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Sharma MK, Stobart M, Akochy PM, Adam H, Janella D, Rabb M, Alawa M, Sekirov I, Tyrrell GJ, Soualhine H. Evaluation of Whole Genome Sequencing-Based Predictions of Antimicrobial Resistance to TB First Line Agents: A Lesson from 5 Years of Data. Int J Mol Sci 2024; 25:6245. [PMID: 38892433 PMCID: PMC11172968 DOI: 10.3390/ijms25116245] [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: 04/13/2024] [Revised: 05/24/2024] [Accepted: 05/31/2024] [Indexed: 06/21/2024] Open
Abstract
Phenotypic susceptibility testing of the Mycobacterium tuberculosis complex (MTBC) isolate requires culture growth, which can delay rapid detection of resistant cases. Whole genome sequencing (WGS) and data analysis pipelines can assist in predicting resistance to antimicrobials used in the treatment of tuberculosis (TB). This study compared phenotypic susceptibility testing results and WGS-based predictions of antimicrobial resistance (AMR) to four first-line antimicrobials-isoniazid, rifampin, ethambutol, and pyrazinamide-for MTBC isolates tested between the years 2018-2022. For this 5-year retrospective analysis, the WGS sensitivity for predicting resistance for isoniazid, rifampin, ethambutol, and pyrazinamide using Mykrobe was 86.7%, 100.0%, 100.0%, and 47.8%, respectively, and the specificity was 99.4%, 99.5%, 98.7%, and 99.9%, respectively. The predictive values improved slightly using Mykrobe corrections applied using TB Profiler, i.e., the WGS sensitivity for isoniazid, rifampin, ethambutol, and pyrazinamide was 92.31%, 100%, 100%, and 57.78%, respectively, and the specificity was 99.63%. 99.45%, 98.93%, and 99.93%, respectively. The utilization of WGS-based testing addresses concerns regarding test turnaround time and enables analysis for MTBC member identification, antimicrobial resistance prediction, detection of mixed cultures, and strain genotyping, all through a single laboratory test. WGS enables rapid resistance detection compared to traditional phenotypic susceptibility testing methods using the WHO TB mutation catalog, providing an insight into lesser-known mutations, which should be added to prediction databases as high-confidence mutations are recognized. The WGS-based methods can support TB elimination efforts in Canada and globally by ensuring the early start of appropriate treatment, rapidly limiting the spread of TB outbreaks.
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Affiliation(s)
- Meenu Kaushal Sharma
- National Reference Centre for Mycobacteriology, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB R3E 3R2, Canada (M.S.)
- Department of Medical Microbiology & Infectious Diseases, University of Manitoba, Winnipeg, MB R3E 0J9, Canada;
| | - Michael Stobart
- National Reference Centre for Mycobacteriology, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB R3E 3R2, Canada (M.S.)
| | - Pierre-Marie Akochy
- Laboratoire de Santé Publique du Québec-Institut National de Santé Publique du Québec, Sainte-Anne-de-Bellevue, QC H9X 3R5, Canada
| | - Heather Adam
- Department of Medical Microbiology & Infectious Diseases, University of Manitoba, Winnipeg, MB R3E 0J9, Canada;
- Diagnostic Services, Shared Health, Winnipeg, MB R3C 3H8, Canada
| | - Debra Janella
- National Reference Centre for Mycobacteriology, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB R3E 3R2, Canada (M.S.)
| | - Melissa Rabb
- National Reference Centre for Mycobacteriology, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB R3E 3R2, Canada (M.S.)
| | - Mohey Alawa
- Regina Qu’Appelle Health Region, Regina, SK S4T 1A5, Canada;
| | - Inna Sekirov
- Public Health Laboratory, B.C. Centre for Disease Control, Vancouver, BC V5Z 4R4, Canada;
| | - Gregory J. Tyrrell
- Division of Diagnostic and Applied Microbiology, Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, AB T6G 2J2, Canada
- Alberta Precision Laboratories Public Health, Edmonton, AB T6G 2J2, Canada
| | - Hafid Soualhine
- National Reference Centre for Mycobacteriology, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB R3E 3R2, Canada (M.S.)
- Department of Medical Microbiology & Infectious Diseases, University of Manitoba, Winnipeg, MB R3E 0J9, Canada;
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Refaya AK, Vetrivel U, Palaniyandi K. Genomic Characterization of IS 6110 Insertions in Mycobacterium orygis. Evol Bioinform Online 2024; 20:11769343241240558. [PMID: 38586439 PMCID: PMC10996354 DOI: 10.1177/11769343241240558] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Accepted: 03/04/2024] [Indexed: 04/09/2024] Open
Abstract
Mycobacterium orygis, a subspecies of the Mycobacterium tuberculosis complex (MTBC), has emerged as a significant concern in the context of One Health, with implications for zoonosis or zooanthroponosis or both. MTBC strains are characterized by the unique insertion element IS6110, which is widely used as a diagnostic marker. IS6110 transposition drives genetic modifications in MTBC, imparting genome plasticity and profound biological consequences. While IS6110 insertions are customarily found in the MTBC genomes, the evolutionary trajectory of strains seems to correlate with the number of IS6110 copies, indicating enhanced adaptability with increasing copy numbers. Here, we present a comprehensive analysis of IS6110 insertions in the M. orygis genome, utilizing ISMapper, and elucidate their genetic consequences in promoting successful host adaptation. Our study encompasses a panel of 67 paired-end reads, comprising 11 isolates from our laboratory and 56 sequences downloaded from public databases. Among these sequences, 91% exhibited high-copy, 4.5% low-copy, and 4.5% lacked IS6110 insertions. We identified 255 insertion loci, including 141 intragenic and 114 intergenic insertions. Most of these loci were either unique or shared among a limited number of isolates, potentially influencing strain behavior. Furthermore, we conducted gene ontology and pathway analysis, using eggNOG-mapper 5.0, on the protein sequences disrupted by IS6110 insertions, revealing 63 genes involved in diverse functions of Gene Ontology and 45 genes participating in various KEGG pathways. Our findings offer novel insights into IS6110 insertions, their preferential insertion regions, and their impact on metabolic processes and pathways, providing valuable knowledge on the genetic changes underpinning IS6110 transposition in M. orygis.
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Affiliation(s)
- Ahmed Kabir Refaya
- Department of Immunology, ICMR-National Institute for Research in Tuberculosis, Chetpet, Chennai, India
| | - Umashankar Vetrivel
- Department of Virology & Biotechnology/Bioinformatics Division, ICMR-National Institute for Research in Tuberculosis, Chetpet, Chennai, India
| | - Kannan Palaniyandi
- Department of Immunology, ICMR-National Institute for Research in Tuberculosis, Chetpet, Chennai, India
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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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