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Affara M, Lagu HI, Achol E, Omari N, Ochido G, Kezakarayagwa E, Kabatesi F, Nduwimana C, Nkeshimana A, Duku Samson D, Awin Nykwec G, Daniel Wani Lako J, Lasuba M, Lojok Deng L, Ezekiely Kelly M, Bernard Mtesigwa Mkama P, Magesa A, Said Ali S, Amour Rashid S, Pimundu G, Muyigi T, Ndidde Nabadda S, Rutayisire R, Kabanda A, Kabalisa E, May J, Nzeyimana E, Katende M, Gehre F. Regional Evaluation of Two SARS-CoV-2 Antigen Rapid Diagnostic Tests in East Africa. Microbiol Spectr 2023; 11:e0489522. [PMID: 37010436 PMCID: PMC10269495 DOI: 10.1128/spectrum.04895-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Accepted: 02/24/2023] [Indexed: 04/04/2023] Open
Abstract
The clinical performance of two rapid antigen tests for the diagnosis of Severe Acute Respiratory Coronavirus (SARS-CoV-2) were regionally evaluated in East African populations. Swabs were collected from 1,432 individuals from five Partner States of the East African Community (Tanzania, Uganda, Burundi, Rwanda and South Sudan). The two rapid antigen tests (Bionote NowCheck COVID-19 Ag and SD Biosensor STANDARD Q COVID-19 Ag) were evaluated against the detection of SARS-CoV-2 RNA by the Reverse Transcription PCR (RT-PCR) gold standard. Of the concordant results with both RT-PCR and rapid antigen test data (862 for Bionote and 852 for SD Biosensor), overall clinical sensitivity was 60% and 50% for the Bionote NowCheck and the SD Biosensor STANDARD Q, respectively. Stratification by viral load, including samples with RT-PCR cycle thresholds (Ct) of <25, improved sensitivity to 90% for both rapid diagnostic tests (RDTs). Overall specificity was good at 99% for both antigen tests. Taken together, the clinical performance of both Ag-RDTs in real world settings within the East African target population was lower than has been reported elsewhere and below the acceptable levels for sensitivity of >80%, as defined by the WHO. Therefore, the rapid antigen test alone should not be used for diagnosis but could be used as part of an algorithm to identify potentially infectious individuals with high viral load. IMPORTANCE Accurate diagnostic tests are essential to both support the management and containment of outbreaks, as well as inform appropriate patient care. In the case of the SARS-CoV-2 pandemic, antigen Rapid Diagnostic Tests (Ag-RDTs) played a major role in this function, enabling widespread testing by untrained individuals, both at home and within health facilities. In East Africa, a number of SARS-CoV-2 Ag-RDTs are available; however, there remains little information on their true test performance within the region, in the hands of the health workers routinely carrying out SARS-CoV-2 diagnostics. This study contributes test performance data for two commonly used SARS-CoV-2 Ag-RDTs in East Africa, which will help inform the use of these RDTs within the region.
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Affiliation(s)
- Muna Affara
- Department for Infectious Disease Epidemiology, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, Germany
- East African Community (EAC), Arusha, Tanzania
| | | | | | - Neema Omari
- Department for Infectious Disease Epidemiology, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, Germany
- East African Community (EAC), Arusha, Tanzania
| | - Grace Ochido
- Department for Infectious Disease Epidemiology, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, Germany
- East African Community (EAC), Arusha, Tanzania
| | - Eric Kezakarayagwa
- National Institute of Public Health, Ministry of Health and Fight Against AIDS, Bujumbura, Burundi
| | - Francine Kabatesi
- National Institute of Public Health, Ministry of Health and Fight Against AIDS, Bujumbura, Burundi
| | - Cassien Nduwimana
- National Institute of Public Health, Ministry of Health and Fight Against AIDS, Bujumbura, Burundi
| | - Anatole Nkeshimana
- National Institute of Public Health, Ministry of Health and Fight Against AIDS, Bujumbura, Burundi
| | - Donald Duku Samson
- Public Health Laboratory and National Blood Transfusion Centre, Ministry of Health, Juba, South Sudan
| | - Gwokpan Awin Nykwec
