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Folliero V, Ferravante C, Iovane V, Salvati A, Crescenzo L, Perna R, Corvino G, Della Rocca MT, Panetta V, Tranfa A, Greco G, Baldoni T, Pagnini U, Finamore E, Giurato G, Nassa G, Coppola M, Atripaldi L, Greco R, D'Argenio A, Foti MG, Abate R, Del Giudice A, Sarnelli B, Weisz A, Iovane G, Pinto R, Franci G, Galdiero M. Whole Genome Sequence Dataset of Mycobacterium tuberculosis Strains from Patients of Campania Region. Sci Data 2024; 11:220. [PMID: 38374088 PMCID: PMC10876956 DOI: 10.1038/s41597-024-03032-6] [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: 12/06/2023] [Accepted: 01/31/2024] [Indexed: 02/21/2024] Open
Abstract
Tuberculosis (TB) is one of the deadliest infectious disorders in the world. To effectively TB manage, an essential step is to gain insight into the lineage of Mycobacterium tuberculosis (MTB) and the distribution of drug resistance. Although the Campania region is declared a cluster area for the infection, to contribute to the effort to understand TB evolution and transmission, still poorly known, we have generated a dataset of 159 genomes of MTB strains, from Campania region collected during 2018-2021, obtained from the analysis of whole genome sequence. The results show that the most frequent MTB lineage is the 4 according for 129 strains (81.11%). Regarding drug resistance, 139 strains (87.4%) were classified as multi susceptible, while the remaining 20 (12.58%) showed drug resistance. Among the drug-resistance strains, 8 were isoniazid-resistant MTB, 4 multidrug-resistant MTB, while only one was classified as pre-extensively drug-resistant MTB. This dataset expands the existing available knowledge on drug resistance and evolution of MTB, contributing to further TB-related genomics studies to improve the management of this disease.
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Affiliation(s)
- Veronica Folliero
- Department of Veterinary Medicine and Animal Productions, University of Naples Federico II, Naples, Italy
- Department of Experimental Medicine, University of Campania "Luigi Vanvitelli", Naples, Italy
| | - Carlo Ferravante
- Department of Medicine, Surgery and Dentistry "Scuola Medica Salernitana", Baronissi, SA, Italy
- Molecular Pathology and Medical Genomics Program, San Giovanni di Dio e Ruggi D'Aragona University Hospital, Salerno, Italy
| | - Valentina Iovane
- Department of Agricultural Sciences, University of Naples Federico II, Portici, Naples, Italy
| | - Annamaria Salvati
- Department of Medicine, Surgery and Dentistry "Scuola Medica Salernitana", Baronissi, SA, Italy
- Molecular Pathology and Medical Genomics Program, San Giovanni di Dio e Ruggi D'Aragona University Hospital, Salerno, Italy
| | - Laura Crescenzo
- Department of Medicine, Surgery and Dentistry "Scuola Medica Salernitana", Baronissi, SA, Italy
| | - Rossella Perna
- Department of Veterinary Medicine and Animal Productions, University of Naples Federico II, Naples, Italy
- Laboratory of Microbiology and Virology, Ospedali dei Colli, Naples, Italy
| | - Giusy Corvino
- Department of Veterinary Medicine and Animal Productions, University of Naples Federico II, Naples, Italy
- Department of Experimental Medicine, University of Campania "Luigi Vanvitelli", Naples, Italy
- UOC Microbiology - Ospedale Cardinale Ascalesi, ASL NA1, Naples, Italy
| | - Maria T Della Rocca
- Department of Veterinary Medicine and Animal Productions, University of Naples Federico II, Naples, Italy
- Department of Experimental Medicine, University of Campania "Luigi Vanvitelli", Naples, Italy
- UOSD Microbiology - AORN Sant 'Anna and San Sebastiano, Caserta, Italy
| | - Vittorio Panetta
- Department of Experimental Medicine, University of Campania "Luigi Vanvitelli", Naples, Italy
- UOSD Microbiology - AORN Sant 'Anna and San Sebastiano, Caserta, Italy
| | - Alessandro Tranfa
- Department of Veterinary Medicine and Animal Productions, University of Naples Federico II, Naples, Italy
- UOC Microbiology and Virology- San Giuseppe Moscati Hospital, Avellino, Italy
| | - Giuseppe Greco
- Department of Veterinary Medicine and Animal Productions, University of Naples Federico II, Naples, Italy
- Department of Experimental Medicine, University of Campania "Luigi Vanvitelli", Naples, Italy
- Clinical Pathology and Microbiology Unit, San Giovanni di Dio e Ruggi D'Aragona University Hospital, Salerno, Italy
| | - Teresa Baldoni
- Department of Veterinary Medicine and Animal Productions, University of Naples Federico II, Naples, Italy
- Department of Experimental Medicine, University of Campania "Luigi Vanvitelli", Naples, Italy
- Laboratory of Microbiology and Virology, Ospedali dei Colli, Naples, Italy
| | - Ugo Pagnini
- Department of Veterinary Medicine and Animal Productions, University of Naples Federico II, Naples, Italy
| | - Emiliana Finamore
- UOC Virology and Microbiology - University Hospital AOU "Luigi Vanvitelli", Naples, Italy
| | - Giorgio Giurato
- Department of Medicine, Surgery and Dentistry "Scuola Medica Salernitana", Baronissi, SA, Italy
| | - Giovanni Nassa
- Department of Medicine, Surgery and Dentistry "Scuola Medica Salernitana", Baronissi, SA, Italy
| | | | - Luigi Atripaldi
- Laboratory of Microbiology and Virology, Ospedali dei Colli, Naples, Italy
| | - Rita Greco
- UOSD Microbiology - AORN Sant 'Anna and San Sebastiano, Caserta, Italy
| | - Annamaria D'Argenio
- UOC Microbiology and Virology- San Giuseppe Moscati Hospital, Avellino, Italy
| | - Maria Grazia Foti
- UOC Microbiology and Virology- San Giuseppe Moscati Hospital, Avellino, Italy
| | - Rosamaria Abate
- UOC Microbiology - Ospedale Cardinale Ascalesi, ASL NA1, Naples, Italy
| | | | - Bruno Sarnelli
- UOC Microbiology - Ospedale Cardinale Ascalesi, ASL NA1, Naples, Italy
| | - Alessandro Weisz
- Department of Medicine, Surgery and Dentistry "Scuola Medica Salernitana", Baronissi, SA, Italy
- Molecular Pathology and Medical Genomics Program, San Giovanni di Dio e Ruggi D'Aragona University Hospital, Salerno, Italy
| | - Giuseppe Iovane
- Department of Veterinary Medicine and Animal Productions, University of Naples Federico II, Naples, Italy
| | - Renato Pinto
- UOD Prevenzione e Sanità Pubblica Veterinaria, Direzione Generale Tutela della Salute - Regione Campania, Naples, Italy
| | - Gianluigi Franci
- Department of Medicine, Surgery and Dentistry "Scuola Medica Salernitana", Baronissi, SA, Italy.
- Clinical Pathology and Microbiology Unit, San Giovanni di Dio e Ruggi D'Aragona University Hospital, Salerno, Italy.
| | - Massimiliano Galdiero
- Department of Experimental Medicine, University of Campania "Luigi Vanvitelli", Naples, Italy.
- UOC Virology and Microbiology - University Hospital AOU "Luigi Vanvitelli", Naples, Italy.
