PMCID: PMC7276699 DOI: 10.1099/mgen.0.000361] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2019] [Accepted: 03/12/2020] [Indexed: 11/21/2022] Open
Abstract
Understanding host and pathogen factors that influence tuberculosis (TB) transmission can inform strategies to eliminate the spread of Mycobacterium tuberculosis (Mtb). Determining transmission links between cases of TB is complicated by a long and variable latency period and undiagnosed cases, although methods are improving through the application of probabilistic modelling and whole-genome sequence analysis. Using a large dataset of 1857 whole-genome sequences and comprehensive metadata from Karonga District, Malawi, over 19 years, we reconstructed Mtb transmission networks using a two-step Bayesian approach that identified likely infector and recipient cases, whilst robustly allowing for incomplete case sampling. We investigated demographic and pathogen genomic variation associated with transmission and clustering in our networks. We found that whilst there was a significant decrease in the proportion of infectors over time, we found higher transmissibility and large transmission clusters for lineage 2 (Beijing) strains. By performing evolutionary convergence testing (phyC) and genome-wide association analysis (GWAS) on transmitting versus non-transmitting cases, we identified six loci, PPE54, accD2, PE_PGRS62, rplI, Rv3751 and Rv2077c, that were associated with transmission. This study provides a framework for reconstructing large-scale Mtb transmission networks. We have highlighted potential host and pathogen characteristics that were linked to increased transmission in a high-burden setting and identified genomic variants that, with validation, could inform further studies into transmissibility and TB eradication.
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Affiliation(s)
- Benjamin Sobkowiak
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
- Present address: Division of Respiratory Medicine, University of British Columbia, Vancouver, Canada, and British Columbia Centre for Disease Control, Vancouver, Canada
| | - Louis Banda
- Malawi Epidemiology and Intervention Research Unit, Malawi
| | - Themba Mzembe
- Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, London, UK
| | - Amelia C. Crampin
- Institute of Health and Wellbeing, University of Glasgow, Glasgow, UK
| | - Judith R. Glynn
- Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, 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
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47
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Gu X, Ding J, Liu W, Yang X, Yao L, Gao X, Zhang M, Yang S, Wen J. Comparative genomics and association analysis identifies virulence genes of Cercospora sojina in soybean. BMC Genomics 2020; 21:172. [PMID: 32075575 PMCID: PMC7032006 DOI: 10.1186/s12864-020-6581-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Accepted: 02/13/2020] [Indexed: 03/01/2023] Open
Abstract
BACKGROUND Recently, a new strain of Cercospora sojina (Race15) has been identified, which has caused the breakdown of resistance in most soybean cultivars in China. Despite this serious yield reduction, little is known about why this strain is more virulent than others. Therefore, we sequenced the Race15 genome and compared it to the Race1 genome sequence, as its virulence is significantly lower. We then re-sequenced 30 isolates of C. sojina from different regions to identifying differential virulence genes using genome-wide association analysis (GWAS). RESULTS The 40.12-Mb Race15 genome encodes 12,607 predicated genes and contains large numbers of gene clusters that have annotations in 11 different common databases. Comparative genomics revealed that although these two genomes had a large number of homologous genes, their genome structures have evolved to introduce 245 specific genes. The most important 5 candidate virulence genes were located on Contig 3 and Contig 1 and were mainly related to the regulation of metabolic mechanisms and the biosynthesis of bioactive metabolites, thereby putatively affecting fungi self-toxicity and reducing host resistance. Our study provides insight into the genomic basis of C. sojina pathogenicity and its infection mechanism, enabling future studies of this disease. CONCLUSIONS Via GWAS, we identified five candidate genes using three different methods, and these candidate genes are speculated to be related to metabolic mechanisms and the biosynthesis of bioactive metabolites. Meanwhile, Race15 specific genes may be linked with high virulence. The genes highly prevalent in virulent isolates should also be proposed as candidates, even though they were not found in our SNP analysis. Future work should focus on using a larger sample size to confirm and refine candidate gene identifications and should study the functional roles of these candidates, in order to investigate their potential roles in C. sojina pathogenicity.
