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Garcia-Basteiro AL, Ehrlich J, Bonnet M, Calnan M, Graham SM, Hermans S, Jarrett A, Lewa R, Mandalakas A, Martinez L, Migliori GB, Ong CWM, Otero L, Rangaka MX, Raviglione MCB, Seaworth B, Ssengooba W, Theron G, Trajman A, Behr MA. A Global Tuberculosis Dictionary: unified terms and definitions for the field of tuberculosis. Lancet Glob Health 2024; 12:e737-e739. [PMID: 38527468 DOI: 10.1016/s2214-109x(24)00083-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2024] [Accepted: 02/15/2024] [Indexed: 03/27/2024]
Affiliation(s)
- Alberto L Garcia-Basteiro
- Centro de Investigação em Saúde de Manhiça, Manhiça 1121, Mozambique; Instituto de Salud Global de Barcelona, Barcelona, Spain.
| | - Joanna Ehrlich
- Instituto de Salud Global de Barcelona, Barcelona, Spain
| | - Maryline Bonnet
- TransVIHMI, University of Montpellier, Institut de Recherche pour le Développement, Institut National de la Santé et de la Recherche Médicale, Montpellier, France
| | | | - Stephen M Graham
- University of Melbourne Department of Paediatrics, Royal Children's Hospital, Melbourne, VIC, Australia
| | - Sabine Hermans
- Department of Global Health, Amsterdam Institute for Global Health and Development, Amsterdam UMC, Amsterdam, Netherlands; Department of Infectious Diseases, Centre for Tropical Medicine and Travel Medicine, Amsterdam UMC, Amsterdam, Netherlands
| | - Adriana Jarrett
- We Are TB, National Tuberculosis Controllers Association, Smyrna, GA, USA
| | | | - Anna Mandalakas
- Department of Pediatrics, Baylor College of Medicine-Texas Children's Hospital, Houston, TX, USA
| | - Leonardo Martinez
- Department of Epidemiology, School of Public Health, Boston University, Boston, MA, USA
| | - Giovanni Battista Migliori
- Servizio di Epidemiologia Clinica delle Malattie Respiratorie, Istituti Clinici Scientifici Maugeri, IRCCS Tradate, Tradate, Italy
| | - Catherine W M Ong
- Infectious Diseases Translational Research Programme and Division of Infectious Diseases, Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Larissa Otero
- School of Medicine and Instituto de Medicina Tropical Alexander von Humboldt, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Molebogeng Xheedha Rangaka
- Institute for Global Health & Medical Research Council Clinical Trials Unit, University College London, London, UK; School of Public Health and Clinical Infectious Disease Research Institute-AFRICA, University of Cape Town, Cape Town, South Africa
| | - Mario C B Raviglione
- Centre for Multidisciplinary Research in Health Science, University of Milan, Milan, Italy
| | - Barbara Seaworth
- University of Texas at Tyler Health Science Center, Tyler, Texas, USA
| | - Willy Ssengooba
- Department of Medical Microbiology, Makerere University, Kampala, Uganda
| | - Grant Theron
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Anete Trajman
- Federal University of Rio de Janeiro, Rio de Janeiro, Brazil; McGill International TB Centre, Montreal, QC, Canada
| | - Marcel A Behr
- McGill International TB Centre, Montreal, QC, Canada
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Behr MA, Edelstein PH, Ramakrishnan L. Rethinking the burden of latent tuberculosis to reprioritize research. Nat Microbiol 2024:10.1038/s41564-024-01683-0. [PMID: 38671272 DOI: 10.1038/s41564-024-01683-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/28/2024]
Affiliation(s)
- Marcel A Behr
- Department of Medicine, McGill University, McGill International TB Centre, Montreal, Quebec, Canada
| | - Paul H Edelstein
- Department of Medicine, University of Cambridge, Cambridge, UK
- MRC Laboratory of Molecular Biology, Cambridge, UK
| | - Lalita Ramakrishnan
- Department of Medicine, University of Cambridge, Cambridge, UK.
- MRC Laboratory of Molecular Biology, Cambridge, UK.
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3
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Biet F, Conde C, Cochard T, Mcintoch FA, Behr MA, Bannantine JP. Complete genome sequence of an ovine ancestral strain of Mycobacterium avium subspecies paratuberculosis 6756. Microbiol Resour Announc 2024; 13:e0120723. [PMID: 38441975 PMCID: PMC11008209 DOI: 10.1128/mra.01207-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Accepted: 02/24/2024] [Indexed: 03/07/2024] Open
Abstract
The complete genome sequence of the most ancestral type SI strain of Mycobacterium avium subspecies paratuberculosis 6756, isolated from a sheep, was determined. The genome was sequenced using PacBio technology, yielding a genome size of 4,830,294 nucleotides with no identified plasmids.
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Affiliation(s)
- Franck Biet
- INRAE, Université de Tours ISP, Nouzilly, France
| | - Cyril Conde
- INRAE, Université de Tours ISP, Nouzilly, France
| | | | | | - Marcel A. Behr
- McGill University Health Centre, Montreal, Quebec, Canada
| | - John P. Bannantine
- USDA-Agricultural Research Service, National Animal Disease Center, Ames, Iowa, USA
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Duffy SC, Marais B, Kapur V, Behr MA. Zoonotic tuberculosis in the 21st century. Lancet Infect Dis 2024; 24:339-341. [PMID: 38307096 DOI: 10.1016/s1473-3099(24)00059-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Accepted: 01/18/2024] [Indexed: 02/04/2024]
Affiliation(s)
- Shannon C Duffy
- Department of Microbiology and Immunology, McGill University, Montreal, QC H4A 3J1, Canada; McGill International TB Centre, McGill University, Montreal, QC H4A 3J1, Canada; The Infectious Diseases and Immunity in Global Health Program, Research Institute of the McGill University Health Centre, Montreal, QC, Canada
| | - Ben Marais
- Sydney Infectious Diseases Institute, University of Sydney, NSW, Australia
| | - Vivek Kapur
- Department of Animal Science and the Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, USA
| | - Marcel A Behr
- Department of Microbiology and Immunology, McGill University, Montreal, QC H4A 3J1, Canada; McGill International TB Centre, McGill University, Montreal, QC H4A 3J1, Canada; Department of Medicine, McGill University, Montreal, QC H4A 3J1, Canada; The Infectious Diseases and Immunity in Global Health Program, Research Institute of the McGill University Health Centre, Montreal, QC, Canada.
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5
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Bannantine JP, Duffy SC, Colombatti Olivieri MA, Behr MA, Biet F, Price NPJ. Genetic and chemical control of tuberculostearic acid production in Mycobacterium avium subspecies paratuberculosis. Microbiol Spectr 2024:e0050824. [PMID: 38501867 DOI: 10.1128/spectrum.00508-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2024] [Accepted: 02/28/2024] [Indexed: 03/20/2024] Open
Abstract
Tuberculostearic acid (TBSA) is a fatty acid unique to mycobacteria and some corynebacteria and has been studied due to its diagnostic value, biofuel properties, and role in membrane dynamics. In this study, we demonstrate that TBSA production can be abrogated either by addition of pivalic acid to mycobacterial growth cultures or by a bfaA gene knockout encoding a flavin adenine dinucleotide (FAD)-binding oxidoreductase. Mycobacterium avium subspecies paratuberculosis (Map) growth and TBSA production were inhibited in 0.5-mg/mL pivalic acid-supplemented cultures, but higher concentrations were needed to have a similar effect in other mycobacteria, including Mycobacterium smegmatis. While Map C-type strains, isolated from cattle and other ruminants, will produce TBSA in the absence of pivalic acid, the S-type Map strains, typically isolated from sheep, do not produce TBSA in any condition. A SAM-dependent methyltransferase encoded by bfaB and FAD-binding oxidoreductase are both required in the two-step biosynthesis of TBSA. However, S-type strains contain a single-nucleotide polymorphism in the bfaA gene, rendering the oxidoreductase enzyme vestigial. This results in the production of an intermediate, termed 10-methylene stearate, which is detected only in S-type strains. Fatty acid methyl ester analysis of a C-type Map bfaA knockout revealed the loss of TBSA production, but the intermediate was present, similar to the S-type strains. Collectively, these results demonstrate the subtle biochemical differences between two primary genetic lineages of Map and other mycobacteria as well as explain the resulting phenotype at the genetic level. These data also suggest that TBSA should not be used as a diagnostic marker for Map.IMPORTANCEBranched-chain fatty acids are a predominant cell wall component among species belonging to the Mycobacterium genus. One of these is TBSA, which is a long-chain middle-branched fatty acid used as a diagnostic marker for Mycobacterium tuberculosis. This fatty acid is also an excellent biolubricant. Control of its production is important for industrial purposes as well as understanding the biology of mycobacteria. In this study, we discovered that a carboxylic acid compound termed pivalic acid inhibits TBSA production in mycobacteria. Furthermore, Map strains from two separate genetic lineages (C-type and S-type) showed differential production of TBSA. Cattle-type strains of Mycobacterium avium subspecies paratuberculosis produce TBSA, while the sheep-type strains do not. This important phenotypic difference is attributed to a single-nucleotide deletion in sheep-type strains of Map. This work sheds further light on the mechanism used by mycobacteria to produce tuberculostearic acid.
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Affiliation(s)
- John P Bannantine
- National Animal Disease Center, USDA Agricultural Research Service, Ames, Iowa, USA
| | - Shannon C Duffy
- Department of Microbiology and Immunology, McGill University, Montreal, Quebec, Canada
| | - María A Colombatti Olivieri
- National Animal Disease Center, USDA Agricultural Research Service, Ames, Iowa, USA
- ARS Participation Program, Oak Ridge Institute for Science and Education (ORISE), Oak Ridge, Tennessee, USA
| | - Marcel A Behr
- Department of Microbiology and Immunology, McGill University, Montreal, Quebec, Canada
| | - Franck Biet
- INRAE, ISP, Université de Tours, Nouzilly, France
| | - Neil P J Price
- National Center for Agricultural Utilization Research, USDA Agricultural Research Service, Peoria, Illinois, USA
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White RG, Fiore-Gartland AJ, Hanekom WA, Vekemans J, Garcia-Basteiro AL, Churchyard G, Rangaka MX, Frick M, Behr MA, Hill PC, Mave V. What is next for BCG revaccination to prevent tuberculosis? Lancet Respir Med 2024; 12:e7-e8. [PMID: 38272048 DOI: 10.1016/s2213-2600(24)00009-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Accepted: 01/16/2024] [Indexed: 01/27/2024]
Affiliation(s)
- Richard G White
- Department of Infectious Disease Epidemiology, London School of Hygiene and Tropical Medicine, London, WC1E 7HT, UK.
| | | | | | - Johan Vekemans
- International AIDS Vaccine Initiative, New York, NY, USA
| | - Alberto L Garcia-Basteiro
- Centro de Investigação em Saúde de Manhiça, Maputo, Mozambique; ISGlobal, Hospital Clínic, Universitat de Barcelona, Barcelona, Spain; Centro de Investigación Biomédica en Red de Enfermedades Infecciosas, Barcelona, Spain
| | | | - Molebogeng X Rangaka
- Institute for Global Health, Medical Research Council Clinical Trials Unit, University College London, London, UK; CIDRI-AFRICA, Institute of Infectious Disease and Molecular Medicine and School of Public Health, University of Cape Town, Cape Town, South Africa
| | - Mike Frick
- Treatment Action Group, New York, NY, USA
| | - Marcel A Behr
- McGill International TB Centre, McGill University, Montreal, QC, Canada
| | | | - Vidya Mave
- Byramjee Jeejeebhoy Government Medical College, Johns Hopkins University Clinical Research Site, Pune, Maharashtra, India; Center for Infectious Diseases in India, Johns Hopkins India, Pune, India
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Hill PC, Cobelens F, Martinez L, Garcia-Basteiro AL, Behr MA, Rangaka MX, Churchyard G, Evans T, Hanekom W, White RG. Reply to McShane. J Infect Dis 2024; 229:616. [PMID: 37897697 DOI: 10.1093/infdis/jiad466] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Accepted: 10/26/2023] [Indexed: 10/30/2023] Open
Affiliation(s)
- Philip C Hill
- Centre for International Health, University of Otago, Dunedin, New Zealand
| | - Frank Cobelens
- Department of Global Health, Amsterdam University Medical Centre, Amsterdam, The Netherlands
- Amsterdam Institute for Global Health and Development, Amsterdam University Medical Centre, Amsterdam, The Netherlands
| | - Leonardo Martinez
- Department of Epidemiology, School of Public Health, Boston University, Boston, Massachusetts, USA
| | - Alberto L Garcia-Basteiro
- Centro de Investigação em Saúde de Manhiça, Maputo, Mozambique
- Instituto de Salud Global, Hospital Clínic-Universitat de Barcelona, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Infecciosas, Barcelona, Spain
| | - Marcel A Behr
- McGill International TB Centre, McGill University, Montreal, Quebec, Canada
| | - Molebogeng X Rangaka
- Institute for Global Health, University College London, London, United Kingdom
- MRC Clinical Trials Unit, University College London, London, United Kingdom
- Centre for Infectious Diseases Research Africa, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Gavin Churchyard
- The Aurum Institute, Parktown, South Africa
- Department of Medicine, Vanderbilt University, Nashville, Tennessee, USA
- School of Public Health, University of the Witwatersrand, Johannesburg, South Africa
| | | | - Willem Hanekom
- Africa Health Research Institute, Durban, KwaZulu-Natal, South Africa
- Division of Infection and Immunity, University College London, London, United Kingdom
| | - Richard G White
- Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, London, United Kingdom
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Maqsood R, Duffy SC, Bin Rashid H, Gill SS, Jabeen C, Arshad N, Umbreen G, Behr MA, Kapur V, Chaudhry M. Molecular detection and characterization of the Mycobacterium tuberculosis complex subspecies responsible for bovine tuberculosis in Punjab, Pakistan. Microbiol Spectr 2024; 12:e0269223. [PMID: 38226805 PMCID: PMC10846167 DOI: 10.1128/spectrum.02692-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Accepted: 11/16/2023] [Indexed: 01/17/2024] Open
Abstract
Bovine tuberculosis (bTB), traditionally associated with Mycobacterium bovis, presents significant public health and economic challenges worldwide. This study investigated the causative agents of bTB in slaughtered cattle and buffalo in Lahore, Pakistan. Of the 3,581 animals screened, 34 were identified with gross TB-like lesions. The lesions were processed for culture, PCR, and Sanger sequencing to identify the causative agents of the disease. The results identified 10 Mycobacterium orygis and 8 Mycobacterium tuberculosis sensu stricto isolates. Whole-genome sequencing was performed on two M. orygis isolates, and the sequences were phylogenetically compared to 93 publicly available M. orygis sequences. The results also demonstrated that the JB21 and JB22 primers, which have been previously commonly applied to detect M. bovis in Pakistan, are unable to distinguish between M. tuberculosis complex subspecies. The identification of M. orygis and M. tuberculosis as causative agents of bTB in this slaughterhouse in Punjab may have important implications in identifying cases of zoonotic TB in humans and applying appropriate molecular tools to identify the prevalence of the disease. The data from this study align with recent findings suggesting M. orygis is the predominant cause of bTB in South Asia.IMPORTANCEThe study findings hold significant relevance to the Journal of Clinical Microbiology, as they directly impact the field. The first-time identification of Mycobacterium orygis and Mycobacterium tuberculosis as the predominant causative agents of bovine tuberculosis in Lahore, Pakistan underscores the urgent need for enhanced diagnostic methods. The study emphasizes the importance of improved assays for the accurate detection and differentiation of Mycobacterium subspecies. Additionally, the research addresses zoonotic risk assessment and public health implications, advocating for a multidisciplinary approach that integrates clinical microbiology with veterinary and human health sectors. These insights contribute to clinical microbiology knowledge, shaping effective strategies for disease prevention, surveillance, and control. The study's potential to advance the field makes it well suited for publication in the Microbiology Spectrum journal.