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Coulibaly G, Georges Togo AC, Somboro AM, Kone M, Traore FG, Diallo F, Degoga B, Somboro A, Dramé HM, Sanogo M, Kodio O, Baya B, Tolofoudie M, Maiga A, Maiga M, Saliba-Shaw K, Diallo S, Doumbia S, Maiga II, Samaké F, Diarra B. Use of light-emitting diode fluorescence microscopy to detect acid-fast bacilli in sputum as proficient alternative tool in the diagnosis of pulmonary tuberculosis in countries with limited resource settings. Int J Mycobacteriol 2023; 12:144-150. [PMID: 37338475 DOI: 10.4103/ijmy.ijmy_13_23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/21/2023] Open
Abstract
Background Despite recent advances in the development of more sensitive technologies for the diagnosis of tuberculosis (TB), in resource-limited settings, the diagnosis continues to rely on sputum smear microscopy. This is because smear microscopy is simple, cost-efficient and the most accessible tool for the diagnosis of TB. Our study evaluated the performance of light-emitting diode fluorescence microscopy (LED-FM) using auramine/rhodamine (auramine) and the fluorescein di-acetate (FDA) vital stain in the diagnostic of pulmonary TB in Bamako, Mali. Methods Sputum smear microscopy was conducted using the FDA and auramine/rhodamine staining procedures on fresh samples using LED-FM to evaluate the Mycobacterium TB (MTB) metabolic activity and to predict contagiousness. Mycobacterial culture assay was utilized as a gold standard method. Results Out of 1401 TB suspected patients, 1354 (96.65%) were retrieved from database, which were MTB complex culture positive, and 47 (3.40%) were culture negative (no mycobacterial growth observed). Out of the 1354 included patients, 1343 (95.86%), were acid-fast bacillus (AFB) positive after direct FDA staining, 1352 (96.50%) AFB positive after direct Auramine, and 1354 (96.65%) AFB positive with indirect auramine after digestion and centrifugation. Overall, the FDA staining method has a sensitivity of 98.82%, while the sensitivity of Auramine with direct observation was 99.48%, and 99.56% with the indirect examination. Conclusion This study showed that, using fresh sputum both auramine/rhodamine and FDA are highly sensitive methods in diagnosing pulmonary TB and could be easily used in countries with limited resource settings.
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Affiliation(s)
- Gagni Coulibaly
- University Clinical Research Center-SEREFO Laboratory, University of Sciences, Techniques and Technologies of Bamako, Bamako, Mali
| | - Antièmé Combo Georges Togo
- University Clinical Research Center-SEREFO Laboratory, University of Sciences, Techniques and Technologies of Bamako, Bamako, Mali
| | - Anou Moise Somboro
- University Clinical Research Center-SEREFO Laboratory, University of Sciences, Techniques and Technologies of Bamako, Bamako, Mali; Medical Biochemistry, School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Mahamadou Kone
- University Clinical Research Center-SEREFO Laboratory, University of Sciences, Techniques and Technologies of Bamako, Bamako, Mali
| | - Fah Gaoussou Traore
- University Clinical Research Center-SEREFO Laboratory, University of Sciences, Techniques and Technologies of Bamako, Bamako, Mali
| | - Fatimata Diallo
- University Clinical Research Center-SEREFO Laboratory, University of Sciences, Techniques and Technologies of Bamako, Bamako, Mali
| | - Boureima Degoga
- University Clinical Research Center-SEREFO Laboratory, University of Sciences, Techniques and Technologies of Bamako, Bamako, Mali
| | - Amadou Somboro
- University Clinical Research Center-SEREFO Laboratory, University of Sciences, Techniques and Technologies of Bamako, Bamako, Mali
| | - Hawa M'baye Dramé
- University Clinical Research Center-SEREFO Laboratory, University of Sciences, Techniques and Technologies of Bamako, Bamako, Mali
| | - Moumine Sanogo
- University Clinical Research Center-SEREFO Laboratory, University of Sciences, Techniques and Technologies of Bamako, Bamako, Mali
| | - Ousmane Kodio
- University Clinical Research Center-SEREFO Laboratory, University of Sciences, Techniques and Technologies of Bamako, Bamako, Mali
| | - Bocar Baya
- University Clinical Research Center-SEREFO Laboratory, University of Sciences, Techniques and Technologies of Bamako, Bamako, Mali
| | - Mohamed Tolofoudie
- University Clinical Research Center-SEREFO Laboratory, University of Sciences, Techniques and Technologies of Bamako, Bamako, Mali
| | - Aminata Maiga
- Laboratory and Hospital Hygiene Services, University Teaching Hospital of Point G, Bamako, Mali
| | - Mamoudou Maiga
- University Clinical Research Center-SEREFO Laboratory, University of Sciences, Techniques and Technologies of Bamako, Bamako, Mali; Center for Innovation in Global Health Technology, Northwestern University, Chicago, Illinois, USA
| | - Katy Saliba-Shaw
- Collaborative Clinical Research Branch, Division of Clinical Research, NIAID/NIH, Bethesda, Maryland, USA
| | - Souleymane Diallo
- University Clinical Research Center-SEREFO Laboratory, University of Sciences, Techniques and Technologies of Bamako, Bamako, Mali
| | - Seydou Doumbia
- University Clinical Research Center-SEREFO Laboratory, University of Sciences, Techniques and Technologies of Bamako, Bamako, Mali
| | | | - Fassé Samaké
- Microbial Biotechnology Laboratory, University of Sciences, Techniques and Technologies of Bamako, Bamako, Mali
| | - Bassirou Diarra
- University Clinical Research Center-SEREFO Laboratory, University of Sciences, Techniques and Technologies of Bamako, Bamako, Mali
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Osei-Wusu S, Otchere ID, Asare P, Ntoumi F, Zumla A, Asante-Poku A, Yeboah-Manu D. Relevance of genomic diversity of Mycobacterium tuberculosis complex in Africa. Int J Infect Dis 2022; 124 Suppl 1:S47-S49. [PMID: 35321844 DOI: 10.1016/j.ijid.2022.03.016] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Revised: 03/09/2022] [Accepted: 03/10/2022] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND The diversity in the lineages of Mycobacterium tuberculosis complex (MTBC) was initially considered insignificant. However, comparative genomics analysis of MTBC have found genomic variation among the genotypes with potential phenotypic implications. OBJECTIVE Therefore, this viewpoint seeks to discuss the impact of the identified genotypic diversity on the physiology of MTBC and the potential implications on TB control. RESULTS Studies conducted in West Africa and other parts of Africa have unravelled the implications of the genomic diversity on phenotypes such as disease outcome, transmission dynamics and host immune response. The understanding of the phenotypic diversity among the different lineages of MTBC may be an important key to the fight against TB. CONCLUSION The relevance of these differences has been observed in the design of new control tools such as diagnostics and anti-TB drugs/vaccines. This only points to the fact that the diversity in MTBC cannot be ignored in future studies especially clinical trials for new vaccines and new anti-TB drugs.
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Affiliation(s)
- Stephen Osei-Wusu
- Noguchi Memorial Institute for Medical Research, College of Health Sciences, University of Ghana, Legon, Accra, Ghana.
| | - Isaac Darko Otchere
- Noguchi Memorial Institute for Medical Research, College of Health Sciences, University of Ghana, Legon, Accra, Ghana.
| | - Prince Asare
- Noguchi Memorial Institute for Medical Research, College of Health Sciences, University of Ghana, Legon, Accra, Ghana.
| | - Francine Ntoumi
- Fondation Congolaise pour la Recherche Médicale (FCRM), Brazzaville, Republic of Congo; Faculty of Sciences and Technology, University Marien Ngouabi, Brazzaville, Republic of Congo; University of Tübingen, Tübingen, Germany.
| | - Alimuddin Zumla
- Division of Infection and Immunity, Center for Clinical Microbiology, University College London, and NIHR Biomedical Research Centre, UCL Hospitals NHS Foundation Trust, London, United Kingdom.
| | - Adwoa Asante-Poku
- Noguchi Memorial Institute for Medical Research, College of Health Sciences, University of Ghana, Legon, Accra, Ghana.
| | - Dorothy Yeboah-Manu
- Noguchi Memorial Institute for Medical Research, College of Health Sciences, University of Ghana, Legon, Accra, Ghana.