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Affiliation(s)
- Xin Gu
- Department of Plant Protection, College of Agriculture, Northeast Agricultural University, Harbin, China
- Jiamusi Branch of Heilongjiang Academy of Agricultural Sciences, Jiamusi, China
| | - Junjie Ding
- Jiamusi Branch of Heilongjiang Academy of Agricultural Sciences, Jiamusi, China
| | - Wei Liu
- Jiamusi Branch of Heilongjiang Academy of Agricultural Sciences, Jiamusi, China
| | - Xiaohe Yang
- Jiamusi Branch of Heilongjiang Academy of Agricultural Sciences, Jiamusi, China
| | - Liangliang Yao
- Jiamusi Branch of Heilongjiang Academy of Agricultural Sciences, Jiamusi, China
| | - Xuedong Gao
- Jiamusi Branch of Heilongjiang Academy of Agricultural Sciences, Jiamusi, China
| | - Maoming Zhang
- Jiamusi Branch of Heilongjiang Academy of Agricultural Sciences, Jiamusi, China
| | - Shuai Yang
- Potato Research Institute, Heilongjiang Academy of Agricultural Sciences, Harbin, 150086, China
| | - Jingzhi Wen
- Department of Plant Protection, College of Agriculture, Northeast Agricultural University, Harbin, China.
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48
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TbD1 deletion as a driver of the evolutionary success of modern epidemic Mycobacterium tuberculosis lineages. Nat Commun 2020; 11:684. [PMID: 32019932 PMCID: PMC7000671 DOI: 10.1038/s41467-020-14508-5] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Accepted: 01/09/2020] [Indexed: 11/29/2022] Open
Abstract
Mycobacterium tuberculosis (Mtb) strains are classified into different phylogenetic lineages (L), three of which (L2/L3/L4) emerged from a common progenitor after the loss of the MmpS6/MmpL6-encoding Mtb-specific deletion 1 region (TbD1). These TbD1-deleted “modern” lineages are responsible for globally-spread tuberculosis epidemics, whereas TbD1-intact “ancestral” lineages tend to be restricted to specific geographical areas, such as South India and South East Asia (L1) or East Africa (L7). By constructing and characterizing a panel of recombinant TbD1-knock-in and knock-out strains and comparison with clinical isolates, here we show that deletion of TbD1 confers to Mtb a significant increase in resistance to oxidative stress and hypoxia, which correlates with enhanced virulence in selected cellular, guinea pig and C3HeB/FeJ mouse infection models, the latter two mirroring in part the development of hypoxic granulomas in human disease progression. Our results suggest that loss of TbD1 at the origin of the L2/L3/L4 Mtb lineages was a key driver for their global epidemic spread and outstanding evolutionary success. Mycobacterium tuberculosis (Mtb) modern strains emerged from a common progenitor after the loss of Mtb-specific deletion 1 region (TbD1). Here, the authors show that deletion of TbD1 correlates with enhanced Mtb virulence in animal models, mirroring the development of hypoxic granulomas in human disease progression.
