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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] [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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Karthik K, Subramanian S, Vinoli Priyadharshini M, Jawahar A, Anbazhagan S, Kathiravan RS, Thomas P, Babu RPA, Gopalan Tirumurugaan K, Raj GD. Whole genome sequencing and comparative genomics of Mycobacterium orygis isolated from different animal hosts to identify specific diagnostic markers. Front Cell Infect Microbiol 2023; 13:1302393. [PMID: 38188626 PMCID: PMC10770871 DOI: 10.3389/fcimb.2023.1302393] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Accepted: 11/22/2023] [Indexed: 01/09/2024] Open
Abstract
Introduction Mycobacterium orygis, a member of MTBC has been identified in higher numbers in the recent years from animals of South Asia. Comparative genomics of this important zoonotic pathogen is not available which can provide data on the molecular difference between other MTBC members. Hence, the present study was carried out to isolate, whole genome sequence M. orygis from different animal species (cattle, buffalo and deer) and to identify molecular marker for the differentiation of M. orygis from other MTBC members. Methods Isolation and whole genome sequencing of M. orygis was carried out for 9 samples (4 cattle, 4 deer and 1 buffalo) died due to tuberculosis. Comparative genomics employing 53 genomes (44 from database and 9 newly sequenced) was performed to identify SNPs, spoligotype, pangenome structure, and region of difference. Results M. orygis was isolated from water buffalo and sambar deer which is the first of its kind report worldwide. Comparative pangenomics of all M. orygis strains worldwide (n= 53) showed a closed pangenome structure which is also reported for the first time. Pairwise SNP between TANUVAS_2, TANUVAS_4, TANUVAS_5, TANUVAS_7 and NIRTAH144 was less than 15 indicating that the same M. orygis strain may be the cause for infection. Region of difference prediction showed absence of RD7, RD8, RD9, RD10, RD12, RD301, RD315 in all the M. orygis analyzed. SNPs in virulence gene, PE35 was found to be unique to M. orygis which can be used as marker for identification. Conclusion The present study is yet another supportive evidence that M. orygis is more prevalent among animals in South Asia and the zoonotic potential of this organism needs to be evaluated.
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Affiliation(s)
- Kumaragurubaran Karthik
- Department of Veterinary Microbiology, Veterinary College and Research Institute, Tamil Nadu Veterinary and Animal Sciences University, Udumalpet, India
| | - Saraswathi Subramanian
- Translational Research Platform for Veterinary Biologicals, Tamil Nadu Veterinary and Animal Sciences University (TANUVAS), Chennai, India
| | - Michael Vinoli Priyadharshini
- Translational Research Platform for Veterinary Biologicals, Tamil Nadu Veterinary and Animal Sciences University (TANUVAS), Chennai, India
| | - Ayyaru Jawahar
- Translational Research Platform for Veterinary Biologicals, Tamil Nadu Veterinary and Animal Sciences University (TANUVAS), Chennai, India
| | - Subbaiyan Anbazhagan
- Indian Council of Medical Research (ICMR)-National Animal Resource Facility for Biomedical Research, Hyderabad, Telangana, India
| | - Ramaiyan Selvaraju Kathiravan
- Translational Research Platform for Veterinary Biologicals, Tamil Nadu Veterinary and Animal Sciences University (TANUVAS), Chennai, India
| | - Prasad Thomas
- Division of Bacteriology and Mycology, Indian Council of Agricultural Research (ICAR)- India Veterinary Research Institute, Bareilly, Uttar Pradesh, India
| | - Ramasamy Parthiban Aravindh Babu
- Translational Research Platform for Veterinary Biologicals, Tamil Nadu Veterinary and Animal Sciences University (TANUVAS), Chennai, India
| | - Krishnaswamy Gopalan Tirumurugaan
- Translational Research Platform for Veterinary Biologicals, Tamil Nadu Veterinary and Animal Sciences University (TANUVAS), Chennai, India
| | - Gopal Dhinakar Raj
- Department of Animal Biotechnology, Madras Veterinary College, Tamil Nadu Veterinary and Animal Sciences University (TANUVAS), Chennai, India