- Public Health Laboratory and National Blood Transfusion Centre, Ministry of Health, Juba, South Sudan
| | - Joseph Daniel Wani Lako
- Public Health Laboratory and National Blood Transfusion Centre, Ministry of Health, Juba, South Sudan
| | - Michael Lasuba
- Public Health Laboratory and National Blood Transfusion Centre, Ministry of Health, Juba, South Sudan
| | - Lul Lojok Deng
- Public Health Laboratory and National Blood Transfusion Centre, Ministry of Health, Juba, South Sudan
| | - Maria Ezekiely Kelly
- Ministry of Health, Dodoma, Tanzania
- National Public Health Laboratory, Dar es Salaam, Tanzania
| | | | - Alex Magesa
- Ministry of Health, Dodoma, Tanzania
- National Public Health Laboratory, Dar es Salaam, Tanzania
| | - Salum Said Ali
- Zanzibar National Public Health Laboratory, Stonetown, Zanzibar
| | | | - Godfrey Pimundu
- National Health Laboratory and Diagnostic Services (NHLDS), Ministry of Health, Kampala, Uganda
| | - Tonny Muyigi
- National Health Laboratory and Diagnostic Services (NHLDS), Ministry of Health, Kampala, Uganda
| | - Susan Ndidde Nabadda
- National Health Laboratory and Diagnostic Services (NHLDS), Ministry of Health, Kampala, Uganda
| | | | | | | | - Jürgen May
- Department for Infectious Disease Epidemiology, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, Germany
- German Center for Infection Research (DZIF), partner site Hamburg-Lübeck-Borstel-Riems, Hamburg, Germany
- Tropical Medicine II, University Medical Center Hamburg-Eppendorf (UKE), Hamburg, Germany
| | | | | | - Florian Gehre
- Department for Infectious Disease Epidemiology, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, Germany
- East African Community (EAC), Arusha, Tanzania
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Kelly ME, Msafiri F, Affara M, Gehre F, Moremi N, Mghamba J, Misinzo G, Thye T, Gatei W, Whistler T, Joachim A, Lema N, Santiago GA. Molecular Characterization and Phylogenetic Analysis of Dengue Fever Viruses in Three Outbreaks in Tanzania Between 2017 and 2019. PLoS Negl Trop Dis 2023; 17:e0011289. [PMID: 37099594 PMCID: PMC10166554 DOI: 10.1371/journal.pntd.0011289] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Revised: 05/08/2023] [Accepted: 04/05/2023] [Indexed: 04/27/2023] Open
Abstract
BACKGROUND Dengue is a disease of public health interest, and Tanzania experienced major outbreaks in 2014 and 2019. Here, we report our findings on the molecular characterization of dengue viruses (DENV) that circulated during two smaller outbreaks (2017 and 2018) and one major epidemic (2019) in Tanzania. METHODOLOGY/PRINCIPAL FINDINGS We tested archived serum samples from 1,381 suspected dengue fever patients, with a median age of 29 (IQR:22-40) years, referred to the National Public Health Laboratory for confirmation of DENV infection. DENV serotypes were identified by reverse transcription polymerase chain reaction (RT-PCR), and specific genotypes were identified by sequencing the envelope glycoprotein gene and phylogenetic inference methods. DENV was confirmed in 823 (59.6%) cases. More than half (54.7%) of patients with dengue fever infection were males, and nearly three-quarters (73%) of the infected individuals were living in Kinondoni district, Dar es Salaam. DENV-3 Genotype III caused the two smaller outbreaks in 2017 and 2018, while DENV-1 Genotype V caused the 2019 epidemic. DENV-1 Genotype I was also detected in one patient in 2019. CONCLUSION/SIGNIFICANCE This study has demonstrated the molecular diversity of dengue viruses circulating in Tanzania. We found that contemporary circulating serotypes did not cause the major epidemic of 2019 but rather due to a serotype shift from DENV-3 (2017/2018) to DENV-1 in 2019. Such a change increases the risk for patients previously infected with a particular serotype to develop severe symptoms upon potential re-infection with a heterologous serotype due to antibody-dependent enhancement of infection. Therefore, the circulation of serotypes emphasizes the need to strengthen the country's dengue surveillance system for better management of patients, early detection of outbreaks, and vaccine development.