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Affiliation(s)
- Rubab Maqsood
- Department of Epidemiology and Public Health, University of Veterinary and Animal Sciences, Lahore, Pakistan
- Institute of Continuing Education and Extension, University of Veterinary and Animal Sciences, Ravi Campus, Pattoki, Pakistan
| | - Shannon C. Duffy
- Department of Microbiology and Immunology, McGill University, Montreal, Quebec, Canada
- The Infectious Diseases and Immunity in Global Health Program, Research Institute of the McGill University Health Centre, Montreal, Quebec, Canada
| | - Hamad Bin Rashid
- Department of Veterinary Surgery and Pet Sciences, University of Veterinary and Animal Sciences, Lahore, Pakistan
| | - Shakera Sadiq Gill
- Department of Epidemiology and Public Health, University of Veterinary and Animal Sciences, Lahore, Pakistan
| | - Chanda Jabeen
- Department of Epidemiology and Public Health, University of Veterinary and Animal Sciences, Lahore, Pakistan
| | - Nimra Arshad
- Department of Epidemiology and Public Health, University of Veterinary and Animal Sciences, Lahore, Pakistan
| | - Gulshan Umbreen
- Department of Epidemiology and Public Health, University of Veterinary and Animal Sciences, Lahore, Pakistan
| | - Marcel A. Behr
- Department of Microbiology and Immunology, McGill University, Montreal, Quebec, Canada
- The Infectious Diseases and Immunity in Global Health Program, Research Institute of the McGill University Health Centre, Montreal, Quebec, Canada
- Department of Medicine, McGill University, Montreal, Quebec, Canada
| | - Vivek Kapur
- Department of Animal Science, The Pennsylvania State University, University Park, Pennsylvania, USA
- The Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, Pennsylvania, USA
| | - Mamoona Chaudhry
- Department of Epidemiology and Public Health, University of Veterinary and Animal Sciences, Lahore, Pakistan
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Danchuk SN, Solomon OE, Kohl TA, Dreyer V, Barilar I, Utpatel C, Niemann S, Soolingen DV, Anthony R, van Ingen J, Michael JS, Behr MA. Challenging the gold standard: the limitations of molecular assays for detection of Mycobacterium tuberculosis heteroresistance. Thorax 2024:thorax-2023-220202. [PMID: 38286614 DOI: 10.1136/thorax-2023-220202] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Accepted: 01/08/2024] [Indexed: 01/31/2024]
Abstract
OBJECTIVES Heteroresistant infections are defined as infections in which a mixture of drug-resistant and drug-susceptible populations are present. In Mycobacterium tuberculosis (M. tb), heteroresistance poses a challenge in diagnosis and has been linked with poor treatment outcomes. We compared the analytical sensitivity of molecular methods, such as GeneXpert and whole genome sequencing (WGS) in detecting heteroresistance when compared with the 'gold standard' phenotypic assay: the agar proportion method (APM). METHODS Using two rounds of proficiency surveys with defined monoresistant BCG strains and mixtures of susceptible/resistant M. tb, we determined the limit of detection (LOD) of known resistance associated mutations. RESULTS The LOD for rifampin-R (RIF-R) detection was 1% using APM, 60% using GeneXpert MTB/RIF, 10% using GeneXpert MTB/RIF Ultra and 10% using WGS. While WGS could detect mutations beyond those associated with RIF resistance, the LOD for these other mutations was also 10%. Additionally, we observed instances where laboratories did not report resistance in the majority population, yet the mutations were present in the raw sequence data. CONCLUSION The gold standard APM detects minority resistant populations at a lower proportion than molecular tests. Mycobacterium bovis BCG strains with defined resistance and extracted DNA from M. tb provided concordant results and can serve in quality control of laboratories offering molecular testing for resistance. Further research is required to determine whether the higher LOD of molecular tests is associated with negative treatment outcomes.
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Affiliation(s)
- Sarah N Danchuk
- Department of Microbiology and Immunology, McGill University, Montreal, Quebec, Canada
- Infectious Diseases and Immunity in Global Health Program, Research Institute of the McGill University Health Centre, Montreal, Quebec, Canada
- McGill International TB Centre, McGill University, Montreal, Quebec, Canada
| | - Ori E Solomon
- Department of Microbiology and Immunology, McGill University, Montreal, Quebec, Canada
- Infectious Diseases and Immunity in Global Health Program, Research Institute of the McGill University Health Centre, Montreal, Quebec, Canada
- McGill International TB Centre, McGill University, Montreal, Quebec, Canada
| | - Thomas Andreas Kohl
- Molecular and Experimental Mycobacteriology, Research Center Borstel Leibniz Lung Center, Borstel, Schleswig-Holstein, Germany
| | - Viola Dreyer
- Molecular and Experimental Mycobacteriology, Research Center Borstel Leibniz Lung Center, Borstel, Schleswig-Holstein, Germany
| | - Ivan Barilar
- German Centre for Infection Research, Research Centre Borstel, Borstel, Germany
| | - Christian Utpatel
- Molecular and Experimental Mycobacteriology, Research Center Borstel Leibniz Lung Center, Borstel, Schleswig-Holstein, Germany
| | - Stefan Niemann
- Research Center Borstel Leibniz Lung Center, Borstel, Schleswig-Holstein, Germany
| | | | | | | | - Joy S Michael
- Microbiology, Christian Medical College and Hospital Vellore, Vellore, Tamil Nadu, India
| | - Marcel A Behr
- Department of Microbiology and Immunology, McGill University, Montreal, Quebec, Canada
- Infectious Diseases and Immunity in Global Health Program, Research Institute of the McGill University Health Centre, Montreal, Quebec, Canada
- McGill International TB Centre, McGill University, Montreal, Quebec, Canada
- Department of Medicine, McGill University, Montreal, Quebec, Canada
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Harrison LB, Kapur V, Behr MA. An imputed ancestral reference genome for the Mycobacterium tuberculosis complex better captures structural genomic diversity for reference-based alignment workflows. Microb Genom 2024; 10:001165. [PMID: 38175684 PMCID: PMC10868604 DOI: 10.1099/mgen.0.001165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Accepted: 12/07/2023] [Indexed: 01/05/2024] Open
Abstract
Reference-based alignment of short-reads is a widely used technique in genomic analysis of the Mycobacterium tuberculosis complex (MTBC) and the choice of reference sequence impacts the interpretation of analyses. The most widely used reference genomes include the ATCC type strain (H37Rv) and the putative MTBC ancestral sequence of Comas et al. both of which are based on a lineage 4 sequence. As such, these reference sequences do not capture all of the structural variation known to be present in the ancestor of the MTBC. To better represent the base of the MTBC, we generated an imputed ancestral genomic sequence, termed MTBC0 from reference-free alignments of closed MTBC genomes. When used as a reference sequence in alignment workflows, MTBC0 mapped more short sequencing reads and called more pairwise SNPs relative to the Comas et al. sequence while exhibiting minimal impact on the overall phylogeny of MTBC. The results also show that MTBC0 provides greater fidelity in capturing genomic variation and allows for the inclusion of regions absent from H37Rv in standard MTBC workflows without additional steps. The use of MTBC0 as an ancestral reference sequence in standard workflows modestly improved read mapping, SNP calling and intuitively facilitates the study of structural variation and evolution in MTBC.
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Affiliation(s)
- Luke B. Harrison
- Department of Medicine, McGill University, Montreal, Quebec H4A 3J1, Canada
- Bacterial Symbionts Evolution, INRS-Centre Armand-Frappier Santé Biotechnologie, Laval, Quebec H7V 1B7, Canada
| | - Vivek Kapur
- Department of Animal Science, The Pennsylvania State University, State College, PA 16802-3500, USA
| | - Marcel A. Behr
- Department of Medicine, McGill University, Montreal, Quebec H4A 3J1, Canada
- McGill International TB Centre, McGill University, Montreal, Quebec H4A 3S5, Canada
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Hill PC, Cobelens F, Martinez L, Behr MA, Churchyard G, Evans T, Fiore-Gartland AJ, Garcia-Basteiro AL, Hanekom W, Rangaka MX, Vekemans J, White RG. An Aspiration to Radically Shorten Phase 3 Tuberculosis Vaccine Trials. J Infect Dis 2023; 228:1150-1153. [PMID: 37607272 DOI: 10.1093/infdis/jiad356] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Revised: 07/06/2023] [Accepted: 08/17/2023] [Indexed: 08/24/2023] Open
Abstract
A new tuberculosis vaccine is a high priority. However, the classical development pathway is a major deterrent. Most tuberculosis cases arise within 2 years after Mycobacterium tuberculosis exposure, suggesting a 3-year trial period should be possible if sample size is large to maximize the number of early exposures. Increased sample size could be facilitated by working alongside optimized routine services for case ascertainment, with strategies for enhanced case detection and safety monitoring. Shortening enrolment could be achieved by simplifying screening criteria and procedures and strengthening site capacity. Together, these measures could enable radically shortened phase 3 tuberculosis vaccine trials.
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Affiliation(s)
- Philip C Hill
- Centre for International Health, University of Otago, Dunedin, New Zealand
| | - Frank Cobelens
- Department of Global Health, Amsterdam University Medical Centre, Amsterdam, The Netherlands
- Amsterdam Institute for Global Health and Development, Amsterdam University Medical Centre, Amsterdam, The Netherlands
| | - Leonardo Martinez
- Department of Epidemiology, School of Public Health, Boston University, Boston, Massachusetts, USA
| | - Marcel A Behr
- McGill International TB Centre, McGill University, Montreal, Quebec, Canada
| | - Gavin Churchyard
- The Aurum Institute, Parktown, South Africa
- Department of Medicine, Vanderbilt University, Nashville, Tennessee, USA
- School of Public Health, University of the Witwatersrand, Johannesburg, South Africa
| | | | - Andrew J Fiore-Gartland
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Alberto L Garcia-Basteiro
- Centro de Investigação em Saúde de Manhiça, Maputo, Mozambique
- Instituto de Salud Global, Hospital Clínic-Universitat de Barcelona, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Infecciosas, Barcelona, Spain
| | - Willem Hanekom
- Africa Health Research Institute, KwaZulu-Natal, Durban, South Africa
- Division of Infection and Immunity, University College London, London, United Kingdom
| | - Molebogeng X Rangaka
- MRC Clinical Trials Unit, University College London, London, United Kingdom
- Institute for Global Health, University College London, London, United Kingdom
- Centre for Infectious Diseases Research Africa, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | | | - Richard G White
- Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, London, United Kingdom
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Duffy SC, Lupien A, Elhaji Y, Farag M, Marcus V, Behr MA. Establishment of persistent enteric mycobacterial infection following streptomycin pre-treatment. Gut Pathog 2023; 15:46. [PMID: 37789445 PMCID: PMC10546655 DOI: 10.1186/s13099-023-00573-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Accepted: 09/21/2023] [Indexed: 10/05/2023] Open
Abstract
Mycobacterium avium subsp. paratuberculosis (MAP) is the causative agent of paratuberculosis, a chronic gastrointestinal disease affecting ruminants. This disease remains widespread in part due to the limitations of available diagnostics and vaccines. A representative small animal model of disease could act as a valuable tool for studying its pathogenesis and to develop new methods for paratuberculosis control, but current models are lacking. Streptomycin pre-treatment can reduce colonization resistance and has previously been shown to improve enteric infection in a Salmonella model. Here, we investigated whether streptomycin pre-treatment of mice followed by MAP gavage could act as a model of paratuberculosis which mimics the natural route of infection and disease development in ruminants. The infection outcomes of MAP were compared to M. avium subsp. hominissuis (MAH), an environmental mycobacterium, and M. bovis and M. orygis, two tuberculous mycobacteria. Streptomycin pre-treatment was shown to consistently improve bacterial infection post-oral inoculation. This model led to chronic MAP infection of the intestines and mesenteric lymph nodes (MLNs) up to 24-weeks post-gavage, however there was no evidence of inflammation or disease. These infection outcomes were found to be specific to MAP. When the model was applied to a bacterium of lesser virulence MAH, the infection was comparatively transient. Mice infected with bacteria of greater virulence, M. bovis or M. orygis, developed chronic intestinal and MLN infection with pulmonary disease similar to zoonotic TB. Our findings suggest that a streptomycin pre-treatment mouse model could be applied to future studies to improve enteric infection with MAP and to investigate other modifications underlying MAP enteritis.
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Affiliation(s)
- Shannon C Duffy
- Department of Microbiology and Immunology, McGill University, Montreal, QC, Canada
- McGill International TB Centre, Montreal, QC, Canada
- The Infectious Diseases and Immunity in Global Health Program, The Research Institute of the McGill University Health Centre, Montreal, QC, Canada
| | - Andréanne Lupien
- Department of Microbiology and Immunology, McGill University, Montreal, QC, Canada
- McGill International TB Centre, Montreal, QC, Canada
- The Infectious Diseases and Immunity in Global Health Program, The Research Institute of the McGill University Health Centre, Montreal, QC, Canada
- Department of Medicine, McGill University, Montreal, QC, Canada
| | - Youssef Elhaji
- Diagnostic Genomic Division, Department of Laboratory Medicine and Pathology, Hamad Medical Corporation, Doha, Qatar
| | - Mina Farag
- Department of Pathology, McGill University, Montreal, QC, Canada
- Department of Laboratory Medicine, Division of Pathology, McGill University Health Center, Montreal, QC, Canada
| | - Victoria Marcus
- Department of Pathology, McGill University, Montreal, QC, Canada
- Department of Laboratory Medicine, Division of Pathology, McGill University Health Center, Montreal, QC, Canada
| | - Marcel A Behr
- Department of Microbiology and Immunology, McGill University, Montreal, QC, Canada.
- McGill International TB Centre, Montreal, QC, Canada.
- The Infectious Diseases and Immunity in Global Health Program, The Research Institute of the McGill University Health Centre, Montreal, QC, Canada.
- Department of Medicine, McGill University, Montreal, QC, Canada.
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13
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Sumanth LJ, Suresh CR, Venkatesan M, Manesh A, Behr MA, Kapur V, Michael JS. Clinical features of human tuberculosis due to Mycobacterium orygis in Southern India. J Clin Tuberc Other Mycobact Dis 2023; 32:100372. [PMID: 37168873 PMCID: PMC10164920 DOI: 10.1016/j.jctube.2023.100372] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/13/2023] Open
Abstract
Mycobacterium orygis is a member of the Mycobacterium tuberculosis complex (MTBC) and causes tuberculosis in a variety of animals, including humans in South Asia. Here, we describe the clinical features associated with 8 human cases of whole genome sequence (WGS) confirmed M. orygis from a tertiary care hospital in South India during 2018-2019. The patient ages ranged from 9 to 51 years, with 5 females and 3 males included. All the patients had extrapulmonary disease with 2 having concomitant pulmonary involvement. Clinical improvement was documented after a full course of anti-tuberculosis therapy in 6 cases for whom follow-up was available. Taken together, the results show that M. orygis causes human tuberculosis in India, with a predominant extrapulmonary disease. Standardized molecular assays of this emerging member of the MTBC are needed to provide further information on the frequency of M. orygis infection in India and other countries where it is found in livestock and domestic wildlife.
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Affiliation(s)
- Lydia Jennifer Sumanth
- Associate Physician, Department of Clinical Microbiology, Christian Medical College, Vellore 632004, Tamil Nadu, India
| | | | - Manigandan Venkatesan
- Research Associate, Department of Clinical Microbiology, Christian Medical College, Vellore 632004, Tamil Nadu, India
| | - Abi Manesh
- Associate Professor, Department of Infectious Diseases, Christian Medical College, Vellore, Tamil Nadu 632004, India
| | - Marcel A. Behr
- Professor of Medicine, McGill International TB Centre, Montreal, Quebec H4A 3S5, Canada
| | - Vivek Kapur
- Professor, Infectious Diseases and Microbiology, The Pennsylvania State University, State College, PA 16802-3500, USA
| | - Joy Sarojini Michael
- Professor, Department of Clinical Microbiology, Christian Medical College, Vellore, Tamil Nadu 632004, India
- Corresponding author.
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14
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Harrison LB, Behr MA. Mutation rates and the molecular epidemiology of Mycobacterium abscessus. Proc Natl Acad Sci U S A 2023; 120:e2307499120. [PMID: 37310999 DOI: 10.1073/pnas.2307499120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023] Open
Affiliation(s)
- Luke B Harrison
- Department of Medicine, McGill University, Montreal, Quebec H4A 3J1, Canada
| | - Marcel A Behr
- Department of Medicine, McGill University, Montreal, Quebec H4A 3J1, Canada
- McGill International TB Centre, McGill University, Montreal, Quebec H4A 3S5, Canada
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15
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Abstract
Mycobacteria are responsible for several human and animal diseases. NOD2 is a pattern recognition receptor that has an important role in mycobacterial recognition. However, the mechanisms by which mutations in NOD2 alter the course of mycobacterial infection remain unclear. Herein, we aimed to review the totality of studies directly addressing the relationship between NOD2 and mycobacteria as a foundation for moving the field forward. NOD2 was linked to mycobacterial infection at 3 levels: (1) genetic, through association with mycobacterial diseases of humans; (2) chemical, through the distinct NOD2 ligand in the mycobacterial cell wall; and (3) immunologic, through heightened NOD2 signaling caused by the unique modification of the NOD2 ligand. The immune response to mycobacteria is shaped by NOD2 signaling, responsible for NF-κB and MAPK activation, and the production of various immune effectors like cytokines and nitric oxide, with some evidence linking this to bacteriologic control. Absence of NOD2 during mycobacterial infection of mice can be detrimental, but the mechanism remains unknown. Conversely, the success of immunization with mycobacteria has been linked to NOD2 signaling and NOD2 has been targeted as an avenue of immunotherapy for diseases even beyond mycobacteria. The mycobacteria-NOD2 interaction remains an important area of study, which may shed light on immune mechanisms in disease.