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Dabitao D, Somboro A, Sanogo I, Diarra B, Achenbach CJ, Holl JL, Baya B, Sanogo M, Wague M, Coulibaly N, Kone M, Drame HB, Tolofoudie M, Kone B, Diarra A, Coulibaly MD, Saliba-Shaw K, Toloba Y, Diakite M, Doumbia S, Klein SL, Bishai WR, Diallo S, Murphy RL. Sex Differences in Active Pulmonary Tuberculosis Outcomes in Mali, West Africa. Am J Trop Med Hyg 2022; 107:433-440. [PMID: 35895582 PMCID: PMC9393465 DOI: 10.4269/ajtmh.21-1141] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Accepted: 03/19/2022] [Indexed: 08/03/2023] Open
Abstract
Men and women often respond differently to infectious diseases and their treatments. Tuberculosis (TB) is a life-threatening communicable disease that affects more men than women globally. Whether male sex is an independent risk factor for unfavorable TB outcomes, however, has not been rigorously investigated in an African context, where individuals are likely exposed to different microbial and environmental factors. We analyzed data collected from a cohort study in Mali by focusing on newly diagnosed active pulmonary TB individuals who were treatment naive. We gathered baseline demographic, clinical, and microbiologic characteristics before treatment initiation and also at three time points during treatment. More males than females were affected with TB, as evidenced by a male-to-female ratio of 2.4:1. In addition, at baseline, males had a significantly higher bacterial count and shorter time to culture positivity as compared with females. Male sex was associated with lower smear negativity rate after 2 months of treatment also known as the intensive phase of treatment, but not at later time points. There was no relationship between patients' sex and mortality from any cause during treatment. This study suggests that sex-based differences in TB outcomes exist, with sex-specific effects on disease outcomes being more pronounced before treatment initiation and during the intensive phase of treatment rather than at later phases of treatment.
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Affiliation(s)
- Djeneba Dabitao
- University Clinical Research Center, Faculty of Pharmacy and Faculty of Medicine and Odonto-Stomatology, University of Sciences, Techniques, and Technologies of Bamako, Mali, West Africa
| | - Amadou Somboro
- University Clinical Research Center, Faculty of Pharmacy and Faculty of Medicine and Odonto-Stomatology, University of Sciences, Techniques, and Technologies of Bamako, Mali, West Africa
| | - Ibrahim Sanogo
- University Clinical Research Center, Faculty of Pharmacy and Faculty of Medicine and Odonto-Stomatology, University of Sciences, Techniques, and Technologies of Bamako, Mali, West Africa
| | - Bassirou Diarra
- University Clinical Research Center, Faculty of Pharmacy and Faculty of Medicine and Odonto-Stomatology, University of Sciences, Techniques, and Technologies of Bamako, Mali, West Africa
| | - Chad J. Achenbach
- Division of Infectious Diseases and Havey Institute for Global Health, Feinberg School of Medicine, Northwestern University, Chicago, Illinois
| | - Jane L. Holl
- Biological Sciences Division, University of Chicago, Chicago, Illinois
| | - Bocar Baya
- University Clinical Research Center, Faculty of Pharmacy and Faculty of Medicine and Odonto-Stomatology, University of Sciences, Techniques, and Technologies of Bamako, Mali, West Africa
| | - Moumine Sanogo
- University Clinical Research Center, Faculty of Pharmacy and Faculty of Medicine and Odonto-Stomatology, University of Sciences, Techniques, and Technologies of Bamako, Mali, West Africa
| | - Mamadou Wague
- University Clinical Research Center, Faculty of Pharmacy and Faculty of Medicine and Odonto-Stomatology, University of Sciences, Techniques, and Technologies of Bamako, Mali, West Africa
| | - Nadie Coulibaly
- University Clinical Research Center, Faculty of Pharmacy and Faculty of Medicine and Odonto-Stomatology, University of Sciences, Techniques, and Technologies of Bamako, Mali, West Africa
| | - Mahamadou Kone
- University Clinical Research Center, Faculty of Pharmacy and Faculty of Medicine and Odonto-Stomatology, University of Sciences, Techniques, and Technologies of Bamako, Mali, West Africa
| | - Hawa Baye Drame
- University Clinical Research Center, Faculty of Pharmacy and Faculty of Medicine and Odonto-Stomatology, University of Sciences, Techniques, and Technologies of Bamako, Mali, West Africa
| | - Mohamed Tolofoudie
- University Clinical Research Center, Faculty of Pharmacy and Faculty of Medicine and Odonto-Stomatology, University of Sciences, Techniques, and Technologies of Bamako, Mali, West Africa
| | - Bourahima Kone
- University Clinical Research Center, Faculty of Pharmacy and Faculty of Medicine and Odonto-Stomatology, University of Sciences, Techniques, and Technologies of Bamako, Mali, West Africa
| | - Ayouba Diarra
- University Clinical Research Center, Faculty of Pharmacy and Faculty of Medicine and Odonto-Stomatology, University of Sciences, Techniques, and Technologies of Bamako, Mali, West Africa
| | - Mamadou D. Coulibaly
- University Clinical Research Center, Faculty of Pharmacy and Faculty of Medicine and Odonto-Stomatology, University of Sciences, Techniques, and Technologies of Bamako, Mali, West Africa
| | - Kathryn Saliba-Shaw
- Collaborative Clinical Research Branch, Division of Clinical Research, National Institutes of Allergy and Infectious Diseases, Bethesda, Maryland
| | - Yacouba Toloba
- University Clinical Research Center, Faculty of Pharmacy and Faculty of Medicine and Odonto-Stomatology, University of Sciences, Techniques, and Technologies of Bamako, Mali, West Africa
| | - Mahamadou Diakite
- University Clinical Research Center, Faculty of Pharmacy and Faculty of Medicine and Odonto-Stomatology, University of Sciences, Techniques, and Technologies of Bamako, Mali, West Africa
| | - Seydou Doumbia
- University Clinical Research Center, Faculty of Pharmacy and Faculty of Medicine and Odonto-Stomatology, University of Sciences, Techniques, and Technologies of Bamako, Mali, West Africa
| | - Sabra L. Klein
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | - William R. Bishai
- Department of Infectious Diseases, Center for Tuberculosis Research, Johns Hopkins School of Medicine, Baltimore, Maryland
| | - Souleymane Diallo
- University Clinical Research Center, Faculty of Pharmacy and Faculty of Medicine and Odonto-Stomatology, University of Sciences, Techniques, and Technologies of Bamako, Mali, West Africa
| | - Robert L. Murphy
- Division of Infectious Diseases and Havey Institute for Global Health, Feinberg School of Medicine, Northwestern University, Chicago, Illinois
- Biological Sciences Division, University of Chicago, Chicago, Illinois
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Effectiveness of the Novel Anti-TB Bedaquiline against Drug-Resistant TB in Africa: A Systematic Review of the Literature. Pathogens 2022; 11:pathogens11060636. [PMID: 35745490 PMCID: PMC9229213 DOI: 10.3390/pathogens11060636] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 05/28/2022] [Accepted: 05/30/2022] [Indexed: 11/23/2022] Open
Abstract
Background: In 2018, an estimated 10.0 million people contracted tuberculosis (TB), and 1.5 million died from it, including 1.25 million HIV-negative persons and 251,000 HIV-associated TB fatalities. Drug-resistant tuberculosis (DR-TB) is an important contributor to global TB mortality. Multi-drug-resistant TB (MDR-TB) is defined as TB resistant to at least isoniazid (INH) and rifampin (RMP), which are recommended by the WHO as essential drugs for treatment. Objective: To investigate the effectiveness of bedaquiline addition to the treatment of drug-resistant TB infections on the African continent. Methodology: The search engine databases Medline, PubMed, Google Scholar, and Embase were used to obtain published data pertaining to DR-TB between 2012 and 2021 in Africa. Included studies had to document clinical characteristics at treatment initiation and outcomes at the end of treatment (i.e., success, failure, recurrence, loss to follow-up, and death). The included studies were used to conduct a meta-analysis. All data analysis and visualization were performed using the R programming environment. The log risk ratios and sample variances were calculated for DR-TB patients treated with BBQ monotherapy vs. BDQ and other drug therapy. To quantify heterogeneity among the included studies, random effect sizes were calculated. Results: A total of 16 studies in Africa from Mozambique (N = 1 study), Eswatini (N = 1 study), Democratic Republic of the Congo (N = 1 study), South Africa (N = 12 studies), and a multicenter study undertaken across Africa (N = 1 study) were included. In total, 22,368 individuals participated in the research studies. Among the patients, (55.2%; 12,350/22,368) were male while 9723/22,368 (44%) were female. Overall, (9%; 2033/22,368) of patients received BDQ monotherapy, while (88%; 19,630/22,368) patients received bedaquiline combined with other antibiotics. In total, (42%; 9465/22,368) of the patients were successfully treated. About (39%; 8653/22,368) of participants finished their therapy, meanwhile (5%; 1166/22,368) did not finish their therapy, while people (0.4%; 99/22,368) were lost to follow up. A total of (42%; 9265/22,368) patients died. Conclusion: Very few studies on bedaquiline usage in DR-TB in Africa have been published to date. Bedaquiline has been shown to enhance DR-TB results in clinical studies and programmatic settings. Hence, the World Health Organization (WHO) has recommended that it be included in DR-TB regimens. However, in the current study limited improvement to DR-TB treatment results were observed using BDQ on the continent. Better in-country monitoring and reporting, as well as multi-country collaborative cohort studies of DR-TB, can expand the knowledge of bedaquiline usage and clinical impact, as well as the risks and benefits throughout the continent.
