1
|
Orgeur M, Sous C, Madacki J, Brosch R. Evolution and emergence of Mycobacterium tuberculosis. FEMS Microbiol Rev 2024; 48:fuae006. [PMID: 38365982 PMCID: PMC10906988 DOI: 10.1093/femsre/fuae006] [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: 11/09/2023] [Revised: 01/12/2024] [Accepted: 02/13/2024] [Indexed: 02/18/2024] Open
Abstract
Tuberculosis (TB) remains one of the deadliest infectious diseases in human history, prevailing even in the 21st century. The causative agents of TB are represented by a group of closely related bacteria belonging to the Mycobacterium tuberculosis complex (MTBC), which can be subdivided into several lineages of human- and animal-adapted strains, thought to have shared a last common ancestor emerged by clonal expansion from a pool of recombinogenic Mycobacterium canettii-like tubercle bacilli. A better understanding of how MTBC populations evolved from less virulent mycobacteria may allow for discovering improved TB control strategies and future epidemiologic trends. In this review, we highlight new insights into the evolution of mycobacteria at the genus level, describing different milestones in the evolution of mycobacteria, with a focus on the genomic events that have likely enabled the emergence and the dominance of the MTBC. We also review the recent literature describing the various MTBC lineages and highlight their particularities and differences with a focus on host preferences and geographic distribution. Finally, we discuss on putative mechanisms driving the evolution of tubercle bacilli and mycobacteria in general, by taking the mycobacteria-specific distributive conjugal transfer as an example.
Collapse
Affiliation(s)
- Mickael Orgeur
- Institut Pasteur, Université Paris Cité, CNRS UMR 6047, Unit for Integrated Mycobacterial Pathogenomics, 75015 Paris, France
| | - Camille Sous
- Institut Pasteur, Université Paris Cité, CNRS UMR 6047, Unit for Integrated Mycobacterial Pathogenomics, 75015 Paris, France
| | - Jan Madacki
- Institut Pasteur, Université Paris Cité, CNRS UMR 6047, Unit for Integrated Mycobacterial Pathogenomics, 75015 Paris, France
- Institut Pasteur, Université Paris Cité, CNRS UMR 2000, Unit for Human Evolutionary Genetics, 75015 Paris, France
| | - Roland Brosch
- Institut Pasteur, Université Paris Cité, CNRS UMR 6047, Unit for Integrated Mycobacterial Pathogenomics, 75015 Paris, France
| |
Collapse
|
2
|
Guan Q, Garbati M, Mfarrej S, AlMutairi T, Laval T, Singh A, Fagbo S, Smyth A, Browne J, urRahman M, Alruwaili A, Hoosen A, Meehan C, Nakajima C, Suzuki Y, Demangel C, Bhatt A, Gordon S, AlAsmari F, Pain A. Insights into the ancestry evolution of the Mycobacterium tuberculosis complex from analysis of Mycobacterium riyadhense. NAR Genom Bioinform 2021; 3:lqab070. [PMID: 34396095 PMCID: PMC8356964 DOI: 10.1093/nargab/lqab070] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2020] [Revised: 06/10/2021] [Accepted: 07/19/2021] [Indexed: 01/08/2023] Open
Abstract
Current evolutionary scenarios posit the emergence of Mycobacterium tuberculosis from an environmental saprophyte through a cumulative process of genome adaptation. Mycobacterium riyadhense, a related bacillus, is being increasingly isolated from human clinical cases with tuberculosis-like symptoms in various parts of the world. To elucidate the evolutionary relationship between M. riyadhense and other mycobacterial species, including members of the M. tuberculosis complex (MTBC), eight clinical isolates of M. riyadhense were sequenced and analyzed. We show, among other features, that M. riyadhense shares a large number of conserved orthologs with M. tuberculosis and shows the expansion of toxin/antitoxin pairs, PE/PPE family proteins compared with other non-tuberculous mycobacteria. We observed M. riyadhense lacks wecE gene which may result in the absence of lipooligosaccharides (LOS) IV. Comparative transcriptomic analysis of infected macrophages reveals genes encoding inducers of Type I IFN responses, such as cytosolic DNA sensors, were relatively less expressed by macrophages infected with M. riyadhense or M. kansasii, compared to BCG or M. tuberculosis. Overall, our work sheds new light on the evolution of M. riyadhense, its relationship to the MTBC, and its potential as a system for the study of mycobacterial virulence and pathogenesis.