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Affiliation(s)
- Jean-Yves Dubé
- Department of Microbiology and Immunology, McGill University, Montréal, Canada
| | - Marcel A Behr
- Department of Medicine, McGill University Health Centre, Montréal, Canada
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16
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Semret M, Behr MA. Selfie-diagnosed tuberculosis. IDCases 2023; 31:e01718. [PMID: 36875150 PMCID: PMC9974454 DOI: 10.1016/j.idcr.2023.e01718] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Revised: 02/12/2023] [Accepted: 02/13/2023] [Indexed: 02/27/2023] Open
Affiliation(s)
- Makeda Semret
- Correspondence to: McGill University Health Centre – Glen site, 1001 Boul Décarie, E05.1514, Montréal, Quebec, Canada H3J1A4.
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17
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Sullivan JR, Yao J, Courtine C, Lupien A, Herrmann J, Müller R, Behr MA. Natural Products Lysobactin and Sorangicin A Show In Vitro Activity against Mycobacterium abscessus Complex. Microbiol Spectr 2022; 10:e0267222. [PMID: 36342177 PMCID: PMC9769517 DOI: 10.1128/spectrum.02672-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Accepted: 10/08/2022] [Indexed: 11/09/2022] Open
Abstract
The prevalence of lung disease caused by Mycobacterium abscessus is increasing among patients with cystic fibrosis. M. abscessus is a multidrug resistant opportunistic pathogen that is notoriously difficult to treat due to a lack of efficacious therapeutic regimens. Currently, there are no standard regimens, and treatment guidelines are based empirically on drug susceptibility testing. Thus, novel antibiotics are required. Natural products represent a vast pool of biologically active compounds that have a history of being a good source of antibiotics. Here, we screened a library of 517 natural products purified from fermentations of various bacteria, fungi, and plants against M. abscessus ATCC 19977. Lysobactin and sorangicin A were active against the M. abscessus complex and drug resistant clinical isolates. These natural products merit further consideration to be included in the M. abscessus drug pipeline. IMPORTANCE The many thousands of people living with cystic fibrosis are at a greater risk of developing a chronic lung infection caused by Mycobacterium abscessus. Since M. abscessus is clinically resistant to most anti-TB drugs available, treatment options are limited to macrolides. Despite macrolide-based therapies, cure rates for M. abscessus lung infections are 50%. Using an in-house library of curated natural products, we identified lysobactin and sorangicin A as novel scaffolds for the future development of antimicrobials for patients with M. abscessus infections.
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Affiliation(s)
- Jaryd R. Sullivan
- Department of Microbiology & Immunology, McGill University, Montréal, Québec, Canada
- Infectious Diseases and Immunity in Global Health Program, Research Institute of the McGill University Health Centre, Montréal, Québec, Canada
- McGill International TB Centre, Montréal, Québec, Canada
| | - Jacqueline Yao
- Infectious Diseases and Immunity in Global Health Program, Research Institute of the McGill University Health Centre, Montréal, Québec, Canada
| | - Christophe Courtine
- Department of Microbiology & Immunology, McGill University, Montréal, Québec, Canada
- Infectious Diseases and Immunity in Global Health Program, Research Institute of the McGill University Health Centre, Montréal, Québec, Canada
| | - Andréanne Lupien
- Infectious Diseases and Immunity in Global Health Program, Research Institute of the McGill University Health Centre, Montréal, Québec, Canada
- McGill International TB Centre, Montréal, Québec, Canada
| | - Jennifer Herrmann
- Department of Microbial Natural Products, Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI),Saarbrücken, Germany
| | - Rolf Müller
- Department of Microbial Natural Products, Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI),Saarbrücken, Germany
- Department of Pharmacy, Saarland University, Saarbrücken, Germany
| | - Marcel A. Behr
- Department of Microbiology & Immunology, McGill University, Montréal, Québec, Canada
- Infectious Diseases and Immunity in Global Health Program, Research Institute of the McGill University Health Centre, Montréal, Québec, Canada
- McGill International TB Centre, Montréal, Québec, Canada
- Department of Medicine, McGill University Health Centre, Montréal, Québec, Canada
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18
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Ortiz-Brizuela E, Menzies D, Behr MA. Testing and Treating Mycobacterium tuberculosis Infection. Med Clin North Am 2022; 106:929-947. [PMID: 36280337 DOI: 10.1016/j.mcna.2022.08.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
After infection with Mycobacterium tuberculosis, a minority of individuals will progress to tuberculosis disease (TB). The risk is higher among persons with well-established risk factors and within the first year after infection. Testing and treating individuals at high risk of progression maximizes the benefits of TB preventive therapy; avoiding testing of low-risk persons will limit potential harms. Several treatment options are available; rifamycin-based regimens offer the best efficacy-safety balance. In this review, we present an overview of the diagnosis and treatment of TB infection, and summarize common clinical scenarios.
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Affiliation(s)
- Edgar Ortiz-Brizuela
- Department of Epidemiology, Biostatistics & Occupational Health, McGill University, 1020 Pine Avenue, West Montreal, H3A 1A2, Canada; McGill International TB Centre, Research Institute of the McGill University Health Centre, 5252 boul.de Maisonneuve, West Montreal, Quebec, H4A 3S5, Canada; Department of Medicine, Insituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán. Vasco de Quiroga 15, Belisario Domínguez Secc 16, Tlalpan, Mexico City, 14000, Mexico
| | - Dick Menzies
- Department of Epidemiology, Biostatistics & Occupational Health, McGill University, 1020 Pine Avenue, West Montreal, H3A 1A2, Canada; McGill International TB Centre, Research Institute of the McGill University Health Centre, 5252 boul.de Maisonneuve, West Montreal, Quebec, H4A 3S5, Canada; Department of Medicine, McGill University, 1001 Decarie Boulevard, Montreal, Quebec, H4A 3J1, Canada
| | - Marcel A Behr
- Department of Epidemiology, Biostatistics & Occupational Health, McGill University, 1020 Pine Avenue, West Montreal, H3A 1A2, Canada; McGill International TB Centre, Research Institute of the McGill University Health Centre, 5252 boul.de Maisonneuve, West Montreal, Quebec, H4A 3S5, Canada; Department of Medicine, McGill University, 1001 Decarie Boulevard, Montreal, Quebec, H4A 3J1, Canada.
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19
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Eshraghisamani R, Mirto AJ, Wang J, Behr MA, Barkema HW, De Buck J. Identification of essential genes in Mycobacterium avium subsp. paratuberculosis genome for persistence in dairy calves. Front Microbiol 2022; 13:994421. [PMID: 36338087 PMCID: PMC9631821 DOI: 10.3389/fmicb.2022.994421] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Accepted: 09/05/2022] [Indexed: 11/02/2023] Open
Abstract
To cause disease Mycobacterium avium subsp. paratuberculosis needs to enter mammalian cells, arrest phagosomal maturation and manipulate the host immune system. The genetic basis of the bacterial capacity to achieve these outcomes remains largely unknown. Identifying these genes would allow us to gain a deeper understanding of MAP's pathogenesis and potentially develop a live attenuated Johne's disease vaccine by knocking out these genes. MAP genes demonstrated to be essential for colonization in the natural host, ruminants, are unknown. Genome-wide transposon mutagenesis and high-throughput sequencing were combined to evaluate the essentiality of each coding region in the bacterial genome to survive in dairy calves. A saturated library of 3,852 MAP Tn mutants, with insertions in 56% of TA sites, interrupting 88% of genes, was created using a MycoMarT7 phagemid containing a mariner transposon. Six calves were inoculated with a high dose of a library of MAP mutants, 1011 CFUs, (input) at 2 weeks of age. Following 2 months of incubation, MAP cells were isolated from the ileum, jejunum, and their associated lymph nodes of calves, resulting in approximately 100,000 colonies grown on solid media across 6 animals (output). Targeted next-generation sequencing was used to identify the disrupted genes in all the mutants in the input pool and the output pool recovered from the tissues to identify in vivo essential genes. Statistical analysis for the determination of essential genes was performed by a Hidden Markov Model (HMM), categorizing genes into essential genes that are devoid of insertions and growth-defect genes whose disruption impairs the growth of the organism. Sequence analysis identified 430 in vivo essential and 260 in vivo growth-defect genes. Gene ontology enrichment analysis of the in vivo essential and growth-defect genes with the highest reduction in the tissues revealed a high representation of genes involved in metabolism and respiration, cell wall and cell processing, virulence, and information pathway processes. This study has systematically identified essential genes for the growth and persistence of MAP in the natural host body.
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Affiliation(s)
- Razieh Eshraghisamani
- Department of Production Animal Health, Faculty of Veterinary Medicine, University of Calgary, Calgary, AB, Canada
| | - Amanda J. Mirto
- Environmental Health and Safety, University of Wisconsin-Madison, Madison, WI, United States
| | - Joyce Wang
- Department of Medicine, Faculty of Medicine, Health Centre, McGill University, Montréal, QC, Canada
| | - Marcel A. Behr
- Department of Medicine, Faculty of Medicine, Health Centre, McGill University, Montréal, QC, Canada
| | - Herman W. Barkema
- Department of Production Animal Health, Faculty of Veterinary Medicine, University of Calgary, Calgary, AB, Canada
| | - Jeroen De Buck
- Department of Production Animal Health, Faculty of Veterinary Medicine, University of Calgary, Calgary, AB, Canada
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20
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Waglechner N, Tullis E, Stephenson AL, Waters V, McIntosh F, Ma J, Jamieson FB, Behr MA, Batt J, Lee RS. Genomic epidemiology of Mycobacterium abscessus in a Canadian cystic fibrosis centre. Sci Rep 2022; 12:16116. [PMID: 36167715 PMCID: PMC9514693 DOI: 10.1038/s41598-022-19666-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Accepted: 09/01/2022] [Indexed: 11/09/2022] Open
Abstract
The Mycobacterium abscessus complex causes significant morbidity and mortality among patients with Cystic Fibrosis (CF). It has been hypothesized that these organisms are transmitted from patient to patient based on genomics. However, few studies incorporate epidemiologic data to confirm this hypothesis. We longitudinally sampled 27 CF and 7 non-CF patients attending a metropolitan hospital in Ontario, Canada from 2013 to 2018. Whole genome sequencing along with epidemiological data was used to evaluate the likelihood of transmission. Overall, the genetic diversity of M. abscessus was large, with a median pairwise distance (IQR) of 1,279 (143-134) SNVs between all Ontario M. abscessus isolates and 2,908 (21-3,204) single nucleotide variants (SNVs) between M. massiliense isolates. This reflects the global diversity of this pathogen, with Ontario isolates widely dispersed throughout global phylogenetic trees of each subspecies. Using a maximum distance of 25 SNVs as a threshold to identify possible transmission, we identified 23 (of 276 total) pairs of closely-related isolates. However, transmission was probable for only one pair based on both genomic and epidemiological data. This suggests that person-to-person transmission of M. abscessus among CF patients is indeed rare and reinforces the critical importance of epidemiological data for inferences of transmission.
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Affiliation(s)
- Nicholas Waglechner
- Dalla Lana School of Public Health, University of Toronto, 155 College St., Toronto, ON, M5T 3M7, Canada.
| | - Elizabeth Tullis
- Adult Cystic Fibrosis Program, Division of Respirology, St. Michael's Hospital, Unity Health Toronto, Toronto, ON, Canada.,Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, ON, Canada
| | - Anne L Stephenson
- Adult Cystic Fibrosis Program, Division of Respirology, St. Michael's Hospital, Unity Health Toronto, Toronto, ON, Canada.,Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, ON, Canada.,Institute of Health Policy, Management and Evaluation, University of Toronto, Toronto, ON, Canada
| | - Valerie Waters
- Department of Pediatrics, Division of Infectious Diseases, Hospital for Sick Children, 555 University Avenue, Toronto, ON, M5G 1X8, Canada
| | - Fiona McIntosh
- Infectious Diseases and Immunity in Global Health Program, Research Institute of the McGill University Health Centre, Montreal, QC, Canada.,McGill International TB Centre, McGill University, Montreal, QC, Canada
| | - Jennifer Ma
- Public Health Ontario, Public Health Ontario Laboratories, 661 University Avenue, Suite 1701, Toronto, ON, M5G 1V2, Canada
| | - Frances B Jamieson
- Public Health Ontario, Public Health Ontario Laboratories, 661 University Avenue, Suite 1701, Toronto, ON, M5G 1V2, Canada
| | - Marcel A Behr
- Infectious Diseases and Immunity in Global Health Program, Research Institute of the McGill University Health Centre, Montreal, QC, Canada.,McGill International TB Centre, McGill University, Montreal, QC, Canada.,Department of Epidemiology, Biostatistics and Occupational Health, McGill University, Montreal, QC, Canada
| | - Jane Batt
- Keenan Research Center for Biomedical Science, St. Michael's Hospital, Toronto, ON, Canada.,Tuberculosis Program, St. Michael's Hospital Unity Health Toronto, Toronto, ON, M5B 1WB, Canada
| | - Robyn S Lee
- Dalla Lana School of Public Health, University of Toronto, 155 College St., Toronto, ON, M5T 3M7, Canada. .,McGill International TB Centre, McGill University, Montreal, QC, Canada. .,Center for Communicable Disease Dynamics, Harvard School of Public Health, Boston, MA, USA.
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21
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Dowdy DW, Behr MA. Estimating annual risk of infection with Mycobacterium tuberculosis - Authors' reply. Lancet Infect Dis 2022; 22:1277-1278. [PMID: 36029782 DOI: 10.1016/s1473-3099(22)00448-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Accepted: 06/23/2022] [Indexed: 06/15/2023]
Affiliation(s)
- David W Dowdy
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA.
| | - Marcel A Behr
- McGill International Tuberculosis Centre and Department of Medicine, McGill University, Montreal, QC, Canada
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22
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Fanti RC, Vasconcelos SNS, Catta-Preta CMC, Sullivan JR, Riboldi GP, Dos Reis CV, Ramos PZ, Edwards AM, Behr MA, Couñago RM. A Target Engagement Assay to Assess Uptake, Potency, and Retention of Antibiotics in Living Bacteria. ACS Infect Dis 2022; 8:1449-1467. [PMID: 35815896 DOI: 10.1021/acsinfecdis.2c00073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
New antibiotics are urgently needed to counter the emergence of antimicrobial-resistant pathogenic bacteria. A major challenge in antibiotic drug discovery is to turn potent biochemical inhibitors of essential bacterial components into effective antimicrobials. This difficulty is underpinned by a lack of methods to investigate the physicochemical properties needed for candidate antibiotics to permeate the bacterial cell envelope and avoid clearance by the action of bacterial efflux pumps. To address these issues, here we used a target engagement assay to measure the equilibrium and kinetic binding parameters of antibiotics targeting dihydrofolate reductase (DHFR) in live bacteria. We also used this assay to identify novel DHFR ligands having antimicrobial activity. We validated this approach using the Gram-negative bacteria Escherichia coli and the emerging human pathogen Mycobacterium abscessus. We expect the use of target engagement assays in bacteria to expedite the discovery and progression of novel, cell-permeable antibiotics with on-target activity.
