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Zhang X, Lam C, Sim E, Martinez E, Crighton T, Marais BJ, Sintchenko V. Genomic characteristics of prospectively sequenced Mycobacterium tuberculosis from respiratory and non-respiratory sources. iScience 2024; 27:110327. [PMID: 39055934 PMCID: PMC11269812 DOI: 10.1016/j.isci.2024.110327] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Revised: 05/23/2024] [Accepted: 06/18/2024] [Indexed: 07/28/2024] Open
Abstract
Understanding the differences between Mycobacterium tuberculosis strains isolated from respiratory and non-respiratory sources may inform clinical care and control strategies. We examined demographic and genomic characteristics of all culture-confirmed M. tuberculosis cultures isolated from respiratory and non-respiratory sources in New South Wales, Australia, from January 2017 to December 2021, using logistic regression models. M. tuberculosis strains from 1,831 patients were sequenced; 64.7% were from respiratory, 32.1% from non-respiratory, and 2.2% from both sources. Female patients had more frequent isolation from a non-respiratory source (p = 0.03), and older adults (≧65 years) from a respiratory source (p < 0.0001). Lineage 2 strains were relatively over-represented among respiratory isolates (p = 0.01). Among 39 cases with sequenced isolates from both sources, 43.6% had 1-10 single nucleotide polymorphism differences. The finding that older adults were more likely to have M. tuberculosis isolated from respiratory sources has relevance for TB control given the expected rise of TB among older adults.
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Affiliation(s)
- Xiaomei Zhang
- Centre for Research Excellence in Tuberculosis (TB-CRE), Centenary Institute, Sydney, NSW, Australia
- Sydney Infectious Diseases Institute (Sydney ID), The University of Sydney, Sydney, NSW, Australia
- Centre for Infectious Diseases and Microbiology-Public Health, Westmead Hospital, Western Sydney Local Health District, Sydney, NSW, Australia
| | - Connie Lam
- Sydney Infectious Diseases Institute (Sydney ID), The University of Sydney, Sydney, NSW, Australia
- Centre for Infectious Diseases and Microbiology-Public Health, Westmead Hospital, Western Sydney Local Health District, Sydney, NSW, Australia
| | - Eby Sim
- Sydney Infectious Diseases Institute (Sydney ID), The University of Sydney, Sydney, NSW, Australia
- Centre for Infectious Diseases and Microbiology-Public Health, Westmead Hospital, Western Sydney Local Health District, Sydney, NSW, Australia
| | - Elena Martinez
- Sydney Infectious Diseases Institute (Sydney ID), The University of Sydney, Sydney, NSW, Australia
- Centre for Infectious Diseases and Microbiology-Public Health, Westmead Hospital, Western Sydney Local Health District, Sydney, NSW, Australia
- NSW Mycobacterium Reference Laboratory, Centre for Infectious Diseases and Microbiology-Laboratory Services, Institute of Clinical Pathology and Medical Research, NSW Health Pathology, Sydney, NSW, Australia
| | - Taryn Crighton
- Centre for Infectious Diseases and Microbiology-Public Health, Westmead Hospital, Western Sydney Local Health District, Sydney, NSW, Australia
- NSW Mycobacterium Reference Laboratory, Centre for Infectious Diseases and Microbiology-Laboratory Services, Institute of Clinical Pathology and Medical Research, NSW Health Pathology, Sydney, NSW, Australia
| | - Ben J. Marais
- Centre for Research Excellence in Tuberculosis (TB-CRE), Centenary Institute, Sydney, NSW, Australia
- Sydney Infectious Diseases Institute (Sydney ID), The University of Sydney, Sydney, NSW, Australia
| | - Vitali Sintchenko
- Centre for Research Excellence in Tuberculosis (TB-CRE), Centenary Institute, Sydney, NSW, Australia
- Sydney Infectious Diseases Institute (Sydney ID), The University of Sydney, Sydney, NSW, Australia
- Centre for Infectious Diseases and Microbiology-Public Health, Westmead Hospital, Western Sydney Local Health District, Sydney, NSW, Australia
- NSW Mycobacterium Reference Laboratory, Centre for Infectious Diseases and Microbiology-Laboratory Services, Institute of Clinical Pathology and Medical Research, NSW Health Pathology, Sydney, NSW, Australia
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Distribution of Mycobacterium tuberculosis Lineages and Drug Resistance in Upper Myanmar. Trop Med Infect Dis 2022; 7:tropicalmed7120448. [PMID: 36548703 PMCID: PMC9781755 DOI: 10.3390/tropicalmed7120448] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Revised: 12/09/2022] [Accepted: 12/16/2022] [Indexed: 12/24/2022] Open
Abstract
Mycobacterium tuberculosis complex (MTBC) is divided into 9 whole genome sequencing (WGS) lineages. Among them, lineages 1−4 are widely distributed. Multi-drug resistant tuberculosis (MDR-TB) is a major public health threat. For effective TB control, there is a need to obtain genetic information on lineages of Mycobacterium tuberculosis (Mtb) and to understand distribution of lineages and drug resistance. This study aimed to describe the distribution of major lineages and drug resistance patterns of Mtb in Upper Myanmar. This was a cross-sectional study conducted with 506 sequenced isolates. We found that the most common lineage was lineage 2 (n = 223, 44.1%). The most common drug resistance mutation found was streptomycin (n = 44, 8.7%). Lineage 2 showed a higher number of MDR-TB compared to other lineages. There were significant associations between lineages of Mtb and drug resistance patterns, and between lineages and geographical locations of Upper Myanmar (p value < 0.001). This information on the distribution of Mtb lineages across the geographical areas will support a lot for the better understanding of TB transmission and control in Myanmar and other neighboring countries. Therefore, closer collaboration in cross border tuberculosis control is recommended.
