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Osei-Wusu S, Tetteh JKA, Musah AB, Ntiamoah DO, Arthur N, Adjei A, Arbues A, Ofori EA, Mensah KA, Galevo SEA, Frempong AF, Asare P, Asante-Poku A, Otchere ID, Kusi KA, Lenz TL, Gagneux S, Portevin D, Yeboah-Manu D. Macrophage susceptibility to infection by Ghanaian Mycobacterium tuberculosis complex lineages 4 and 5 varies with self-reported ethnicity. Front Cell Infect Microbiol 2023; 13:1163993. [PMID: 37645380 PMCID: PMC10461633 DOI: 10.3389/fcimb.2023.1163993] [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: 02/11/2023] [Accepted: 07/24/2023] [Indexed: 08/31/2023] Open
Abstract
Background The epidemiology of Mycobacterium tuberculosis complex (MTBC) lineage 5 (L5) infections in Ghana revealed a significantly increased prevalence in Ewes compared to other self-reported ethnic groups. In that context, we sought to investigate the early phase of tuberculosis (TB) infection using ex vivo infection of macrophages derived from the blood of Ewe and Akan ethnic group volunteers with MTBC L4 and L5 strains. Methods The study participants consisted of 16 controls, among which self-reported Akan and Ewe ethnicity was equally represented, as well as 20 cured TB cases consisting of 11 Akans and 9 Ewes. Peripheral blood mononuclear cells were isolated from both healthy controls and cured TB cases. CD14+ monocytes were isolated and differentiated into monocyte-derived macrophages (MDMs) before infection with L4 or L5 endemic strains. The bacterial load was assessed after 2 hours (uptake) as well as 3 and 7 days post-infection. Results We observed a higher capacity of MDMs from Ewes to phagocytose L4 strains (p < 0.001), translating into a higher bacillary load on day 7 (p < 0.001) compared to L5, despite the higher replication rate of L5 in Ewe MDMs (fold change: 1.4 vs. 1.2, p = 0.03) among the controls. On the contrary, within macrophages from Akans, we observed a significantly higher phagocytic uptake of L5 (p < 0.001) compared to L4, also translating into a higher load on day 7 (p = 0.04). However, the replication rate of L4 in Akan MDMs was higher than that of L5 (fold change: L4 = 1.2, L4 = 1.1, p = 0.04). Although there was no significant difference in the uptake of L4 and L5 among cured TB cases, there was a higher bacterial load of both L4 (p = 0.02) and L5 (p = 0.02) on day 7 in Ewe MDMs. Conclusion Our results suggest that host ethnicity (driven by host genetic diversity), MTBC genetic diversity, and individual TB infection history are all acting together to modulate the outcome of macrophage infections by MTBC.
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Affiliation(s)
- Stephen Osei-Wusu
- Noguchi Memorial Institute for Medical Research, University of Ghana, Legon, Ghana
- West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), University of Ghana, Legon, Ghana
| | - John K. A. Tetteh
- Noguchi Memorial Institute for Medical Research, University of Ghana, Legon, Ghana
| | - Abdul Basit Musah
- Noguchi Memorial Institute for Medical Research, University of Ghana, Legon, Ghana
| | | | - Nelly Arthur
- Department of Chest Diseases, Korle-Bu Teaching Hospital, Accra, Ghana
| | - Abraham Adjei
- Department of Chest Diseases, Korle-Bu Teaching Hospital, Accra, Ghana
| | - Ainhoa Arbues
- Swiss Tropical and Public Health Institute, Allschwil, Switzerland
- University of Basel, Basel, Switzerland
| | - Ebenezer Addo Ofori
- Noguchi Memorial Institute for Medical Research, University of Ghana, Legon, Ghana
| | - Kwadwo Akyea Mensah
- Noguchi Memorial Institute for Medical Research, University of Ghana, Legon, Ghana
| | | | - Abena Frema Frempong
- Noguchi Memorial Institute for Medical Research, University of Ghana, Legon, Ghana
| | - Prince Asare
- Noguchi Memorial Institute for Medical Research, University of Ghana, Legon, Ghana
| | - Adwoa Asante-Poku
- Noguchi Memorial Institute for Medical Research, University of Ghana, Legon, Ghana
| | - Isaac Darko Otchere
- Noguchi Memorial Institute for Medical Research, University of Ghana, Legon, Ghana
| | - Kwadwo Asamoah Kusi
- Noguchi Memorial Institute for Medical Research, University of Ghana, Legon, Ghana
| | - Tobias L. Lenz
- Research Group for Evolutionary Immunogenomics, Department of Biology, University of Hamburg, Hamburg, Germany
| | - Sebastien Gagneux
- Swiss Tropical and Public Health Institute, Allschwil, Switzerland
- University of Basel, Basel, Switzerland
| | - Damien Portevin
- Swiss Tropical and Public Health Institute, Allschwil, Switzerland
- University of Basel, Basel, Switzerland
| | - Dorothy Yeboah-Manu
- Noguchi Memorial Institute for Medical Research, University of Ghana, Legon, Ghana
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Owusu W, van Vliet AHM, Riddell NE, Stewart G, Akwani WC, Aryeetey S, Arthur RA, Sylverken AA, Hingley-Wilson SM. A multiplex PCR assay for the differentiation of Mycobacterium tuberculosis complex reveals high rates of mixed-lineage tuberculosis infections among patients in Ghana. Front Cell Infect Microbiol 2023; 13:1125079. [PMID: 37077529 PMCID: PMC10108843 DOI: 10.3389/fcimb.2023.1125079] [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: 12/15/2022] [Accepted: 03/17/2023] [Indexed: 04/05/2023] Open
Abstract
In low-resource settings with high tuberculosis (TB) burdens, lack of rapid diagnostic methods for detection and differentiation of Mycobacterium tuberculosis complex (MTBC) is a major challenge affecting TB management. This study utilized comparative genomic analyses of MTBC lineages; M. tuberculosis, M. africanum Lineages 5/6 and M. bovis to identify lineage-specific genes. Primers were designed for the development of a Multiplex PCR assay which was successful in differentiating the MTBC lineages. There was no cross-reaction with other respiratory pathogens tested. Validation of the assay using clinical samples was performed with sputum DNA extracts from 341 clinically confirmed active TB patients. It was observed that 24.9% of cases were caused by M. tuberculosis, while M. africanum L5 & L6 reported 9.0% and 14.4%, respectively. M. bovis infection was the least frequently detected lineage with 1.8%. Also, 27.0% and 17.0% of the cases were PCR negative and unspeciated, respectively. However, mixed-lineage TB infections were recorded at a surprising 5.9%. This multiplex PCR assay will allow speciation of MTBC lineages in low-resource regions, providing rapid differentiation of TB infections to select appropriate medication at the earliest possible time point. It will also be useful in epidemiological surveillance studies providing reliable information on the prevalence of TB lineages as well as identifying difficult to treat cases of mixed-lineage tuberculosis infections.
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Affiliation(s)
- Wellington Owusu
- Department of Microbial Sciences, School of Biosciences, Faculty of Health and Medical Sciences, University of Surrey, Guildford, United Kingdom
| | - Arnoud H. M. van Vliet
- Department of Comparative Biomedical Sciences, School of Veterinary Medicine, Faculty of Health and Medical Sciences, University of Surrey, Guildford, United Kingdom
| | - Natalie E. Riddell
- Department of Biochemical Sciences, School of Biosciences and Medicine, University of Surrey, Guildford, United Kingdom
| | - Graham Stewart
- Department of Microbial Sciences, School of Biosciences, Faculty of Health and Medical Sciences, University of Surrey, Guildford, United Kingdom
| | - Winifred C. Akwani
- Department of Microbial Sciences, School of Biosciences, Faculty of Health and Medical Sciences, University of Surrey, Guildford, United Kingdom
| | - Sherihane Aryeetey
- Kumasi Centre for Collaborative Research in Tropical Medicine, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Rejoice Agyeiwaa Arthur
- Kumasi Centre for Collaborative Research in Tropical Medicine, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Augustina Angelina Sylverken
- Kumasi Centre for Collaborative Research in Tropical Medicine, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
- Department of Theoretical and Applied Biology, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Suzanne M. Hingley-Wilson
- Department of Microbial Sciences, School of Biosciences, Faculty of Health and Medical Sciences, University of Surrey, Guildford, United Kingdom
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3
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Need for speed: Key driver of host cell migration varies among mycobacteria. Cell 2022; 185:4467-4469. [PMID: 36423577 DOI: 10.1016/j.cell.2022.10.029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Revised: 10/26/2022] [Accepted: 10/27/2022] [Indexed: 11/24/2022]
Abstract
In this issue of Cell, Saelens et al. describe a new function for mycobacterial Type VII secretion systems: manipulation of host cell migration. They find that a substantial proportion of global TB cases arise from bacteria lacking this function, raising questions about its role in pathoadaptation of Mycobacterium tuberculosis.
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Soler-Camargo NC, Silva-Pereira TT, Zimpel CK, Camacho MF, Zelanis A, Aono AH, Patané JS, Dos Santos AP, Guimarães AMS. The rate and role of pseudogenes of the Mycobacterium tuberculosis complex. Microb Genom 2022; 8. [PMID: 36250787 DOI: 10.1099/mgen.0.000876] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Whole-genome sequence analyses have significantly contributed to the understanding of virulence and evolution of the Mycobacterium tuberculosis complex (MTBC), the causative pathogens of tuberculosis. Most MTBC evolutionary studies are focused on single nucleotide polymorphisms and deletions, but rare studies have evaluated gene content, whereas none has comprehensively evaluated pseudogenes. Accordingly, we describe an extensive study focused on quantifying and predicting possible functions of MTBC and Mycobacterium canettii pseudogenes. Using NCBI's PGAP-detected pseudogenes, we analysed 25 837 pseudogenes from 158 MTBC and M. canetii strains and combined transcriptomics and proteomics of M. tuberculosis H37Rv to gain insights about pseudogenes' expression. Our results indicate significant variability concerning rate and conservancy of in silico predicted pseudogenes among different ecotypes and lineages of tuberculous mycobacteria and pseudogenization of important virulence factors and genes of the metabolism and antimicrobial resistance/tolerance. We show that in silico predicted pseudogenes contribute considerably to MTBC genetic diversity at the population level. Moreover, the transcription machinery of M. tuberculosis can fully transcribe most pseudogenes, indicating intact promoters and recent pseudogene evolutionary emergence. Proteomics of M. tuberculosis and close evaluation of mutational lesions driving pseudogenization suggest that few in silico predicted pseudogenes are likely capable of neofunctionalization, nonsense mutation reversal, or phase variation, contradicting the classical definition of pseudogenes. Such findings indicate that genome annotation should be accompanied by proteomics and protein function assays to improve its accuracy. While indels and insertion sequences are the main drivers of the observed mutational lesions in these species, population bottlenecks and genetic drift are likely the evolutionary processes acting on pseudogenes' emergence over time. Our findings unveil a new perspective on MTBC's evolution and genetic diversity.
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Affiliation(s)
- Naila Cristina Soler-Camargo
- Laboratory of Applied Research in Mycobacteria, Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, SP, Brazil.,Department of Preventive Veterinary Medicine and Animal Health, College of Veterinary Medicine, University of São Paulo, São Paulo, SP, Brazil
| | - Taiana Tainá Silva-Pereira
- Laboratory of Applied Research in Mycobacteria, Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, SP, Brazil
| | - Cristina Kraemer Zimpel
- Laboratory of Applied Research in Mycobacteria, Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, SP, Brazil.,Department of Preventive Veterinary Medicine and Animal Health, College of Veterinary Medicine, University of São Paulo, São Paulo, SP, Brazil
| | - Maurício F Camacho
- Functional Proteomics Laboratory, Federal University of São Paulo (UNIFESP), São José dos Campos, SP, Brazil
| | - André Zelanis
- Functional Proteomics Laboratory, Federal University of São Paulo (UNIFESP), São José dos Campos, SP, Brazil
| | - Alexandre H Aono
- Center of Molecular Biology and Genetic Engineering, University of Campinas, Campinas, SP, Brazil.,Institute of Science and Technology, Federal University of São Paulo (UNIFESP), São José dos Campos, SP, Brazil
| | | | | | - Ana Marcia Sá Guimarães
- Laboratory of Applied Research in Mycobacteria, Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, SP, Brazil.,Department of Comparative Pathobiology, College of Veterinary Medicine, Purdue University
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5
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Ncube P, Bagheri B, Goosen WJ, Miller MA, Sampson SL. Evidence, Challenges, and Knowledge Gaps Regarding Latent Tuberculosis in Animals. Microorganisms 2022; 10:microorganisms10091845. [PMID: 36144447 PMCID: PMC9503773 DOI: 10.3390/microorganisms10091845] [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: 08/12/2022] [Revised: 09/08/2022] [Accepted: 09/09/2022] [Indexed: 01/30/2023] Open
Abstract
Mycobacterium bovis and other Mycobacterium tuberculosis complex (MTBC) pathogens that cause domestic animal and wildlife tuberculosis have received considerably less attention than M. tuberculosis, the primary cause of human tuberculosis (TB). Human TB studies have shown that different stages of infection can exist, driven by host–pathogen interactions. This results in the emergence of heterogeneous subpopulations of mycobacteria in different phenotypic states, which range from actively replicating (AR) cells to viable but slowly or non-replicating (VBNR), viable but non-culturable (VBNC), and dormant mycobacteria. The VBNR, VBNC, and dormant subpopulations are believed to underlie latent tuberculosis (LTB) in humans; however, it is unclear if a similar phenomenon could be happening in animals. This review discusses the evidence, challenges, and knowledge gaps regarding LTB in animals, and possible host–pathogen differences in the MTBC strains M. tuberculosis and M. bovis during infection. We further consider models that might be adapted from human TB research to investigate how the different phenotypic states of bacteria could influence TB stages in animals. In addition, we explore potential host biomarkers and mycobacterial changes in the DosR regulon, transcriptional sigma factors, and resuscitation-promoting factors that may influence the development of LTB.
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6
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Mascarell P, de la Rica A, Padilla S, Ruiz-García M, López-Escudero J, García-Abellán J, Botella Á, Masiá M, Gutiérrez F. Pericarditis caused by Mycobacterium africanum: case report. BMC Infect Dis 2022; 22:628. [PMID: 35850703 PMCID: PMC9290226 DOI: 10.1186/s12879-022-07540-x] [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: 11/02/2021] [Accepted: 06/15/2022] [Indexed: 11/26/2022] Open
Abstract
Background Mycobacterium africanum is a member of the Mycobacterium tuberculosis complex (MTBC) and is endemic in West Africa, where it causes up to half of all cases of pulmonary tuberculosis. Here, we report the first isolation of Mycobacterium africanum from the pericardial effusion culture of a patient with tuberculous pericarditis. Case presentation A 31-year-old man, native from Senegal, came to the emergency room with massive pericardial effusion and cardiac tamponade requiring pericardiocentesis. M. africanum subtype II was identified in the pericardial fluid. The patient completed 10 months of standard treatment, with a favorable outcome. Conclusions We report the first case of tuberculous pericarditis caused by Mycobacterium africanum, which provide evidence that this microorganism can cause pericardial disease and must be considered in patients from endemic areas presenting with pericardial effusion.