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Affiliation(s)
- Rebeka C Fanti
- Centro de Química Medicinal (CQMED), Centro de Biologia Molecular e Engenharia Genética (CBMEG), Universidade Estadual de Campinas (UNICAMP), Campinas 13083-886, Brazil.,Post-Graduate Program in Genetics and Molecular Biology (PGBM), UNICAMP, Campinas 13083-970, Brazil
| | - Stanley N S Vasconcelos
- Centro de Química Medicinal (CQMED), Centro de Biologia Molecular e Engenharia Genética (CBMEG), Universidade Estadual de Campinas (UNICAMP), Campinas 13083-886, Brazil
| | - Carolina M C Catta-Preta
- Centro de Química Medicinal (CQMED), Centro de Biologia Molecular e Engenharia Genética (CBMEG), Universidade Estadual de Campinas (UNICAMP), Campinas 13083-886, Brazil
| | - Jaryd R Sullivan
- Department of Microbiology & Immunology, McGill University, Montréal H3A 2B4, Canada.,Infectious Diseases and Immunity in Global Health Program, Research Institute of the McGill University Health Centre, Montréal H4A 3J1, Canada.,McGill International TB Centre, Montréal H4A 3S5, Canada
| | - Gustavo P Riboldi
- Centro de Química Medicinal (CQMED), Centro de Biologia Molecular e Engenharia Genética (CBMEG), Universidade Estadual de Campinas (UNICAMP), Campinas 13083-886, Brazil
| | - Caio V Dos Reis
- Centro de Química Medicinal (CQMED), Centro de Biologia Molecular e Engenharia Genética (CBMEG), Universidade Estadual de Campinas (UNICAMP), Campinas 13083-886, Brazil
| | - Priscila Z Ramos
- Centro de Química Medicinal (CQMED), Centro de Biologia Molecular e Engenharia Genética (CBMEG), Universidade Estadual de Campinas (UNICAMP), Campinas 13083-886, Brazil
| | - Aled M Edwards
- Structural Genomics Consortium, 101 College Street, Toronto M5G 1L7, Canada
| | - Marcel A Behr
- Department of Microbiology & Immunology, McGill University, Montréal H3A 2B4, Canada.,Infectious Diseases and Immunity in Global Health Program, Research Institute of the McGill University Health Centre, Montréal H4A 3J1, Canada.,McGill International TB Centre, Montréal H4A 3S5, Canada.,Department of Medicine, McGill University Health Centre, Montréal H4A 3J1, Canada
| | - Rafael M Couñago
- Centro de Química Medicinal (CQMED), Centro de Biologia Molecular e Engenharia Genética (CBMEG), Universidade Estadual de Campinas (UNICAMP), Campinas 13083-886, Brazil.,Post-Graduate Program in Genetics and Molecular Biology (PGBM), UNICAMP, Campinas 13083-970, Brazil
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23
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Garcia-Basteiro AL, White RG, Tait D, Schmidt AC, Rangaka MX, Quaife M, Nemes E, Mogg R, Hill PC, Harris RC, Hanekom WA, Frick M, Fiore-Gartland A, Evans T, Dagnew AF, Churchyard G, Cobelens F, Behr MA, Hatherill M. End-point definition and trial design to advance tuberculosis vaccine development. Eur Respir Rev 2022; 31:220044. [PMID: 35675923 PMCID: PMC9488660 DOI: 10.1183/16000617.0044-2022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Accepted: 04/04/2022] [Indexed: 11/05/2022] Open
Abstract
Tuberculosis (TB) remains a leading infectious cause of death worldwide and the coronavirus disease 2019 pandemic has negatively impacted the global TB burden of disease indicators. If the targets of TB mortality and incidence reduction set by the international community are to be met, new more effective adult and adolescent TB vaccines are urgently needed. There are several new vaccine candidates at different stages of clinical development. Given the limited funding for vaccine development, it is crucial that trial designs are as efficient as possible. Prevention of infection (POI) approaches offer an attractive opportunity to accelerate new candidate vaccines to advance into large and expensive prevention of disease (POD) efficacy trials. However, POI approaches are limited by imperfect current tools to measure Mycobacterium tuberculosis infection end-points. POD trials need to carefully consider the type and number of microbiological tests that define TB disease and, if efficacy against subclinical (asymptomatic) TB disease is to be tested, POD trials need to explore how best to define and measure this form of TB. Prevention of recurrence trials are an alternative approach to generate proof of concept for efficacy, but optimal timing of vaccination relative to treatment must still be explored. Novel and efficient approaches to efficacy trial design, in addition to an increasing number of candidates entering phase 2-3 trials, would accelerate the long-standing quest for a new TB vaccine.
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Affiliation(s)
- Alberto L Garcia-Basteiro
- Centro de Investigação em Sade de Manhiça (CISM), Maputo, Mozambique
- ISGlobal, Hospital Clínic - Universitat de Barcelona, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Infecciosas (CIBERINFECT), Barcelona, Spain
| | | | - Dereck Tait
- International AIDS Vaccine Initiative (IAVI) NPC, Cape Town, South Africa
| | | | - Molebogeng X Rangaka
- Institute for Global Health and MRC Clinical Trials Unit at University College London, London, UK
- CIDRI-AFRICA, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Matthew Quaife
- London School of Hygiene and Tropical Medicine, London, UK
| | - Elisa Nemes
- South African Tuberculosis Vaccine Initiative, Institute of Infectious Disease and Molecular Medicine and Division of Immunology, Dept of Pathology, University of Cape Town, Cape Town, South Africa
| | - Robin Mogg
- Takeda Pharmaceutical Company Limited, Cambridge, MA, USA
| | - Philip C Hill
- Centre for International Health, University of Otago, Dunedin, New Zealand
| | - Rebecca C Harris
- London School of Hygiene and Tropical Medicine, London, UK
- Sanofi Pasteur, Singapore
| | - Willem A Hanekom
- Africa Health Research Institute, KwaZulu-Natal, South Africa
- Division of Infection and Immunity, University College London, London, UK
| | - Mike Frick
- Treatment Action Group, New York, NY, USA
| | - Andrew Fiore-Gartland
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | | | - Alemnew F Dagnew
- Bill and Melinda Gates Medical Research Institute, Cambridge, MA, USA
| | - Gavin Churchyard
- The Aurum Institute, Parktown, South Africa
- Vanderbilt University, Nashville, TN, USA
- University of the Witwatersrand, Johannesburg, South Africa
| | - Frank Cobelens
- Dept of Global Health and Amsterdam Institute for Global health and development, Amsterdam University Medical Centres, Amsterdam, The Netherlands
| | - Marcel A Behr
- Dept of Medicine, McGill University; McGill International TB Centre, Montreal, QC, Canada
| | - Mark Hatherill
- South African Tuberculosis Vaccine Initiative, Institute of Infectious Disease and Molecular Medicine and Division of Immunology, Dept of Pathology, University of Cape Town, Cape Town, South Africa
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Dowdy DW, Behr MA. Are we underestimating the annual risk of infection with Mycobacterium tuberculosis in high-burden settings? Lancet Infect Dis 2022; 22:e271-e278. [PMID: 35526558 DOI: 10.1016/s1473-3099(22)00153-0] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Revised: 02/06/2022] [Accepted: 02/23/2022] [Indexed: 12/17/2022]
Abstract
The annual risk of infection with Mycobacterium tuberculosis determines a population's exposure level and thus the fraction of incident tuberculosis resulting from recent infection (often considered as having occurred within the past 2 years). Contemporary annual risk of infection estimates centre around 1% in most high-burden countries. We present three arguments why these estimates-primarily derived from cross-sectional tuberculin surveys in young school children (aged 5-12 years)-might underrepresent the true annual risk of infection. First, young children are expected to have lower risk of infection than older adolescents and adults (ie, those aged 15 years and older). Second, exposure might not lead to a positive test result in some individuals. Third, cross-sectional surveys might overlook transient immune responses. Accounting for these biases, the true annual risk of infection among adults in high-burden settings is probably closer to 5-10%. Consequently, most tuberculosis in those settings should reflect infection within the past 2 years rather than remote infection occurring many years ago. Under this reframing, major reductions in tuberculosis incidence could be achievable by focusing on the minority of people who have been recently infected.
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Affiliation(s)
- David W Dowdy
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA.
| | - Marcel A Behr
- McGill International Tuberculosis Centre and Department of Medicine, McGill University, Montreal, QC, Canada
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25
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Dubé JY, McIntosh F, Behr MA. Mice Dually Disrupted for Nod2 and Mincle Manifest Early Bacteriological Control but Late Susceptibility During Mycobacterium tuberculosis Infection. Front Immunol 2022; 13:862992. [PMID: 35418999 PMCID: PMC8995500 DOI: 10.3389/fimmu.2022.862992] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Accepted: 03/04/2022] [Indexed: 11/13/2022] Open
Abstract
Pattern recognition receptors Mincle and NOD2 have been implicated in mycobacterial immunity. However, knockout (KO) animal infection studies with Mycobacterium tuberculosis (Mtb) have had mild/delayed phenotypes. Given that genetic susceptibility to infectious diseases can be polygenic, we hypothesized that murine double knockout (DKO) of Mincle and Nod2 would result in exacerbation of altered immunity to mycobacterial infection leading to a more extreme phenotype than either KO alone. To test this hypothesis, we monitored bacterial burden, immune responses and survival following in vivo infections with Mtb in DKO mice for comparison to wildtype (WT) and single KOs. Bacterial burden and immune responses were not significantly affected at 3 and 6 weeks after infection in all mutant mice. At later timepoints, Nod2-KO mice had reduced survival compared to wildtype mice, and Mincle-KO survival was intermediate. Unexpectedly, dual disruption had no further effect; rather, DKO mice phenocopied Nod2-KO mice. We observed that Mtb-related death, exclusively in mice with disrupted Nod2, was accompanied by greater pulmonary cell death and distinct large necrotic foci. Therefore, determining how these receptors contribute to mycobacterial resistance will require analysis of immunophenotypes and their consequences on host pathology.
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Affiliation(s)
- Jean-Yves Dubé
- Department of Microbiology and Immunology, McGill University, Montréal, QC, Canada.,Infectious Diseases and Immunity in Global Health Program, Research Institute of the McGill University Health Centre, Montréal, QC, Canada.,McGill International TB Centre, Montréal, QC, Canada
| | - Fiona McIntosh
- Infectious Diseases and Immunity in Global Health Program, Research Institute of the McGill University Health Centre, Montréal, QC, Canada.,McGill International TB Centre, Montréal, QC, Canada
| | - Marcel A Behr
- Department of Microbiology and Immunology, McGill University, Montréal, QC, Canada.,Infectious Diseases and Immunity in Global Health Program, Research Institute of the McGill University Health Centre, Montréal, QC, Canada.,McGill International TB Centre, Montréal, QC, Canada.,Department of Medicine, McGill University Health Centre, Montréal, QC, Canada
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26
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Affiliation(s)
- Menonli Adjobimey
- National Tuberculosis Program of Bénin Cotonou, Bénin.,Health Sciences Faculty Abomey Calavi University Cotonou, Bénin
| | - Marcel A Behr
- Department of Medicine McGill University Montreal, Quebec, Canada.,McGill International TB Centre McGill University Montreal, Quebec, Canada.,Research Institute of the McGill University Health Centre Montreal, Quebec, Canada
| | - Dick Menzies
- Department of Medicine McGill University Montreal, Quebec, Canada.,McGill International TB Centre McGill University Montreal, Quebec, Canada.,Research Institute of the McGill University Health Centre Montreal, Quebec, Canada
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27
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Sullivan JR, Lupien A, Kalthoff E, Hamela C, Taylor L, Munro KA, Schmeing TM, Kremer L, Behr MA. Efficacy of epetraborole against Mycobacterium abscessus is increased with norvaline. PLoS Pathog 2021; 17:e1009965. [PMID: 34637487 PMCID: PMC8535176 DOI: 10.1371/journal.ppat.1009965] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Revised: 10/22/2021] [Accepted: 09/23/2021] [Indexed: 12/16/2022] Open
Abstract
Mycobacterium abscessus is the most common rapidly growing non-tuberculous mycobacteria to cause pulmonary disease in patients with impaired lung function such as cystic fibrosis. M. abscessus displays high intrinsic resistance to common antibiotics and inducible resistance to macrolides like clarithromycin. As such, M. abscessus is clinically resistant to the entire regimen of front-line M. tuberculosis drugs, and treatment with antibiotics that do inhibit M. abscessus in the lab results in cure rates of 50% or less. Here, we identified epetraborole (EPT) from the MMV pandemic response box as an inhibitor against the essential protein leucyl-tRNA synthetase (LeuRS) in M. abscessus. EPT protected zebrafish from lethal M. abscessus infection and did not induce self-resistance nor against clarithromycin. Contrary to most antimycobacterials, the whole-cell activity of EPT was greater against M. abscessus than M. tuberculosis, but crystallographic and equilibrium binding data showed that EPT binds LeuRSMabs and LeuRSMtb with similar residues and dissociation constants. Since EPT-resistant M. abscessus mutants lost LeuRS editing activity, these mutants became susceptible to misaminoacylation with leucine mimics like the non-proteinogenic amino acid norvaline. Proteomic analysis revealed that when M. abscessus LeuRS mutants were fed norvaline, leucine residues in proteins were replaced by norvaline, inducing the unfolded protein response with temporal changes in expression of GroEL chaperonins and Clp proteases. This supports our in vitro data that supplementation of media with norvaline reduced the emergence of EPT mutants in both M. abscessus and M. tuberculosis. Furthermore, the combination of EPT and norvaline had improved in vivo efficacy compared to EPT in a murine model of M. abscessus infection. Our results emphasize the effectiveness of EPT against the clinically relevant cystic fibrosis pathogen M. abscessus, and these findings also suggest norvaline adjunct therapy with EPT could be beneficial for M. abscessus and other mycobacterial infections like tuberculosis. Current antimycobacterial drugs are inadequate to handle the increasing number of non-tuberculous mycobacteria infections that eclipse tuberculosis infections in many developed countries. Of particular importance for cystic fibrosis patients, Mycobacterium abscessus is notoriously difficult to treat where patients spend extended time on antibiotics with cure rates comparable to extreme drug resistant M. tuberculosis. Here, we identified epetraborole (EPT) with in vitro and in vivo activities against M. abscessus. We showed that EPT targets the editing domain of the leucyl-tRNA synthetase (LeuRS) and that escape mutants lost LeuRS editing activity, making these mutants susceptible to misaminoacylation with leucine mimics. Most importantly, combination therapy of EPT and norvaline limited the rate of EPT resistance in both M. abscessus and M. tuberculosis, and this was the first study to demonstrate improved in vivo efficacy of EPT and norvaline compared to EPT in a murine model of M. abscessus pulmonary infection. The demonstration of norvaline adjunct therapy with EPT for M. abscessus infections is promising for cystic fibrosis patients and could translate to other mycobacterial infections, such as tuberculosis.
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Affiliation(s)
- Jaryd R. Sullivan
- Department of Microbiology & Immunology, McGill University, Montréal, Canada
- Infectious Diseases and Immunity in Global Health Program, Research Institute of the McGill University Health Centre, Montréal, Canada
- McGill International TB Centre, Montréal, Canada
| | - Andréanne Lupien
- Infectious Diseases and Immunity in Global Health Program, Research Institute of the McGill University Health Centre, Montréal, Canada
- McGill International TB Centre, Montréal, Canada
| | - Elias Kalthoff
- Department of Biochemistry, McGill University, Montréal, Canada
- Centre de Recherche en Biologie Structural, McGill University, Montréal, Canada
| | - Claire Hamela
- Centre National de la Recherche Scientifique UMR 9004, Institut de Recherche en Infectiologie de Montpellier (IRIM), Université de Montpellier, Montpellier, France
| | - Lorne Taylor
- Clinical Proteomics Platform, Research Institute of the McGill University Health Centre, Montréal, Canada
| | - Kim A. Munro
- Department of Biochemistry, McGill University, Montréal, Canada
- Centre de Recherche en Biologie Structural, McGill University, Montréal, Canada
| | - T. Martin Schmeing
- Department of Biochemistry, McGill University, Montréal, Canada
- Centre de Recherche en Biologie Structural, McGill University, Montréal, Canada
| | - Laurent Kremer
- Centre National de la Recherche Scientifique UMR 9004, Institut de Recherche en Infectiologie de Montpellier (IRIM), Université de Montpellier, Montpellier, France
- INSERM, IRIM, Montpellier, France
| | - Marcel A. Behr
- Department of Microbiology & Immunology, McGill University, Montréal, Canada
- Infectious Diseases and Immunity in Global Health Program, Research Institute of the McGill University Health Centre, Montréal, Canada
- McGill International TB Centre, Montréal, Canada
- Department of Medicine, McGill University Health Centre, Montréal, Canada
- * E-mail:
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28
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Benea C, Rendon L, Papenburg J, Frenette C, Imacoudene A, McDonald EG, Nguyen QD, Rajda E, Tran E, Vameghestahbanati M, Benedetti A, Behr MA, Smith BM. Evaluation of a home-based 7-day infection control strategy for healthcare workers following high-risk exposure to severe acute respiratory coronavirus virus 2 (SARS-CoV-2): A cohort study. Infect Control Hosp Epidemiol 2021; 42:1194-1197. [PMID: 33323137 PMCID: PMC7783088 DOI: 10.1017/ice.2020.1389] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Revised: 12/07/2020] [Accepted: 12/10/2020] [Indexed: 12/11/2022]
Abstract
OBJECTIVE Evidence-based infection control strategies are needed for healthcare workers (HCWs) following high-risk exposure to severe acute respiratory coronavirus virus 2 (SARS-CoV-2). In this study, we evaluated the negative predictive value (NPV) of a home-based 7-day infection control strategy. METHODS HCWs advised by their infection control or occupational health officer to self-isolate due to a high-risk SARS-CoV-2 exposure were enrolled between May and October 2020. The strategy consisted of symptom-triggered nasopharyngeal SARS-CoV-2 RNA testing from day 0 to day 7 after exposure and standardized home-based nasopharyngeal swab and saliva testing on day 7. The NPV of this strategy was calculated for (1) clinical coronavirus disease 2019 (COVID-19) diagnosis from day 8-14 after exposure, and for (2) asymptomatic SARS-CoV-2 detected by standardized nasopharyngeal swab and saliva specimens collected at days 9, 10, and 14 after exposure. Interim results are reported in the context of a second wave threatening this essential workforce. RESULTS Among 30 HCWs enrolled, the mean age was 31 years (SD, ±9), and 24 (80%) were female. Moreover, 3 were diagnosed with COVID-19 by day 14 after exposure (secondary attack rate, 10.0%), and all cases were detected using the 7-day infection control strategy: the NPV for subsequent clinical COVID-19 or asymptomatic SARS-CoV-2 detection by day 14 was 100.0% (95% CI, 93.1%-100.0%). CONCLUSIONS Among HCWs with high-risk exposure to SARS-CoV-2, a home-based 7-day infection control strategy may have a high NPV for subsequent COVID-19 and asymptomatic SARS-CoV-2 detection. Ongoing data collection and data sharing are needed to improve the precision of the estimated NPV, and here we report interim results to inform infection control strategies in light of a second wave threatening this essential workforce.