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Saelens JW, Sweeney MI, Viswanathan G, Xet-Mull AM, Jurcic Smith KL, Sisk DM, Hu DD, Cronin RM, Hughes EJ, Brewer WJ, Coers J, Champion MM, Champion PA, Lowe CB, Smith CM, Lee S, Stout JE, Tobin DM. An ancestral mycobacterial effector promotes dissemination of infection. Cell 2022; 185:4507-4525.e18. [PMID: 36356582 PMCID: PMC9691622 DOI: 10.1016/j.cell.2022.10.019] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Revised: 08/27/2022] [Accepted: 10/16/2022] [Indexed: 11/11/2022]
Abstract
The human pathogen Mycobacterium tuberculosis typically causes lung disease but can also disseminate to other tissues. We identified a M. tuberculosis (Mtb) outbreak presenting with unusually high rates of extrapulmonary dissemination and bone disease. We found that the causal strain carried an ancestral full-length version of the type VII-secreted effector EsxM rather than the truncated version present in other modern Mtb lineages. The ancestral EsxM variant exacerbated dissemination through enhancement of macrophage motility, increased egress of macrophages from established granulomas, and alterations in macrophage actin dynamics. Reconstitution of the ancestral version of EsxM in an attenuated modern strain of Mtb altered the migratory mode of infected macrophages, enhancing their motility. In a zebrafish model, full-length EsxM promoted bone disease. The presence of a derived nonsense variant in EsxM throughout the major Mtb lineages 2, 3, and 4 is consistent with a role for EsxM in regulating the extent of dissemination.
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Affiliation(s)
- Joseph W Saelens
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Mollie I Sweeney
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Gopinath Viswanathan
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Ana María Xet-Mull
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Kristen L Jurcic Smith
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Dana M Sisk
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Daniel D Hu
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Rachel M Cronin
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Erika J Hughes
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC 27710, USA
| | - W Jared Brewer
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Jörn Coers
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC 27710, USA; Department of Immunology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Matthew M Champion
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, USA; Eck Institute for Global Health, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Patricia A Champion
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN 46556, USA; Eck Institute for Global Health, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Craig B Lowe
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Clare M Smith
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Sunhee Lee
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC 27710, USA; Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA; Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX 77555, USA.
| | - Jason E Stout
- Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA; Division of Infectious Diseases and International Health, Duke University School of Medicine, Durham, NC 27710, USA.
| | - David M Tobin
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC 27710, USA; Department of Immunology, Duke University School of Medicine, Durham, NC 27710, USA.
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Disseminated tuberculosis with paradoxical reactions caused by a Mycobacterium tuberculosis strain belonging to the Indo-Oceanic lineage: An imported case in Japan. J Infect Chemother 2022; 28:965-970. [DOI: 10.1016/j.jiac.2022.02.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Revised: 12/30/2021] [Accepted: 02/06/2022] [Indexed: 11/20/2022]
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Saelens JW, Viswanathan G, Tobin DM. Mycobacterial Evolution Intersects With Host Tolerance. Front Immunol 2019; 10:528. [PMID: 30967867 PMCID: PMC6438904 DOI: 10.3389/fimmu.2019.00528] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Accepted: 02/27/2019] [Indexed: 12/12/2022] Open
Abstract
Over the past 200 years, tuberculosis (TB) has caused more deaths than any other infectious disease, likely infecting more people than it has at any other time in human history. Mycobacterium tuberculosis (Mtb), the etiologic agent of TB, is an obligate human pathogen that has evolved through the millennia to become an archetypal human-adapted pathogen. This review focuses on the evolutionary framework by which Mtb emerged as a specialized human pathogen and applies this perspective to the emergence of specific lineages that drive global TB burden. We consider how evolutionary pressures, including transmission dynamics, host tolerance, and human population patterns, may have shaped the evolution of diverse mycobacterial genomes.
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Affiliation(s)
- Joseph W. Saelens
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC, United States
| | - Gopinath Viswanathan
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC, United States
| | - David M. Tobin
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC, United States
- Department of Immunology, Duke University School of Medicine, Durham, NC, United States
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Comprehensive Analysis and Comparison on the Codon Usage Pattern of Whole Mycobacterium tuberculosis Coding Genome from Different Area. BIOMED RESEARCH INTERNATIONAL 2018; 2018:3574976. [PMID: 29854746 PMCID: PMC5964552 DOI: 10.1155/2018/3574976] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/13/2017] [Revised: 02/25/2018] [Accepted: 03/28/2018] [Indexed: 11/18/2022]
Abstract
Phenomenon of unequal use of synonymous codons in Mycobacterium tuberculosis is common. Codon usage bias not only plays an important regulatory role at the level of gene expression, but also helps in improving the accuracy and efficiency of translation. Meanwhile, codon usage pattern of Mycobacterium tuberculosis genome is important for interpreting evolutionary characteristics in species. In order to investigate the codon usage pattern of the Mycobacterium tuberculosis genome, 12 Mycobacterium tuberculosis genomes from different area are downloaded from the GeneBank. The correlations between G3, GC12, whole GC content, codon adaptation index, codon bias index, and so on of Mycobacterium tuberculosis genomes are calculated. The ENC-plot, relationship between A3/(A3 + T3) and G3/(G3 + C3), GC12 versus GC3 plot, and the RSCU of overall/separated genomes all show that the codon usage bias exists in all 12 Mycobacterium tuberculosis genomes. Lastly, relationship between CBI and the equalization of ENC shows a strong negative correlation between them. The relationship between protein length and GC content (GC3 and GC12) shows that more obvious differences in the GC content may be in shorter protein. These results show that codon usage bias existing in the Mycobacterium tuberculosis genomes could be used for further study on their evolutionary phenomenon.
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