Collapse
Affiliation(s)
- Qingtian Guan
- Pathogen Genomics Laboratory, BESE Division, King Abdullah University of Science and Technology (KAUST), Thuwal-Jeddah, 23955, Saudi Arabia
| | - Musa Garbati
- King Fahad Medical City (KFMC), Riyadh, 11525, Saudi Arabia
| | - Sara Mfarrej
- Pathogen Genomics Laboratory, BESE Division, King Abdullah University of Science and Technology (KAUST), Thuwal-Jeddah, 23955, Saudi Arabia
| | | | - Thomas Laval
- Immunobiology of Infection Unit, Institut Pasteur, INSERM U1221, Paris, France
- Université Paris Diderot, Sorbonne Paris Cité, 75205 CEDEX 13, Paris, France
| | | | | | | | - John A Browne
- UCD School of Agriculture and Food Science, University College Dublin, Dublin, D04 W6F6, Ireland
| | | | - Alya Alruwaili
- King Fahad Medical City (KFMC), Riyadh, 11525, Saudi Arabia
| | - Anwar Hoosen
- King Fahad Medical City (KFMC), Riyadh, 11525, Saudi Arabia
| | - Conor J Meehan
- School of Chemistry and Biosciences, University of Bradford, Bradford, BD7 1AZ, UK
| | - Chie Nakajima
- Global Institution for Collaborative Research and Education, Hokkaido University, Kita 20 Nishi 10, Kita-ku, Sapporo, Japan
- Research Center for Zoonosis Control, Hokkaido University, Kita 20 Nishi 10, Kita-ku, Sapporo, Japan
| | - Yasuhiko Suzuki
- Global Institution for Collaborative Research and Education, Hokkaido University, Kita 20 Nishi 10, Kita-ku, Sapporo, Japan
- Research Center for Zoonosis Control, Hokkaido University, Kita 20 Nishi 10, Kita-ku, Sapporo, Japan
| | | | | | | | | | - Arnab Pain
- To whom correspondence should be addressed. Tel: +966 54 470 0687;
| |
Collapse
|
3
|
Baadani AM, Ballool S, Alhemyadi S, Sallam L, ALsufyani E, Alghamdi A, Alfahad W. The clinical outcome of HIV infection at a tertiary care center in Riyadh, Saudi Arabia. Saudi Med J 2021; 41:965-970. [PMID: 32893278 PMCID: PMC7557546 DOI: 10.15537/smj.2020.9.25274] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Objectives: To investigate clinical characteristics and the outcome of people living with HIV (PLWHIV) at tertiary care center in Riyadh, Saudi Arabia. Methods: The present retrospective, observational study was carried between 2000-2019 at Prince Sultan Military Medical City (PSMMC), Riyadh, Saudi Arabia. The demographic and clinical characteristics of 137 PLWHIV patients were collected by reviewing the medical data record. Results: Of the total 137 PLWHIV, 78.8% were male and 21.2% were female. At care entry, the most opportunistic infections found were the cytomegalovirus infections. cytomegalovirus (CMV) infections in 13.8% of patients, tuberculosis (8%), AIDS associated malignancy (10.9%), hepatitis B (5.8%), NTM (3.6%), hepatitis C (2.2%). In the present study, more than half of the patients received integrase based combination therapy. The highest number (n=20) of patients were diagnosed in 2018. Conclusions: Our findings describe the clinical characteristics and outcomes of PLWHIV at a major tertiary referral hospital in Saudi Arabia. The non AIDS related disease is the major cause of death in HIV infected patients. Early diagnosis and initiation of antiretroviral therapy resulted in a significant decrease in morbidity and mortality.