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Affiliation(s)
- Carla Benea
- Department of Medicine, McGill University, Montréal, Quebec, Canada
| | - Laura Rendon
- Department of Medicine, McGill University, Montréal, Quebec, Canada
| | - Jesse Papenburg
- Department of Medicine, McGill University, Montréal, Quebec, Canada
- Research Institute of the McGill University Health Centre, Montréal, Quebec, Canada
| | - Charles Frenette
- Department of Medicine, McGill University, Montréal, Quebec, Canada
| | - Ahmed Imacoudene
- Department of Medicine, McGill University, Montréal, Quebec, Canada
| | - Emily G. McDonald
- Department of Medicine, McGill University, Montréal, Quebec, Canada
- Research Institute of the McGill University Health Centre, Montréal, Quebec, Canada
| | - Quoc D. Nguyen
- Centre hospitalier de l’Université de Montréal, Montréal, Quebec, Canada
- Centre de recherche du Centre hospitalier de l’Université de Montréal, Montréal, Quebec, Canada
| | - Ewa Rajda
- Department of Medicine, McGill University, Montréal, Quebec, Canada
| | - Estelle Tran
- Department of Medicine, McGill University, Montréal, Quebec, Canada
| | - Motahareh Vameghestahbanati
- Department of Medicine, McGill University, Montréal, Quebec, Canada
- Research Institute of the McGill University Health Centre, Montréal, Quebec, Canada
| | - Andrea Benedetti
- Department of Medicine, McGill University, Montréal, Quebec, Canada
- Research Institute of the McGill University Health Centre, Montréal, Quebec, Canada
- Department of Epidemiology, Biostatistical and Occupational Health, McGill University, Montréal, Quebec, Canada
| | - Marcel A. Behr
- Department of Medicine, McGill University, Montréal, Quebec, Canada
- Research Institute of the McGill University Health Centre, Montréal, Quebec, Canada
- Department of Epidemiology, Biostatistical and Occupational Health, McGill University, Montréal, Quebec, Canada
| | - Benjamin M. Smith
- Department of Medicine, McGill University, Montréal, Quebec, Canada
- Research Institute of the McGill University Health Centre, Montréal, Quebec, Canada
- Department of Epidemiology, Biostatistical and Occupational Health, McGill University, Montréal, Quebec, Canada
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29
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Affiliation(s)
- Frédéric J Veyrier
- Bacterial Symbionts Evolution, Institut National de la Recherche Scientifique, Centre Armand-Frappier Santé Biotechnologie, Laval, Quebec, Canada
| | - Marcel A Behr
- Department of Medicine and McGill International TB Centre, McGill University, Montreal, Quebec, Canada.
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30
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Lange C, Aaby P, Behr MA, Donald PR, Kaufmann SHE, Netea MG, Mandalakas AM. 100 years of Mycobacterium bovis bacille Calmette-Guérin. Lancet Infect Dis 2021; 22:e2-e12. [PMID: 34506734 DOI: 10.1016/s1473-3099(21)00403-5] [Citation(s) in RCA: 64] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Revised: 06/29/2021] [Accepted: 07/05/2021] [Indexed: 12/13/2022]
Abstract
Mycobacterium bovis bacille Calmette-Guérin (BCG), an experimental vaccine designed to protect cattle from bovine tuberculosis, was administered for the first time to a newborn baby in Paris in 1921. Over the past century, BCG has saved tens of millions of lives and has been given to more humans than any other vaccine. It remains the sole tuberculosis vaccine licensed for use in humans. BCG provides long-lasting strong protection against miliary and meningeal tuberculosis in children, but it is less effective for the prevention of pulmonary tuberculosis, especially in adults. Evidence mainly from the past two decades suggests that BCG has non-specific benefits against non-tuberculous infections in newborn babies and in older adults, and offers immunotherapeutic benefit in certain malignancies such as non-muscle invasive bladder cancer. However, as a live attenuated vaccine, BCG can cause localised or disseminated infections in immunocompromised hosts, which can also occur following intravesical installation of BCG for the treatment of bladder cancer. The legacy of BCG includes fundamental discoveries about tuberculosis-specific and non-specific immunity and the demonstration that tuberculosis is a vaccine-preventable disease, providing a foundation for new vaccines to hasten tuberculosis elimination.
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Affiliation(s)
- Christoph Lange
- Division of Clinical Infectious Diseases, Medical Clinic, Research Center Borstel, Borstel, Germany; German Center for Infection Research (DZIF) Tuberculosis Unit, Borstel, Germany; Respiratory Medicine and International Health, University of Lübeck, Lübeck, Germany; Global TB Program, Baylor College of Medicine and Texas Children's Hospital, Houston, TX, USA.
| | - Peter Aaby
- Bandim Health Project, Indepth Network, Bissau, Guinea-Bissau; Bandim Health Project, Southern Danish University, Copenhagen, Denmark
| | - Marcel A Behr
- McGill International TB Centre and Department of Medicine, McGill University, Montreal, QC, Canada
| | - Peter R Donald
- Desmond Tutu TB Centre, Department of Paediatrics and Child Health, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Stefan H E Kaufmann
- Max Planck Institute for Infection Biology, Berlin, Germany; Max Planck Institute for Biophysical Chemistry, Göttingen, Germany; Hagler Institute for Advanced Study, Texas A&M University, College Station, TX, USA
| | - Mihai G Netea
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, Netherlands; Department of Immunology and Metabolism, Life and Medical Sciences Institute, University of Bonn, Bonn, Germany
| | - Anna M Mandalakas
- Global TB Program, Baylor College of Medicine and Texas Children's Hospital, Houston, TX, USA
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31
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Dubé JY, Fava VM, Schurr E, Behr MA. Underwhelming or Misunderstood? Genetic Variability of Pattern Recognition Receptors in Immune Responses and Resistance to Mycobacterium tuberculosis. Front Immunol 2021; 12:714808. [PMID: 34276708 PMCID: PMC8278570 DOI: 10.3389/fimmu.2021.714808] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Accepted: 06/17/2021] [Indexed: 12/23/2022] Open
Abstract
Human genetic control is thought to affect a considerable part of the outcome of infection with Mycobacterium tuberculosis (Mtb). Most of us deal with the pathogen by containment (associated with clinical "latency") or sterilization, but tragically millions each year do not. After decades of studies on host genetic susceptibility to Mtb infection, genetic variation has been discovered to play a role in tuberculous immunoreactivity and tuberculosis (TB) disease. Genes encoding pattern recognition receptors (PRRs) enable a consistent, molecularly direct interaction between humans and Mtb which suggests the potential for co-evolution. In this review, we explore the roles ascribed to PRRs during Mtb infection and ask whether such a longstanding and intimate interface between our immune system and this pathogen plays a critical role in determining the outcome of Mtb infection. The scientific evidence to date suggests that PRR variation is clearly implicated in altered immunity to Mtb but has a more subtle role in limiting the pathogen and pathogenesis. In contrast to 'effectors' like IFN-γ, IL-12, Nitric Oxide and TNF that are critical for Mtb control, 'sensors' like PRRs are less critical for the outcome of Mtb infection. This is potentially due to redundancy of the numerous PRRs in the innate arsenal, such that Mtb rarely goes unnoticed. Genetic association studies investigating PRRs during Mtb infection should therefore be designed to investigate endophenotypes of infection - such as immunological or clinical variation - rather than just TB disease, if we hope to understand the molecular interface between innate immunity and Mtb.
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Affiliation(s)
- Jean-Yves Dubé
- Department of Microbiology and Immunology, McGill University, Montreal, QC, Canada
- Program in Infectious Diseases and Immunity in Global Health, The Research Institute of the McGill University Health Centre, Montreal, QC, Canada
- McGill International TB Centre, McGill University, Montreal, QC, Canada
| | - Vinicius M. Fava
- Program in Infectious Diseases and Immunity in Global Health, The Research Institute of the McGill University Health Centre, Montreal, QC, Canada
- McGill International TB Centre, McGill University, Montreal, QC, Canada
| | - Erwin Schurr
- Department of Microbiology and Immunology, McGill University, Montreal, QC, Canada
- Program in Infectious Diseases and Immunity in Global Health, The Research Institute of the McGill University Health Centre, Montreal, QC, Canada
- McGill International TB Centre, McGill University, Montreal, QC, Canada
- Department of Human Genetics, Faculty of Medicine, McGill University, Montreal, QC, Canada
- Department of Medicine, Faculty of Medicine, McGill University, Montreal, QC, Canada
| | - Marcel A. Behr
- Department of Microbiology and Immunology, McGill University, Montreal, QC, Canada
- Program in Infectious Diseases and Immunity in Global Health, The Research Institute of the McGill University Health Centre, Montreal, QC, Canada
- McGill International TB Centre, McGill University, Montreal, QC, Canada
- Department of Medicine, Faculty of Medicine, McGill University, Montreal, QC, Canada
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32
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Alvarez GG, Zwerling AA, Duncan C, Pease C, Van Dyk D, Behr MA, Lee RS, Mulpuru S, Pakhale S, Cameron DW, Aaron SD, Patterson M, Allen J, Sullivan K, Jolly A, Sharma MK, Jamieson FB. Molecular Epidemiology of Mycobacterium tuberculosis To Describe the Transmission Dynamics Among Inuit Residing in Iqaluit Nunavut Using Whole-Genome Sequencing. Clin Infect Dis 2021; 72:2187-2195. [PMID: 32293676 DOI: 10.1093/cid/ciaa420] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Accepted: 04/10/2020] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND In the last decade, tuberculosis (TB) incidence among Inuit in the Canadian Arctic has been rising. Our aim was to better understand the transmission dynamics of TB in this remote region of Canada using whole-genome sequencing. METHODS Isolates from patients who had culture-positive pulmonary TB in Iqaluit, Nunavut, between 2009 and 2015 underwent whole-genome sequencing (WGS). The number of transmission events between cases within clusters was calculated using a threshold of a ≤3 single nucleotide polymorphism (SNP) difference between isolates and then combined with detailed epidemiological data using a reproducible novel algorithm. Social network analysis of epidemiological data was used to support the WGS data analysis. RESULTS During the study period, 140 Mycobacterium tuberculosis isolates from 135 cases were sequenced. Four clusters were identified, all from Euro-American lineage. One cluster represented 62% of all cases that were sequenced over the entire study period. In this cluster, 2 large chains of transmission were associated with 3 superspreading events in a homeless shelter. One of the superspreading events was linked to a nonsanctioned gambling house that resulted in further transmission. Shelter to nonshelter transmission was also confirmed. An algorithm developed for the determination of transmission events demonstrated very good reproducibility (κ score .98, 95% confidence interval, .97-1.0). CONCLUSIONS Our study suggests that socioeconomic factors, namely residing in a homeless shelter and spending time in a gambling house, combined with the superspreading event effect may have been significant factors explaining the rise in cases in this predominantly Inuit Arctic community.
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Affiliation(s)
- Gonzalo G Alvarez
- School of Epidemiology and Public Health, University of Ottawa, Ottawa, Ontario, Canada.,Ottawa Hospital Research Institute, Ottawa, Ontario, Canada.,Department of Medicine, The Ottawa Hospital, Ottawa, Ontario, Canada.,McGill International Tuberculosis Centre, McGill University Health Centre, Montreal, Quebec, Canada
| | - Alice A Zwerling
- School of Epidemiology and Public Health, University of Ottawa, Ottawa, Ontario, Canada.,McGill International Tuberculosis Centre, McGill University Health Centre, Montreal, Quebec, Canada
| | - Carla Duncan
- Public Health Ontario Laboratory, Public Health Ontario, Toronto, Ontario, Canada
| | - Christopher Pease
- Ottawa Hospital Research Institute, Ottawa, Ontario, Canada.,Department of Medicine, The Ottawa Hospital, Ottawa, Ontario, Canada
| | | | - Marcel A Behr
- McGill International Tuberculosis Centre, McGill University Health Centre, Montreal, Quebec, Canada.,The Research Institute of the McGill University Health Centre, Montreal, Quebec, Canada
| | - Robyn S Lee
- McGill International Tuberculosis Centre, McGill University Health Centre, Montreal, Quebec, Canada.,The Research Institute of the McGill University Health Centre, Montreal, Quebec, Canada
| | - Sunita Mulpuru
- School of Epidemiology and Public Health, University of Ottawa, Ottawa, Ontario, Canada.,Ottawa Hospital Research Institute, Ottawa, Ontario, Canada.,Department of Medicine, The Ottawa Hospital, Ottawa, Ontario, Canada
| | - Smita Pakhale
- School of Epidemiology and Public Health, University of Ottawa, Ottawa, Ontario, Canada.,Ottawa Hospital Research Institute, Ottawa, Ontario, Canada.,Department of Medicine, The Ottawa Hospital, Ottawa, Ontario, Canada
| | - D William Cameron
- School of Epidemiology and Public Health, University of Ottawa, Ottawa, Ontario, Canada.,Ottawa Hospital Research Institute, Ottawa, Ontario, Canada.,Department of Medicine, The Ottawa Hospital, Ottawa, Ontario, Canada
| | - Shawn D Aaron
- School of Epidemiology and Public Health, University of Ottawa, Ottawa, Ontario, Canada.,Ottawa Hospital Research Institute, Ottawa, Ontario, Canada.,Department of Medicine, The Ottawa Hospital, Ottawa, Ontario, Canada
| | - Michael Patterson
- Department of Health, Government of Nunavut, Iqaluit, Nunavut, Canada
| | - Jean Allen
- Nunavut Tunngavik Inc, Iqaluit, Nunavut, Canada
| | - Kathryn Sullivan
- School of Medicine, University of Ottawa, Ottawa, Ontario, Canada
| | - Anne Jolly
- School of Epidemiology and Public Health, University of Ottawa, Ottawa, Ontario, Canada
| | - Meenu K Sharma
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada.,Department of Medical Microbiology and Infectious Diseases, Max Rady College of Medicine, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Frances B Jamieson
- Public Health Ontario Laboratory, Public Health Ontario, Toronto, Ontario, Canada.,Department of Medicine and Pathobiology, Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
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33
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Duncan D, Lupien A, Behr MA, Auclair K. Effect of pH on the antimicrobial activity of the macrophage metabolite itaconate. Microbiology (Reading) 2021; 167. [PMID: 34020726 DOI: 10.1099/mic.0.001050] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The production of itaconate by macrophages was only discovered in 2011. An increasing number of studies have since revealed essential biological functions for this small molecule, ranging from antimicrobial to immunomodulator. The antibacterial role of itaconate has however been questioned because the estimated concentration of itaconate in macrophages (low-millimolar) is lower than the minimum inhibitory concentration (MIC) of itaconate reported for several bacterial strains (low-to-mid-millimolar). We note that some of these investigations have tended to ignore the high acidity of this small diacid (pKas 3.85 and 5.45), thereby potentially biassing activity measurements. We measured the MIC of itaconate in Escherichia coli (not known to metabolize itaconate) and in Salmonella enterica serovar Typhimurium (known to metabolize itaconate) at varying pH values to probe the effect that pH has on itaconate toxicity. Herein, we demonstrate that the antimicrobial effect of itaconate is dependent upon the pH of the media and that itaconate does have antimicrobial activity at biologically relevant pH and concentrations. Under nutrient-poor conditions, the antimicrobial activity of itaconate in both E. coli and S. Typhimurium increased approximately 200-fold when the pH was dropped by one unit, whereas itaconate was not found to be toxic under nutrient rich conditions. Our results also reveal that the activity of itaconate is synergistic with acidity, yet is not a function of increased permeability with protonation. Similar experiments performed with succinate (a pKa-matched diacid) yielded drastically different results, consistent with a target-based mechanism of action for itaconate. Overall, our work shows the importance of controlling the pH when performing experiments with itaconic acid.
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Affiliation(s)
- Dustin Duncan
- Department of Chemistry, McGill University, Montreal, Quebec, Canada
| | - Andréanne Lupien
- McGill International TB Centre, McGill University, Montreal, Quebec, Canada.,Department of Medicine, McGill University, Montreal, Quebec, Canada
| | - Marcel A Behr
- McGill International TB Centre, McGill University, Montreal, Quebec, Canada.,Department of Medicine, McGill University, Montreal, Quebec, Canada
| | - Karine Auclair
- Department of Chemistry, McGill University, Montreal, Quebec, Canada
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34
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Luo T, Xu P, Zhang Y, Porter JL, Ghanem M, Liu Q, Jiang Y, Li J, Miao Q, Hu B, Howden BP, Fyfe JAM, Globan M, He W, He P, Wang Y, Liu H, Takiff HE, Zhao Y, Chen X, Pan Q, Behr MA, Stinear TP, Gao Q. Population genomics provides insights into the evolution and adaptation to humans of the waterborne pathogen Mycobacterium kansasii. Nat Commun 2021; 12:2491. [PMID: 33941780 PMCID: PMC8093194 DOI: 10.1038/s41467-021-22760-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Accepted: 03/16/2021] [Indexed: 02/02/2023] Open
Abstract
Mycobacterium kansasii can cause serious pulmonary disease. It belongs to a group of closely-related species of non-tuberculous mycobacteria known as the M. kansasii complex (MKC). Here, we report a population genomics analysis of 358 MKC isolates from worldwide water and clinical sources. We find that recombination, likely mediated by distributive conjugative transfer, has contributed to speciation and on-going diversification of the MKC. Our analyses support municipal water as a main source of MKC infections. Furthermore, nearly 80% of the MKC infections are due to closely-related M. kansasii strains, forming a main cluster that apparently originated in the 1900s and subsequently expanded globally. Bioinformatic analyses indicate that several genes involved in metabolism (e.g., maintenance of the methylcitrate cycle), ESX-I secretion, metal ion homeostasis and cell surface remodelling may have contributed to M. kansasii's success and its ongoing adaptation to the human host.