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Affiliation(s)
- Paula Mascarell
- Infectious Diseases Unit, Hospital General Universitario de Elche, Alicante, Spain.
| | - Alba de la Rica
- Microbiology Service, Hospital General Universitario de Elche, Alicante, Spain
| | - Sergio Padilla
- Infectious Diseases Unit, Hospital General Universitario de Elche, Alicante, Spain
| | | | - José López-Escudero
- Infectious Diseases Unit, Hospital General Universitario de Elche, Alicante, Spain
| | | | - Ángela Botella
- Infectious Diseases Unit, Hospital General Universitario de Elche, Alicante, Spain
| | - Mar Masiá
- Infectious Diseases Unit, Hospital General Universitario de Elche, Alicante, Spain
| | - Félix Gutiérrez
- Infectious Diseases Unit, Hospital General Universitario de Elche, Alicante, Spain
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7
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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: 10] [Impact Index Per Article: 5.0] [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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8
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Sanchez CR, Hidalgo-Hermoso E. Mycobacterium tuberculosis sensu stricto in African Apes, What Is Its True Health Impact? Pathogens 2022; 11:484. [PMID: 35631005 PMCID: PMC9145341 DOI: 10.3390/pathogens11050484] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 04/06/2022] [Accepted: 04/14/2022] [Indexed: 11/30/2022] Open
Abstract
Since the Symposium on Mycobacterial Infections of Zoo Animals held at the National Zoological Park, Smithsonian Institution in 1976, our understanding of tuberculosis (TB) in non-domestic animals has greatly expanded. Throughout the past decades, this knowledge has resulted in improved zoo-habitats and facilities design, stricter biosecurity measures, and advanced diagnostic methods, including molecular techniques, that have significantly decreased the number of clinical disease caused by Mycobacterium tuberculosis in apes under human care settings. In the other hand, exponential growth of human populations has led to human encroachment in wildlife habitat which has resulted in increased inter-species contact and recurrent conflict between humans and wild animals. Although it is widely accepted that non-human primates are susceptible to M. tb infection, opinions differ with regard to the susceptibility to develop disease amongst different taxa. Specifically, some authors suggest that African apes are less susceptible to clinical tuberculosis than other species of primates. The aim of this review article is to evaluate the current scientific literature to determine the actual health impact of disease caused by Mycobacterium tuberculosis and more specifically Mycobacterium tuberculosis sensu stricto in African apes. The literature review included literature databases: Web of Science, Pubmed, Scopus, Wiley, Springer and Science direct, without temporal limit and proceedings of annual conferences in the field of wildlife health. Our general inclusion criteria included information about serological, molecular, pathological (macroscopic and/or microscopic), and clinical evidence of TB in African apes; while our, our more stringent inclusion selection criteria required that in addition to a gross pathology, a molecular test confirmed Mycobacterium tuberculosis sensu stricto as the cause of disease or death. We identified eleven reports of tuberculosis in African apes; of those, only four reports met the more stringent selection criteria that confirmed M. tb sensu stricto in six individuals. All reports that confirmed M. tb sensu stricto originated from zoological collections. Our review suggests that there is little evidence of disease or mortality caused by M. tb in the different species of African apes both under human care and free ranging populations. Additional studies are needed in free-ranging, semi-captive populations (sanctuaries) and animals under human care (zoos and rescue centers) to definitely conclude that this mycobacteria has a limited health effect in African ape species.
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Affiliation(s)
- Carlos R. Sanchez
- Veterinary Medical Center, Oregon Zoo, Portland, 4001 SW Canyon Rd., Portland, OR 97221, USA
| | - Ezequiel Hidalgo-Hermoso
- Conservation and Research Department, Parque Zoologico Buin Zoo, Panamericana Sur Km 32, Buin 01730, Chile;
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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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10
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Ter Beek L, Bolhuis MS, Jager-Wittenaar H, Brijan RXD, Sturkenboom MGG, Kerstjens HAM, de Lange WCM, Tiberi S, van der Werf TS, Alffenaar JWC, Akkerman OW. Malnutrition assessment methods in adult patients with tuberculosis: a systematic review. BMJ Open 2021; 11:e049777. [PMID: 35344503 PMCID: PMC8719177 DOI: 10.1136/bmjopen-2021-049777] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Accepted: 11/19/2021] [Indexed: 12/18/2022] Open
Abstract
OBJECTIVES Malnutrition is associated with a twofold higher risk of dying in patients with tuberculosis (TB) and considered an important potentially reversible risk factor for failure of TB treatment. The construct of malnutrition has three domains: intake or uptake of nutrition; body composition and physical and cognitive function. The objectives of this systematic review are to identify malnutrition assessment methods, and to quantify how malnutrition assessment methods capture the international consensus definition for malnutrition, in patients with TB. DESIGN Different assessment methods were identified. We determined the extent of capturing of the three domains of malnutrition, that is, intake or uptake of nutrition, body composition and physical and cognitive function. RESULTS Seventeen malnutrition assessment methods were identified in 69 included studies. In 53/69 (77%) of studies, body mass index was used as the only malnutrition assessment method. Three out of 69 studies (4%) used a method that captured all three domains of malnutrition. CONCLUSIONS Our study focused on published articles. Implementation of new criteria takes time, which may take longer than the period covered by this review. Most patients with TB are assessed for only one aspect of the conceptual definition of malnutrition. The use of international consensus criteria is recommended to establish uniform diagnostics and treatment of malnutrition. PROSPERO REGISTRATION NUMBER CRD42019122832.
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Affiliation(s)
- Lies Ter Beek
- Department of Pulmonary Diseases and Tuberculosis, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
- Tuberculosis Center Beatrixoord, University of Groningen, University Medical Center Groningen, Haren, The Netherlands
- Department of Health Sciences, Faculty of Science, Vrije Universiteit Amsterdam, and Amsterdam Public Health Research Institute, Amsterdam, The Netherlands
| | - Mathieu S Bolhuis
- Department of Clinical Pharmacy and Pharmacology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Harriët Jager-Wittenaar
- Research Group Healthy Ageing, Allied Health Care and Nursing, Hanze University of Applied Sciences, Groningen, The Netherlands
- Department of Oral and Maxillofacial Surgery, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - René X D Brijan
- Department of Health Sciences, Faculty of Science, Vrije Universiteit Amsterdam, and Amsterdam Public Health Research Institute, Amsterdam, The Netherlands
| | - Marieke G G Sturkenboom
- Department of Clinical Pharmacy and Pharmacology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Huib A M Kerstjens
- Department of Pulmonary Diseases and Tuberculosis, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Wiel C M de Lange
- Department of Pulmonary Diseases and Tuberculosis, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
- Tuberculosis Center Beatrixoord, University of Groningen, University Medical Center Groningen, Haren, The Netherlands
| | - Simon Tiberi
- Department of Infection, Barts Health NHS Trust, London, UK
- Blizard Institute, Queen Mary University of London, London, UK
| | - Tjip S van der Werf
- Department of Pulmonary Diseases and Tuberculosis, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
- Department of Internal Medicine, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Jan-Willem C Alffenaar
- Faculty of Medicine and Health, University of Sydney, School of Pharmacy, Sydney, New South Wales, Australia
- Westmead Hospital, Sydney, New South Wales, Australia
- Marie Bashir Institute for Infectious Diseases and Biosecurity, University of Sydney, Sydney, Australia
| | - Onno W Akkerman
- Department of Pulmonary Diseases and Tuberculosis, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
- Tuberculosis Center Beatrixoord, University of Groningen, University Medical Center Groningen, Haren, The Netherlands
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11
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Osei-Wusu S, Otchere ID, Morgan P, Musah AB, Siam IM, Asandem D, Afum T, Asare P, Asante-Poku A, Kusi KA, Gagneux S, Yeboah-Manu D. Genotypic and phenotypic diversity of Mycobacterium tuberculosis complex genotypes prevalent in West Africa. PLoS One 2021; 16:e0255433. [PMID: 34437584 PMCID: PMC8389432 DOI: 10.1371/journal.pone.0255433] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Accepted: 07/15/2021] [Indexed: 12/13/2022] Open
Abstract
Findings from previous comparative genomics studies of the Mycobacterium tuberculosis complex (MTBC) suggest genomic variation among the genotypes may have phenotypic implications. We investigated the diversity in the phenotypic profiles of the main prevalent MTBC genotypes in West Africa. Thirty-six whole genome sequenced drug susceptible MTBC isolates belonging to lineages 4, 5 and 6 were included in this study. The isolates were phenotypically characterized for urease activity, tween hydrolysis, Thiophen-2-Carboxylic Acid Hydrazide (TCH) susceptibility, nitric oxide production, and growth rate in both liquid (7H9) and solid media (7H11 and Löwenstein–Jensen (L-J)). Lineage 4 isolates showed the highest growth rate in both liquid (p = 0.0003) and on solid (L-J) media supplemented with glycerol (p<0.001) or pyruvate (p = 0.005). L6 isolates optimally utilized pyruvate compared to glycerol (p<0.001), whereas L5 isolates grew similarly on both media (p = 0.05). Lineage 4 isolates showed the lowest average time to positivity (TTP) (p = 0.01; Average TTP: L4 = 15days, L5 = 16.7days, L6 = 29.7days) and the highest logCFU/mL (p = 0.04; average logCFU/mL L4 = 5.9, L5 = 5.0, L6 = 4.4) on 7H11 supplemented with glycerol, but there was no significant difference in growth on 7H11 supplemented with pyruvate (p = 0.23). The highest release of nitrite was recorded for L5 isolates, followed by L4 and L6 isolates. However, the reverse was observed in the urease activity for the lineages. All isolates tested were resistant to TCH except for one L6 isolate. Comparative genomic analyses revealed several mutations that might explain the diverse phenotypic profiles of these isolates. Our findings showed significant phenotypic diversity among the MTBC lineages used for this study.
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Affiliation(s)
- Stephen Osei-Wusu
- Noguchi Memorial Institute for Medical Research, University of Ghana, Legon, Ghana
- West African Centre for Cell Biology of Infectious Pathogens, University of Ghana, Legon, Ghana
| | - Isaac Darko Otchere
- Noguchi Memorial Institute for Medical Research, University of Ghana, Legon, Ghana
- West African Centre for Cell Biology of Infectious Pathogens, University of Ghana, Legon, Ghana
| | - Portia Morgan
- Noguchi Memorial Institute for Medical Research, University of Ghana, Legon, Ghana
- West African Centre for Cell Biology of Infectious Pathogens, University of Ghana, Legon, Ghana
| | - Abdul Basit Musah
- Noguchi Memorial Institute for Medical Research, University of Ghana, Legon, Ghana
| | - Ishaque Mintah Siam
- Noguchi Memorial Institute for Medical Research, University of Ghana, Legon, Ghana
| | - Diana Asandem
- Noguchi Memorial Institute for Medical Research, University of Ghana, Legon, Ghana
- West African Centre for Cell Biology of Infectious Pathogens, University of Ghana, Legon, Ghana
| | - Theophilus Afum
- Noguchi Memorial Institute for Medical Research, University of Ghana, Legon, Ghana
| | - Prince Asare
- Noguchi Memorial Institute for Medical Research, University of Ghana, Legon, Ghana
- West African Centre for Cell Biology of Infectious Pathogens, University of Ghana, Legon, Ghana
| | - Adwoa Asante-Poku
- Noguchi Memorial Institute for Medical Research, University of Ghana, Legon, Ghana
| | - Kwadwo Asamoah Kusi
- Noguchi Memorial Institute for Medical Research, University of Ghana, Legon, Ghana
- West African Centre for Cell Biology of Infectious Pathogens, University of Ghana, Legon, Ghana
| | - Sebastien Gagneux
- Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Dorothy Yeboah-Manu
- Noguchi Memorial Institute for Medical Research, University of Ghana, Legon, Ghana
- West African Centre for Cell Biology of Infectious Pathogens, University of Ghana, Legon, Ghana
- * E-mail:
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12
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Asare P, Asante-Poku A, Osei-Wusu S, Otchere ID, Yeboah-Manu D. The Relevance of Genomic Epidemiology for Control of Tuberculosis in West Africa. Front Public Health 2021; 9:706651. [PMID: 34368069 PMCID: PMC8342769 DOI: 10.3389/fpubh.2021.706651] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Accepted: 06/29/2021] [Indexed: 12/30/2022] Open
Abstract
Tuberculosis (TB), an airborne infectious disease caused by Mycobacterium tuberculosis complex (MTBC), remains a global health problem. West Africa has a unique epidemiology of TB that is characterized by medium- to high-prevalence. Moreover, the geographical restriction of M. africanum to the sub-region makes West Africa have an extra burden to deal with a two-in-one pathogen. The region is also burdened with low case detection, late reporting, poor treatment adherence leading to development of drug resistance and relapse. Sporadic studies conducted within the subregion report higher burden of drug resistant TB (DRTB) than previously thought. The need for more sensitive and robust tools for routine surveillance as well as to understand the mechanisms of DRTB and transmission dynamics for the design of effective control tools, cannot be overemphasized. The advancement in molecular biology tools including traditional fingerprinting and next generation sequencing (NGS) technologies offer reliable tools for genomic epidemiology. Genomic epidemiology provides in-depth insight of the nature of pathogens, circulating strains and their spread as well as prompt detection of the emergence of new strains. It also offers the opportunity to monitor treatment and evaluate interventions. Furthermore, genomic epidemiology can be used to understand potential emergence and spread of drug resistant strains and resistance mechanisms allowing the design of simple but rapid tools. In this review, we will describe the local epidemiology of MTBC, highlight past and current investigations toward understanding their biology and spread as well as discuss the relevance of genomic epidemiology studies to TB control in West Africa.
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Affiliation(s)
- Prince Asare
- College of Health Sciences, Noguchi Memorial Institute for Medical Research, University of Ghana, Accra, Ghana
| | - Adwoa Asante-Poku
- College of Health Sciences, Noguchi Memorial Institute for Medical Research, University of Ghana, Accra, Ghana
| | - Stephen Osei-Wusu
- College of Health Sciences, Noguchi Memorial Institute for Medical Research, University of Ghana, Accra, Ghana
| | - Isaac Darko Otchere
- College of Health Sciences, Noguchi Memorial Institute for Medical Research, University of Ghana, Accra, Ghana
| | - Dorothy Yeboah-Manu
- College of Health Sciences, Noguchi Memorial Institute for Medical Research, University of Ghana, Accra, Ghana
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13
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Chidumayo NN. Estimation of Brucella and Mycobacterium bovis contamination in bovine milk in Africa. INTERNATIONAL JOURNAL OF ONE HEALTH 2021. [DOI: 10.14202/ijoh.2021.37-41] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Background and Aim: Bovine brucellosis and tuberculosis are zoonotic bacterial diseases transmitted through the consumption of raw milk and dairy products. Many developed countries have eliminated bovine brucellosis and tuberculosis in their cattle herds, however, the diseases are still endemic in Africa. Despite the public health risk of these pathogens, the sale and consumption of unpasteurized milk are still common in some African countries. This study aimed to estimate the prevalence of Brucella and Mycobacterium bovis in bovine milk.