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49
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Palucci I, Maulucci G, De Maio F, Sali M, Romagnoli A, Petrone L, Fimia GM, Sanguinetti M, Goletti D, De Spirito M, Piacentini M, Delogu G. Inhibition of Transglutaminase 2 as a Potential Host-Directed Therapy Against Mycobacterium tuberculosis. Front Immunol 2020; 10:3042. [PMID: 32038614 PMCID: PMC6992558 DOI: 10.3389/fimmu.2019.03042] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Accepted: 12/11/2019] [Indexed: 12/14/2022] Open
Abstract
Host-directed therapies (HDTs) are emerging as a potential valid support in the treatment of drug-resistant tuberculosis (TB). Following our recent report indicating that genetic and pharmacological inhibition of transglutaminase 2 (TG2) restricts Mycobacterium tuberculosis (Mtb) replication in macrophages, we aimed to investigate the potentials of the TG2 inhibitors cystamine and cysteamine as HDTs against TB. We showed that both cysteamine and cystamine restricted Mtb replication in infected macrophages when provided at equimolar concentrations and did not exert any antibacterial activity when administered directly on Mtb cultures. Interestingly, infection of differentiated THP-1 mRFP-GFP-LC3B cells followed by the determination of the autophagic intermediates pH distribution (AIPD) showed that cystamine inhibited the autophagic flux while restricting Mtb replication. Moreover, both cystamine and cysteamine had a similar antimicrobial activity in primary macrophages infected with a panel of Mtb clinical strains belonging to different phylogeographic lineages. Evaluation of cysteamine and cystamine activity in the human ex vivo model of granuloma-like structures (GLS) further confirmed the ability of these drugs to restrict Mtb replication and to reduce the size of GLS. The antimicrobial activity of the TG2 inhibitors synergized with a second-line anti-TB drug as amikacin in human monocyte-derived macrophages and in the GLS model. Overall, the results of this study support the potential usefulness of the TG2-inhibitors cysteamine and cystamine as HDTs against TB.
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Affiliation(s)
- Ivana Palucci
- Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy.,Institute of Microbiology, Università Cattolica del Sacro Cuore, Rome, Italy
| | - Giuseppe Maulucci
- Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy.,Institute of Physics, Università Cattolica del Sacro Cuore, Rome, Italy
| | - Flavio De Maio
- Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy.,Institute of Microbiology, Università Cattolica del Sacro Cuore, Rome, Italy
| | - Michela Sali
- Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy.,Institute of Microbiology, Università Cattolica del Sacro Cuore, Rome, Italy
| | - Alessandra Romagnoli
- Electron Microscopy and Cell Biology Unit, Department of Epidemiology and Preclinical Research, "L. Spallanzani" National Institute for Infectious Diseases (INMI), IRCCS, Rome, Italy
| | - Linda Petrone
- Translational Research Unit, Department of Epidemiology and Preclinical Research, "L. Spallanzani" National Institute for Infectious Diseases (INMI), IRCCS, Rome, Italy
| | - Gian Maria Fimia
- Electron Microscopy and Cell Biology Unit, Department of Epidemiology and Preclinical Research, "L. Spallanzani" National Institute for Infectious Diseases (INMI), IRCCS, Rome, Italy.,Department of Molecular Medicine, Sapienza University of Rome, Rome, Italy
| | - Maurizio Sanguinetti
- Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy.,Institute of Microbiology, Università Cattolica del Sacro Cuore, Rome, Italy
| | - Delia Goletti
- Translational Research Unit, Department of Epidemiology and Preclinical Research, "L. Spallanzani" National Institute for Infectious Diseases (INMI), IRCCS, Rome, Italy
| | - Marco De Spirito
- Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy.,Institute of Physics, Università Cattolica del Sacro Cuore, Rome, Italy
| | - Mauro Piacentini
- Electron Microscopy and Cell Biology Unit, Department of Epidemiology and Preclinical Research, "L. Spallanzani" National Institute for Infectious Diseases (INMI), IRCCS, Rome, Italy.,Department of Biology, University of Rome "Tor Vergata", Rome, Italy
| | - Giovanni Delogu
- Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy.,Institute of Microbiology, Università Cattolica del Sacro Cuore, Rome, Italy.,Mater Olbia Hospital, Olbia, Italy
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50
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Ofori-Anyinam B, Riley AJ, Jobarteh T, Gitteh E, Sarr B, Faal-Jawara TI, Rigouts L, Senghore M, Kehinde A, Onyejepu N, Antonio M, de Jong BC, Gehre F, Meehan CJ. Comparative genomics shows differences in the electron transport and carbon metabolic pathways of Mycobacterium africanum relative to Mycobacterium tuberculosis and suggests an adaptation to low oxygen tension. Tuberculosis (Edinb) 2020; 120:101899. [PMID: 32090860 PMCID: PMC7049902 DOI: 10.1016/j.tube.2020.101899] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Revised: 12/31/2019] [Accepted: 01/05/2020] [Indexed: 12/21/2022]
Abstract
The geographically restricted Mycobacterium africanum lineages (MAF) are primarily found in West Africa, where they account for a significant proportion of tuberculosis. Despite this phenomenon, little is known about the co-evolution of these ancient lineages with West Africans. MAF and M. tuberculosis sensu stricto lineages (MTB) differ in their clinical, in vitro and in vivo characteristics for reasons not fully understood. Therefore, we compared genomes of 289 MAF and 205 MTB clinical isolates from the 6 main human-adapted M. tuberculosis complex lineages, for mutations in their Electron Transport Chain and Central Carbon Metabolic pathway in order to explain these metabolic differences. Furthermore, we determined, in silico, whether each mutation could affect the function of genes encoding enzymes in these pathways. We found more mutations with the potential to affect enzymes in these pathways in MAF lineages compared to MTB lineages. We also found that similar mutations occurred in these pathways between MAF and some MTB lineages. Generally, our findings show further differences between MAF and MTB lineages that may have contributed to the MAF clinical and growth phenotype and indicate potential adaptation of MAF lineages to a distinct ecological niche, which we suggest includes areas characterized by low oxygen tension.
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Affiliation(s)
- Boatema Ofori-Anyinam
- Mycobacteriology Unit, Institute of Tropical Medicine, Antwerp, Belgium; Vaccines and Immunity Theme, Medical Research Council Unit, Banjul, Gambia; Center for Global Health Security and Diplomacy, Ottawa, Canada
| | - Abi Janet Riley
- Vaccines and Immunity Theme, Medical Research Council Unit, Banjul, Gambia
| | - Tijan Jobarteh
- Vaccines and Immunity Theme, Medical Research Council Unit, Banjul, Gambia
| | - Ensa Gitteh
- Vaccines and Immunity Theme, Medical Research Council Unit, Banjul, Gambia
| | - Binta Sarr
- Vaccines and Immunity Theme, Medical Research Council Unit, Banjul, Gambia
| | | | - Leen Rigouts
- Mycobacteriology Unit, Institute of Tropical Medicine, Antwerp, Belgium; Department of Biomedical Sciences, Antwerp University, Antwerp, Belgium
| | - Madikay Senghore
- Vaccines and Immunity Theme, Medical Research Council Unit, Banjul, Gambia
| | - Aderemi Kehinde
- Department of Medical Microbiology & Parasitology, University College Hospital, Ibadan, Nigeria; Department of Medical Microbiology & Parasitology, College of Medicine, University of Ibadan, Ibadan, Nigeria
| | - Nneka Onyejepu
- Center for Tuberculosis Research, Nigeria Institute of Medical Research, Lagos, Nigeria
| | - Martin Antonio
- Vaccines and Immunity Theme, Medical Research Council Unit, Banjul, Gambia; Division of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, United Kingdom; Medical School, University of Warwick, Coventry, United Kingdom
| | - Bouke C de Jong
- Mycobacteriology Unit, Institute of Tropical Medicine, Antwerp, Belgium
| | - Florian Gehre
- Mycobacteriology Unit, Institute of Tropical Medicine, Antwerp, Belgium; Vaccines and Immunity Theme, Medical Research Council Unit, Banjul, Gambia; Bernhard-Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - Conor J Meehan
- Mycobacteriology Unit, Institute of Tropical Medicine, Antwerp, Belgium; School of Chemistry and Biosciences, University of Bradford, Bradford, United Kingdom.
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