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Affiliation(s)
- Tao Luo
- grid.13291.380000 0001 0807 1581Department of Pathogen Biology, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, China ,grid.8547.e0000 0001 0125 2443Shanghai Institute of Infectious Disease and Biosecurity, Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), Shanghai Medical College and School of Basic Medical Sciences, Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
| | - Peng Xu
- grid.8547.e0000 0001 0125 2443Shanghai Institute of Infectious Disease and Biosecurity, Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), Shanghai Medical College and School of Basic Medical Sciences, Shanghai Public Health Clinical Center, Fudan University, Shanghai, China ,grid.417409.f0000 0001 0240 6969Key Laboratory of Characteristic Infectious Disease & Bio-safety Development of Guizhou Province Education Department, Institute of Life Sciences, Zunyi Medical University, Zunyi, China
| | - Yangyi Zhang
- Department of Tuberculosis Control, Shanghai Municipal Centre for Disease Control and Prevention, Shanghai, China
| | - Jessica L. Porter
- grid.1008.90000 0001 2179 088XDepartment of Microbiology and Immunology, Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Vic Australia ,grid.1008.90000 0001 2179 088XDoherty Applied Microbial Genomics, Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Vic Australia
| | - Marwan Ghanem
- grid.14709.3b0000 0004 1936 8649Department of Microbiology and Immunology, McGill University and McGill International TB Centre, Montreal, Quebec Canada
| | - Qingyun Liu
- grid.8547.e0000 0001 0125 2443Shanghai Institute of Infectious Disease and Biosecurity, Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), Shanghai Medical College and School of Basic Medical Sciences, Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
| | - Yuan Jiang
- Department of Tuberculosis Control, Shanghai Municipal Centre for Disease Control and Prevention, Shanghai, China
| | - Jing Li
- Department of Tuberculosis Control, Shanghai Municipal Centre for Disease Control and Prevention, Shanghai, China
| | - Qing Miao
- grid.8547.e0000 0001 0125 2443Department of Infectious Diseases, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Bijie Hu
- grid.8547.e0000 0001 0125 2443Department of Infectious Diseases, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Benjamin P. Howden
- grid.1008.90000 0001 2179 088XDepartment of Microbiology and Immunology, Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Vic Australia ,grid.1008.90000 0001 2179 088XDoherty Applied Microbial Genomics, Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Vic Australia ,grid.1008.90000 0001 2179 088XMicrobiological Diagnostic Unit Public Health Laboratory, Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria 3000 Australia
| | - Janet A. M. Fyfe
- grid.429299.d0000 0004 0452 651XVictorian Infectious Diseases Reference Laboratory, Doherty Institute for Infection and Immunity, Melbourne Health, Melbourne, Vic Australia
| | - Maria Globan
- grid.429299.d0000 0004 0452 651XVictorian Infectious Diseases Reference Laboratory, Doherty Institute for Infection and Immunity, Melbourne Health, Melbourne, Vic Australia
| | - Wencong He
- grid.198530.60000 0000 8803 2373Chinese Center for Disease Control and Prevention and Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing, China
| | - Ping He
- grid.198530.60000 0000 8803 2373Chinese Center for Disease Control and Prevention and Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing, China
| | - Yiting Wang
- grid.198530.60000 0000 8803 2373Chinese Center for Disease Control and Prevention and Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing, China
| | - Houming Liu
- grid.263817.9Department of Clinical Laboratory, The Third People’s Hospital of Shenzhen, Southern University of Science and Technology, Shenzhen, China
| | - Howard E. Takiff
- grid.428999.70000 0001 2353 6535Unité de Pathogenetique Integrée Mycobacterienne, Institut Pasteur, Paris, France ,grid.418243.80000 0001 2181 3287Laboratorio de Genética Molecular, CMBC, IVIC, Caracas, Venezuela ,Shenzhen Nanshan Center for Chronic Disease Control, Shenzhen, China
| | - Yanlin Zhao
- grid.198530.60000 0000 8803 2373Chinese Center for Disease Control and Prevention and Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing, China
| | - Xinchun Chen
- grid.263488.30000 0001 0472 9649Guangdong Provincial Key Laboratory of Regional Immunity and Diseases, Department of Pathogen Biology, Shenzhen University School of Medicine, Shenzhen, China
| | - Qichao Pan
- Department of Tuberculosis Control, Shanghai Municipal Centre for Disease Control and Prevention, Shanghai, China
| | - Marcel A. Behr
- grid.14709.3b0000 0004 1936 8649Department of Microbiology and Immunology, McGill University and McGill International TB Centre, Montreal, Quebec Canada
| | - Timothy P. Stinear
- grid.1008.90000 0001 2179 088XDepartment of Microbiology and Immunology, Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Vic Australia ,grid.1008.90000 0001 2179 088XDoherty Applied Microbial Genomics, Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Vic Australia
| | - Qian Gao
- grid.8547.e0000 0001 0125 2443Shanghai Institute of Infectious Disease and Biosecurity, Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), Shanghai Medical College and School of Basic Medical Sciences, Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
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35
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Danchuk SN, Behr MA. Bacille Calmette-Guérin: One Hundred Years, One Hundred Questions. Clin Infect Dis 2021; 71:1894-1895. [PMID: 31677382 DOI: 10.1093/cid/ciz1083] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Accepted: 10/29/2019] [Indexed: 11/14/2022] Open
Affiliation(s)
- Sarah N Danchuk
- Department of Microbiology and Immunology, McGill University, Montreal, Quebec, Canada.,Infectious Diseases and Immunity in Global Health Program, Research Institute of the McGill University Health Centre, Montreal, Quebec, Canada.,McGill International TB Centre, Montreal, Quebec, Canada
| | - Marcel A Behr
- Department of Microbiology and Immunology, McGill University, Montreal, Quebec, Canada.,Infectious Diseases and Immunity in Global Health Program, Research Institute of the McGill University Health Centre, Montreal, Quebec, Canada.,McGill International TB Centre, Montreal, Quebec, Canada.,Department of Medicine, McGill University Health Centre, Montreal, Quebec, Canada
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36
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Affiliation(s)
- Marcel A Behr
- Department of Medicine.,McGill International Tuberculosis Centre, and
| | - Eva Kaufmann
- Department of Medicine.,Meakins-Christie Laboratories, McGill University, Montreal, Quebec, Canada
| | - Jacalyn Duffin
- Hannah Professor Emerita of the History of Medicine, Queen's University, Kingston, Ontario, Canada
| | - Paul H Edelstein
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania; and.,Molecular Immunity Unit MRC, Laboratory of Molecular Biology and Cambridge Institute of Therapeutic Immunology and Infectious Diseases, Department of Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Lalita Ramakrishnan
- Molecular Immunity Unit MRC, Laboratory of Molecular Biology and Cambridge Institute of Therapeutic Immunology and Infectious Diseases, Department of Medicine, University of Cambridge, Cambridge, United Kingdom
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37
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Cheng B, Behr MA, Howden BP, Cohen T, Lee RS. Reporting practices for genomic epidemiology of tuberculosis: a systematic review of the literature using STROME-ID guidelines as a benchmark. Lancet Microbe 2021; 2:e115-e129. [PMID: 33842904 PMCID: PMC8034592 DOI: 10.1016/s2666-5247(20)30201-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
BACKGROUND Pathogen genomics have become increasingly important in infectious disease epidemiology and public health. The Strengthening the Reporting of Molecular Epidemiology for Infectious Diseases (STROME-ID) guidelines were developed to outline a minimum set of criteria that should be reported in genomic epidemiology studies to facilitate assessment of study quality. We evaluate such reporting practices, using tuberculosis as an example. METHODS For this systematic review, we initially searched MEDLINE, Embase Classic, and Embase on May 3, 2017, using the search terms "tuberculosis" and "genom* sequencing". We updated this initial search on April 23, 2019, and also included a search of bioRxiv at this time. We included studies in English, French, or Spanish that recruited patients with microbiologically confirmed tuberculosis and used whole genome sequencing for typing of strains. Non-human studies, conference abstracts, and literature reviews were excluded. For each included study, the number and proportion of fulfilled STROME-ID criteria were recorded by two reviewers. A comparison of the mean proportion of fulfilled STROME-ID criteria before and after publication of the STROME-ID guidelines (in 2014) was done using a two-tailed t test. Quasi-Poisson regression and tobit regression were used to examine associations between study characteristics and the number and proportion of fulfilled STROME-ID criteria. This study was registered with PROSPERO, CRD42017064395. FINDINGS 976 titles and abstracts were identified by our primary search, with an additional 16 studies identified in bioRxiv. 114 full texts (published between 2009 and 2019) were eligible for inclusion. The mean proportion of STROME-ID criteria fulfilled was 50% (SD 12; range 16-75). The proportion of criteria fulfilled was similar before and after STROME-ID publication (51% [SD 11] vs 46% [14], p=0·26). The number of criteria reported (among those applicable to all studies) was not associated with impact factor, h-index, country of affiliation of senior author, or sample size of isolates. Similarly, the proportion of criteria fulfilled was not associated with these characteristics, with the exception of a sample size of isolates of 277 or more (the highest quartile). In terms of reproducibility, 100 (88%) studies reported which bioinformatic tools were used, but only 33 (33%) reported corresponding version numbers. Sequencing data were available for 86 (75%) studies. INTERPRETATION The reporting of STROME-ID criteria in genomic epidemiology studies of tuberculosis between 2009 and 2019 was low, with implications for assessment of study quality. The considerable proportion of studies without bioinformatics version numbers or sequencing data available highlights a key concern for reproducibility.
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Affiliation(s)
- Brianna Cheng
- Department of Epidemiology, Biostatistics and Occupational Health, McGill University, Montreal, QC, Canada
| | - Marcel A Behr
- Department of Epidemiology, Biostatistics and Occupational Health, McGill University, Montreal, QC, Canada
| | - Benjamin P Howden
- The Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | | | - Robyn S Lee
- Epidemiology Division, Dalla Lana School of Public Health, University of Toronto, Toronto, ON, Canada
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38
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Behr MA, Divangahi M, Schurr E. Lessons From Bacille Calmette-Guérin for SARS-CoV-2 Vaccine Candidates. J Infect Dis 2021; 223:189-191. [PMID: 33535239 PMCID: PMC7798939 DOI: 10.1093/infdis/jiaa637] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Accepted: 10/05/2020] [Indexed: 11/13/2022] Open
Abstract
Developers of severe acute respiratory syndrome coronavirus 2 vaccines should consider some of the lessons from a "new" vaccine introduced in 1921, namely bacille Calmette-Guérin.
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Affiliation(s)
- Marcel A Behr
- Department of Medicine, McGill University, Montreal, Quebec, Canada.,McGill International TB Centre, Montreal, Quebec, Canada.,Infectious Diseases and Immunity in Global Health, McGill University Health Centre Research Institute, Montreal, Quebec, Canada.,McGill Interdisciplinary Initiative in Infection and Immunity, Montreal, Quebec, Canada
| | - Maziar Divangahi
- Department of Medicine, McGill University, Montreal, Quebec, Canada.,McGill International TB Centre, Montreal, Quebec, Canada.,McGill Interdisciplinary Initiative in Infection and Immunity, Montreal, Quebec, Canada.,Meakins-Christie Laboratories, Montreal, Quebec, Canada
| | - Erwin Schurr
- Department of Medicine, McGill University, Montreal, Quebec, Canada.,McGill International TB Centre, Montreal, Quebec, Canada.,Infectious Diseases and Immunity in Global Health, McGill University Health Centre Research Institute, Montreal, Quebec, Canada.,McGill Interdisciplinary Initiative in Infection and Immunity, Montreal, Quebec, Canada
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39
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Clemmensen HS, Dube JY, McIntosh F, Rosenkrands I, Jungersen G, Aagaard C, Andersen P, Behr MA, Mortensen R. In vivo antigen expression regulates CD4 T cell differentiation and vaccine efficacy against Mycobacterium tuberculosis infection. bioRxiv 2021:2021.02.02.429488. [PMID: 33564764 PMCID: PMC7872352 DOI: 10.1101/2021.02.02.429488] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
New vaccines are urgently needed against Mycobacterium tuberculosis (Mtb), which kills more than 1.4 million people each year. CD4 T cell differentiation is a key determinant of protective immunity against Mtb, but it is not fully understood how host-pathogen interactions shape individual antigen-specific T cell populations and their protective capacity. Here, we investigated the immunodominant Mtb antigen, MPT70, which is upregulated in response to IFN-γ or nutrient/oxygen deprivation of in vitro infected macrophages. Using a murine aerosol infection model, we compared the in vivo expression kinetics of MPT70 to a constitutively expressed antigen, ESAT-6, and analysed their corresponding CD4 T cell phenotype and vaccine-protection. For wild-type Mtb, we found that in vivo expression of MPT70 was delayed compared to ESAT-6. This delayed expression was associated with induction of less differentiated MPT70-specific CD4 T cells but, compared to ESAT-6, also reduced protection after vaccination. In contrast, infection with an MPT70-overexpressing Mtb strain promoted highly differentiated KLRG1+CX3CR1+ CD4 T cells with limited lung-homing capacity. Importantly, this differentiated phenotype could be prevented by vaccination and, against the overexpressing strain, vaccination with MPT70 conferred similar protection as ESAT-6. Together our data indicate that high in vivo antigen expression drives T cells towards terminal differentiation and that targeted vaccination with adjuvanted protein can counteract this phenomenon by maintaining T cells in a protective less-differentiated state. These observations shed new light on host-pathogen interactions and provide guidance on how future Mtb vaccines can be designed to tip the immune-balance in favor of the host.
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Affiliation(s)
- Helena Strand Clemmensen
- Department of Infectious Disease Immunology, Statens Serum Institut, Denmark
- Department of Health Technology, Technical University of Denmark
| | - Jean-Yves Dube
- Department of Microbiology and Immunology, McGill University, Montréal, Canada
- Infectious Diseases and Immunity in Global Health Program, Research Institute of the McGill University Health Centre, Montréal, Canada
- McGill International TB Centre, Montréal, Canada
| | - Fiona McIntosh
- Infectious Diseases and Immunity in Global Health Program, Research Institute of the McGill University Health Centre, Montréal, Canada
- McGill International TB Centre, Montréal, Canada
| | - Ida Rosenkrands
- Department of Infectious Disease Immunology, Statens Serum Institut, Denmark
| | - Gregers Jungersen
- Department of Infectious Disease Immunology, Statens Serum Institut, Denmark
- Department of Health Technology, Technical University of Denmark
| | - Claus Aagaard
- Department of Infectious Disease Immunology, Statens Serum Institut, Denmark
| | - Peter Andersen
- Department of Infectious Disease Immunology, Statens Serum Institut, Denmark
- Department of Immunology and Microbiology, University of Copenhagen
| | - Marcel A. Behr
- Department of Microbiology and Immunology, McGill University, Montréal, Canada
- Infectious Diseases and Immunity in Global Health Program, Research Institute of the McGill University Health Centre, Montréal, Canada
- McGill International TB Centre, Montréal, Canada
- Department of Medicine, McGill University Health Centre, Montréal, Canada
| | - Rasmus Mortensen
- Department of Infectious Disease Immunology, Statens Serum Institut, Denmark
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40
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Rufai SB, McIntosh F, Poojary I, Chothe S, Sebastian A, Albert I, Praul C, Venkatesan M, Mahata G, Maity H, Dandapat P, Michael JS, Katani R, Kapur V, Behr MA. Complete Genome Sequence of Mycobacterium orygis Strain 51145. Microbiol Resour Announc 2021; 10:e01279-20. [PMID: 33414309 PMCID: PMC8407732 DOI: 10.1128/mra.01279-20] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Accepted: 11/24/2020] [Indexed: 11/20/2022] Open
Abstract
We report the complete 4,352,172-bp genome sequence of Mycobacterium orygis strain 51145 assembled into a single circular chromosome. Comparative genomic analyses with other lineages of the Mycobacterium tuberculosis complex can provide insights into the biology, evolution, and epidemiology of this important group of pathogenic mycobacteria.