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Silva ML, Cá B, Osório NS, Rodrigues PNS, Maceiras AR, Saraiva M. Tuberculosis caused by Mycobacterium africanum: Knowns and unknowns. PLoS Pathog 2022; 18:e1010490. [PMID: 35617217 PMCID: PMC9135246 DOI: 10.1371/journal.ppat.1010490] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Tuberculosis (TB), one of the deadliest threats to human health, is mainly caused by 2 highly related and human-adapted bacteria broadly known as Mycobacterium tuberculosis and Mycobacterium africanum. Whereas M. tuberculosis is widely spread, M. africanum is restricted to West Africa, where it remains a significant cause of tuberculosis. Although several differences have been identified between these 2 pathogens, M. africanum remains a lot less studied than M. tuberculosis. Here, we discuss the genetic, phenotypic, and clinical similarities and differences between strains of M. tuberculosis and M. africanum. We also discuss our current knowledge on the immune response to M. africanum and how it possibly articulates with distinct disease progression and with the geographical restriction attributed to this pathogen. Understanding the functional impact of the diversity existing in TB-causing bacteria, as well as incorporating this diversity in TB research, will contribute to the development of better, more specific approaches to tackle TB.
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Affiliation(s)
- Marta L. Silva
- i3S - Instituto de Investigação e Inovação em Saúde, University of Porto, Porto, Portugal
- IBMC - Instituto de Biologia Molecular e Celular, University of Porto, Porto, Portugal
- Doctoral Program in Molecular and Cell Biology, ICBAS - Instituto de Ciências Biomédicas Abel Salazar, University of Porto, Porto, Portugal
| | - Baltazar Cá
- INASA - Instituto Nacional de Saúde Pública da Guiné-Bissau, Bissau, Guinea-Bissau
- Bandim Health Project, Indepth Network, Bissau, Guinea-Bissau
| | - Nuno S. Osório
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Campus Gualtar, Braga, Portugal
- ICVS/3B’s - PT Government Associate Laboratory, Braga/Guimarães, Portugal
| | - Pedro N. S. Rodrigues
- i3S - Instituto de Investigação e Inovação em Saúde, University of Porto, Porto, Portugal
- IBMC - Instituto de Biologia Molecular e Celular, University of Porto, Porto, Portugal
| | - Ana Raquel Maceiras
- i3S - Instituto de Investigação e Inovação em Saúde, University of Porto, Porto, Portugal
- IBMC - Instituto de Biologia Molecular e Celular, University of Porto, Porto, Portugal
| | - Margarida Saraiva
- i3S - Instituto de Investigação e Inovação em Saúde, University of Porto, Porto, Portugal
- IBMC - Instituto de Biologia Molecular e Celular, University of Porto, Porto, Portugal
- * E-mail:
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7
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Balamurugan M, Banerjee R, Kasibhatla SM, Achalere A, Joshi R. Understanding the Genetic Diversity of Mycobacterium africanum Using Phylogenetics and Population Genomics Approaches. Front Genet 2022; 13:800083. [PMID: 35495132 PMCID: PMC9043288 DOI: 10.3389/fgene.2022.800083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2021] [Accepted: 03/14/2022] [Indexed: 11/13/2022] Open
Abstract
A total of two lineages of Mycobacterium tuberculosis var. africanum (Maf), L5 and L6, which are members of the Mycobacterium tuberculosis complex (MTBC), are responsible for causing tuberculosis in West Africa. Regions of difference (RDs) are usually used for delineation of MTBC. With increased data availability, single nucleotide polymorphisms (SNPs) promise to provide better resolution. Publicly available 380 Maf samples were analyzed for identification of “core-cluster-specific-SNPs,” while additional 270 samples were used for validation. RD-based methods were used for lineage-assignment, wherein 31 samples remained unidentified. The genetic diversity of Maf was estimated based on genome-wide SNPs using phylogeny and population genomics approaches. Lineage-based clustering (L5 and L6) was observed in the whole genome phylogeny with distinct sub-clusters. Population stratification using both model-based and de novo approaches supported the same observations. L6 was further delineated into three sub-lineages (L6.1–L6.3), whereas L5 was grouped as L5.1 and L5.2 based on the occurrence of RD711. L5.1 and L5.2 were further divided into two (L5.1.1 and L5.1.2) and four (L5.2.1–L5.2.4) sub-clusters, respectively. Unassigned samples could be assigned to definite lineages/sub-lineages based on clustering observed in phylogeny along with high-confidence posterior membership scores obtained during population stratification. Based on the (sub)-clusters delineated, “core-cluster-specific-SNPs” were derived. Synonymous SNPs (137 in L5 and 128 in L6) were identified as biomarkers and used for validation. Few of the cluster-specific missense variants in L5 and L6 belong to the central carbohydrate metabolism pathway which include His6Tyr (Rv0946c), Glu255Ala (Rv1131), Ala309Gly (Rv2454c), Val425Ala and Ser112Ala (Rv1127c), Gly198Ala (Rv3293) and Ile137Val (Rv0363c), Thr421Ala (Rv0896), Arg442His (Rv1248c), Thr218Ile (Rv1122), and Ser381Leu (Rv1449c), hinting at the differential growth attenuation. Genes harboring multiple (sub)-lineage-specific “core-cluster” SNPs such as Lys117Asn, Val447Met, and Ala455Val (Rv0066c; icd2) present across L6, L6.1, and L5, respectively, hinting at the association of these SNPs with selective advantage or host-adaptation. Cluster-specific SNPs serve as additional markers along with RD-regions for Maf delineation. The identified SNPs have the potential to provide insights into the genotype–phenotype correlation and clues for endemicity of Maf in the African population.
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Kone B, Somboro AM, Kone M, Holl JL, Baya B, Dabitao D, Diallo D, Diarra B, Kone A, Sarro YDS, Sanogo M, Togo AC, Murphy RL, Diallo S, Coulibaly N, Camara F, Samake S, Diakite M, Doumbia S, Maiga M. Molecular epidemiology and genetic diversity of Mycobacterium tuberculosis complex in referral health centers of Bamako, Mali: What is new? Int J Infect Dis 2022; 117:204-211. [PMID: 35134562 PMCID: PMC9055845 DOI: 10.1016/j.ijid.2022.01.061] [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: 09/22/2021] [Revised: 01/22/2022] [Accepted: 01/27/2022] [Indexed: 11/29/2022] Open
Abstract
Background and Aims: Tuberculosis (TB) remains an important global health issue worldwide. Despite this scourge threatening many human lives, especially in developing countries, thus far, no advanced molecular epidemiology study using recent and more accurate tools has been conducted in Mali. Therefore, this study aimed to use variable-number tandem repeats of mycobacterial interspersed repetitive units (MIRU-VNTR) technology coupled with the spoligotyping method to accurately determine the hot spots and establish the epidemiological transmission links of TB in Bamako, Mali. Methods: In a cross-sectional study, 245 isolates of Mycobacterium tuberculosis complex (MTBC) were characterized using spoligotyping and MIRU-VNTR, and an epidemiological investigation was conducted. Results: Of the 245 isolates, 184 (75.1%) were formally identified. The most widespread strain was the Cameroon strain (83; 45.1%). Eight major clusters were identified: Ghana (27; 14.7%), West African 2 (22; 12%), Haarlem (13; 7.1%), H37Rv (t) (8; 4.3%), Latin American Mediterranean (8; 4.3%), and Uganda I and II (6; 3.3%). Statistical analysis showed a significant difference between lineages from the respective referral health centers of Bamako, Mali (P = 0.01). Conclusion: This study establishes, for the first time, an accurate spatial distribution of circulating MTB strains in Bamako, Mali. The data was used to identify strains and “hot spots” causing TB infection and can also be used for more targeted public health responses, particularly for hot spots of drug-resistant strains.