Materials and Methods: A conceptual model for milk contamination was constructed and 1 million simulations were performed using data from published articles.
Results: Brucella milk contamination was estimated at a median of 8.68% (interquartile range [IQR]: 5.95-11.97%; range: 2.41-25.16%). The median prevalence of M. bovis was estimated at 6.86% (IQR: 4.25-9.40%; range: 0.01-15.16%).
Conclusion: These results indicate that there is a risk of Brucella and M. bovis transmission through the consumption of unpasteurized milk. The findings of this study highlight the need to improve the safety and quality of informally marketed milk in the region.
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Affiliation(s)
- Nozyechi Ngulube Chidumayo
- Department of Clinical Studies, University of Zambia, School of Veterinary Medicine, P. O. Box 32379, Lusaka, Zambia
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14
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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: 57] [Impact Index Per Article: 19.0] [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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15
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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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16
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Patients infected with Mycobacterium africanum versus Mycobacterium tuberculosis possess distinct intestinal microbiota. PLoS Negl Trop Dis 2020; 14:e0008230. [PMID: 32401750 PMCID: PMC7219701 DOI: 10.1371/journal.pntd.0008230] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Accepted: 03/17/2020] [Indexed: 12/15/2022] Open
Abstract
Background Mycobacterium tuberculosis complex (MTBC), the causative agent of tuberculosis (TB), is composed of eight subspecies. TB in West Africa, in contrast to other geographical regions, is caused by Mycobacterium africanum (MAF) in addition to M. tuberculosis (MTB), with both infections presenting similar symptoms. Nevertheless, MAF is considered to be hypovirulent in comparison with MTB and less likely to progress to active disease. In this study, we asked whether MAF and MTB infected patients possess distinct intestinal microbiomes and characterized how these microbiota communities are affected by anti-tuberculosis therapy (ATT). Additionally, we assessed if the changes in microbiota composition following infection correlate with pathogen induced alterations in host blood-gene expression. Methods A longitudinal, clinical study of MAF infected, MTB infected patients assessed at diagnosis and two months after start of ATT, and healthy, endemic controls was conducted to compare compositions of the fecal microbiome as determined by 16S rRNA sequencing. A blood transcriptome analysis was also performed on a subset of subjects in each group by microarray and the results cross-compared with the same individual’s microbiota composition. Findings MAF participants have distinct microbiomes compared with MTB patients, displaying decreased diversity and increases in Enterobacteriaceae with respect to healthy participants not observed in the latter patient group. Interestingly, this observed elevation in Enterobacteriaceae positively correlated with enhanced inflammatory gene expression in peripheral blood and was reversed after initiation of ATT. Interpretation Our findings indicate that MAF and MTB have distinct associations with the gut microbiome that may be reflective of the differential susceptibility of West Africans to these two co-endemic infections either as biomarkers or as a contributing determinant. Mycobacterium africanum (MAF) is a hypovirulent mycobacterium species that is co-endemic with Mycobacterium tuberculosis (MTB) in West Africa and is selectively responsible for up to half the tuberculosis cases in this region. Why some individuals become infected with MAF versus MTB is unclear but has been suggested to be determined by differential host immune competency. Since the microbiome has now been implicated in numerous studies to generally influence host resistance to disease, we investigated whether differences in the intestinal microbiota might associate with MAF as compared with MTB infection. This report presents the first analysis of the intestinal microbiome of MAF-infected subjects as well as a comparison with the microbiota of co-endemic MTB patients and reveals that the microbiota of individuals with MAF infection display both decreased diversity and distinct differences in microbial taxa when compared to both MTB-infected and healthy controls. Furthermore, our data reveal for the first time in TB patients a correlation between the abundance of certain taxa and host blood transcriptional changes related to immune function. Our study also establishes that antibiotic treatment induces parallel changes in the gut microbiota of MAF- and MTB-infected patients. Although not directly addressed in the present study, the findings presented here raise the possibility that the microbiota or other host physiologic or immune factors closely associated with it may be a factor underlying the differential susceptibility of West Africans to MAF infection. In addition, the data identify certain commensal taxa that could be tested in future studies as specific determinants of this association.
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17
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Zimpel CK, Patané JSL, Guedes ACP, de Souza RF, Silva-Pereira TT, Camargo NCS, de Souza Filho AF, Ikuta CY, Neto JSF, Setubal JC, Heinemann MB, Guimaraes AMS. Global Distribution and Evolution of Mycobacterium bovis Lineages. Front Microbiol 2020; 11:843. [PMID: 32477295 PMCID: PMC7232559 DOI: 10.3389/fmicb.2020.00843] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Accepted: 04/08/2020] [Indexed: 12/31/2022] Open
Abstract
Mycobacterium bovis is the main causative agent of zoonotic tuberculosis in humans and frequently devastates livestock and wildlife worldwide. Previous studies suggested the existence of genetic groups of M. bovis strains based on limited DNA markers (a.k.a. clonal complexes), and the evolution and ecology of this pathogen has been only marginally explored at the global level. We have screened over 2,600 publicly available M. bovis genomes and newly sequenced four wildlife M. bovis strains, gathering 1,969 genomes from 23 countries and at least 24 host species, including humans, to complete a phylogenomic analyses. We propose the existence of four distinct global lineages of M. bovis (Lb1, Lb2, Lb3, and Lb4) underlying the current disease distribution. These lineages are not fully represented by clonal complexes and are dispersed based on geographic location rather than host species. Our data divergence analysis agreed with previous studies reporting independent archeological data of ancient M. bovis (South Siberian infected skeletons at ∼2,000 years before present) and indicates that extant M. bovis originated between 715 and 3,556 years BP, with later emergence in the New World and Oceania, likely influenced by trades among countries.
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Affiliation(s)
- Cristina Kraemer Zimpel
- Laboratory of Applied Research in Mycobacteria, Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil.,Department of Preventive Veterinary Medicine and Animal Health, School of Veterinary Medicine and Animal Sciences, University of São Paulo, São Paulo, Brazil
| | - José Salvatore L Patané
- Department of Biochemistry, Institute of Chemistry, University of São Paulo, São Paulo, Brazil.,Laboratory of Cellular Cycle, Butantan Institute, São Paulo, Brazil
| | - Aureliano Coelho Proença Guedes
- Laboratory of Protein Structure and Evolution, Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Robson F de Souza
- Laboratory of Protein Structure and Evolution, Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Taiana T Silva-Pereira
- Laboratory of Applied Research in Mycobacteria, Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil.,Department of Preventive Veterinary Medicine and Animal Health, School of Veterinary Medicine and Animal Sciences, University of São Paulo, São Paulo, Brazil
| | - Naila C Soler Camargo
- Laboratory of Applied Research in Mycobacteria, Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil.,Department of Preventive Veterinary Medicine and Animal Health, School of Veterinary Medicine and Animal Sciences, University of São Paulo, São Paulo, Brazil
| | - Antônio F de Souza Filho
- Department of Preventive Veterinary Medicine and Animal Health, School of Veterinary Medicine and Animal Sciences, University of São Paulo, São Paulo, Brazil
| | - Cássia Y Ikuta
- Department of Preventive Veterinary Medicine and Animal Health, School of Veterinary Medicine and Animal Sciences, University of São Paulo, São Paulo, Brazil
| | - José Soares Ferreira Neto
- Department of Preventive Veterinary Medicine and Animal Health, School of Veterinary Medicine and Animal Sciences, University of São Paulo, São Paulo, Brazil
| | - João Carlos Setubal
- Department of Biochemistry, Institute of Chemistry, University of São Paulo, São Paulo, Brazil.,Biocomplexity Institute of Virginia Tech, Blacksburg, VA, United States
| | - Marcos Bryan Heinemann
- Department of Preventive Veterinary Medicine and Animal Health, School of Veterinary Medicine and Animal Sciences, University of São Paulo, São Paulo, Brazil
| | - Ana Marcia Sa Guimaraes
- Laboratory of Applied Research in Mycobacteria, Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
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18
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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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19
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Ofori-Anyinam B, Riley AJ, Jobarteh T, Gitteh E, Sarr B, Faal-Jawara TI, Rigouts L, Senghore M, Kehinde A, Onyejepu N, Antonio M, de Jong BC, Gehre F, Meehan CJ. Comparative genomics shows differences in the electron transport and carbon metabolic pathways of Mycobacterium africanum relative to Mycobacterium tuberculosis and suggests an adaptation to low oxygen tension. Tuberculosis (Edinb) 2020; 120:101899. [PMID: 32090860 PMCID: PMC7049902 DOI: 10.1016/j.tube.2020.101899] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Revised: 12/31/2019] [Accepted: 01/05/2020] [Indexed: 12/21/2022]
Abstract
The geographically restricted Mycobacterium africanum lineages (MAF) are primarily found in West Africa, where they account for a significant proportion of tuberculosis. Despite this phenomenon, little is known about the co-evolution of these ancient lineages with West Africans. MAF and M. tuberculosis sensu stricto lineages (MTB) differ in their clinical, in vitro and in vivo characteristics for reasons not fully understood. Therefore, we compared genomes of 289 MAF and 205 MTB clinical isolates from the 6 main human-adapted M. tuberculosis complex lineages, for mutations in their Electron Transport Chain and Central Carbon Metabolic pathway in order to explain these metabolic differences. Furthermore, we determined, in silico, whether each mutation could affect the function of genes encoding enzymes in these pathways. We found more mutations with the potential to affect enzymes in these pathways in MAF lineages compared to MTB lineages. We also found that similar mutations occurred in these pathways between MAF and some MTB lineages. Generally, our findings show further differences between MAF and MTB lineages that may have contributed to the MAF clinical and growth phenotype and indicate potential adaptation of MAF lineages to a distinct ecological niche, which we suggest includes areas characterized by low oxygen tension.
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Affiliation(s)
- Boatema Ofori-Anyinam
- Mycobacteriology Unit, Institute of Tropical Medicine, Antwerp, Belgium; Vaccines and Immunity Theme, Medical Research Council Unit, Banjul, Gambia; Center for Global Health Security and Diplomacy, Ottawa, Canada
| | - Abi Janet Riley
- Vaccines and Immunity Theme, Medical Research Council Unit, Banjul, Gambia
| | - Tijan Jobarteh
- Vaccines and Immunity Theme, Medical Research Council Unit, Banjul, Gambia
| | - Ensa Gitteh
- Vaccines and Immunity Theme, Medical Research Council Unit, Banjul, Gambia
| | - Binta Sarr
- Vaccines and Immunity Theme, Medical Research Council Unit, Banjul, Gambia
| | | | - Leen Rigouts
- Mycobacteriology Unit, Institute of Tropical Medicine, Antwerp, Belgium; Department of Biomedical Sciences, Antwerp University, Antwerp, Belgium
| | - Madikay Senghore
- Vaccines and Immunity Theme, Medical Research Council Unit, Banjul, Gambia
| | - Aderemi Kehinde
- Department of Medical Microbiology & Parasitology, University College Hospital, Ibadan, Nigeria; Department of Medical Microbiology & Parasitology, College of Medicine, University of Ibadan, Ibadan, Nigeria
| | - Nneka Onyejepu
- Center for Tuberculosis Research, Nigeria Institute of Medical Research, Lagos, Nigeria
| | - Martin Antonio
- Vaccines and Immunity Theme, Medical Research Council Unit, Banjul, Gambia; Division of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, United Kingdom; Medical School, University of Warwick, Coventry, United Kingdom
| | - Bouke C de Jong
- Mycobacteriology Unit, Institute of Tropical Medicine, Antwerp, Belgium
| | - Florian Gehre
- Mycobacteriology Unit, Institute of Tropical Medicine, Antwerp, Belgium; Vaccines and Immunity Theme, Medical Research Council Unit, Banjul, Gambia; Bernhard-Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - Conor J Meehan
- Mycobacteriology Unit, Institute of Tropical Medicine, Antwerp, Belgium; School of Chemistry and Biosciences, University of Bradford, Bradford, United Kingdom.
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20
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Cá B, Fonseca KL, Sousa J, Maceiras AR, Machado D, Sanca L, Rabna P, Rodrigues PNS, Viveiros M, Saraiva M. Experimental Evidence for Limited in vivo Virulence of Mycobacterium africanum. Front Microbiol 2019; 10:2102. [PMID: 31552007 PMCID: PMC6746983 DOI: 10.3389/fmicb.2019.02102] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Accepted: 08/26/2019] [Indexed: 02/03/2023] Open
Abstract
Tuberculosis remains a public health problem and a main cause of death to humans. Both Mycobacterium tuberculosis and Mycobacterium africanum cause tuberculosis. In contrast to M. tuberculosis, which is geographically spread, M. africanum is restricted to West Africa. Differences have also been found in the growth rate and type of disease caused by M. africanum, globally suggesting an attenuation of this bacteria. In this study, we used the mouse model of infection to follow the dynamics of M. africanum infection in terms of bacterial burdens and tissue pathology, as well as the immune response triggered. Our findings support a lower virulence of M. africanum as compared to M. tuberculosis, including in mice lacking IFN-γ, a major protective cytokine in tuberculosis. Furthermore, the lung immune response triggered by M. africanum infection in wild-type animals was characterized by a discrete influx of leukocytes and a modest transcriptional upregulation of inflammatory mediators. Our findings contribute to elucidate the pathogenesis of M. africanum, supporting the hypothesis that this is an attenuated member of the tuberculosis-causing bacteria. Understanding the biology of M. africanum and how it interacts with the host to establish infection will have implications for our knowledge of TB and for the development of novel and better tools to control this devastating disease.
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Affiliation(s)
- Baltazar Cá
- i3S - Instituto de Investigação e Inovação em Saúde, Porto, Portugal.,Instituto de Biologia Molecular e Celular, Universidade do Porto, Porto, Portugal.,Programa de Pós-Graduação Ciência para o Desenvolvimento, Instituto Gulbenkian de Ciência, Oeiras, Portugal.,Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto, Porto, Portugal.,Instituto Nacional de Saúde Pública/Projeto de Saúde de Bandim, Bissau, Guinea-Bissau
| | - Kaori L Fonseca
- i3S - Instituto de Investigação e Inovação em Saúde, Porto, Portugal.,Instituto de Biologia Molecular e Celular, Universidade do Porto, Porto, Portugal.,Programa de Pós-Graduação Ciência para o Desenvolvimento, Instituto Gulbenkian de Ciência, Oeiras, Portugal.,Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto, Porto, Portugal
| | - Jeremy Sousa
- i3S - Instituto de Investigação e Inovação em Saúde, Porto, Portugal.,Instituto de Biologia Molecular e Celular, Universidade do Porto, Porto, Portugal.,Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto, Porto, Portugal
| | - Ana Raquel Maceiras
- i3S - Instituto de Investigação e Inovação em Saúde, Porto, Portugal.,Instituto de Biologia Molecular e Celular, Universidade do Porto, Porto, Portugal
| | - Diana Machado
- Global Health and Tropical Medicine, Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa, Lisbon, Portugal
| | - Lilica Sanca
- Instituto Nacional de Saúde Pública/Projeto de Saúde de Bandim, Bissau, Guinea-Bissau
| | - Paulo Rabna
- Instituto Nacional de Saúde Pública/Projeto de Saúde de Bandim, Bissau, Guinea-Bissau
| | - Pedro N S Rodrigues
- i3S - Instituto de Investigação e Inovação em Saúde, Porto, Portugal.,Instituto de Biologia Molecular e Celular, Universidade do Porto, Porto, Portugal.,Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto, Porto, Portugal
| | - Miguel Viveiros
- Global Health and Tropical Medicine, Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa, Lisbon, Portugal
| | - Margarida Saraiva
- i3S - Instituto de Investigação e Inovação em Saúde, Porto, Portugal.,Instituto de Biologia Molecular e Celular, Universidade do Porto, Porto, Portugal
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21
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Chakravarti A, Soualhine H, Sharma M, Rivest P, Poirier L, Lavallée C. Indigenous Transmission of Mycobacterium africanum in Canada: A Case Series and Cluster Analysis. Open Forum Infect Dis 2019; 6:ofz088. [PMID: 30949534 PMCID: PMC6441568 DOI: 10.1093/ofid/ofz088] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2018] [Accepted: 03/04/2019] [Indexed: 11/15/2022] Open
Abstract
Mycobacterium africanum is an important cause of human tuberculosis and is found almost exclusively in West Africa. We identified a cluster of patients in Montreal, Canada, with M africanum disease that share identical genotypic signatures by mycobacterial interspersed repetitive unit-variable number tandem repeat (MIRU-VNTR) typing and a putative epidemiological link, thus providing evidence of possible local transmission of M africanum in Montreal over a 10-year period.