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Affiliation(s)
- Syed Beenish Rufai
- Department of Microbiology and Immunology, McGill University, Montreal, Quebec, Canada
- McGill International TB Centre, Montreal, Quebec, Canada
- Infectious Diseases and Immunity in Global Health Program, Research Institute of the McGill University Health Centre, Montréal, Canada
| | - Fiona McIntosh
- McGill International TB Centre, Montreal, Quebec, Canada
- Infectious Diseases and Immunity in Global Health Program, Research Institute of the McGill University Health Centre, Montréal, Canada
| | - Indira Poojary
- Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, Pennsylvania, USA
| | - Shubhada Chothe
- Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, Pennsylvania, USA
| | - Aswathy Sebastian
- Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, Pennsylvania, USA
| | - Istvan Albert
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, Pennsylvania, USA
| | - Craig Praul
- Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, Pennsylvania, USA
| | - Manigandan Venkatesan
- Department of Clinical Microbiology, Christian Medical College Vellore, Vellore, India
| | - Gibarni Mahata
- Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, Pennsylvania, USA
| | - Hindol Maity
- Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, Pennsylvania, USA
- Cisgen Biotech Discoveries, Chennai, India
| | - Premanshu Dandapat
- Indian Veterinary Research Institute, Eastern Region Station, Kolkata, West Bengal, India
| | - Joy Sarojini Michael
- Department of Clinical Microbiology, Christian Medical College Vellore, Vellore, India
| | - Robab Katani
- Infectious Diseases and Immunity in Global Health Program, Research Institute of the McGill University Health Centre, Montréal, Canada
- Department of Animal Science and the Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, Pennsylvania, USA
| | - Vivek Kapur
- Infectious Diseases and Immunity in Global Health Program, Research Institute of the McGill University Health Centre, Montréal, Canada
- Department of Animal Science and the Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, Pennsylvania, USA
| | - Marcel A Behr
- Department of Microbiology and Immunology, McGill University, Montreal, Quebec, Canada
- McGill International TB Centre, Montreal, Quebec, Canada
- Infectious Diseases and Immunity in Global Health Program, Research Institute of the McGill University Health Centre, Montréal, Canada
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41
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Khan N, Downey J, Sanz J, Kaufmann E, Blankenhaus B, Pacis A, Pernet E, Ahmed E, Cardoso S, Nijnik A, Mazer B, Sassetti C, Behr MA, Soares MP, Barreiro LB, Divangahi M. M. tuberculosis Reprograms Hematopoietic Stem Cells to Limit Myelopoiesis and Impair Trained Immunity. Cell 2020; 183:752-770.e22. [PMID: 33125891 PMCID: PMC7599081 DOI: 10.1016/j.cell.2020.09.062] [Citation(s) in RCA: 125] [Impact Index Per Article: 31.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Revised: 06/23/2020] [Accepted: 09/02/2020] [Indexed: 12/20/2022]
Abstract
A greater understanding of hematopoietic stem cell (HSC) regulation is required for dissecting protective versus detrimental immunity to pathogens that cause chronic infections such as Mycobacterium tuberculosis (Mtb). We have shown that systemic administration of Bacille Calmette-Guérin (BCG) or β-glucan reprograms HSCs in the bone marrow (BM) via a type II interferon (IFN-II) or interleukin-1 (IL1) response, respectively, which confers protective trained immunity against Mtb. Here, we demonstrate that, unlike BCG or β-glucan, Mtb reprograms HSCs via an IFN-I response that suppresses myelopoiesis and impairs development of protective trained immunity to Mtb. Mechanistically, IFN-I signaling dysregulates iron metabolism, depolarizes mitochondrial membrane potential, and induces cell death specifically in myeloid progenitors. Additionally, activation of the IFN-I/iron axis in HSCs impairs trained immunity to Mtb infection. These results identify an unanticipated immune evasion strategy of Mtb in the BM that controls the magnitude and intrinsic anti-microbial capacity of innate immunity to infection.
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Affiliation(s)
- Nargis Khan
- Meakins-Christie Laboratories, Department of Medicine, Department of Microbiology and Immunology, Department of Pathology, McGill University, Montreal, QC, Canada; McGill International TB Centre, McGill University Health Centre, Montreal, QC, Canada
| | - Jeffrey Downey
- Meakins-Christie Laboratories, Department of Medicine, Department of Microbiology and Immunology, Department of Pathology, McGill University, Montreal, QC, Canada; McGill International TB Centre, McGill University Health Centre, Montreal, QC, Canada
| | - Joaquin Sanz
- Department of Theoretical Physics, University of Zaragoza, Institute BIFI for Bio-computation and Physics of Complex Systems, University of Zaragoza, Zaragoza, Spain
| | - Eva Kaufmann
- Meakins-Christie Laboratories, Department of Medicine, Department of Microbiology and Immunology, Department of Pathology, McGill University, Montreal, QC, Canada; McGill International TB Centre, McGill University Health Centre, Montreal, QC, Canada
| | | | - Alain Pacis
- Department of Medicine, Genetic Section, University of Chicago, Chicago, IL, USA
| | - Erwan Pernet
- Meakins-Christie Laboratories, Department of Medicine, Department of Microbiology and Immunology, Department of Pathology, McGill University, Montreal, QC, Canada; McGill International TB Centre, McGill University Health Centre, Montreal, QC, Canada
| | - Eisha Ahmed
- Meakins-Christie Laboratories, Department of Medicine, Department of Microbiology and Immunology, Department of Pathology, McGill University, Montreal, QC, Canada
| | | | - Anastasia Nijnik
- Department of Physiology, Complex Traits Group, McGill University, Montreal, QC, Canada
| | - Bruce Mazer
- Meakins-Christie Laboratories, Department of Medicine, Department of Microbiology and Immunology, Department of Pathology, McGill University, Montreal, QC, Canada
| | - Christopher Sassetti
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, MA, USA
| | - Marcel A Behr
- McGill International TB Centre, McGill University Health Centre, Montreal, QC, Canada
| | | | - Luis B Barreiro
- Department of Medicine, Genetic Section, University of Chicago, Chicago, IL, USA
| | - Maziar Divangahi
- Meakins-Christie Laboratories, Department of Medicine, Department of Microbiology and Immunology, Department of Pathology, McGill University, Montreal, QC, Canada; McGill International TB Centre, McGill University Health Centre, Montreal, QC, Canada.
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42
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Duffy SC, Srinivasan S, Michael JS, Behr MA, Kapur V. Mycobacterium orygis: a zoonosis, zooanthroponosis, or both? – Authors' reply. The Lancet Microbe 2020; 1:e241. [DOI: 10.1016/s2666-5247(20)30145-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Accepted: 08/25/2020] [Indexed: 11/29/2022] Open
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43
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Veyrier FJ, Nieves C, Lefrancois LH, Trigui H, Vincent AT, Behr MA. RskA Is a Dual Function Activator-Inhibitor That Controls SigK Activity Across Distinct Bacterial Genera. Front Microbiol 2020; 11:558166. [PMID: 33013790 PMCID: PMC7509140 DOI: 10.3389/fmicb.2020.558166] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Accepted: 08/14/2020] [Indexed: 01/25/2023] Open
Abstract
It has been previously shown that RskA, the anti-Sigma factor K of Mycobacterium tuberculosis, inhibits SigK and that mutations in RskA promote high expression of the SigK regulon. The latter observation led us to hypothesize that RskA mutations lead to loss of the anti-Sigma factor function. In this report, we used natural and artificial mutations in RskA to determine the basis of the SigK-RskA partnership. Consistent with predictions, the N-terminal cytoplasmic portion of RskA was sufficient on its own to inhibit SigK. Unexpectedly, RskA also served as an activator of SigK. This activation depended on the same N-terminal region and was enhanced by the membrane-extracellular portion of RskA. Based on this, we engineered similar truncations in a Gram-negative bacterium, namely Yersinia enterocolitica. Again, we observed that, with specific alterations of RskA, we were able to enhance SigK activity. Together these results support an alternative mechanism of anti-Sigma factor function, that we could term modulator (activator-inhibitor) in both Actinobacteria and Gram-negative bacteria, suggesting that Sigma factor activation by anti-Sigma factors could be under-recognized.
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Affiliation(s)
- Frédéric J Veyrier
- Bacterial Symbionts Evolution, Centre Armand-Frappier Santé Biotechnologie, Institut National de la Recherche Scientifique, Université du Québec, Laval, QC, Canada
- McGill International TB Centre, Montreal, QC, Canada
| | - Cecilia Nieves
- Bacterial Symbionts Evolution, Centre Armand-Frappier Santé Biotechnologie, Institut National de la Recherche Scientifique, Université du Québec, Laval, QC, Canada
- McGill International TB Centre, Montreal, QC, Canada
| | - Louise H Lefrancois
- McGill International TB Centre, Montreal, QC, Canada
- Department of Medicine, McGill University, Montreal, QC, Canada
| | - Hana Trigui
- Bacterial Symbionts Evolution, Centre Armand-Frappier Santé Biotechnologie, Institut National de la Recherche Scientifique, Université du Québec, Laval, QC, Canada
- McGill International TB Centre, Montreal, QC, Canada
| | - Antony T Vincent
- Bacterial Symbionts Evolution, Centre Armand-Frappier Santé Biotechnologie, Institut National de la Recherche Scientifique, Université du Québec, Laval, QC, Canada
- McGill International TB Centre, Montreal, QC, Canada
| | - Marcel A Behr
- McGill International TB Centre, Montreal, QC, Canada
- Department of Medicine, McGill University, Montreal, QC, Canada
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El-Zein M, Gotlieb W, Gilbert L, Hemmings R, Behr MA, Franco EL. Dual staining for p16/Ki-67 to detect high-grade cervical lesions: Results from the Screening Triage Ascertaining Intraepithelial Neoplasia by Immunostain Testing study. Int J Cancer 2020; 148:492-501. [PMID: 32781481 DOI: 10.1002/ijc.33250] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Revised: 07/13/2020] [Accepted: 08/03/2020] [Indexed: 12/13/2022]
Abstract
We compared clinical performance of p16/Ki-67 dual-stained cytology and human papillomavirus (HPV) genotyping, via different algorithms-alone, or in combination with cytology-to identify cervical intraepithelial neoplasia grade 2 or worse (CIN2+) and grade 3 or worse (CIN3+) in women referred to as colposcopy. We included 492 cervical specimens (134 normal, 130 CIN1, 99 CIN2, 121 CIN3, 8 cancers) randomly selected from 1158 specimens with valid conventional cytology, HPV (cobas 4800 HPV test) and biopsy results. Dual-stained cytology was retrospectively performed (CINtec PLUS assay) on PreservCyt material; slides were read by a cytologist and confirmed by two pathologists, blinded to cytology, biopsy and genotyping results. Sensitivity and specificity (95% confidence intervals in parentheses) of dual-stained cytology to detect CIN2+ and CIN3+ were compared to other screening tests available for the same women. Positivity rate for dual-stained cytology increased with histological severity: 30.6% in normal, 41.5% in CIN1, 72.7% in CIN2, 86.8% in CIN3 and 87.5% in cancer. Dual-stained cytology alone had lower sensitivity than HPV testing for CIN2+ [80.7% (75.0-85.6) vs 89.9% (85.3-93.5)] and CIN3+ [86.8% (79.7-92.1) vs 92.3% (86.2-96.2)]. However, corresponding specificity values were higher [64.0% (57.9-69.8) vs 56.1% (49.8-62.1) for CIN2+; 54.0% (48.7-59.2) vs 44.4% (39.2-49.6) for CIN3+]. Combining dual-stained cytology with an ASC-US abnormality threshold decreased specificity to 31.4% (25.9-37.4) for CIN2+ and 24.2% (19.9-29.0) for CIN3+. The corresponding values considering low squamous intraepithelial lesion threshold values were 42.8% (36.8-49.0) and 35.0% (30.1-40.1). Dual-stained cytology and HPV testing exhibited similar performance, although the former improved the specificity by 7.9% and 9.6% for CIN2+ and CIN3+, respectively.
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Affiliation(s)
- Mariam El-Zein
- Division of Cancer Epidemiology, McGill University, Montréal, Quebec, Canada
| | - Walter Gotlieb
- Division of Gynecologic Oncology and Colposcopy, McGill University-Jewish General Hospital, Montréal, Quebec, Canada
| | - Lucy Gilbert
- Gynecologic Cancer Service, McGill University Health Centre-Glen Site Cedars Cancer Centre, Montréal, Quebec, Canada
| | - Robert Hemmings
- Department of Obstetrics and Gynecology, McGill University Health Centre-St Mary's Hospital Centre, Montréal, Quebec, Canada
| | - Marcel A Behr
- Department of Medicine, McGill University Health Centre, Montréal, Quebec, Canada
| | - Eduardo L Franco
- Division of Cancer Epidemiology, McGill University, Montréal, Quebec, Canada
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45
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Duffy SC, Srinivasan S, Schilling MA, Stuber T, Danchuk SN, Michael JS, Venkatesan M, Bansal N, Maan S, Jindal N, Chaudhary D, Dandapat P, Katani R, Chothe S, Veerasami M, Robbe-Austerman S, Juleff N, Kapur V, Behr MA. Reconsidering Mycobacterium bovis as a proxy for zoonotic tuberculosis: a molecular epidemiological surveillance study. Lancet Microbe 2020; 1:e66-e73. [PMID: 32642742 PMCID: PMC7325494 DOI: 10.1016/s2666-5247(20)30038-0] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Background Zoonotic tuberculosis is defined as human infection with Mycobacterium bovis. Although globally, India has the largest number of human tuberculosis cases and the largest cattle population, in which bovine tuberculosis is endemic, the burden of zoonotic tuberculosis is unknown. The aim of this study was to obtain estimates of the human prevalence of animal-associated members of the Mycobacterium tuberculosis complex (MTBC) at a large referral hospital in India. Methods We did a molecular epidemiological surveillance study of 940 positive mycobacteria growth indicator tube (MGIT) cultures, collected from patients visiting the outpatient department at Christian Medical College (Vellore, India) with suspected tuberculosis between Oct 1, 2018, and March 31, 2019. A PCR-based approach was applied to subspeciate cultures. Isolates identified as MTBC other than M tuberculosis or as inconclusive on PCR were subject to whole-genome sequencing (WGS), and phylogenetically compared with publicly available MTBC sequences from south Asia. Sequences from WGS were deposited in the National Center for Biotechnology Information Sequence Read Archive, accession number SRP226525 (BioProject database number PRJNA575883). Findings The 940 MGIT cultures were from 548 pulmonary and 392 extrapulmonary samples. A conclusive identification was obtained for all 940 isolates; wild-type M bovis was not identified. The isolates consisted of M tuberculosis (913 [97·1%] isolates), Mycobacterium orygis (seven [0·7%]), M bovis BCG (five [0·5%]), and non-tuberculous mycobacteria (15 [1·6%]). Subspecies were assigned for 25 isolates by WGS, which were analysed against 715 MTBC sequences from south Asia. Among the 715 genomes, no M bovis was identified. Four isolates of cattle origin were dispersed among human sequences within M tuberculosis lineage 1, and the seven M orygis isolates from human MGIT cultures were dispersed among sequences from cattle. Interpretation M bovis prevalence in humans is an inadequate proxy of zoonotic tuberculosis. The recovery of M orygis from humans highlights the need to use a broadened definition, including MTBC subspecies such as M orygis, to investigate zoonotic tuberculosis. The identification of M tuberculosis in cattle also reinforces the need for One Health investigations in countries with endemic bovine tuberculosis. Funding Bill & Melinda Gates Foundation, Canadian Institutes for Health Research.