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Affiliation(s)
- Bourahima Kone
- University Clinical Research Center (UCRC) Laboratory, University of Sciences, Techniques and Technologies of Bamako (USTTB), Bamako, Mali.
| | - Anou M Somboro
- University Clinical Research Center (UCRC) Laboratory, University of Sciences, Techniques and Technologies of Bamako (USTTB), Bamako, Mali; School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Mahamadou Kone
- University Clinical Research Center (UCRC) Laboratory, University of Sciences, Techniques and Technologies of Bamako (USTTB), Bamako, Mali
| | - Jane L Holl
- Center for Healthcare Delivery Science and Innovation, University of Chicago, Chicago, Illinois, USA
| | - Bocar Baya
- University Clinical Research Center (UCRC) Laboratory, University of Sciences, Techniques and Technologies of Bamako (USTTB), Bamako, Mali
| | - Djeneba Dabitao
- University Clinical Research Center (UCRC) Laboratory, University of Sciences, Techniques and Technologies of Bamako (USTTB), Bamako, Mali
| | - Dramane Diallo
- University Clinical Research Center (UCRC) Laboratory, University of Sciences, Techniques and Technologies of Bamako (USTTB), Bamako, Mali
| | - Bassirou Diarra
- University Clinical Research Center (UCRC) Laboratory, University of Sciences, Techniques and Technologies of Bamako (USTTB), Bamako, Mali
| | - Amadou Kone
- University Clinical Research Center (UCRC) Laboratory, University of Sciences, Techniques and Technologies of Bamako (USTTB), Bamako, Mali
| | - Yeya Dit Sadio Sarro
- University Clinical Research Center (UCRC) Laboratory, University of Sciences, Techniques and Technologies of Bamako (USTTB), Bamako, Mali
| | - Moumine Sanogo
- University Clinical Research Center (UCRC) Laboratory, University of Sciences, Techniques and Technologies of Bamako (USTTB), Bamako, Mali
| | - Antieme Cg Togo
- University Clinical Research Center (UCRC) Laboratory, University of Sciences, Techniques and Technologies of Bamako (USTTB), Bamako, Mali
| | - Robert L Murphy
- Biomedical Engineering Department, Northwestern University, Evanston, Illinois, USA
| | - Souleymane Diallo
- University Clinical Research Center (UCRC) Laboratory, University of Sciences, Techniques and Technologies of Bamako (USTTB), Bamako, Mali
| | - Nadie Coulibaly
- University Clinical Research Center (UCRC) Laboratory, University of Sciences, Techniques and Technologies of Bamako (USTTB), Bamako, Mali
| | - Fatoumata Camara
- University Clinical Research Center (UCRC) Laboratory, University of Sciences, Techniques and Technologies of Bamako (USTTB), Bamako, Mali
| | - Seydou Samake
- University Clinical Research Center (UCRC) Laboratory, University of Sciences, Techniques and Technologies of Bamako (USTTB), Bamako, Mali
| | - Mahamadou Diakite
- University Clinical Research Center (UCRC) Laboratory, University of Sciences, Techniques and Technologies of Bamako (USTTB), Bamako, Mali
| | - Seydou Doumbia
- University Clinical Research Center (UCRC) Laboratory, University of Sciences, Techniques and Technologies of Bamako (USTTB), Bamako, Mali
| | - Mamoudou Maiga
- University Clinical Research Center (UCRC) Laboratory, University of Sciences, Techniques and Technologies of Bamako (USTTB), Bamako, Mali; Biomedical Engineering Department, Northwestern University, Evanston, Illinois, USA.
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Tolofoudie M, Somboro A, Diarra B, Sarro YS, Drame HB, Togo ACG, Sanogo M, Dembele A, Togun T, Nkereuwem E, Baya B, Konate B, Egere U, Traore M, Maiga M, Saliba-Shaw K, Kampmann B, Diallo S, Doumbia S, Sylla M. Isoniazid preventive therapy in child household contacts of adults with active TB in Bamako, Mali. Public Health Action 2021; 11:191-195. [PMID: 34956847 PMCID: PMC8680184 DOI: 10.5588/pha.21.0061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Accepted: 08/16/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND AND OBJECTIVE Isoniazid preventive therapy (IPT) is known to reduce the risk of developing active TB in about 59% in children aged ⩽15 years. We assessed adherence, completion and adverse events among children who were household contacts of a newly diagnosed adult with smear-positive TB in Bamako, Mali. METHODS Children aged <15 years living in the same house with an adult smear-positive index case were enrolled in the study in the Bamako Region after consent was obtained from the parent or legal guardian. Adherence was assessed based on the number of tablets consumed during 6 months. RESULTS A total of 260 children aged <15 years were identified as household contacts of 207 adult patients with smear-positive TB during the study period. Among all child contacts, 130/260 (50.0%) were aged 0-4 years and were eligible for IPT; 128/130 (98.5%) were started on IPT and 83/128 (64.8%) completed with good adherence at the end of the 6 months, and without any significant adverse events. CONCLUSION We successfully implemented IPT with good acceptance, but low completion rate. The Mali National TB Program and partners should expand this strategy to reach more children in Bamako and the whole country and create greater awareness in the population.