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Affiliation(s)
- Arpita Chakravarti
- Department of Microbiology and Adult Infectious Diseases, Centre Hospitalier de l’Université de Montréal, Canada
| | - Hafid Soualhine
- National Reference Centre for Mycobacteriology, Public Health Agency of Canada, Winnipeg
| | - Meenu Sharma
- National Reference Centre for Mycobacteriology, Public Health Agency of Canada, Winnipeg
| | - Paul Rivest
- Direction de Santé Publique, Centre Intégré Universitaire de Soins et de Services Sociaux du Centre-Sud-de-l’Île-de-Montréal, Canada
| | - Louise Poirier
- Department of Microbiology, Maisonneuve-Rosemont Hospital, Montreal, Canada
| | - Christian Lavallée
- Department of Microbiology and Adult Infectious Diseases, Maisonneuve-Rosemont Hospital, Montreal, Canada
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22
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Kone A, Diarra B, Cohen K, Diabate S, Kone B, Diakite MT, Diarra H, Sanogo M, Togo ACG, Sarro YDS, Baya B, Coulibaly N, Kodio O, Achenbach CJ, Murphy RL, Holl JL, Siddiqui S, Doumbia S, Bishai WR, Diallo S, Maiga M. Differential HLA allele frequency in Mycobacterium africanum vs Mycobacterium tuberculosis in Mali. HLA 2019; 93:24-31. [PMID: 30516034 DOI: 10.1111/tan.13448] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2018] [Revised: 10/22/2018] [Accepted: 11/28/2018] [Indexed: 11/28/2022]
Abstract
Tuberculosis (TB) is caused by Mycobacterium tuberculosis complex (MTBC), however, the distribution and frequency of MTBC lineages and sublineages vary in different parts of the globe. Mycobacterium africanum, a member of MTBC is responsible for a large percentage of TB cases in West Africa, however, it is rarely identified outside of this part of the World. Whether or not differential HLA polymorphism (an important host factor) is contributing to the geographic restriction of M. africanum to West Africa is unknown. Here, we conducted a cohort study in Mali of newly diagnosed individuals with active pulmonary TB and normal healthy controls. The MTBC isolates were spoligotyped to determine the TB study groups (M. tuberculosis sensu stricto LAM10 and M. africanum), and HLA typing was performed on peripheral blood. Unlike previous reports on other populations, we found that HLA class-I alleles were significantly associated with active TB disease in this population. HLA-B alleles (B*07:02, B*08:01, B*14:02, B*15:03, B*15:10, B*18:01, B*42:01, B*42:02, B*51:01 and B*81:01) were significantly associated with M. africanum (40%-45%) and M. tuberculosis (75%) compared with healthy controls. Many HLA-A alleles (A*02:05, A*34:02, A*66:01 and A*68:02) were also associated with both TB groups (65%-70%). However, many class II HLA-DR variants were found to be associated with M. tuberculosis but not M. africanum with the exception of the DRB1*03:01, which was associated with both groups. The differential HLA distribution observed in this study might be at least partially responsible for the geographical restriction of M. africanum infections to West Africa.
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Affiliation(s)
- Amadou Kone
- University of Sciences, Techniques and Technologies of Bamako (USTTB), Bamako, Mali
| | - Bassirou Diarra
- University of Sciences, Techniques and Technologies of Bamako (USTTB), Bamako, Mali
| | - Keira Cohen
- Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Seydou Diabate
- University of Sciences, Techniques and Technologies of Bamako (USTTB), Bamako, Mali
| | - Bourahima Kone
- University of Sciences, Techniques and Technologies of Bamako (USTTB), Bamako, Mali
| | - Mahamane T Diakite
- University of Sciences, Techniques and Technologies of Bamako (USTTB), Bamako, Mali
| | - Hawa Diarra
- University of Sciences, Techniques and Technologies of Bamako (USTTB), Bamako, Mali
| | - Moumine Sanogo
- University of Sciences, Techniques and Technologies of Bamako (USTTB), Bamako, Mali
| | - Antieme C G Togo
- University of Sciences, Techniques and Technologies of Bamako (USTTB), Bamako, Mali
| | - Yeya Dit Sadio Sarro
- University of Sciences, Techniques and Technologies of Bamako (USTTB), Bamako, Mali
| | - Bocar Baya
- University of Sciences, Techniques and Technologies of Bamako (USTTB), Bamako, Mali
| | - Nadie Coulibaly
- University of Sciences, Techniques and Technologies of Bamako (USTTB), Bamako, Mali
| | - Ousmane Kodio
- University of Sciences, Techniques and Technologies of Bamako (USTTB), Bamako, Mali
| | | | | | | | - Sophia Siddiqui
- National Institute of Allergic and Infectious Diseases, Rockville, Maryland
| | - Seydou Doumbia
- University of Sciences, Techniques and Technologies of Bamako (USTTB), Bamako, Mali
| | - William R Bishai
- Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Souleymane Diallo
- University of Sciences, Techniques and Technologies of Bamako (USTTB), Bamako, Mali
| | - Mamoudou Maiga
- University of Sciences, Techniques and Technologies of Bamako (USTTB), Bamako, Mali.,Northwestern University, Chicago, Illinois
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23
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Diarra B, Kone M, Togo ACG, Sarro YDS, Cisse AB, Somboro A, Degoga B, Tolofoudie M, Kone B, Sanogo M, Baya B, Kodio O, Maiga M, Belson M, Orsega S, Krit M, Dao S, Maiga II, Murphy RL, Rigouts L, Doumbia S, Diallo S, de Jong BC. Mycobacterium africanum (Lineage 6) shows slower sputum smear conversion on tuberculosis treatment than Mycobacterium tuberculosis (Lineage 4) in Bamako, Mali. PLoS One 2018; 13:e0208603. [PMID: 30540823 PMCID: PMC6291124 DOI: 10.1371/journal.pone.0208603] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Accepted: 11/20/2018] [Indexed: 11/19/2022] Open
Abstract
Objective Ancestral M. tuberculosis complex lineages such as M. africanum are underrepresented among retreatment patients and those with drug resistance. To test the hypothesis that they respond faster to TB treatment, we determined the rate of smear conversion of new pulmonary tuberculosis patients in Bamako, Mali by the main MTBc lineages. Methods Between 2015 and 2017, we conducted a prospective cohort study of new smear positive pulmonary tuberculosis patients in Bamako. Confirmed MTBc isolates underwent genotyping by spoligotyping for lineage classification. Patients were followed at 1 month (M), 2M and 5M to measure smear conversion in auramine (AR) and Fluorescein DiAcetate (FDA) vital stain microscopy. Result All the first six human MTBc lineages were represented in the population, plus M. bovis in 0.8% of the patients. The most widely represented lineage was the modern Euro-American lineage (L) 4, 57%, predominantly the T family, followed by L6 (M. africanum type 2) in 22.9%. Ancestral lineages 1, 5, 6 and M. bovis combined amounted to 28.8%. Excluding 25 patients with rifampicin resistance, smear conversion, both by AR and FDA, occurred later in L6 compared to L4 (HR 0.80 (95% CI 0.66–0.97) for AR, and HR 0.81 (95%CI 0.68–0.97) for FDA). In addition we found that HIV negative status, higher BMI at day 0, and patients with smear grade at baseline ≤ 1+ were associated with earlier smear conversion. Conclusion The six major human lineages of the MTBc all circulate in Bamako. Counter to our hypothesis, we found that patients diseased with modern M. tuberculosis complex L4 respond faster to TB treatment than those with M. africanum L6.
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Affiliation(s)
- Bassirou Diarra
- University Clinical Research Center (UCRC)-SEREFO-Laboratory, University of Sciences, Techniques and Technologies of Bamako (USTTB), Bamako, Mali
- Institute of Tropical Medicine, Department of Biomedical Sciences, Antwerp, Belgium
- Department of Biomedical Sciences, Antwerp University, Antwerp, Belgium
- * E-mail:
| | - Mahamadou Kone
- 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
| | - Yeya dit Sadio Sarro
- University Clinical Research Center (UCRC)-SEREFO-Laboratory, University of Sciences, Techniques and Technologies of Bamako (USTTB), Bamako, Mali
| | - Aissata Boubakar Cisse
- Laboratoire National de Référence des Mycobactéries (LNR), Institut National de Recherche en Santé publique (INRSP), Bamako, Mali
| | - Amadou Somboro
- University Clinical Research Center (UCRC)-SEREFO-Laboratory, University of Sciences, Techniques and Technologies of Bamako (USTTB), Bamako, Mali
| | - Boureima Degoga
- University Clinical Research Center (UCRC)-SEREFO-Laboratory, University of Sciences, Techniques and Technologies of Bamako (USTTB), Bamako, Mali
| | - Mohamed Tolofoudie
- 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
| | - Moumine Sanogo
- University Clinical Research Center (UCRC)-SEREFO-Laboratory, University of Sciences, Techniques and Technologies of Bamako (USTTB), Bamako, Mali
| | - Bocar Baya
- 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
| | - Mamoudou Maiga
- Global Health, Northwestern University, Chicago, IL, United States of America
| | - Michael Belson
- Collaborative Clinical Research Branch, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, Bethesda, Maryland, United States of America
| | - Susan Orsega
- Collaborative Clinical Research Branch, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, Bethesda, Maryland, United States of America
| | - Meryam Krit
- Institute of Tropical Medicine, Department of Biomedical Sciences, Antwerp, Belgium
| | - Sounkalo Dao
- University Clinical Research Center (UCRC)-SEREFO-Laboratory, University of Sciences, Techniques and Technologies of Bamako (USTTB), Bamako, Mali
| | - Ibrahim Izétiegouma Maiga
- Laboratoire d’analyses Médicales et Hygiène Hospitalière du Centre Hospitalier Universitaire du Point-G, Bamako, Mali
| | - Robert L. Murphy
- Global Health, Northwestern University, Chicago, IL, United States of America
| | - Leen Rigouts
- Institute of Tropical Medicine, Department of Biomedical Sciences, Antwerp, Belgium
- Department of Biomedical Sciences, Antwerp University, Antwerp, Belgium
| | - 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
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24
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Otchere ID, Coscollá M, Sánchez-Busó L, Asante-Poku A, Brites D, Loiseau C, Meehan C, Osei-Wusu S, Forson A, Laryea C, Yahayah AI, Baddoo A, Ansa GA, Aboagye SY, Asare P, Borrell S, Gehre F, Beckert P, Kohl TA, N'dira S, Beisel C, Antonio M, Niemann S, de Jong BC, Parkhill J, Harris SR, Gagneux S, Yeboah-Manu D. Comparative genomics of Mycobacterium africanum Lineage 5 and Lineage 6 from Ghana suggests distinct ecological niches. Sci Rep 2018; 8:11269. [PMID: 30050166 PMCID: PMC6062541 DOI: 10.1038/s41598-018-29620-2] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2017] [Accepted: 07/16/2018] [Indexed: 11/09/2022] Open
Abstract
Mycobacterium africanum (Maf) causes a substantial proportion of human tuberculosis in some countries of West Africa, but little is known on this pathogen. We compared the genomes of 253 Maf clinical isolates from Ghana, including N = 175 Lineage 5 (L5) and N = 78 Lineage 6 (L6). We found that the genomic diversity of L6 was higher than in L5 despite the smaller sample size. Regulatory proteins appeared to evolve neutrally in L5 but under purifying selection in L6. Even though over 90% of the human T cell epitopes were conserved in both lineages, L6 showed a higher ratio of non-synonymous to synonymous single nucleotide variation in these epitopes overall compared to L5. Of the 10% human T cell epitopes that were variable, most carried mutations that were lineage-specific. Our findings indicate that Maf L5 and L6 differ in some of their population genomic characteristics, possibly reflecting different selection pressures linked to distinct ecological niches.
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Affiliation(s)
- Isaac Darko Otchere
- Noguchi Memorial Institute for Medical Research, University of Ghana, Legon, Accra, Ghana
- Department of Biochemistry, Cell and Molecular Biology, University of Ghana, Legon, Accra, Ghana
| | - Mireia Coscollá
- Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Leonor Sánchez-Busó
- Wellcome Trust Sanger Institute, University of Cambridge, Hinxton, United Kingdom
| | - Adwoa Asante-Poku
- 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
| | - Chloe Loiseau
- Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Conor Meehan
- Institute of Tropical Medicine, Antwerp, Belgium
| | - Stephen Osei-Wusu
- Noguchi Memorial Institute for Medical Research, University of Ghana, Legon, Accra, Ghana
| | - Audrey Forson
- Chest Clinic, Korle-Bu Teaching Hospital, Accra, Ghana
| | | | | | - Akosua Baddoo
- Chest Clinic, Korle-Bu Teaching Hospital, Accra, Ghana
| | - Gloria Akosua Ansa
- Public Health Department, University of Ghana Hospital, Legon, Accra, Ghana
| | - Samuel Yaw Aboagye
- 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
| | - Sonia Borrell
- Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Florian Gehre
- Institute of Tropical Medicine, Antwerp, Belgium
- Medical Research Council Unit The Gambia at The London School of Hygiene and Tropical Medicine, Banjul, The Gambia
| | - Patrick Beckert
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Germany
- German Center for Infection Research, Partner Site Hamburg-Borstel-Lübeck, Lübeck, Germany
| | - Thomas A Kohl
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Germany
- German Center for Infection Research, Partner Site Hamburg-Borstel-Lübeck, Lübeck, Germany
| | - Sanoussi N'dira
- National Reference Laboratory for Mycobacteria, Cotonou, Benin
| | - Christian Beisel
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | - Martin Antonio
- Medical Research Council Unit The Gambia at The London School of Hygiene and Tropical Medicine, Banjul, The Gambia
- Division of Microbiology & Immunity, Warwick Medical School, University of Warwick, Coventry, CV4 7AL, UK
| | - Stefan Niemann
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Germany
- German Center for Infection Research, Partner Site Hamburg-Borstel-Lübeck, Lübeck, Germany
| | - Bouke C de Jong
- Institute of Tropical Medicine, Antwerp, Belgium
- Medical Research Council Unit The Gambia at The London School of Hygiene and Tropical Medicine, Banjul, The Gambia
| | - Julian Parkhill
- Wellcome Trust Sanger Institute, University of Cambridge, Hinxton, United Kingdom
| | - Simon R Harris
- Wellcome Trust Sanger Institute, University of Cambridge, Hinxton, United Kingdom
| | - Sebastien Gagneux
- Swiss Tropical and Public Health Institute, Basel, Switzerland.