Collapse
Affiliation(s)
- Abeer M Baadani
- Division of Infectious Diseases, Department of Medicine, Prince Sultan Military Medical City, Riyadh, Kingdom of Saudi Arabia. E-mail.
| | | | | | | | | | | | | |
Collapse
|
4
|
Alenazi TH, Alanazi BS, Alsaedy A, Khair A, Solomon R, Al Johani SM. Mycobacterium riyadhense as the opportunistic infection that lead to HIV diagnosis: A report of 2 cases and literature review. J Infect Public Health 2018; 12:285-288. [PMID: 29884324 DOI: 10.1016/j.jiph.2018.05.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2017] [Revised: 05/19/2018] [Accepted: 05/21/2018] [Indexed: 11/17/2022] Open
Abstract
Human immunodeficiency virus (HIV) infection usually presents with a wide range of manifestations. Although HIV patients are prone to pulmonary infections by opportunistic pathogens in the late stage of AIDS, manifesting the disease with pulmonary infections caused by Mycobacterium riyadhense (newly identified non-tuberculous mycobacteria) is extremely rare with only one case reported in the literature. We are describing two previously healthy patients who presented with M. riyadhense lung infection and were subsequently found to have HIV, illustrating the need for considering the possibility M. riyadhense lung infection as a presenting illness of HIV.
Collapse
Affiliation(s)
- Thamer H Alenazi
- Infection Prevention and Control Department, King Abdulaziz Medical City, Ministry of National Guard Health Affairs, Riyadh, Saudi Arabia; College of Medicine, King Saud Bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia.
| | - Bashayer S Alanazi
- College of Medicine, King Saud Bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia
| | - Abdulrahman Alsaedy
- College of Medicine, King Saud Bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia; Division of Infectious Diseases, Department of Medicine, King Abdulaziz Medical City, Ministry of National Guard Health Affairs, Riyadh, Saudi Arabia
| | - Abdulmoneim Khair
- Pulmonary Division, Department of Medicine, King Abdulaziz Medical City, Ministry of National Guard Health Affairs, Riyadh, Saudi Arabia
| | - Rifat Solomon
- Microbiology Division, Pathology and Laboratory Medicine, King Abdulaziz Medical City, Ministry of National Guard Health Affairs, Riyadh, Saudi Arabia
| | - Sameera M Al Johani
- Microbiology Division, Pathology and Laboratory Medicine, King Abdulaziz Medical City, Ministry of National Guard Health Affairs, Riyadh, Saudi Arabia; College of Science and Health Professions, King Saud Bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia
| |
Collapse
|
5
|
The first Saudi Arabian national inventory study revealed the upcoming challenges of highly diverse non-tuberculous mycobacterial diseases. PLoS Negl Trop Dis 2018; 12:e0006515. [PMID: 29799845 PMCID: PMC5991771 DOI: 10.1371/journal.pntd.0006515] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Revised: 06/07/2018] [Accepted: 05/09/2018] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND Incidences of nontuberculous mycobacteria (NTM) causing pulmonary and extrapulmonary diseases are reportedly increasing globally and the current epidemiologic situation in Saudi Arabia remains unclear. To study such trend, we carried out a nationwide systematic epidemiological study focusing on NTM diseases for the first time in the country. METHODS/PRINCIPLE FINDINGS A nationwide collection of NTM isolates with clinical and demographical data was conducted for a period of 24 months. Primary species identification was carried out by line probe assays followed by sequencing of 16S rRNA, 16S-23S ITS region, rpoB and hsp65 genes. The laboratory findings were comprehensively analysed against demographical and clinical data. A total of 527 isolates were enrolled with a higher proportion of Saudi citizens (76.5%), elderly (>60 years) patients (34.2%), and male gender (65.3%) respectively. Overall, 75.1% isolates were pulmonary origin with a proven clinical significance of 44.7%. In total, 34 NTM species including 17 rare species were identified, in addition to 8 'undefined' isolates. M.simiae (22.6%), M.fortuitum (18.1%) and M.abscessus (17.8%) were predominant species. Interestingly, 27 new cases of clinically relevant M.riyadhense were also noticed (Primary data on emergence of rare NTM species and M.riyadhense has been recently reported). Results showed, rare clinical events such as mycobacteremia, cecum abscess, peritonitis and ascites caused by M.wolinskyi, M.holsaticum, M.duvalii and M.monacence respectively. Diabetes mellitus (P value-0.04) and previous history of tuberculosis (P value- 0.001) were identified as independent risk factors associated with NTM diseases. CONCLUSIONS/SIGNIFICANCE NTM disease spectrum and pathogen diversity is an emerging challenge to any nation, including Saudi Arabia. Therefore, more priorities will be given to NTM's with an immediate initiative to develop diagnostic infrastructures and disease management plans.
Collapse
|