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Affiliation(s)
- M Tolofoudie
- University Clinical Research Center, University of Sciences, Techniques and Technologies of Bamako, Bamako, Mali
| | - A Somboro
- University Clinical Research Center, University of Sciences, Techniques and Technologies of Bamako, Bamako, Mali
| | - B Diarra
- University Clinical Research Center, University of Sciences, Techniques and Technologies of Bamako, Bamako, Mali
| | - Y S Sarro
- University Clinical Research Center, University of Sciences, Techniques and Technologies of Bamako, Bamako, Mali
| | - H B Drame
- University Clinical Research Center, University of Sciences, Techniques and Technologies of Bamako, Bamako, Mali
| | - A C G Togo
- University Clinical Research Center, University of Sciences, Techniques and Technologies of Bamako, Bamako, Mali
| | - M Sanogo
- University Clinical Research Center, University of Sciences, Techniques and Technologies of Bamako, Bamako, Mali
| | - A Dembele
- Department of Paediatrics, University Teaching Hospital of Gabriel Toure, Bamako, Mali
| | - T Togun
- Vaccines and Immunity Theme, Medical Research Council Unit-The Gambia, Banjul, The Gambia
| | - E Nkereuwem
- Vaccines and Immunity Theme, Medical Research Council Unit-The Gambia, Banjul, The Gambia
| | - B Baya
- University Clinical Research Center, University of Sciences, Techniques and Technologies of Bamako, Bamako, Mali
| | - B Konate
- National Tuberculosis Control Program, Ministry of Health and Public Hygiene, Bamako, Mali
| | - U Egere
- Vaccines and Immunity Theme, Medical Research Council Unit-The Gambia, Banjul, The Gambia
| | - M Traore
- Health Referral Center Five, Ministry of Health and Social Development, Bamako, Mali
| | - M Maiga
- Center for Innovation in Global Health Technology, Northwestern University, Chicago, IL, USA
| | - K Saliba-Shaw
- Collaborative Clinical Research Branch, Division of Clinical Research, National Institute of Allergy and Infectious Diseases/National Institutes of Health, Bethesda, MD, USA
| | - B Kampmann
- Vaccines and Immunity Theme, Medical Research Council Unit-The Gambia, Banjul, The Gambia
| | - S Diallo
- University Clinical Research Center, University of Sciences, Techniques and Technologies of Bamako, Bamako, Mali
| | - S Doumbia
- University Clinical Research Center, University of Sciences, Techniques and Technologies of Bamako, Bamako, Mali
| | - M Sylla
- Department of Paediatrics, University Teaching Hospital of Gabriel Toure, Bamako, Mali
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Mekonnen D, Derbie A, Mihret A, Yimer SA, Tønjum T, Gelaw B, Nibret E, Munshae A, Waddell SJ, Aseffa A. Lipid droplets and the transcriptome of Mycobacterium tuberculosis from direct sputa: a literature review. Lipids Health Dis 2021; 20:129. [PMID: 34602073 PMCID: PMC8487580 DOI: 10.1186/s12944-021-01550-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Accepted: 09/09/2021] [Indexed: 11/21/2022] Open
Abstract
Mycobacterium tuberculosis (Mtb), the main etiology of tuberculosis (TB), is predominantly an intracellular pathogen that has caused infection, disease and death in humans for centuries. Lipid droplets (LDs) are dynamic intracellular organelles that are found across the evolutionary tree of life. This review is an evaluation of the current state of knowledge regarding Mtb-LD formation and associated Mtb transcriptome directly from sputa.Based on the LD content, Mtb in sputum may be classified into three groups: LD positive, LD negative and LD borderline. However, the clinical and evolutionary importance of each state is not well elaborated. Mounting evidence supports the view that the presence of LD positive Mtb bacilli in sputum is a biomarker of slow growth, low energy state, towards lipid degradation, and drug tolerance. In Mtb, LD may serve as a source of chemical energy, scavenger of toxic compounds, prevent destruction of Mtb through autophagy, delay trafficking of lysosomes towards the phagosome, and contribute to Mtb persistence. It is suggest that LD is a key player in the induction of a spectrum of phenotypic and metabolic states of Mtb in the macrophage, granuloma and extracellular sputum microenvironment. Tuberculosis patients with high proportion of LD positive Mtb in pretreatment sputum was associated with higher rate of poor treatment outcome, indicating that LD may have a clinical application in predicting treatment outcome.The propensity for LD formation among Mtb lineages is largely unknown. The role of LD on Mtb transmission and disease phenotype (pulmonary TB vs extra-pulmonary TB) is not well understood. Thus, further studies are needed to understand the relationships between LD positivity and Mtb lineage, Mtb transmission and clinical types.
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Affiliation(s)
- Daniel Mekonnen
- Department of Medical Microbiology, College of Medicine and Health Sciences, Bahir Dar University, Bahir Dar, Ethiopia.
- Institute of Biotechnology, Bahir Dar University, Bahir Dar, Ethiopia.
| | - Awoke Derbie
- Department of Medical Microbiology, College of Medicine and Health Sciences, Bahir Dar University, Bahir Dar, Ethiopia
- Institute of Biotechnology, Bahir Dar University, Bahir Dar, Ethiopia
- The Centre for Innovative Drug Development and Therapeutic Trials for Africa (CDT-Africa), Addis Ababa University, Addis Ababa, Ethiopia
| | - Adane Mihret
- Armauer Hansen Research Institute, Jimma Road, ALERT Compound, PO Box 1005, Addis Ababa, Ethiopia
- Department of Medical Microbiology, Immunology and Parasitology, College of Medicine and Health Sciences, Addis Ababa University, Addis Ababa, Ethiopia
| | - Solomon Abebe Yimer
- Department of Microbiology, University of Oslo, PO Box 1071, Blindern, NO-0316, Oslo, Norway
- Coalition for Epidemic Preparedness Innovations, CEPI, P.O. Box 123, Torshov, 0412, Oslo, Norway
| | - Tone Tønjum
- Department of Microbiology, University of Oslo, PO Box 1071, Blindern, NO-0316, Oslo, Norway
- Department of Microbiology, Oslo University Hospital, PO Box 4950, Nydalen, NO-0424, Oslo, Norway
| | - Baye Gelaw
- Department of Medical Microbiology, School of Biomedical and Laboratory Sciences, College of Medicine and Health Sciences, University of Gondar, Gondar, Ethiopia
| | - Endalkachew Nibret
- Institute of Biotechnology, Bahir Dar University, Bahir Dar, Ethiopia
- Department of Biology, Bahir Dar University, Bahir Dar, Ethiopia
| | - Abaineh Munshae
- Institute of Biotechnology, Bahir Dar University, Bahir Dar, Ethiopia
- Department of Biology, Bahir Dar University, Bahir Dar, Ethiopia
| | - Simon J Waddell
- Department of Global Health and Infection, Brighton and Sussex Medical School, University of Sussex, Brighton, BN1 9PX, UK
| | - Abraham Aseffa
- Armauer Hansen Research Institute, Jimma Road, ALERT Compound, PO Box 1005, Addis Ababa, Ethiopia
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11
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Molecular epidemiology and drug susceptibility profiles of Mycobacterium tuberculosis complex isolates from Northern Ghana. Int J Infect Dis 2021; 109:294-303. [PMID: 34273514 DOI: 10.1016/j.ijid.2021.07.020] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Revised: 06/30/2021] [Accepted: 07/03/2021] [Indexed: 01/19/2023] Open
Abstract
OBJECTIVE We conducted a cross-sectional study in the five administrative regions of Northern Ghana to determine the diversity of Mycobacterium tuberculosis complex (MTBC) sub/lineages and their susceptibility to isoniazid (INH) and rifampicin (RIF). METHODS Sputum specimens were collected and cultured from 566 pulmonary tuberculosis patients reporting to 17 health facilities from 2015 to 2019. Mycobacterial isolates obtained from solid cultures were confirmed as members of the MTBC by PCR amplification of IS6110 and rpoß and assigned lineages and sub-lineages using spoligotyping. RESULTS Of 294 mycobacterial isolates recovered, MTBC species identified were: M. tuberculosis sensu stricto (Mtbss) 241 (82.0%), M. africanum 41 (13.9%) and M. bovis four (1.4%) with eight (2.7%) unidentified. The human-adapted lineages (L) identified (N=279) were L1 (8/279, 2.9%), L2 (15/279, 5.4%), L3 (7/279, 2.5%), L4 (208/279, 74.5%), L5 (13/279, 4.7%) and L6 (28/279, 10.0%) with three unidentified lineages. Among the 208 L4, the dominant sub-lineages in the region were the Cameroon 120/208 (57.7%) and Ghana 50/208 (24.0%). We found 4.4% (13/294) and 0.7% (2/294) of the patients infected with MTBC isolates resistant to INH only and RIF only, respectively, with 2.4% (7/294) being infected with MDR strains. Whereas L6 was associated with the elderly, we identified that the Ghana sub-lineage of L4 was associated with both INH and MDR (p<0.05), making them important TB pathogens in Northern Ghana and a growing public health concern.
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12
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Coscolla M, Gagneux S, Menardo F, Loiseau C, Ruiz-Rodriguez P, Borrell S, Otchere ID, Asante-Poku A, Asare P, Sánchez-Busó L, Gehre F, Sanoussi CN, Antonio M, Affolabi D, Fyfe J, Beckert P, Niemann S, Alabi AS, Grobusch MP, Kobbe R, Parkhill J, Beisel C, Fenner L, Böttger EC, Meehan CJ, Harris SR, de Jong BC, Yeboah-Manu D, Brites D. Phylogenomics of Mycobacterium africanum reveals a new lineage and a complex evolutionary history. Microb Genom 2021; 7:000477. [PMID: 33555243 PMCID: PMC8208692 DOI: 10.1099/mgen.0.000477] [Citation(s) in RCA: 62] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Accepted: 10/29/2020] [Indexed: 01/08/2023] Open
Abstract
Human tuberculosis (TB) is caused by members of the Mycobacterium tuberculosis complex (MTBC). The MTBC comprises several human-adapted lineages known as M. tuberculosis sensu stricto, as well as two lineages (L5 and L6) traditionally referred to as Mycobacterium africanum. Strains of L5 and L6 are largely limited to West Africa for reasons unknown, and little is known of their genomic diversity, phylogeography and evolution. Here, we analysed the genomes of 350 L5 and 320 L6 strains, isolated from patients from 21 African countries, plus 5 related genomes that had not been classified into any of the known MTBC lineages. Our population genomic and phylogeographical analyses showed that the unclassified genomes belonged to a new group that we propose to name MTBC lineage 9 (L9). While the most likely ancestral distribution of L9 was predicted to be East Africa, the most likely ancestral distribution for both L5 and L6 was the Eastern part of West Africa. Moreover, we found important differences between L5 and L6 strains with respect to their phylogeographical substructure and genetic diversity. Finally, we could not confirm the previous association of drug-resistance markers with lineage and sublineages. Instead, our results indicate that the association of drug resistance with lineage is most likely driven by sample bias or geography. In conclusion, our study sheds new light onto the genomic diversity and evolutionary history of M. africanum, and highlights the need to consider the particularities of each MTBC lineage for understanding the ecology and epidemiology of TB in Africa and globally.