- University of Basel, Basel, Switzerland.
| | - Dorothy Yeboah-Manu
- Noguchi Memorial Institute for Medical Research, University of Ghana, Legon, Accra, Ghana.
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25
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Brites D, Gagneux S. The Nature and Evolution of Genomic Diversity in the Mycobacterium tuberculosis Complex. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017; 1019:1-26. [DOI: 10.1007/978-3-319-64371-7_1] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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26
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Sanoussi CN, Affolabi D, Rigouts L, Anagonou S, de Jong B. Genotypic characterization directly applied to sputum improves the detection of Mycobacterium africanum West African 1, under-represented in positive cultures. PLoS Negl Trop Dis 2017; 11:e0005900. [PMID: 28863143 PMCID: PMC5599059 DOI: 10.1371/journal.pntd.0005900] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2017] [Revised: 09/14/2017] [Accepted: 08/23/2017] [Indexed: 01/06/2023] Open
Abstract
BACKGROUND This study aimed to compare the prevalence of Mycobacterium tuberculosis complex (MTBc) lineages between direct genotyping (on sputum) and indirect genotyping (on culture), to characterize potential culture bias against difficult growers. METHODOLOGY/PRINCIPAL FINDINGS Smear-positive sputa from consecutive new tuberculosis patients diagnosed in Cotonou, (Benin) were included, before patients had started treatment. An aliquot of decontaminated sputum was used for direct spoligotyping, and another aliquot was cultured on Löwenstein Jensen (LJ) medium (90 days), for indirect spoligotyping. After DNA extraction, spoligotyping was done according to the standard method for all specimens, and patterns obtained from sputa were compared versus those from the derived culture isolates. From 199 patient's sputa, 146 (73.4%) yielded a positive culture. In total, direct spoligotyping yielded a pattern in 98.5% (196/199) of the specimens, versus 73.4% (146/199) for indirect spoligotyping on cultures. There was good agreement between sputum- and isolate derived patterns: 94.4% (135/143) at spoligotype level and 96.5% (138/143) at (sub)lineage level. Two of the 8 pairs with discrepant pattern were suggestive of mixed infection in sputum. Ancestral lineages (Lineage 1, and M. africanum Lineages 5 and 6) were less likely to grow in culture (OR = 0.30, 95%CI (0.14 to 0.64), p = 0.0016); especially Lineage 5 (OR = 0.37 95%CI (0.17 to 0.79), p = 0.010). Among modern lineages, Lineage 4 was over-represented in positive-culture specimens (OR = 3.01, 95%CI (1.4 to 6.51), p = 0.005). CONCLUSIONS/ SIGNIFICANCE Ancestral lineages, especially M. africanum West African 1 (Lineage 5), are less likely to grow in culture relative to modern lineages, especially M. tuberculosis Euro-American (Lineage 4). Direct spoligotyping on smear positive sputum is effective and efficient compared to indirect spoligotyping of cultures. It allows for a more accurate unbiased determination of the population structure of the M. tuberculosis complex. TRIAL REGISTRATION ClinicalTrials.gov NCT02744469.
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Affiliation(s)
- C. N’Dira Sanoussi
- Mycobacteriology Unit, Institute of Tropical Medicine, Antwerp, Belgium
- Laboratoire de Référence des Mycobactéries, Centre National Hospitalier Universitaire de Pneumo-Phtisiologie de Cotonou, National Tuberculosis Programme, Cotonou, Benin
- Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
| | - Dissou Affolabi
- Laboratoire de Référence des Mycobactéries, Centre National Hospitalier Universitaire de Pneumo-Phtisiologie de Cotonou, National Tuberculosis Programme, Cotonou, Benin
| | - Leen Rigouts
- Mycobacteriology Unit, Institute of Tropical Medicine, Antwerp, Belgium
- Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
| | - Séverin Anagonou
- Laboratoire de Référence des Mycobactéries, Centre National Hospitalier Universitaire de Pneumo-Phtisiologie de Cotonou, National Tuberculosis Programme, Cotonou, Benin
| | - Bouke de Jong
- Mycobacteriology Unit, Institute of Tropical Medicine, Antwerp, Belgium
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Adetifa IMO, Kendall L, Donkor S, Lugos MD, Hammond AS, Owiafe PK, Ota MOC, Brookes RH, Hill PC. Mycobacterium tuberculosis Infection in Close Childhood Contacts of Adults with Pulmonary Tuberculosis is Increased by Secondhand Exposure to Tobacco. Am J Trop Med Hyg 2017; 97:429-432. [PMID: 28722570 PMCID: PMC5544071 DOI: 10.4269/ajtmh.16-0611] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2016] [Accepted: 04/06/2017] [Indexed: 11/07/2022] Open
Abstract
Tobacco use is a major risk factor for tuberculosis (TB). Secondhand smoke (SHS) is also a risk factor for TB and to a lesser extent, Mycobacterium tuberculosis infection without disease. We investigated the added risk of M. tuberculosis infection due to SHS exposure in childhood contacts of TB cases in The Gambia. Participants were childhood household contacts aged ≤ 14 years of newly diagnosed pulmonary TB (PTB) cases. The intensity of exposure to the case was categorized according to whether contacts slept in the same room, same house, or a different house as the case. Contacts were tested with an enzyme-linked immunospot interferon gamma release assay. In multivariate regression models, M. tuberculosis infection was associated with increasing exposure to a case (odds ratios [OR]: 3.9, 95% confidence interval [CI]: 2.11-71.4, P < 0.001]) and with male gender (OR: 1.5 [95% CI: 1.12-2.11], P = 0.008). Tobacco use caused a 3-fold increase in the odds of M. tuberculosis infection in children who slept closest to a case who smoked within the same home compared with a nonsmoking case (OR: 8.0 [95% CI: 2.74-23.29] versus 2.4 [95% CI: 1.17-4.92], P < 0.001). SHS exposure as an effect modifier appears to greatly increase the risk of M. tuberculosis infection in children exposed to PTB cases. Smoking cessation campaigns may be important for reducing transmission of M. tuberculosis to children within households.
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Affiliation(s)
- Ifedayo M. O. Adetifa
- Department of Infectious Diseases Epidemiology, London School of Hygiene and Tropical Medicine, London, United Kingdom
- College of Medicine, University of Lagos, Lagos, Nigeria
- Disease Control and Elimination Theme, Medical Research Council Unit The Gambia, Fajara, The Gambia
| | - Lindsay Kendall
- Disease Control and Elimination Theme, Medical Research Council Unit The Gambia, Fajara, The Gambia
| | - Simon Donkor
- Disease Control and Elimination Theme, Medical Research Council Unit The Gambia, Fajara, The Gambia
| | - Moses D. Lugos
- Disease Control and Elimination Theme, Medical Research Council Unit The Gambia, Fajara, The Gambia
- Department of Medical Laboratory Science, University of Jos, Plateau, Nigeria
| | - Abdulrahman S. Hammond
- Disease Control and Elimination Theme, Medical Research Council Unit The Gambia, Fajara, The Gambia
| | - Patrick K. Owiafe
- Disease Control and Elimination Theme, Medical Research Council Unit The Gambia, Fajara, The Gambia
| | - Martin O. C. Ota
- World Health Organization-Regional Office for Africa, Brazzaville, Congo
| | - Roger H. Brookes
- Bioprocess Research and Development, Sanofi Pasteur, Toronto, Ontario, Canada
| | - Philip C. Hill
- Department of Preventive and Social Medicine, Centre for International Health and the Otago International Health Research Network, University of Otago School of Medicine, Dunedin, New Zealand
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28
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Ofori-Anyinam B, Dolganov G, Van T, Davis JL, Walter ND, Garcia BJ, Voskuil M, Fissette K, Diels M, Driesen M, Meehan CJ, Yeboah-Manu D, Coscolla M, Gagneux S, Antonio M, Schoolnik G, Gehre F, de Jong BC. Significant under expression of the DosR regulon in M. tuberculosis complex lineage 6 in sputum. Tuberculosis (Edinb) 2017; 104:58-64. [PMID: 28454650 PMCID: PMC5421582 DOI: 10.1016/j.tube.2017.03.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2016] [Revised: 02/21/2017] [Accepted: 03/02/2017] [Indexed: 11/19/2022]
Abstract
Mycobacterium africanum lineage (L) 6 is an important pathogen in West Africa, causing up to 40% of pulmonary tuberculosis (TB). The biology underlying the clinical differences between M. africanum and M. tuberculosis sensu stricto remains poorly understood. We performed ex vivo expression of 2179 genes of the most geographically dispersed cause of human TB, M. tuberculosis L4 and the geographically restricted, M. africanum L6 directly from sputa of 11 HIV-negative TB patients from The Gambia who had not started treatment. The DosR regulon was the most significantly decreased category in L6 relative to L4. Further, we identified nonsynonymous mutations in major DosR regulon genes of 44 L6 genomes of TB patients from The Gambia and Ghana. Using Lebek's test, we assessed differences in oxygen requirements for growth. L4 grew only at the aerobic surface while L6 grew throughout the medium. In the host, the DosR regulon is critical for M. tuberculosis in adaptation to oxygen limitation. However, M. africanum L6 appears to have adapted to growth under hypoxic conditions or to different biological niches. The observed under expression of DosR in L6 fits with the genomic changes in DosR genes, microaerobic growth and the association with extrapulmonary disease.
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Affiliation(s)
- Boatema Ofori-Anyinam
- Mycobacteriology Unit, Institute of Tropical Medicine (ITM), Nationalestraat 155, 2000, Antwerp, Belgium; Vaccines and Immunity Theme, Medical Research Council (MRC) Unit, The Gambia, Atlantic Boulevard, Fajara, P.O. Box 273, Banjul, Gambia
| | - Gregory Dolganov
- Department of Microbiology and Immunology, Stanford University, 299 Campus Drive, Stanford, CA, 94305, USA
| | - Tran Van
- Department of Microbiology and Immunology, Stanford University, 299 Campus Drive, Stanford, CA, 94305, USA
| | - J Lucian Davis
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, 60 College Street, P.O. Box 208034, New Haven, CT, 06520-8034, USA; Department of Pulmonary, Critical Care, and Sleep Medicine, Yale School of Medicine, P.O. Box 208057, 300 Cedar Street TAC - 441 South, New Haven, CT, 06520-8057, USA
| | - Nicholas D Walter
- Division of Pulmonary Sciences and Critical Care Medicine, University of Colorado Denver, Building 500 - 13001 E, 17th Place, Campus Box C290, Aurora, CO, 80045, USA; Pulmonary Section, Denver Veterans Affairs Medical Center, 1055 Clermont Street, Denver, CO, 80220, USA; Integrated Center for Genes, Environment, & Health, National Jewish Health, Smith Building; A647, 1400 Jackson Street, Denver, CO, 80206, USA
| | - Benjamin J Garcia
- Integrated Center for Genes, Environment, & Health, National Jewish Health, Smith Building; A647, 1400 Jackson Street, Denver, CO, 80206, USA; Computational Bioscience Program, University of Colorado Denver, Building 500 - 13001 E, 17th Place, Campus Box C290, Aurora, CO, 80045, USA
| | - Marty Voskuil
- Department of Immunology and Microbiology, University of Colorado School of Medicine, 12800 E. 19th Ave., Mail Stop 8333, Aurora, CO, 80045, USA
| | - Kristina Fissette
- Mycobacteriology Unit, Institute of Tropical Medicine (ITM), Nationalestraat 155, 2000, Antwerp, Belgium
| | - Maren Diels
- Mycobacteriology Unit, Institute of Tropical Medicine (ITM), Nationalestraat 155, 2000, Antwerp, Belgium
| | - Michèle Driesen
- Mycobacteriology Unit, Institute of Tropical Medicine (ITM), Nationalestraat 155, 2000, Antwerp, Belgium
| | - Conor J Meehan
- Mycobacteriology Unit, Institute of Tropical Medicine (ITM), Nationalestraat 155, 2000, Antwerp, Belgium
| | - Dorothy Yeboah-Manu
- Noguchi Memorial Institute for Medical Research, University of Ghana, P.O. Box LG 581, Legon, Accra, Ghana
| | - Mireia Coscolla
- Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, P.O. Box 4002, Basel, Switzerland; University of Basel, Petersplatz 1, P.O. Box 4001, Basel, Switzerland
| | - Sebastien Gagneux
- Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, P.O. Box 4002, Basel, Switzerland; University of Basel, Petersplatz 1, P.O. Box 4001, Basel, Switzerland
| | - Martin Antonio
- Vaccines and Immunity Theme, Medical Research Council (MRC) Unit, The Gambia, Atlantic Boulevard, Fajara, P.O. Box 273, Banjul, Gambia
| | - Gary Schoolnik
- Department of Microbiology and Immunology, Stanford University, 299 Campus Drive, Stanford, CA, 94305, USA
| | - Florian Gehre
- Mycobacteriology Unit, Institute of Tropical Medicine (ITM), Nationalestraat 155, 2000, Antwerp, Belgium; Vaccines and Immunity Theme, Medical Research Council (MRC) Unit, The Gambia, Atlantic Boulevard, Fajara, P.O. Box 273, Banjul, Gambia
| | - Bouke C de Jong
- Mycobacteriology Unit, Institute of Tropical Medicine (ITM), Nationalestraat 155, 2000, Antwerp, Belgium.
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Tientcheu LD, Koch A, Ndengane M, Andoseh G, Kampmann B, Wilkinson RJ. Immunological consequences of strain variation within the Mycobacterium tuberculosis complex. Eur J Immunol 2017; 47:432-445. [PMID: 28150302 PMCID: PMC5363233 DOI: 10.1002/eji.201646562] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2016] [Revised: 01/26/2017] [Accepted: 01/31/2017] [Indexed: 11/11/2022]
Abstract
In 2015, there were an estimated 10.4 million new cases of tuberculosis (TB) globally, making it one of the leading causes of death due to an infectious disease. TB is caused by members of the Mycobacterium tuberculosis complex (MTBC), with human disease resulting from infection by M. tuberculosis sensu stricto and M. africanum. Recent progress in genotyping techniques, in particular the increasing availability of whole genome sequence data, has revealed previously under appreciated levels of genetic diversity within the MTBC. Several studies have shown that this genetic diversity may translate into differences in TB transmission, clinical manifestations of disease, and host immune responses. This suggests the existence of MTBC genotype‐dependent host–pathogen interactions which may influence the outcome of infection and progression of disease. In this review, we highlight the studies demonstrating differences in innate and adaptive immunological outcomes consequent on MTBC genetic diversity, and discuss how these differences in immune response might influence the development of TB vaccines, diagnostics and new therapies.