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Affiliation(s)
| | - Frank Msafiri
- Department of Microbiology and Immunology, Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
| | - Muna Affara
- Bernhard Nocht Institute for Tropical Medicine, Infectious Disease Epidemiology Department, Hamburg, Germany
- East African Community Secretariat, Health Department, Arusha, Tanzania
| | - Florian Gehre
- Bernhard Nocht Institute for Tropical Medicine, Infectious Disease Epidemiology Department, Hamburg, Germany
- East African Community Secretariat, Health Department, Arusha, Tanzania
| | - Nyambura Moremi
- National Public Health Laboratory, Ministry of Health, Dar es Salaam, Tanzania
| | - Janeth Mghamba
- Department of Epidemiology, Ministry of Health, Dodoma, Tanzania
| | - Gerald Misinzo
- SACIDS Foundation for One Health, Sokoine University of Agriculture, Morogoro, Tanzania
| | - Thorsten Thye
- Bernhard Nocht Institute for Tropical Medicine, Infectious Disease Epidemiology Department, Hamburg, Germany
| | - Wangeci Gatei
- Centers for Disease Control and Prevention, Division of Global Health Protection, Atlanta, Georgia, United States of America
| | - Toni Whistler
- Centers for Disease Control and Prevention, Division of Global Health Protection, Atlanta, Georgia, United States of America
| | - Agricola Joachim
- Department of Microbiology and Immunology, Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
| | - Nsiande Lema
- Tanzania Field Epidemiology and Laboratory Training Program, Dar es Salaam, Tanzania
| | - Gilberto A Santiago
- Centers for Disease Control and Prevention, Division of Vector-Borne Diseases, Dengue Branch, San Juan, Puerto Rico, United States of America
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Ejo M, Torrea G, Diro E, Abebe A, Kassa M, Girma Y, Tesfa E, Ejigu K, Uwizeye C, Gehre F, de Jong BC, Rigouts L. Strain diversity and gene mutations associated with presumptive multidrug-resistant Mycobacterium tuberculosis complex isolates in Northwest Ethiopia. J Glob Antimicrob Resist 2023; 32:167-175. [PMID: 36470362 DOI: 10.1016/j.jgar.2022.11.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Revised: 08/25/2022] [Accepted: 11/25/2022] [Indexed: 12/07/2022] Open
Abstract
OBJECTIVES In this study, we assessed the genetic diversity and gene mutations that confer resistance to rifampicin (RIF), isoniazid (INH), fluoroquinolone (FQ), and second-line injectable (SLI) drugs in RIF-resistant (RR)/multidrug-resistant tuberculosis (MDR-TB) isolates in Northwest Ethiopia. METHODS Spoligotyping was used to assign isolates to TB lineages (Ls), and Hain line probe assays were used to detect resistance to RIF, INH, and FQs, and SLIs. RESULTS Among 130 analyzed strains, 68.5% were RR, and four major Mycobacterium tuberculosis complex lineages (L1, L3, L4, and L7) were identified with a predominance of the Euro-American L4 (72, 54.7%), while L7 genotypes were less common (3, 2.3%). Overall, the L4-T3-ETH (41, 32.0%), L3-CAS1-Delhi (29, 22.7%), and L3-CAS1-Killi (19, 14.8%) families were most common. Line probe analysis showed that among rpoB mutants, 65.2% were S450L, while 87.8% of katG mutants were S315T. Only three isolates showed mutation (c-15t) at the inhA gene, and no double mutation with katG and inhA genes was found. Six strains, two each of L1, L3, and L4, were resistant to FQs, having gyrA mutations (D94G, S91P), of which three isolates had additional resistance to SLI (rrs A1401G or C1402T mutations) including one isolate with low-level kanamycin (KAN) resistance. CONCLUSIONS This study showed a predominance of L4-T3-ETH, L3-CAS1-Delhi, and L3-CAS1-Killi families, with a high rate of rpoB_S450L and katG_S315T mutations and a low proportion of gyrA and rrs mutations. L7 was less frequently observed in this study. Further investigations are, therefore, needed to understand L7 and other lineages with undefined mutations.
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Affiliation(s)
- Mebrat Ejo
- Mycobacteriology Unit, Institute of Tropical Medicine, Antwerp, Belgium; Department of Biomedical Sciences, University of Gondar, Gondar, Ethiopia; Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium.
| | - Gabriela Torrea
- Mycobacteriology Unit, Institute of Tropical Medicine, Antwerp, Belgium
| | - Ermias Diro
- Department of Internal Medicine, University of Gondar, Gondar, Ethiopia; MDR-TB Treatment and Follow-up Center, University of Gondar Specialized Hospital, Gondar, Ethiopia
| | - Ayenesh Abebe
- TB culture laboratory, University of Gondar Specialized Hospital, Gondar, Ethiopia
| | - Meseret Kassa
- TB culture laboratory, University of Gondar Specialized Hospital, Gondar, Ethiopia
| | - Yilak Girma
- TB culture laboratory, University of Gondar Specialized Hospital, Gondar, Ethiopia
| | - Eyasu Tesfa
- MDR-TB Treatment and Follow-up Center, University of Gondar Specialized Hospital, Gondar, Ethiopia
| | - Kefialew Ejigu
- TB culture laboratory, Amhara Public Health Institute, Bahir Dar, Ethiopia
| | - Cecile Uwizeye
- Mycobacteriology Unit, Institute of Tropical Medicine, Antwerp, Belgium
| | - Florian Gehre
- Department of Infectious Disease Epidemiology, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, Germany; East African Community Secretariat, Arusha, Tanzania