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Affiliation(s)
- Mireia Coscolla
- ISysBio, University of Valencia-FISABIO Joint Unit, Valencia, Spain
| | - Sebastien Gagneux
- Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Fabrizio Menardo
- Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Chloé Loiseau
- Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | | | - Sonia Borrell
- Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Isaac Darko Otchere
- Noguchi Memorial Institute for Medical Research, University of Ghana, Legon, Accra, Ghana
| | - Adwoa Asante-Poku
- Noguchi Memorial Institute for Medical Research, University of Ghana, Legon, Accra, Ghana
| | - Prince Asare
- Noguchi Memorial Institute for Medical Research, University of Ghana, Legon, Accra, Ghana
| | - Leonor Sánchez-Busó
- Centre for Genomic Pathogen Surveillance, Big Data Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
| | - Florian Gehre
- Infectious Disease Epidemiology Department, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, Germany
- Health Department, East African Community (EAC), Arusha, Tanzania
| | - C. N’Dira Sanoussi
- Laboratoire de Référence des Mycobactéries, Ministry of Health, Cotonou, Bénin
- Mycobacteriology Unit, Institute of Tropical Medicine, Antwerp, Belgium
| | - Martin Antonio
- London School of Hygiene and Tropical Medicine, London, UK
| | - Dissou Affolabi
- Laboratoire de Référence des Mycobactéries, Ministry of Health, Cotonou, Bénin
| | - Janet Fyfe
- Mycobacterium Reference Laboratory, Victoria Infectious Diseases Reference Laboratory, Peter Doherty Institute, Melbourne, Victoria, Australia
| | - Patrick Beckert
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Germany
- Partner Site Hamburg-Lübeck-Borstel-Riems, German Center for Infection Research, Borstel, Germany
| | - Stefan Niemann
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Germany
- Partner Site Hamburg-Lübeck-Borstel-Riems, German Center for Infection Research, Borstel, Germany
| | - Abraham S. Alabi
- Centre de Recherches Médicales en Lambaréné (Cermel), Lambaréné, Gabon
| | - Martin P. Grobusch
- Centre de Recherches Médicales en Lambaréné (Cermel), Lambaréné, Gabon
- Institut für Tropenmedizin, Deutsches Zentrum fuer Infektionsforschung, University of Tübingen, Tübingen, Germany
- Center of Tropical Medicine and Travel Medicine, Department of Infectious Diseases, Amsterdam University Medical Centers, Amsterdam Infection and Immunity, Amsterdam Public Health, University of Amsterdam, Amsterdam, The Netherlands
| | - Robin Kobbe
- First Department of Medicine, Division of Infectious Diseases, University Medical Center Hamburg-Eppendorf, Germany
| | - Julian Parkhill
- Department of Veterinary Medicine, University of Cambridge, Madingley Road, Cambridge, UK
| | - Christian Beisel
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
| | - Lukas Fenner
- Institute of Social and Preventive Medicine, University of Bern, Bern, Switzerland
| | - Erik C. Böttger
- Institute of Medical Microbiology, University of Zürich, Zürich, Switzerland
| | - Conor J. Meehan
- School of Chemistry and Biosciences, University of Bradford, Bradford, UK
| | - Simon R. Harris
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
- Microbiotica Limited, Bioinnovation Centre, Wellcome Genome Campus, Cambridge, CB10 1DR, UK
| | - Bouke C. de Jong
- Mycobacteriology Unit, Institute of Tropical Medicine, Antwerp, Belgium
| | - Dorothy Yeboah-Manu
- Noguchi Memorial Institute for Medical Research, University of Ghana, Legon, Accra, Ghana
| | - Daniela Brites
- Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
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Characterization of Mycobacterium tuberculosis var. africanum isolated from a patient with pulmonary tuberculosis in Brazil. INFECTION GENETICS AND EVOLUTION 2020; 85:104550. [PMID: 32920193 DOI: 10.1016/j.meegid.2020.104550] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2020] [Revised: 08/01/2020] [Accepted: 09/04/2020] [Indexed: 11/22/2022]
Abstract
Human tuberculosis (TB) is caused by members of the Mycobacterium tuberculosis complex (MTBC), including Mycobacterium tuberculosis var. tuberculosis (MTB) and Mycobacterium tuberculosis var. africanum (MAF). While MTB is isolated worldwide, MAF is almost completely restricted to the African continent, and despite the historical proximity between Brazil and Africa during the slave trade, no case of TB being caused by MAF has been reported in Brazil to date. We hereby describe the first case of TB caused by MAF in Brazil comparing its genome against the published ones. A female patient who had never visited Africa presented with clinical symptoms typical of pulmonary TB. Based on 16S rRNA gene sequencing, the cultured isolate was identified as belonging to MTBC and partial sequence of the hsp65 gene was identical to that of MAF. This was confirmed by genotyping based on detection of Single Nucleotide Polymorphism (SNP), Region of Difference (RD) and spoligotyping. The isolate presented the Shared International Typing (SIT) 181. In the whole-genome comparison against MAF genomes available on published EMBL-EBI European Nucleotide Archive (ENA), the Brazilian genome (MAFBRA00707) was identified as belonging to Lineage 6 and clustered with isolates from The Gambia. This is the first report of the isolation of MAF from a patient from Brazil, without evidence of having any contact with an African index case.
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14
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Baya B, Diarra B, Diabate S, Kone B, Goita D, Sarro YDS, Cohen K, Holl JL, Achenbach CJ, Tolofoudie M, Togo ACG, Sanogo M, Kone A, Kodio O, Dabitao D, Coulibaly N, Siddiqui S, Diop S, Bishai W, Dao S, Doumbia S, Murphy RL, Diallo S, Maiga M. Association of Mycobacterium africanum Infection with Slower Disease Progression Compared with Mycobacterium tuberculosis in Malian Patients with Tuberculosis. Am J Trop Med Hyg 2020; 102:36-41. [PMID: 31733052 PMCID: PMC6947796 DOI: 10.4269/ajtmh.19-0264] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Mycobacterium africanum (MAF) is known to endemically cause up to 40–50% of all pulmonary TB in West Africa. The aim of this study was to compare MAF with Mycobacterium tuberculosis (MTB) with regard to time from symptom onset to TB diagnosis, and clinical and radiological characteristics. A cross-sectional study was conducted in Bamako, Mali, between August 2014 and July 2016. Seventy-seven newly diagnosed pulmonary TB patients who were naive to treatment were enrolled at Mali’s University Clinical Research Center. Sputum cultures were performed to confirm the diagnosis and spoligotyping to identify the mycobacterial strain. Univariate and multivariate analyses were used to identify factors associated with disease progression. Overall, the frequency of female patients was 25% in MAF infection and only 10.0% in MTB infection (OR = 2.9), and MAF was more represented in patients aged ≥ 30 years (57.1% versus 36.7% [OR = 2.3]). More MAF- than MTB-infected patients had a history of a prior TB contact (32.1% versus 14.3% [OR = 2.8]). The mean duration between cough onset and TB diagnosis was 111 days (∼3.7 months) for MAF and 72 days (∼2.4 months) for MTB (P = 0.007). In a multivariate regression, weight loss (body mass index [BMI] < 18.5 kg/m2) and cough duration (> 4 months) were strongly associated with MAF infection (OR = 5.20 [1.49–18.26], P = 0.010, and 4.74 [1.2–18.58], P = 0.02), respectively. Our data show that MAF infection was significantly associated with lower BMI and a longer time between symptom onset and TB diagnosis than MTB. This supports the concept that MAF infection may have slower disease progression and less severe cough symptoms than MTB.