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Affiliation(s)
- Leopold D Tientcheu
- Vaccines and Immunity Theme, Medical Research Council Unit, The Gambia, Banjul, The Gambia.,Department of Biochemistry, Faculty of Science, University of Yaoundé 1, Yaoundé, Cameroon
| | - Anastasia Koch
- Wellcome Centre for Infectious Diseases Research in Africa, Institute of Infectious Disease and Molecular Medicine and Department of Medicine, University of Cape Town, Observatory, Republic of South Africa
| | - Mthawelenga Ndengane
- Wellcome Centre for Infectious Diseases Research in Africa, Institute of Infectious Disease and Molecular Medicine and Department of Medicine, University of Cape Town, Observatory, Republic of South Africa
| | - Genevieve Andoseh
- Department of Biochemistry, Faculty of Science, University of Yaoundé 1, Yaoundé, Cameroon
| | - Beate Kampmann
- Vaccines and Immunity Theme, Medical Research Council Unit, The Gambia, Banjul, The Gambia.,Department of Medicine, Imperial College, London, United Kingdom
| | - Robert J Wilkinson
- Wellcome Centre for Infectious Diseases Research in Africa, Institute of Infectious Disease and Molecular Medicine and Department of Medicine, University of Cape Town, Observatory, Republic of South Africa.,Department of Medicine, Imperial College, London, United Kingdom.,The Francis Crick Institute, London, United Kingdom
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30
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Thirunavukkarasu S, Plain KM, de Silva K, Marais BJ, Whittington RJ. Applying the One Health Concept to Mycobacterial Research - Overcoming Parochialism. Zoonoses Public Health 2017; 64:401-422. [PMID: 28084673 DOI: 10.1111/zph.12334] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2016] [Indexed: 12/27/2022]
Abstract
Mycobacterial infections remain a public health problem. Historically important, globally ubiquitous and with a wide host range, we are still struggling to control mycobacterial infections in humans and animals. While previous reviews have focused on individual mycobacterial infections in either humans or animals, a comprehensive review of the zoonotic aspect of mycobacteria in the context of the One Health initiative is lacking. With the purpose of providing a concise and comprehensive resource, we have collated literature to address the zoonotic potential of different mycobacterial species and elaborate on the necessity for an inter-sectorial approach to attain a new vision to combat mycobacterial infections.
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Affiliation(s)
- S Thirunavukkarasu
- Faculty of Veterinary Science, School of Life and Environmental Sciences, University of Sydney, Sydney, NSW, Australia.,Boise Veterans Affairs Medical Center, Boise, ID, USA
| | - K M Plain
- Faculty of Veterinary Science, School of Life and Environmental Sciences, University of Sydney, Sydney, NSW, Australia
| | - K de Silva
- Faculty of Veterinary Science, School of Life and Environmental Sciences, University of Sydney, Sydney, NSW, Australia
| | - B J Marais
- Marie Bashir Institute for Infectious Diseases and Biosecurity and the Centre for Research Excellence in Emerging Infections, University of Sydney, Sydney, NSW, Australia
| | - R J Whittington
- Faculty of Veterinary Science, School of Life and Environmental Sciences, University of Sydney, Sydney, NSW, Australia
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31
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Copin R, Wang X, Louie E, Escuyer V, Coscolla M, Gagneux S, Palmer GH, Ernst JD. Within Host Evolution Selects for a Dominant Genotype of Mycobacterium tuberculosis while T Cells Increase Pathogen Genetic Diversity. PLoS Pathog 2016; 12:e1006111. [PMID: 27973588 PMCID: PMC5189959 DOI: 10.1371/journal.ppat.1006111] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2016] [Revised: 12/27/2016] [Accepted: 12/05/2016] [Indexed: 12/14/2022] Open
Abstract
Molecular epidemiological assessments, drug treatment optimization, and development of immunological interventions all depend on understanding pathogen adaptation and genetic variation, which differ for specific pathogens. Mycobacterium tuberculosis is an exceptionally successful human pathogen, yet beyond knowledge that this bacterium has low overall genomic variation but acquires drug resistance mutations, little is known of the factors that drive its population genomic characteristics. Here, we compared the genetic diversity of the bacteria that established infection to the bacterial populations obtained from infected tissues during murine M. tuberculosis pulmonary infection and human disseminated M. bovis BCG infection. We found that new mutations accumulate during in vitro culture, but that in vivo, purifying selection against new mutations dominates, indicating that M. tuberculosis follows a dominant lineage model of evolution. Comparing bacterial populations passaged in T cell-deficient and immunocompetent mice, we found that the presence of T cells is associated with an increase in the diversity of the M. tuberculosis genome. Together, our findings put M. tuberculosis genetic evolution in a new perspective and clarify the impact of T cells on sequence diversity of M. tuberculosis.
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Affiliation(s)
- Richard Copin
- Division of Infectious Diseases, Department of Medicine, New York University School of Medicine, New York, NY, United States of America
| | - Xueying Wang
- Department of Mathematics and Statistics, Washington State University, Pullman, WA, United States of America
| | - Eddie Louie
- Division of Infectious Diseases, Department of Medicine, New York University School of Medicine, New York, NY, United States of America
| | - Vincent Escuyer
- Microbiology laboratory, Wadsworth Center, New York State Department of Health, Albany, NY, United States of America
| | - Mireia Coscolla
- Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Sebastien Gagneux
- Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Guy H. Palmer
- Paul G. Allen School for Global Animal Health, Washington State University, Pullman, WA, United States of America
| | - Joel D. Ernst
- Division of Infectious Diseases, Department of Medicine, New York University School of Medicine, New York, NY, United States of America
- Department of Microbiology, New York University School of Medicine, New York, NY, United States of America
- Department of Pathology, New York University School of Medicine, New York, NY, United States of America
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32
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Sharma A, Bloss E, Heilig CM, Click ES. Tuberculosis Caused by Mycobacterium africanum, United States, 2004-2013. Emerg Infect Dis 2016; 22:396-403. [PMID: 26886258 PMCID: PMC4766873 DOI: 10.3201/eid2203.151505] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Mycobacterium africanum is endemic to West Africa and causes tuberculosis (TB). We reviewed reported cases of TB in the United States during 2004-2013 that had lineage assigned by genotype (spoligotype and mycobacterial interspersed repetitive unit variable number tandem repeats). M. africanum caused 315 (0.4%) of 73,290 TB cases with lineage assigned by genotype. TB caused by M. africanum was associated more with persons from West Africa (adjusted odds ratio [aOR] 253.8, 95% CI 59.9-1,076.1) and US-born black persons (aOR 5.7, 95% CI 1.2-25.9) than with US-born white persons. TB caused by M. africanum did not show differences in clinical characteristics when compared with TB caused by M. tuberculosis. Clustered cases defined as >2 cases in a county with identical 24-locus mycobacterial interspersed repetitive unit genotypes, were less likely for M. africanum (aOR 0.1, 95% CI 0.1-0.4), which suggests that M. africanum is not commonly transmitted in the United States.
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Yeboah-Manu D, Asare P, Asante-Poku A, Otchere ID, Osei-Wusu S, Danso E, Forson A, Koram KA, Gagneux S. Spatio-Temporal Distribution of Mycobacterium tuberculosis Complex Strains in Ghana. PLoS One 2016; 11:e0161892. [PMID: 27564240 PMCID: PMC5001706 DOI: 10.1371/journal.pone.0161892] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2016] [Accepted: 08/12/2016] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND There is a perception that genomic differences in the species/lineages of the nine species making the Mycobacterium tuberculosis complex (MTBC) may affect the efficacy of distinct control tools in certain geographical areas. We therefore analyzed the prevalence and spatial distribution of MTBC species and lineages among isolates from pulmonary TB cases over an 8-year period, 2007-2014. METHODOLOGY Mycobacterial species isolated by culture from consecutively recruited pulmonary tuberculosis patients presenting at selected district/sub-district health facilities were confirmed as MTBC by IS6110 and rpoß PCR and further assigned lineages and sub lineages by spoligotyping and large sequence polymorphism PCR (RDs 4, 9, 12, 702, 711) assays. Patient characteristics, residency, and risks were obtained with a structured questionnaire. We used SaTScan and ArcMap analyses to identify significantly clustered MTBC lineages within selected districts and spatial display, respectively. RESULTS Among 2,551 isolates, 2,019 (79.1%), 516 (20.2%) and 16 (0.6%) were identified as M. tuberculosis sensu stricto (MTBss), M. africanum (Maf), 15 M. bovis and 1 M. caprae, respectively. The proportions of MTBss and Maf were fairly constant within the study period. Maf spoligotypes were dominated by Spoligotype International Type (SIT) 331 (25.42%), SIT 326 (15.25%) and SIT 181 (14.12%). We found M. bovis to be significantly higher in Northern Ghana (1.9% of 212) than Southern Ghana (0.5% of 2339) (p = 0.020). Using the purely spatial and space-time analysis, seven significant MTBC lineage clusters (p< 0.05) were identified. Notable among the clusters were Ghana and Cameroon sub-lineages found to be associated with north and south, respectively. CONCLUSION This study demonstrated that overall, 79.1% of TB in Ghana is caused by MTBss and 20% by M. africanum. Unlike some West African Countries, we did not observe a decline of Maf prevalence in Ghana.
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Affiliation(s)
- Dorothy Yeboah-Manu
- Noguchi Memorial Institute for Medical Research, University of Ghana, Legon, Accra, Ghana
- * E-mail:
| | - P. Asare
- Noguchi Memorial Institute for Medical Research, University of Ghana, Legon, Accra, Ghana
| | - A. Asante-Poku
- Noguchi Memorial Institute for Medical Research, University of Ghana, Legon, Accra, Ghana
| | - I. D. Otchere
- Noguchi Memorial Institute for Medical Research, University of Ghana, Legon, Accra, Ghana
| | - S. Osei-Wusu
- Noguchi Memorial Institute for Medical Research, University of Ghana, Legon, Accra, Ghana
| | - E. Danso
- Noguchi Memorial Institute for Medical Research, University of Ghana, Legon, Accra, Ghana
| | - A. Forson
- Department of Chest Diseases, Korle-Bu Teaching Hospital, Korle-bu, Accra, Ghana
| | - K. A. Koram
- Noguchi Memorial Institute for Medical Research, University of Ghana, Legon, Accra, Ghana
| | - Sebastien Gagneux
- Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
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Bhavanam S, Rayat GR, Keelan M, Kunimoto D, Drews SJ. Understanding the pathophysiology of the human TB lung granuloma using in vitro granuloma models. Future Microbiol 2016; 11:1073-89. [PMID: 27501829 DOI: 10.2217/fmb-2016-0005] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Tuberculosis remains a major human health threat that infects one in three individuals worldwide. Infection with Mycobacterium tuberculosis is a standoff between host and bacteria in the formation of a granuloma. This review will introduce a variety of bacterial and host factors that impact individual granuloma fates. The authors describe advances in the development of in vitro granuloma models, current evidence surrounding infection and granuloma development, and the applicability of existing in vitro models in the study of human disease. In vitro models of infection help improve our understanding of pathophysiology and allow for the discovery of other potential models of study.
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Affiliation(s)
- Sudha Bhavanam
- Department of Laboratory Medicine & Pathology, University of Alberta, Edmonton, Alberta, Canada.,Department of Surgery, Surgical-Medical Research Institute, Alberta Diabetes Institute, University of Alberta, Edmonton, Alberta, Canada.,Department of Laboratory Medicine & Pathology, University of Alberta, Edmonton, Alberta, Canada.,Department of Medicine, University of Alberta, Edmonton, Alberta, Canada.,Provincial Laboratory for Public Health, Department of Laboratory Medicine & Pathology, University of Alberta, Edmonton, Alberta, Canada
| | - Gina R Rayat
- Department of Laboratory Medicine & Pathology, University of Alberta, Edmonton, Alberta, Canada.,Department of Surgery, Surgical-Medical Research Institute, Alberta Diabetes Institute, University of Alberta, Edmonton, Alberta, Canada.,Department of Laboratory Medicine & Pathology, University of Alberta, Edmonton, Alberta, Canada.,Department of Medicine, University of Alberta, Edmonton, Alberta, Canada.,Provincial Laboratory for Public Health, Department of Laboratory Medicine & Pathology, University of Alberta, Edmonton, Alberta, Canada
| | - Monika Keelan
- Department of Laboratory Medicine & Pathology, University of Alberta, Edmonton, Alberta, Canada.,Department of Surgery, Surgical-Medical Research Institute, Alberta Diabetes Institute, University of Alberta, Edmonton, Alberta, Canada.,Department of Laboratory Medicine & Pathology, University of Alberta, Edmonton, Alberta, Canada.,Department of Medicine, University of Alberta, Edmonton, Alberta, Canada.,Provincial Laboratory for Public Health, Department of Laboratory Medicine & Pathology, University of Alberta, Edmonton, Alberta, Canada
| | - Dennis Kunimoto
- Department of Laboratory Medicine & Pathology, University of Alberta, Edmonton, Alberta, Canada.,Department of Surgery, Surgical-Medical Research Institute, Alberta Diabetes Institute, University of Alberta, Edmonton, Alberta, Canada.,Department of Laboratory Medicine & Pathology, University of Alberta, Edmonton, Alberta, Canada.,Department of Medicine, University of Alberta, Edmonton, Alberta, Canada.,Provincial Laboratory for Public Health, Department of Laboratory Medicine & Pathology, University of Alberta, Edmonton, Alberta, Canada
| | - Steven J Drews
- Department of Laboratory Medicine & Pathology, University of Alberta, Edmonton, Alberta, Canada.,Department of Surgery, Surgical-Medical Research Institute, Alberta Diabetes Institute, University of Alberta, Edmonton, Alberta, Canada.,Department of Laboratory Medicine & Pathology, University of Alberta, Edmonton, Alberta, Canada.,Department of Medicine, University of Alberta, Edmonton, Alberta, Canada.,Provincial Laboratory for Public Health, Department of Laboratory Medicine & Pathology, University of Alberta, Edmonton, Alberta, Canada
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Ofori-Anyinam B, Kanuteh F, Agbla SC, Adetifa I, Okoi C, Dolganov G, Schoolnik G, Secka O, Antonio M, de Jong BC, Gehre F. Impact of the Mycobaterium africanum West Africa 2 Lineage on TB Diagnostics in West Africa: Decreased Sensitivity of Rapid Identification Tests in The Gambia. PLoS Negl Trop Dis 2016; 10:e0004801. [PMID: 27387550 PMCID: PMC4936735 DOI: 10.1371/journal.pntd.0004801] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2016] [Accepted: 06/02/2016] [Indexed: 01/19/2023] Open
Abstract
Background MPT64 rapid speciation tests are increasingly being used in diagnosis of tuberculosis (TB). Mycobacterium africanum West Africa 2 (Maf 2) remains an important cause of TB in West Africa and causes one third of disease in The Gambia. Since the introduction of MPT64 antigen tests, a higher than expected rate of suspected non-tuberculous mycobacteria (NTM) was seen among AFB smear positive TB suspects, which led us to prospectively assess sensitivity of the MPT64 antigen test in our setting. Methodology/Principal Findings We compared the abundance of mRNA encoded by the mpt64 gene in sputa of patients with untreated pulmonary TB caused by Maf 2 and Mycobacterium tuberculosis (Mtb). Subsequently, prospectively collected sputum samples from presumptive TB patients were inoculated in the BACTEC MGIT 960 System. One hundred and seventy-three acid fast bacilli (AFB)-positive and blood agar negative MGIT cultures were included in the study. Cultures were tested on the day of MGIT positivity with the BD MGIT TBc Identification Test. A random set of positives and all negatives were additionally tested with the SD Bioline Ag MPT64 Rapid. MPT64 negative cultures were further incubated at 37°C and retested until positive. Bacteria were spoligotyped and assigned to different lineages. Maf 2 isolates were 2.52-fold less likely to produce a positive test result and sensitivity ranged from 78.4% to 84.3% at the beginning and end of the recommended 10 day testing window, respectively. There was no significant difference between the tests. We further showed that the decreased rapid test sensitivity was attributable to variations in mycobacterial growth behavior and the smear grades of the patient. Conclusions/Significance In areas where Maf 2 is endemic MPT64 tests should be cautiously used and MPT64 negative results confirmed by a second technique, such as nucleic acid amplification tests, to avoid their misclassification as NTMs. Diagnostics for rapid confirmation of positive liquid cultures presumptive of Mycobacterium tuberculosis bacteria, based on the detection of the MPT64 antigen, are being used in many TB diagnostic laboratories worldwide. Of note, diagnostic performance of these tests in West Africa, where TB is uniquely caused by the geographically restricted Mycobacterium africanum (Maf 1 and 2) and Mycobacterium tuberculosis lineages, has not been properly assessed. Although M. tuberculosis and M. africanum are genetically related, they differ in various aspects. Amongst several differences, Maf 2 grows significantly slower than Mtb bacteria. Because secretion of the MTP64 protein is dependent on the bacterial growth rate, we found that the MPT64 rapid test performance for detecting Maf 2 was lower in our setting in The Gambia. These findings might be relevant for other West African Maf 2 endemic countries where this rapid test is commonly used, as Maf 2 infected patients might have been missed in the past. Our finding emphasizes the need to thoroughly consider the presence of bacterial variants specific to certain regions during product development and implementation of novel diagnostic tests.