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Affiliation(s)
- Shannon C Duffy
- Department of Microbiology and Immunology, McGill University, Montreal, QC, Canada.,McGill International Tuberculosis Centre, McGill University, Montreal, QC, Canada.,Infectious Diseases and Immunity in Global Health Program, Research Institute of the McGill University Health Centre, Montreal, QC, Canada
| | - Sreenidhi Srinivasan
- Department of Animal Science and the Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, USA
| | - Megan A Schilling
- Department of Animal Science and the Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, USA
| | - Tod Stuber
- National Veterinary Services Laboratories, Animal and Plant Health Inspection Service, US Department of Agriculture, Ames, IA, USA
| | - Sarah N Danchuk
- Department of Microbiology and Immunology, McGill University, Montreal, QC, Canada.,McGill International Tuberculosis Centre, McGill University, Montreal, QC, Canada.,Infectious Diseases and Immunity in Global Health Program, Research Institute of the McGill University Health Centre, Montreal, QC, Canada
| | - Joy S Michael
- Department of Clinical Microbiology, Christian Medical College Vellore, Vellore, India
| | - Manigandan Venkatesan
- Department of Clinical Microbiology, Christian Medical College Vellore, Vellore, India
| | - Nitish Bansal
- Department of Veterinary Public Health and Epidemiology, College of Veterinary Sciences, Lala Lajpat Rai University of Veterinary and Animal Sciences, Hisar, India
| | - Sushila Maan
- Department of Animal Biotechnology, College of Veterinary Sciences, Lala Lajpat Rai University of Veterinary and Animal Sciences, Hisar, India
| | - Naresh Jindal
- Department of Veterinary Public Health and Epidemiology, College of Veterinary Sciences, Lala Lajpat Rai University of Veterinary and Animal Sciences, Hisar, India
| | - Deepika Chaudhary
- Department of Veterinary Public Health and Epidemiology, College of Veterinary Sciences, Lala Lajpat Rai University of Veterinary and Animal Sciences, Hisar, India
| | - Premanshu Dandapat
- Eastern Regional Station, Indian Veterinary Research Institute, Indian Council of Agricultural Research, Kolkata, India
| | - Robab Katani
- Department of Animal Science and the Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, USA
| | - Shubhada Chothe
- Department of Animal Science and the Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, USA
| | | | - Suelee Robbe-Austerman
- National Veterinary Services Laboratories, Animal and Plant Health Inspection Service, US Department of Agriculture, Ames, IA, USA
| | | | - Vivek Kapur
- Department of Animal Science and the Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, USA
| | - Marcel A Behr
- Department of Microbiology and Immunology, McGill University, Montreal, QC, Canada.,McGill International Tuberculosis Centre, McGill University, Montreal, QC, Canada.,Department of Medicine, McGill University, Montreal, QC, Canada.,Infectious Diseases and Immunity in Global Health Program, Research Institute of the McGill University Health Centre, Montreal, QC, Canada
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46
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Dubé JY, McIntosh F, Zarruk JG, David S, Nigou J, Behr MA. Synthetic mycobacterial molecular patterns partially complete Freund's adjuvant. Sci Rep 2020; 10:5874. [PMID: 32246076 PMCID: PMC7125112 DOI: 10.1038/s41598-020-62543-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Accepted: 03/13/2020] [Indexed: 12/03/2022] Open
Abstract
Complete Freund's adjuvant (CFA) has historically been one of the most useful tools of immunologists. Essentially comprised of dead mycobacteria and mineral oil, we asked ourselves what is special about the mycobacterial part of this adjuvant, and could it be recapitulated synthetically? Here, we demonstrate the essentiality of N-glycolylated peptidoglycan plus trehalose dimycolate (both unique in mycobacteria) for the complete adjuvant effect using knockouts and chemical complementation. A combination of synthetic N-glycolyl muramyl dipeptide and minimal trehalose dimycolate motif GlcC14C18 was able to upregulate dendritic cell effectors, plus induce experimental autoimmunity qualitatively similar but quantitatively milder compared to CFA. This research outlines how to substitute CFA with a consistent, molecularly-defined adjuvant which may inform the design of immunotherapeutic agents and vaccines benefitting from cell-mediated immunity. We also anticipate using synthetic microbe-associated molecular patterns (MAMPs) to study mycobacterial immunity and immunopathogenesis.
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Affiliation(s)
- Jean-Yves Dubé
- Department of Microbiology and Immunology, McGill University, Montréal, Canada.
- Infectious Diseases and Immunity in Global Health Program, Research Institute of the McGill University Health Centre, Montréal, Canada.
- McGill International TB Centre, Montréal, Canada.
| | - Fiona McIntosh
- Infectious Diseases and Immunity in Global Health Program, Research Institute of the McGill University Health Centre, Montréal, Canada
- McGill International TB Centre, Montréal, Canada
| | - Juan G Zarruk
- Centre for Research in Neuroscience, Research Institute of the McGill University Health Centre, Montréal, Canada
| | - Samuel David
- Centre for Research in Neuroscience, Research Institute of the McGill University Health Centre, Montréal, Canada
| | - Jérôme Nigou
- Institut de Pharmacologie et de Biologie Structurale, Université de Toulouse, CNRS, Université Paul Sabatier, Toulouse, France
| | - Marcel A Behr
- Department of Microbiology and Immunology, McGill University, Montréal, Canada.
- Infectious Diseases and Immunity in Global Health Program, Research Institute of the McGill University Health Centre, Montréal, Canada.
- McGill International TB Centre, Montréal, Canada.
- Department of Medicine, McGill University Health Centre, Montréal, Canada.
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47
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El-Zein M, Cheishvili D, Gotlieb W, Gilbert L, Hemmings R, Behr MA, Szyf M, Franco EL. Genome-wide DNA methylation profiling identifies two novel genes in cervical neoplasia. Int J Cancer 2020; 147:1264-1274. [PMID: 31983058 DOI: 10.1002/ijc.32880] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2019] [Revised: 12/03/2019] [Accepted: 01/03/2020] [Indexed: 12/27/2022]
Abstract
DNA methylation analysis may improve risk stratification in cervical screening. We used a pan-epigenomic approach to identify new methylation markers along the continuum of cervical intraepithelial neoplasia (CIN) to cervical cancer. Physician-collected samples (54 normal, 50 CIN1, 40 CIN2 and 42 CIN3) were randomly selected from women at a single-center colposcopy clinic. Extracted DNA was subjected to Illumina Infinium EPIC array analysis, and methylation was assessed blinded to histopathological and clinical data. CpG sites whose state of methylation correlated with lesion grade were assessed (Spearman correlation), and a weighted methylation score was calculated comparing normal to CIN3. Validation of the top selected genes was performed in an independent cohort (100 normal, 50 CIN1, 50 CIN2, 50 CIN3 and 8 cervical cancers) of new patients, referred for colposcopic examination at three hospitals, using targeted DNA methylation Illumina amplicon sequencing. The relationship between a combined weighted marker score and progression from normal through precancerous lesions and cervical cancer was compared using one-way ANOVA. Our analyses revealed 7,715 CpGs whose methylation level correlated with progression (from normal to CIN1, CIN2 and CIN3), with a significant trend of increased methylation with lesion grade. We shortlisted a bigenic (hyaluronan synthase 1, HAS1 and ATPase phospholipid transporting 10A, ATP10A corresponding to cg03419058 and cg13944175 sites) marker set; r = 0.55, p < 0.0001. Validation of the four most discriminating genes (CA10, DPP10, FMN2 and HAS1) showed a significant correlation between methylation levels and disease progression (p-value < 2.2 × 10-16 , adjusted R2 = 0.952). Translational research of the identified genes to future clinical applications is warranted.
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Affiliation(s)
- Mariam El-Zein
- Division of Cancer Epidemiology, McGill University, Montréal, QC, Canada.,Gerald Bronfman Department of Oncology, McGill University, Montréal, QC, Canada
| | - David Cheishvili
- Gerald Bronfman Department of Oncology, McGill University, Montréal, QC, Canada.,HKG Epitherapeutics, Science Park, Hong Kong.,Montreal EpiTerapia Inc., Montreal, QC, Canada
| | - Walter Gotlieb
- Division of Gynecologic Oncology and Colposcopy, McGill University, Jewish General Hospital, Montréal, QC, Canada
| | - Lucy Gilbert
- Gynecologic Cancer Service, McGill University Health Centre, Glen Site Cedars Cancer Centre, Montréal, QC, Canada
| | - Robert Hemmings
- Department of Obstetrics and Gynecology, McGill University Health Centre - St Mary's Hospital Centre, Montréal, QC, Canada
| | - Marcel A Behr
- Department of Medicine, McGill University Health Centre, Montréal, QC, Canada
| | - Moshe Szyf
- HKG Epitherapeutics, Science Park, Hong Kong.,Montreal EpiTerapia Inc., Montreal, QC, Canada.,Department of Pharmacology and Therapeutics, McGill University, Montréal, QC, Canada
| | - Eduardo L Franco
- Division of Cancer Epidemiology, McGill University, Montréal, QC, Canada.,Gerald Bronfman Department of Oncology, McGill University, Montréal, QC, Canada
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48
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Lee RS, Proulx JF, McIntosh F, Behr MA, Hanage WP. Previously undetected super-spreading of Mycobacterium tuberculosis revealed by deep sequencing. eLife 2020; 9:e53245. [PMID: 32014110 PMCID: PMC7012596 DOI: 10.7554/elife.53245] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Accepted: 01/19/2020] [Indexed: 12/14/2022] Open
Abstract
Tuberculosis disproportionately affects the Canadian Inuit. To address this, it is imperative we understand transmission dynamics in this population. We investigate whether 'deep' sequencing can provide additional resolution compared to standard sequencing, using a well-characterized outbreak from the Arctic (2011-2012, 50 cases). Samples were sequenced to ~500-1000x and reads were aligned to a novel local reference genome generated with PacBio SMRT sequencing. Consensus and heterogeneous variants were identified and compared across genomes. In contrast with previous genomic analyses using ~50x depth, deep sequencing allowed us to identify a novel super-spreader who likely transmitted to up to 17 other cases during the outbreak (35% of the remaining cases that year). It is increasingly evident that within-host diversity should be incorporated into transmission analyses; deep sequencing may facilitate more accurate detection of super-spreaders and transmission clusters. This has implications not only for TB, but all genomic studies of transmission - regardless of pathogen.
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Affiliation(s)
- Robyn S Lee
- Epidemiology Division, Dalla Lana School of Public HealthUniversity of TorontoTorontoCanada
- Center for Communicable Disease DynamicsHarvard TH Chan School of Public HealthBostonUnited States
- Department of EpidemiologyHarvard TH Chan School of Public HealthBostonUnited States
| | | | - Fiona McIntosh
- The Research Institute of McGill University Health CentreMontréalCanada
| | - Marcel A Behr
- The Research Institute of McGill University Health CentreMontréalCanada
| | - William P Hanage
- Center for Communicable Disease DynamicsHarvard TH Chan School of Public HealthBostonUnited States
- Department of EpidemiologyHarvard TH Chan School of Public HealthBostonUnited States
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49
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Fox GJ, Nguyen CB, Nguyen TA, Tran PT, Marais BJ, Graham SM, Nguyen BH, Velen K, Dowdy DW, Mason P, Britton WJ, Behr MA, Benedetti A, Menzies D, Nguyen VN, Marks GB. Levofloxacin versus placebo for the treatment of latent tuberculosis among contacts of patients with multidrug-resistant tuberculosis (the VQUIN MDR trial): a protocol for a randomised controlled trial. BMJ Open 2020; 10:e033945. [PMID: 31900274 PMCID: PMC6955503 DOI: 10.1136/bmjopen-2019-033945] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
INTRODUCTION Treatment of latent tuberculosis infection (LTBI) plays a substantial role in the prevention of drug-susceptible tuberculosis (TB). However, clinical trials to evaluate the efficacy of preventive therapy for presumed multidrug-resistant (MDR) LTBI are lacking. This trial aims to evaluate the efficacy of the antibiotic levofloxacin in preventing the development of active TB among latently infected contacts of index patients with MDR-TB. METHODS AND ANALYSIS A double-blind placebo-controlled parallel group randomised controlled trial will be conducted in 10 provinces of Vietnam. Household contacts living with patients with bacteriologically confirmed rifampicin-resistant or MDR-TB will be eligible for recruitment if they have a positive tuberculin skin test or are known to be immunosuppressed, and do not have active TB. Participants will be randomised to receive either levofloxacin or placebo tablets once per day for 6 months. Screening for incident TB will be performed at 6 months intervals. The primary study outcome is the incidence of bacteriologically confirmed TB within 30 months after randomisation. Analysis will be by intention to treat, using Poisson regression. ETHICS Ethical approval from the University of Sydney Human Research Ethics Committee was obtained on 29 April 2015 (2014/929), and from the Vietnam Ministry of Health Institutional Review Board on 30 September 2015 (4040/QD-BYT). DISSEMINATION Findings of the study will be published in peer-reviewed publications and conference presentations. TRIAL REGISTRATION NUMBER ACTRN12616000215426.
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Affiliation(s)
- Greg J Fox
- Central Clinical School, The University of Sydney Faculty of Medicine and Health, Sydney, New South Wales, Australia
- Woolcock Institute of Medical Research, Glebe, New South Wales, Australia
| | - Cam Binh Nguyen
- Woolcock Institute of Medical Research, Glebe, New South Wales, Australia
| | - Thu Anh Nguyen
- Woolcock Institute of Medical Research, Glebe, New South Wales, Australia
| | - Phuong Thuy Tran
- Woolcock Institute of Medical Research, Glebe, New South Wales, Australia
| | - Ben J Marais
- The University of Sydney Faculty of Medicine and Health, Sydney, New South Wales, Australia
- The University of Sydney Marie Bashir Institute for Infectious Diseases and Biosecurity, Sydney, New South Wales, Australia
| | - Steve M Graham
- Murdoch Childrens Research Institute, Parkville, Victoria, Australia
- Department of Paediatrics, The University of Melbourne, Melbourne, Victoria, Australia
| | | | - Kavi Velen
- Woolcock Institute of Medical Research, Glebe, New South Wales, Australia
- The University of Sydney Faculty of Medicine and Health, Sydney, New South Wales, Australia
| | - David W Dowdy
- Department of Epidemiology, John Hopkins Bloomberg, Baltimore, Maryland, USA
| | - Paul Mason
- Taronga Institute of Science and Learning, Taronga Conservation Society, Sydney, New South Wales, Australia
| | - Warwick J Britton
- The University of Sydney Faculty of Medicine and Health, Sydney, New South Wales, Australia
- Tuberculosis Research Program, The Centenary Institute of Cancer Medicine and Cell Biology, Sydney, New South Wales, Australia
| | - Marcel A Behr
- Department of Medicine, McGill University, Montreal, Quebec, Canada
- McGill International Tuberculosis Centre, McGill University, Montreal, Quebec, Canada
| | - Andrea Benedetti
- Departments of Medicine and of Epidemiology, Biostatistics & Occupational Health, McGill University, Montreal, Quebec, Canada
| | - Dick Menzies
- McGill International Tuberculosis Centre, McGill University, Montreal, Quebec, Canada
| | | | - Guy B Marks
- Woolcock Institute of Medical Research, Glebe, New South Wales, Australia
- South Western Sydney Clinical School, University of New South Wales, Sydney, New South Wales, Australia
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50
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Danchuk SN, McIntosh F, Jamieson FB, May K, Behr MA. Bacillus Calmette-Guérin strains with defined resistance mutations: a new tool for tuberculosis laboratory quality control. Clin Microbiol Infect 2019; 26:384.e5-384.e8. [PMID: 31705996 DOI: 10.1016/j.cmi.2019.10.033] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Revised: 10/23/2019] [Accepted: 10/29/2019] [Indexed: 11/28/2022]
Abstract
OBJECTIVE Laboratory quality control (QC) is essential to assess the reliability of tuberculosis diagnostic testing. To provide safe QC reagents for the detection of drug-resistant Mycobacterium tuberculosis, we generated antibiotic-resistant mycobacterial strains of attenuated virulence (M. bovis bacillus Calmette-Guérin (BCG)). METHODS Seven mono-resistant BCG strains were developed by introducing resistance-conferring mutations into wild-type BCG strains. Mutations were confirmed by dideoxynucleotide sequencing. Phenotypic resistance was quantified by microbroth dilution to determine the MIC90. The capacity of two commercial tests (GeneXpert TB/RIF and Genotype MTBDRplus) to detect resistance-conferring mutations was evaluated independently. RESULTS Our panel included BCG strains with mutations in rpoB (S450L, I491F), katG (deletion at AA428), gyrA (D94G), rpsL (K43R) and Rv0678c (S63R). These mutations translated respectively into phenotypic resistance to rifampin (MIC ≥8 mg/L), isoniazid (MIC ≥8 mg/L), moxifloxacin (MIC 4 mg/L) and streptomycin (MIC ≥8 mg/L); the Rv0678c mutant showed decreased susceptibility to both clofazimine (MIC 4 mg/L) and bedaqualine (MIC 1 mg/L). GeneXpert (Cepheid) and Genotype MTBDRplus (Hain Lifesciences) both called the rpoB S450L strain rifampin-resistant and the I491F mutant rifampin-susceptible, as expected based on single nucleotide polymorphism positions. Likewise, MTBDRplus called the novel katG deletion mutant isoniazid susceptible despite phenotypic resistance. CONCLUSION BCG strains engineered to be mono-resistant to anti-tuberculosis drugs can be used as safe QC reagents for tuberculosis diagnostics and drug susceptibility testing.
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Affiliation(s)
- S N Danchuk
- Department of Microbiology and Immunology, McGill University, Montreal, Quebec, Canada; Infectious Diseases and Immunity in Global Health Program, Research Institute of the McGill University Health Centre, Montreal, Quebec, Canada; McGill International TB Centre, Montreal, Quebec, Canada
| | - F McIntosh
- Infectious Diseases and Immunity in Global Health Program, Research Institute of the McGill University Health Centre, Montreal, Quebec, Canada; McGill International TB Centre, Montreal, Quebec, Canada
| | - F B Jamieson
- Public Health Ontario, Toronto, Ontario, Canada; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - K May
- Public Health Ontario, Toronto, Ontario, Canada
| | - M A Behr
- Department of Microbiology and Immunology, McGill University, Montreal, Quebec, Canada; Infectious Diseases and Immunity in Global Health Program, Research Institute of the McGill University Health Centre, Montreal, Quebec, Canada; McGill International TB Centre, Montreal, Quebec, Canada.
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