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Affiliation(s)
- Bocar Baya
- University Clinical Research Center (UCRC)-SEREFO Laboratory-University of Sciences, Techniques and Technologies of Bamako (USTTB), Bamako, Mali
| | - Bassirou Diarra
- University Clinical Research Center (UCRC)-SEREFO Laboratory-University of Sciences, Techniques and Technologies of Bamako (USTTB), Bamako, Mali
| | - Seydou Diabate
- University Clinical Research Center (UCRC)-SEREFO Laboratory-University of Sciences, Techniques and Technologies of Bamako (USTTB), Bamako, Mali
| | - Bourahima Kone
- University Clinical Research Center (UCRC)-SEREFO Laboratory-University of Sciences, Techniques and Technologies of Bamako (USTTB), Bamako, Mali
| | - Drissa Goita
- University Clinical Research Center (UCRC)-SEREFO Laboratory-University of Sciences, Techniques and Technologies of Bamako (USTTB), Bamako, Mali
| | - Yeya Dit Sadio Sarro
- University Clinical Research Center (UCRC)-SEREFO Laboratory-University of Sciences, Techniques and Technologies of Bamako (USTTB), Bamako, Mali
| | - Keira Cohen
- Johns Hopkins University School of Medicine, Baltimore, Maryland
| | | | | | - Mohamed Tolofoudie
- University Clinical Research Center (UCRC)-SEREFO Laboratory-University of Sciences, Techniques and Technologies of Bamako (USTTB), Bamako, Mali
| | - Antieme Combo Georges Togo
- University Clinical Research Center (UCRC)-SEREFO Laboratory-University of Sciences, Techniques and Technologies of Bamako (USTTB), Bamako, Mali
| | - Moumine Sanogo
- University Clinical Research Center (UCRC)-SEREFO Laboratory-University of Sciences, Techniques and Technologies of Bamako (USTTB), Bamako, Mali
| | - Amadou Kone
- University Clinical Research Center (UCRC)-SEREFO Laboratory-University of Sciences, Techniques and Technologies of Bamako (USTTB), Bamako, Mali
| | - Ousmane Kodio
- University Clinical Research Center (UCRC)-SEREFO Laboratory-University of Sciences, Techniques and Technologies of Bamako (USTTB), Bamako, Mali
| | - Djeneba Dabitao
- University Clinical Research Center (UCRC)-SEREFO Laboratory-University of Sciences, Techniques and Technologies of Bamako (USTTB), Bamako, Mali
| | - Nadie Coulibaly
- University Clinical Research Center (UCRC)-SEREFO Laboratory-University of Sciences, Techniques and Technologies of Bamako (USTTB), Bamako, Mali
| | - Sophia Siddiqui
- National Institutes of Allergic and Infectious Diseases (NIAID), Rockville, Maryland
| | - Samba Diop
- University Clinical Research Center (UCRC)-SEREFO Laboratory-University of Sciences, Techniques and Technologies of Bamako (USTTB), Bamako, Mali
| | - William Bishai
- Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Sounkalo Dao
- University Clinical Research Center (UCRC)-SEREFO Laboratory-University of Sciences, Techniques and Technologies of Bamako (USTTB), Bamako, Mali
| | - Seydou Doumbia
- University Clinical Research Center (UCRC)-SEREFO Laboratory-University of Sciences, Techniques and Technologies of Bamako (USTTB), Bamako, Mali
| | | | - Souleymane Diallo
- University Clinical Research Center (UCRC)-SEREFO Laboratory-University of Sciences, Techniques and Technologies of Bamako (USTTB), Bamako, Mali
| | - Mamoudou Maiga
- Northwestern University, Chicago, Illinois.,University Clinical Research Center (UCRC)-SEREFO Laboratory-University of Sciences, Techniques and Technologies of Bamako (USTTB), Bamako, Mali
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15
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Ejo M, Hassane-Harouna S, Souleymane MB, Lempens P, Dockx J, Uwizeye C, De Rijk P, Decroo T, Diro E, Torrea G, Rigouts L, Piubello A, de Jong BC. Multidrug-resistant patients receiving treatment in Niger who are infected with M. tuberculosis Cameroon family convert faster in smear and culture than those with M. tuberculosis Ghana family. Tuberculosis (Edinb) 2020; 122:101922. [PMID: 32275231 DOI: 10.1016/j.tube.2020.101922] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Revised: 03/19/2020] [Accepted: 03/19/2020] [Indexed: 10/24/2022]
Abstract
In this study, we analyzed the M. tuberculosis complex (MTBc) population structure among multidrug-resistant TB (MDR-TB) patients in Niger and tested whether the Cameroon family displayed a slower response to MDR-TB treatment. We genotyped baseline clinical isolates that had been collected from pulmonary MDR-TB patients recruited consecutively between 2008 and 2016 in Niger. Spoligotyping was used to analyze the genetic diversity of mycobacterial lineages, and Kaplan Meier's analysis to compare treatment outcomes. A total of 222 MTBc isolates were genotyped; 204 (91,9%) were identified as the Euro-American L4 lineage, with the Ghana family (106, 47,4%) and the Cameroon family (63, 28,4%) being predominant. Patients infected by Cameroon family isolates 61(96,8%) showed faster conversion (log-rank p < 0.01) than those infected with Ghana family isolates (91,5%), and were more likely to experience favorable outcome (adjusted odds ratio [aOR] 4.4; 95%CI 1.1-17.9]; p = 0.015). We found no association between MTBc families and second-line drug resistance profiles (p > 0.05). Our findings show that MDR-TB in Niger is caused by major spoligotypes of the Euro-American L4; with more rapid smear and culture conversion in patients infected with the Cameroon family. These first insights may alert clinicians that slow conversion may be associated with the type of infecting strain.
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Affiliation(s)
- Mebrat Ejo
- Institute of Tropical Medicine (ITM), Nationalestraat 155, B-2000, Antwerpen, Belgium; University of Gondar, P. Box 196, Gondar, Ethiopia; University of Antwerp, Campus Drie Eiken, Universiteitsplein 1, B- 2610, Antwerpen, Wilrijk, Antwerp, Belgium
| | | | | | - Pauline Lempens
- Institute of Tropical Medicine (ITM), Nationalestraat 155, B-2000, Antwerpen, Belgium
| | - Jeroen Dockx
- University of Antwerp, Campus Drie Eiken, Universiteitsplein 1, B- 2610, Antwerpen, Wilrijk, Antwerp, Belgium
| | - Cecile Uwizeye
- Institute of Tropical Medicine (ITM), Nationalestraat 155, B-2000, Antwerpen, Belgium
| | - Pim De Rijk
- Institute of Tropical Medicine (ITM), Nationalestraat 155, B-2000, Antwerpen, Belgium
| | - Tom Decroo
- Institute of Tropical Medicine (ITM), Nationalestraat 155, B-2000, Antwerpen, Belgium; Research Foundation Flanders, Brussels, Belgium
| | - Ermias Diro
- University of Gondar, P. Box 196, Gondar, Ethiopia
| | - Gabriela Torrea
- Institute of Tropical Medicine (ITM), Nationalestraat 155, B-2000, Antwerpen, Belgium
| | - Leen Rigouts
- Institute of Tropical Medicine (ITM), Nationalestraat 155, B-2000, Antwerpen, Belgium; University of Antwerp, Campus Drie Eiken, Universiteitsplein 1, B- 2610, Antwerpen, Wilrijk, Antwerp, Belgium
| | - Alberto Piubello
- Damien Foundation, Brussels, Belgium; International Union Against Tuberculosis and Lung Disease, Paris, France
| | - Bouke C de Jong
- Institute of Tropical Medicine (ITM), Nationalestraat 155, B-2000, Antwerpen, Belgium.
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