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Affiliation(s)
- Boatema Ofori-Anyinam
- Mycobacteriology Unit, Institute of Tropical Medicine (ITM), Antwerp, Belgium
- Vaccines and Immunity Theme, Medical Research Council (MRC) Unit, Serrekunda, The Gambia
| | - Fatoumatta Kanuteh
- Vaccines and Immunity Theme, Medical Research Council (MRC) Unit, Serrekunda, The Gambia
| | - Schadrac C. Agbla
- Vaccines and Immunity Theme, Medical Research Council (MRC) Unit, Serrekunda, The Gambia
| | - Ifedayo Adetifa
- Disease Control and Elimination Theme, Medical Research Council (MRC) Unit, Serrekunda, The Gambia
- Department of Infectious Diseases Epidemiology, London School of Hygiene & Tropical Medicine, London, United Kingdom
| | - Catherine Okoi
- Vaccines and Immunity Theme, Medical Research Council (MRC) Unit, Serrekunda, The Gambia
| | - Gregory Dolganov
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford University, Stanford, California, United States of America
| | - Gary Schoolnik
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford University, Stanford, California, United States of America
| | - Ousman Secka
- Vaccines and Immunity Theme, Medical Research Council (MRC) Unit, Serrekunda, The Gambia
| | - Martin Antonio
- Vaccines and Immunity Theme, Medical Research Council (MRC) Unit, Serrekunda, The Gambia
- Division of Microbiology & Immunity, Warwick Medical School, Coventry, United Kingdom
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, United Kingdom
| | - Bouke C. de Jong
- Mycobacteriology Unit, Institute of Tropical Medicine (ITM), Antwerp, Belgium
- Vaccines and Immunity Theme, Medical Research Council (MRC) Unit, Serrekunda, The Gambia
- Division of Infectious Diseases, New York University, New York, New York, United States of America
| | - Florian Gehre
- Mycobacteriology Unit, Institute of Tropical Medicine (ITM), Antwerp, Belgium
- Vaccines and Immunity Theme, Medical Research Council (MRC) Unit, Serrekunda, The Gambia
- * E-mail:
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Tientcheu LD, Haks MC, Agbla SC, Sutherland JS, Adetifa IM, Donkor S, Quinten E, Daramy M, Antonio M, Kampmann B, Ottenhoff THM, Dockrell HM, Ota MO. Host Immune Responses Differ between M. africanum- and M. tuberculosis-Infected Patients following Standard Anti-tuberculosis Treatment. PLoS Negl Trop Dis 2016; 10:e0004701. [PMID: 27192147 PMCID: PMC4871581 DOI: 10.1371/journal.pntd.0004701] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2016] [Accepted: 04/19/2016] [Indexed: 11/19/2022] Open
Abstract
Epidemiological differences exist between Mycobacterium africanum (Maf)- and Mycobacterium tuberculosis (Mtb)-infected patients, but to date, contributing host factors have not been characterised. We analysed clinical outcomes, as well as soluble markers and gene expression profiles in unstimulated, and ESAT6/CFP-10-, whole-Maf- and Mtb-stimulated blood samples of 26 Maf- and 49 Mtb-HIV-negative tuberculosis patients before, and after 2 and 6 months of anti-tuberculosis therapy. Before treatment, both groups had similar clinical parameters, but differed in few cytokines concentration and gene expression profiles. Following treatment the body mass index, skinfold thickness and chest X-ray scores showed greater improvement in the Mtb- compared to Maf-infected patients, after adjusting for age, sex and ethnicity (p = 0.02; 0.04 and 0.007, respectively). In addition, in unstimulated blood, IL-12p70, IL12A and TLR9 were significantly higher in Maf-infected patients, while IL-15, IL-8 and MIP-1α were higher in Mtb-infected patients. Overnight stimulation with ESAT-6/CFP-10 induced significantly higher levels of IFN-γ and TNF-α production, as well as gene expression of CCL4, IL1B and TLR4 in Mtb- compared to Maf-infected patients. Our study confirms differences in clinical features and immune genes expression and concentration of proteins associated with inflammatory processes between Mtb- and Maf-infected patients following anti-tuberculosis treatment These findings have public health implications for treatment regimens, and biomarkers for tuberculosis diagnosis and susceptibility.
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Affiliation(s)
- Leopold D. Tientcheu
- Vaccines and Immunity Theme, Medical Research Council Unit, The Gambia, Banjul, The Gambia
- Department of Immunology and Infection, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
- Department of Biochemistry, Faculty of Science, University of Yaoundé 1, Yaoundé, Cameroon
- * E-mail: ;
| | - Mariëlle C. Haks
- Department of Infectious Diseases, Leiden University Medical Center, Leiden, The Netherlands
| | - Schadrac C. Agbla
- Vaccines and Immunity Theme, Medical Research Council Unit, The Gambia, Banjul, The Gambia
- Department of Medical Statistics, Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Jayne S. Sutherland
- Vaccines and Immunity Theme, Medical Research Council Unit, The Gambia, Banjul, The Gambia
| | - Ifedayo M. Adetifa
- Disease Control and Elimination Theme, Medical Research Council Unit, The Gambia, Fajara, The Gambia
- Department of Infectious Diseases Epidemiology, Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Simon Donkor
- Vaccines and Immunity Theme, Medical Research Council Unit, The Gambia, Banjul, The Gambia
| | - Edwin Quinten
- Department of Infectious Diseases, Leiden University Medical Center, Leiden, The Netherlands
| | - Mohammed Daramy
- Vaccines and Immunity Theme, Medical Research Council Unit, The Gambia, Banjul, The Gambia
| | - Martin Antonio
- Vaccines and Immunity Theme, Medical Research Council Unit, The Gambia, Banjul, The Gambia
- Department of Pathogen Molecular Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, United Kingdom
- Microbiology and Infection Unit, Warwick Medical School, University of Warwick, Coventry, United Kingdom
| | - Beate Kampmann
- Vaccines and Immunity Theme, Medical Research Council Unit, The Gambia, Banjul, The Gambia
| | - Tom H. M. Ottenhoff
- Department of Infectious Diseases, Leiden University Medical Center, Leiden, The Netherlands
| | - Hazel M. Dockrell
- Department of Immunology and Infection, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Martin O. Ota
- Vaccines and Immunity Theme, Medical Research Council Unit, The Gambia, Banjul, The Gambia
- World Health Organization Regional Office for Africa, Brazzaville, Congo
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Winglee K, Manson McGuire A, Maiga M, Abeel T, Shea T, Desjardins CA, Diarra B, Baya B, Sanogo M, Diallo S, Earl AM, Bishai WR. Whole Genome Sequencing of Mycobacterium africanum Strains from Mali Provides Insights into the Mechanisms of Geographic Restriction. PLoS Negl Trop Dis 2016; 10:e0004332. [PMID: 26751217 PMCID: PMC4713829 DOI: 10.1371/journal.pntd.0004332] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2015] [Accepted: 12/05/2015] [Indexed: 01/05/2023] Open
Abstract
Background Mycobacterium africanum, made up of lineages 5 and 6 within the Mycobacterium tuberculosis complex (MTC), causes up to half of all tuberculosis cases in West Africa, but is rarely found outside of this region. The reasons for this geographical restriction remain unknown. Possible reasons include a geographically restricted animal reservoir, a unique preference for hosts of West African ethnicity, and an inability to compete with other lineages outside of West Africa. These latter two hypotheses could be caused by loss of fitness or altered interactions with the host immune system. Methodology/Principal Findings We sequenced 92 MTC clinical isolates from Mali, including two lineage 5 and 24 lineage 6 strains. Our genome sequencing assembly, alignment, phylogeny and average nucleotide identity analyses enabled us to identify features that typify lineages 5 and 6 and made clear that these lineages do not constitute a distinct species within the MTC. We found that in Mali, lineage 6 and lineage 4 strains have similar levels of diversity and evolve drug resistance through similar mechanisms. In the process, we identified a putative novel streptomycin resistance mutation. In addition, we found evidence of person-to-person transmission of lineage 6 isolates and showed that lineage 6 is not enriched for mutations in virulence-associated genes. Conclusions This is the largest collection of lineage 5 and 6 whole genome sequences to date, and our assembly and alignment data provide valuable insights into what distinguishes these lineages from other MTC lineages. Lineages 5 and 6 do not appear to be geographically restricted due to an inability to transmit between West African hosts or to an elevated number of mutations in virulence-associated genes. However, lineage-specific mutations, such as mutations in cell wall structure, secretion systems and cofactor biosynthesis, provide alternative mechanisms that may lead to host specificity. Mycobacterium africanum consists of two lineages, lineages 5 and 6, within the Mycobacterium tuberculosis complex (MTC) that cause human tuberculosis in West Africa, but are found rarely outside of this region. Our analysis of the whole genome sequences of 26 lineage 5 and 6 isolates, and 66 isolates from other lineages within the MTC, reveal that M. africanum does not meet modern criteria to be considered an independent species. We analyzed drug resistance-associated genes and found that drug resistance evolves within these lineages through similar mechanisms as observed for the rest of the MTC in Mali. Though we did not see an elevated number of mutations in virulence-associated genes in these two lineages, we identified a number of lineage-specific mutations, pseudogenes and changes in gene content that may impact virulence and host specificity, and improve, overall, our understanding of what make these lineages unique.
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Affiliation(s)
- Kathryn Winglee
- Center for Tuberculosis Research, Department of Medicine, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Abigail Manson McGuire
- Genome Sequencing and Analysis Program, The Broad Institute of MIT & Harvard, Cambridge, Massachusetts, United States of America
| | - Mamoudou Maiga
- Center for Tuberculosis Research, Department of Medicine, Johns Hopkins University, Baltimore, Maryland, United States of America
- Project SEREFO (Centre de Recherche et de Formation sur le VIH/Sida et la Tuberculose)/University of Sciences, Technics and Technologies of Bamako (USTTB), Bamako, Mali
| | - Thomas Abeel
- Genome Sequencing and Analysis Program, The Broad Institute of MIT & Harvard, Cambridge, Massachusetts, United States of America
- Delft Bioinformatics Lab, Delft University of Technology, Delft, The Netherlands
| | - Terrance Shea
- Genome Sequencing and Analysis Program, The Broad Institute of MIT & Harvard, Cambridge, Massachusetts, United States of America
| | - Christopher A. Desjardins
- Genome Sequencing and Analysis Program, The Broad Institute of MIT & Harvard, Cambridge, Massachusetts, United States of America
| | - Bassirou Diarra
- Project SEREFO (Centre de Recherche et de Formation sur le VIH/Sida et la Tuberculose)/University of Sciences, Technics and Technologies of Bamako (USTTB), Bamako, Mali
| | - Bocar Baya
- Project SEREFO (Centre de Recherche et de Formation sur le VIH/Sida et la Tuberculose)/University of Sciences, Technics and Technologies of Bamako (USTTB), Bamako, Mali
| | - Moumine Sanogo
- Project SEREFO (Centre de Recherche et de Formation sur le VIH/Sida et la Tuberculose)/University of Sciences, Technics and Technologies of Bamako (USTTB), Bamako, Mali
| | - Souleymane Diallo
- Project SEREFO (Centre de Recherche et de Formation sur le VIH/Sida et la Tuberculose)/University of Sciences, Technics and Technologies of Bamako (USTTB), Bamako, Mali
| | - Ashlee M. Earl
- Genome Sequencing and Analysis Program, The Broad Institute of MIT & Harvard, Cambridge, Massachusetts, United States of America
- * E-mail: (AME); (WRB)
| | - William R. Bishai
- Center for Tuberculosis Research, Department of Medicine, Johns Hopkins University, Baltimore, Maryland, United States of America
- * E-mail: (AME); (WRB)
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Abstract
The causative agent of human tuberculosis (TB), Mycobacterium tuberculosis, is an obligate pathogen that evolved to exclusively persist in human populations. For M. tuberculosis to transmit from person to person, it has to cause pulmonary disease. Therefore, M. tuberculosis virulence has likely been a significant determinant of the association between M. tuberculosis and humans. Indeed, the evolutionary success of some M. tuberculosis genotypes seems at least partially attributable to their increased virulence. The latter possibly evolved as a consequence of human demographic expansions. If co-evolution occurred, humans would have counteracted to minimize the deleterious effects of M. tuberculosis virulence. The fact that human resistance to infection has a strong genetic basis is a likely consequence of such a counter-response. The genetic architecture underlying human resistance to M. tuberculosis remains largely elusive. However, interactions between human genetic polymorphisms and M. tuberculosis genotypes have been reported. Such interactions are consistent with local adaptation and allow for a better understanding of protective immunity in TB. Future 'genome-to-genome' studies, in which locally associated human and M. tuberculosis genotypes are interrogated in conjunction, will help identify new protective antigens for the development of better TB vaccines.