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Islam MR, Sharma MK, KhunKhun R, Shandro C, Sekirov I, Tyrrell GJ, Soualhine H. Whole genome sequencing-based identification of human tuberculosis caused by animal-lineage Mycobacterium orygis. J Clin Microbiol 2023; 61:e0026023. [PMID: 37877705 PMCID: PMC10662373 DOI: 10.1128/jcm.00260-23] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Accepted: 09/11/2023] [Indexed: 10/26/2023] Open
Abstract
A recently described member of the Mycobacterium tuberculosis complex (MTBC) is Mycobacterium orygis, which can cause disease primarily in animals but also in humans. Although M. orygis has been reported from different geographic regions around the world, due to a lack of proper identification techniques, the contribution of this emerging pathogen to the global burden of zoonotic tuberculosis is not fully understood. In the present work, we report single nucleotide polymorphism (SNP) analysis using whole genome sequencing (WGS) that can accurately identify M. orygis and differentiate it from other members of the MTBC species. WGS-based SNP analysis was performed for 61 isolates from different provinces in Canada that were identified as M. orygis. A total of 56 M. orygis sequences from the public databases were also included in the analysis. Several unique SNPs in the gyrB, PPE55, Rv2042c, leuS, mmpL6, and mmpS6 genes were used to determine their effectiveness as genetic markers for the identification of M. orygis. To the best of our knowledge, five of these SNPs, viz., gyrB 277 (A→G), gyrB 1478 (T→C), leuS 1064 (A→T), mmpL6 486 (T→C), and mmpS6 334 (C→G), are reported for the first time in this study. Our results also revealed several SNPs specific to other species within MTBC. The phylogenetic analysis shows that the studied genomes were genetically diverse and clustered with M. orygis sequences of human and animal origin reported from different geographic locations. Therefore, the present study provides a new insight into the high-confidence identification of M. orygis from MTBC species based on WGS data, which can be useful for reference and diagnostic laboratories.
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Affiliation(s)
- Md Rashedul Islam
- National Reference Centre for Mycobacteriology, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | - Meenu K. Sharma
- National Reference Centre for Mycobacteriology, 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
| | - Rupinder KhunKhun
- BC Center for Disease Control Public Health Laboratory, Vancouver, British Columbia, Canada
| | - Cary Shandro
- Provincial Laboratory for Public Health, Alberta Precision Labs, Edmonton, Alberta, Canada
| | - Inna Sekirov
- BC Center for Disease Control Public Health Laboratory, Vancouver, British Columbia, Canada
| | - Gregory J. Tyrrell
- Provincial Laboratory for Public Health, Alberta Precision Labs, Edmonton, Alberta, Canada
| | - Hafid Soualhine
- National Reference Centre for Mycobacteriology, 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
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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] [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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Threat from Mycobacterium orygis-associated tuberculosis in south Asia. THE LANCET MICROBE 2022; 3:e641-e642. [DOI: 10.1016/s2666-5247(22)00149-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2022] [Accepted: 05/18/2022] [Indexed: 11/19/2022] Open
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A rare presentation of Mycobacterium africanum after two decades: a case report from Brunei Darussalam. Western Pac Surveill Response J 2022; 13:1-4. [PMID: 36688180 PMCID: PMC9831599 DOI: 10.5365/wpsar.2022.13.3.926] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
Mycobacterium africanum is endemic to West Africa and is rare outside this region. Most of the people infected with
M. africanum outside Africa are migrants from affected parts of Africa. We report a rare case of pulmonary tuberculosis (TB) secondary to M. africanum in a man in Brunei Darussalam who had lived and worked in Guinea, West Africa for 6 years more than 20 years ago. He had been well until December 2020, when he presented with a chronic cough and was diagnosed with coinfections of Klebsiella pneumoniae and M. africanum, and newly diagnosed diabetes mellitus. This case highlights an interesting manifestation of pulmonary TB secondary to M. africanum in a patient whose last exposure was 20 years ago, contributed to by development of diabetes mellitus.
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