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Affiliation(s)
- Daniela Brites
- Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute and University of Basel, Basel, Switzerland
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Tientcheu LD, Maertzdorf J, Weiner J, Adetifa IM, Mollenkopf HJ, Sutherland JS, Donkor S, Kampmann B, Kaufmann SHE, Dockrell HM, Ota MO. Differential transcriptomic and metabolic profiles of M. africanum- and M. tuberculosis-infected patients after, but not before, drug treatment. Genes Immun 2015; 16:347-55. [PMID: 26043170 PMCID: PMC4515549 DOI: 10.1038/gene.2015.21] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2015] [Revised: 04/15/2015] [Accepted: 04/24/2015] [Indexed: 12/11/2022]
Abstract
The epidemiology of Mycobacterium tuberculosis (Mtb) and M. africanum (Maf) suggest differences in their virulence, but the host immune profile to better understand the pathogenesis of tuberculosis (TB) have not been studied. We compared the transcriptomic and metabolic profiles between Mtb and Maf-infected TB cases to identify host biomarkers associated with lineages-specific pathogenesis and response to anti-TB chemotherapy. Venous blood samples from Mtb- and Maf-infected patients obtained before and after anti-TB treatment were analysed for cell composition, gene expression and metabolic profiles. Prior to treatment, similar transcriptomic profiles were seen in Maf- and Mtb-infected patients. In contrast, post-treatment, over 1600 genes related to immune responses and metabolic diseases were differentially expressed between the groups. Notably, the upstream regulator hepatocyte nuclear factor 4-alpha (HNF4α), which regulated 15% of these genes, was markedly enriched. Serum metabolic profiles were similar in both group pre-treatment, but the decline in pro-inflammatory metabolites post-treatment were most pronounced in Mtb-infected patients. Together, the differences in both peripheral blood transcriptomic and serum metabolic profiles between Maf- and Mtb-infected patients observed over the treatment period, might be indicative of intrinsic host factors related to susceptibility to TB and/or differential efficacy of the standard anti-TB treatment on the two lineages.
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Affiliation(s)
- L D Tientcheu
- 1] Vaccinology Theme, Medical Research Council Unit, The Gambia, Banjul, The Gambia [2] Department of Immunology and Infection, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK [3] Department of Biochemistry, Faculty of Science, University of Yaoundé 1, Yaoundé, Cameroon
| | - J Maertzdorf
- Department of Immunology, Max Planck Institute for Infection Biology, Berlin, Germany
| | - J Weiner
- Department of Immunology, Max Planck Institute for Infection Biology, Berlin, Germany
| | - I M Adetifa
- Disease Control and Elimination Theme, Medical Research Council Unit-The Gambia, Fajara, The Gambia
| | - H-J Mollenkopf
- Department of Immunology, Max Planck Institute for Infection Biology, Berlin, Germany
| | - J S Sutherland
- Vaccinology Theme, Medical Research Council Unit, The Gambia, Banjul, The Gambia
| | - S Donkor
- Vaccinology Theme, Medical Research Council Unit, The Gambia, Banjul, The Gambia
| | - B Kampmann
- Vaccinology Theme, Medical Research Council Unit, The Gambia, Banjul, The Gambia
| | - S H E Kaufmann
- Department of Immunology, Max Planck Institute for Infection Biology, Berlin, Germany
| | - H M Dockrell
- Department of Immunology and Infection, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
| | - M O Ota
- 1] Vaccinology Theme, Medical Research Council Unit, The Gambia, Banjul, The Gambia [2] World Health Organization Regional Office for Africa, Brazzaville, Congo
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Ejo M, Gehre F, Barry MD, Sow O, Bah NM, Camara M, Bah B, Uwizeye C, Nduwamahoro E, Fissette K, De Rijk P, Merle C, Olliaro P, Burgos M, Lienhardt C, Rigouts L, de Jong BC. First insights into circulating Mycobacterium tuberculosis complex lineages and drug resistance in Guinea. INFECTION GENETICS AND EVOLUTION 2015; 33:314-9. [PMID: 26004194 PMCID: PMC4503999 DOI: 10.1016/j.meegid.2015.05.022] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2015] [Revised: 05/19/2015] [Accepted: 05/20/2015] [Indexed: 11/23/2022]
Abstract
First insight into resistance levels and genetic diversity of TB in Guinea. Rapid expansion of drug-resistance prone LAM10 Cameroon family. Population structure reveals less ‘ancestral’ TB than in surrounding countries. Knowledge of genetic diversity is relevant for tuberculosis control programs.
In this study we assessed first-line anti-tuberculosis drug resistance and the genotypic distribution of Mycobacterium tuberculosis complex (MTBC) isolates that had been collected from consecutive new tuberculosis patients enrolled in two clinical trials conducted in Guinea between 2005 and 2010. Among the total 359 MTBC strains that were analyzed in this study, 22.8% were resistant to at least one of the first line anti-tuberculosis drugs, including 2.5% multidrug resistance and 17.5% isoniazid resistance, with or without other drugs. In addition, further characterization of isolates from a subset of the two trials (n = 184) revealed a total of 80 different spoligotype patterns, 29 “orphan” and 51 shared patterns. We identified the six major MTBC lineages of human relevance, with predominance of the Euro-American lineage. In total, 132 (71.7%) of the strains were genotypically clustered, and further analysis (using the DESTUS model) suggesting significantly faster spread of LAM10_CAM family (p = 0.00016). In conclusion, our findings provide a first insight into drug resistance and the population structure of the MTBC in Guinea, with relevance for public health scientists in tuberculosis control programs.
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Affiliation(s)
- Mebrat Ejo
- Institute of Tropical Medicine (ITM), Antwerp, Belgium; University of Gondar, Gondar, Ethiopia
| | - Florian Gehre
- Institute of Tropical Medicine (ITM), Antwerp, Belgium; Medical Research Council (MRC), Fajara, Gambia.
| | | | - Oumou Sow
- Reference Laboratory for Mycobacteria, Conakry, Guinea; National University Hospital IgnaceDeen, Conakry, Guinea
| | | | - Mory Camara
- Reference Laboratory for Mycobacteria, Conakry, Guinea
| | - Boubacar Bah
- National University Hospital IgnaceDeen, Conakry, Guinea
| | | | | | | | - Pim De Rijk
- Institute of Tropical Medicine (ITM), Antwerp, Belgium
| | - Corinne Merle
- London School of Hygiene and Tropical Medicine, London, UK; UNICEF/UNDP/World Bank/WHO Special Programme for Research and Training in Tropical Diseases (TDR), Geneva, Switzerland
| | - Piero Olliaro
- UNICEF/UNDP/World Bank/WHO Special Programme for Research and Training in Tropical Diseases (TDR), Geneva, Switzerland; Centre for Tropical Medicine, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Marcos Burgos
- Division of Infectious Diseases, Department of Internal Medicine, University of New Mexico, Albuquerque, United States
| | - Christian Lienhardt
- Clinical Trial Division, International Union against Tuberculosis and Lung Disease, Paris, France; World Health Organization, Geneva, Switzerland
| | - Leen Rigouts
- Institute of Tropical Medicine (ITM), Antwerp, Belgium; University of Antwerp, Antwerp, Belgium
| | - Bouke C de Jong
- Institute of Tropical Medicine (ITM), Antwerp, Belgium; Medical Research Council (MRC), Fajara, Gambia; New York University (NYU), New York, United States
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Coscolla M, Gagneux S. Consequences of genomic diversity in Mycobacterium tuberculosis. Semin Immunol 2014; 26:431-44. [PMID: 25453224 PMCID: PMC4314449 DOI: 10.1016/j.smim.2014.09.012] [Citation(s) in RCA: 278] [Impact Index Per Article: 27.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/29/2014] [Revised: 09/29/2014] [Accepted: 09/30/2014] [Indexed: 11/29/2022]
Abstract
The causative agent of human tuberculosis, Mycobacterium tuberculosis complex (MTBC), comprises seven phylogenetically distinct lineages associated with different geographical regions. Here we review the latest findings on the nature and amount of genomic diversity within and between MTBC lineages. We then review recent evidence for the effect of this genomic diversity on mycobacterial phenotypes measured experimentally and in clinical settings. We conclude that overall, the most geographically widespread Lineage 2 (includes Beijing) and Lineage 4 (also known as Euro-American) are more virulent than other lineages that are more geographically restricted. This increased virulence is associated with delayed or reduced pro-inflammatory host immune responses, greater severity of disease, and enhanced transmission. Future work should focus on the interaction between MTBC and human genetic diversity, as well as on the environmental factors that modulate these interactions.
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Affiliation(s)
- Mireia Coscolla
- Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, Socinstrasse 57, 4002 Basel, Switzerland; University of Basel, Petersplatz 1, Basel 4003, Switzerland
| | - Sebastien Gagneux
- Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, Socinstrasse 57, 4002 Basel, Switzerland; University of Basel, Petersplatz 1, Basel 4003, Switzerland.
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Doughty EL, Sergeant MJ, Adetifa I, Antonio M, Pallen MJ. Culture-independent detection and characterisation of Mycobacterium tuberculosis and M. africanum in sputum samples using shotgun metagenomics on a benchtop sequencer. PeerJ 2014; 2:e585. [PMID: 25279265 PMCID: PMC4179564 DOI: 10.7717/peerj.585] [Citation(s) in RCA: 92] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2014] [Accepted: 08/28/2014] [Indexed: 01/27/2023] Open
Abstract
Tuberculosis remains a major global health problem. Laboratory diagnostic methods that allow effective, early detection of cases are central to management of tuberculosis in the individual patient and in the community. Since the 1880s, laboratory diagnosis of tuberculosis has relied primarily on microscopy and culture. However, microscopy fails to provide species- or lineage-level identification and culture-based workflows for diagnosis of tuberculosis remain complex, expensive, slow, technically demanding and poorly able to handle mixed infections. We therefore explored the potential of shotgun metagenomics, sequencing of DNA from samples without culture or target-specific amplification or capture, to detect and characterise strains from the Mycobacterium tuberculosis complex in smear-positive sputum samples obtained from The Gambia in West Africa. Eight smear- and culture-positive sputum samples were investigated using a differential-lysis protocol followed by a kit-based DNA extraction method, with sequencing performed on a benchtop sequencing instrument, the Illumina MiSeq. The number of sequence reads in each sputum-derived metagenome ranged from 989,442 to 2,818,238. The proportion of reads in each metagenome mapping against the human genome ranged from 20% to 99%. We were able to detect sequences from the M. tuberculosis complex in all eight samples, with coverage of the H37Rv reference genome ranging from 0.002X to 0.7X. By analysing the distribution of large sequence polymorphisms (deletions and the locations of the insertion element IS6110) and single nucleotide polymorphisms (SNPs), we were able to assign seven of eight metagenome-derived genomes to a species and lineage within the M. tuberculosis complex. Two metagenome-derived mycobacterial genomes were assigned to M. africanum, a species largely confined to West Africa; the others that could be assigned belonged to lineages T, H or LAM within the clade of "modern" M. tuberculosis strains. We have provided proof of principle that shotgun metagenomics can be used to detect and characterise M. tuberculosis sequences from sputum samples without culture or target-specific amplification or capture, using an accessible benchtop-sequencing platform, the Illumina MiSeq, and relatively simple DNA extraction, sequencing and bioinformatics protocols. In our hands, sputum metagenomics does not yet deliver sufficient depth of coverage to allow sequence-based sensitivity testing; it remains to be determined whether improvements in DNA extraction protocols alone can deliver this or whether culture, capture or amplification steps will be required. Nonetheless, we can foresee a tipping point when a unified automated metagenomics-based workflow might start to compete with the plethora of methods currently in use in the diagnostic microbiology laboratory.
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Affiliation(s)
- Emma L. Doughty
- Microbiology and Infection Unit, Warwick Medical School, University of Warwick, Coventry, United Kingdom
| | - Martin J. Sergeant
- Microbiology and Infection Unit, Warwick Medical School, University of Warwick, Coventry, United Kingdom
| | | | - Martin Antonio
- Microbiology and Infection Unit, Warwick Medical School, University of Warwick, Coventry, United Kingdom
- Medical Research Council Unit, Fajara, The Gambia
| | - Mark J. Pallen
- Microbiology and Infection Unit, Warwick Medical School, University of Warwick, Coventry, United Kingdom
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Bold TD, Davis DC, Penberthy KK, Cox LM, Ernst JD, de Jong BC. Impaired fitness of Mycobacterium africanum despite secretion of ESAT-6. J Infect Dis 2012; 205:984-90. [PMID: 22301632 PMCID: PMC3282571 DOI: 10.1093/infdis/jir883] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2011] [Accepted: 10/28/2011] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND When compared with Mycobacterium tuberculosis, individuals that live in the same household as an active case of smear-positive pulmonary tuberculosis exposed to M. africanum progress less frequently to active disease within 2 years. A putative ESX-1 secretion apparatus member, Rv3879c, is mutated in M. africanum, and individuals infected with M. africanum less frequently demonstrate T-cell responses to the ESX-1-secreted virulence factor ESAT-6 than those infected with M. tuberculosis. We hypothesized that less frequent progression is caused by impaired secretion of ESAT-6. METHODS We analyzed in vivo growth and in vitro secretion of ESAT-6 and CFP-10, comparing M. tuberculosis to M. africanum and a strain of M. africanum complemented with M. tuberculosis Rv3879c. RESULTS ESAT-6 and CFP-10 secretion were similar for all strains, although these were enriched in M. africanum cell lysates, suggesting a modest ESX-1 secretion defect unrelated to the Rv3879c mutation. In mice, M. africanum demonstrated smaller bacterial population sizes than M. tuberculosis but similar numbers and frequencies of ESAT-6-responsive T cells in the lungs. CONCLUSIONS These results confirm impaired fitness of M. africanum in vivo and indicate that Rv3879c is not required for secretion of ESAT-6 or for its presentation as an antigen to T cells in vivo.
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Affiliation(s)
| | | | | | - Laura M. Cox
- Department of Medicine, Division of Infectious Diseases
| | - Joel D. Ernst
- Department of Medicine, Division of Infectious Diseases
- Department of Pathology
- Department of Microbiology, New York University School of Medicine, New York
| | - Bouke C. de Jong
- Department of Medicine, Division of Infectious Diseases
- Institute of Tropical Medicine, Antwerp, Belgium
- Medical Research Council Laboratories, The Gambia
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de Jong BC, Antonio M, Gagneux S. Mycobacterium africanum--review of an important cause of human tuberculosis in West Africa. PLoS Negl Trop Dis 2010; 4:e744. [PMID: 20927191 PMCID: PMC2946903 DOI: 10.1371/journal.pntd.0000744] [Citation(s) in RCA: 169] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Mycobacterium africanum consists of two phylogenetically distinct lineages within the Mycobacterium tuberculosis complex, known as M. africanum West African 1 and M. africanum West African 2. These lineages are restricted to West Africa, where they cause up to half of human pulmonary tuberculosis. In this review we discuss the definition of M. africanum, describe the prevalence and restricted geographical distribution of M. africanum West African 1 and 2, review the occurrence of M. africanum in animals, and summarize the phenotypic differences described thus far between M. africanum and M. tuberculosis sensu stricto.
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Affiliation(s)
- Bouke C de Jong
- MRC Laboratories, Bacterial Diseases Programme, Fajara, The Gambia.
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