| | - Bouke C de Jong
- Mycobacteriology Unit, Institute of Tropical Medicine, Antwerp, Belgium
| | - Leen Rigouts
- Mycobacteriology Unit, Institute of Tropical Medicine, Antwerp, Belgium; Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
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Gehre F, Lagu H, Achol E, Omari N, Ochido G, Duraffour S, Hinzmann J, Kezakarayagwa E, Kabatesi F, Nkeshimana A, Nyandwi J, Samson DD, Nykwec GA, Lokore ML, Deng LL, Kelly ME, Mkama PBM, Magesa A, Beyanga M, Roba A, Ndia M, Lokamar P, Kiiru J, Kabanda A, Mukagatare I, Kabalisa E, Rutayisire R, Sewanyana I, Nambozo EJ, Muyigi T, Pimundu G, May J, Katende M, Nabadda S, Nzeyimana E, Affara M. The East African Community’s mobile laboratory network’s rapid response during the first 2 weeks of the Ebola Sudan virus disease (SVD) outbreak in Uganda and pandemic preparedness activities in South Sudan, Rwanda, Tanzania, Burundi, Kenya. BMJ Glob Health 2022; 7:bmjgh-2022-011073. [DOI: 10.1136/bmjgh-2022-011073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Accepted: 11/19/2022] [Indexed: 12/15/2022] Open
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Affara M, Lagu HI, Achol E, Karamagi R, Omari N, Ochido G, Kezakarayagwa E, Kabatesi F, Nkeshimana A, Roba A, Ndia MN, Abudo MU, Kabanda A, Mpabuka E, Mwikarago EI, Kutjok PE, Samson DD, Deng LL, Moremi N, Kelly ME, Mkama PBM, Magesa A, Balinandi SK, Pimundu G, Nabadda SN, Puradiredja DI, Hinzmann J, Duraffour S, Gabriel M, Ruge G, Loag W, Ayiko R, Sonoiya SS, May J, Katende MJ, Gehre F. The East African Community (EAC) mobile laboratory networks in Kenya, Burundi, Tanzania, Rwanda, Uganda, and South Sudan-from project implementation to outbreak response against Dengue, Ebola, COVID-19, and epidemic-prone diseases. BMC Med 2021; 19:160. [PMID: 34238298 PMCID: PMC8266482 DOI: 10.1186/s12916-021-02028-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Accepted: 06/09/2021] [Indexed: 11/12/2022] Open
Abstract
BACKGROUND East Africa is home to 170 million people and prone to frequent outbreaks of viral haemorrhagic fevers and various bacterial diseases. A major challenge is that epidemics mostly happen in remote areas, where infrastructure for Biosecurity Level (BSL) 3/4 laboratory capacity is not available. As samples have to be transported from the outbreak area to the National Public Health Laboratories (NPHL) in the capitals or even flown to international reference centres, diagnosis is significantly delayed and epidemics emerge. MAIN TEXT The East African Community (EAC), an intergovernmental body of Burundi, Rwanda, Tanzania, Kenya, Uganda, and South Sudan, received 10 million € funding from the German Development Bank (KfW) to establish BSL3/4 capacity in the region. Between 2017 and 2020, the EAC in collaboration with the Bernhard-Nocht-Institute for Tropical Medicine (Germany) and the Partner Countries' Ministries of Health and their respective NPHLs, established a regional network of nine mobile BSL3/4 laboratories. These rapidly deployable laboratories allowed the region to reduce sample turn-around-time (from days to an average of 8h) at the centre of the outbreak and rapidly respond to epidemics. In the present article, the approach for implementing such a regional project is outlined and five major aspects (including recommendations) are described: (i) the overall project coordination activities through the EAC Secretariat and the Partner States, (ii) procurement of equipment, (iii) the established laboratory setup and diagnostic panels, (iv) regional training activities and capacity building of various stakeholders and (v) completed and ongoing field missions. The latter includes an EAC/WHO field simulation exercise that was conducted on the border between Tanzania and Kenya in June 2019, the support in molecular diagnosis during the Tanzanian Dengue outbreak in 2019, the participation in the Ugandan National Ebola response activities in Kisoro district along the Uganda/DRC border in Oct/Nov 2019 and the deployments of the laboratories to assist in SARS-CoV-2 diagnostics throughout the region since early 2020. CONCLUSIONS The established EAC mobile laboratory network allows accurate and timely diagnosis of BSL3/4 pathogens in all East African countries, important for individual patient management and to effectively contain the spread of epidemic-prone diseases.
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Affiliation(s)
- Muna Affara
- Department for Infectious Disease Epidemiology, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, Germany.,East African Community (EAC), Arusha, Tanzania
| | | | | | | | - Neema Omari
- Department for Infectious Disease Epidemiology, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, Germany.,East African Community (EAC), Arusha, Tanzania
| | - Grace Ochido
- Department for Infectious Disease Epidemiology, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, Germany.,East African Community (EAC), Arusha, Tanzania
| | - Eric Kezakarayagwa
- National Institute of Public Health, Ministry of Health and Fight Against AIDS, Bujumbura, Burundi
| | - Francine Kabatesi
- National Institute of Public Health, Ministry of Health and Fight Against AIDS, Bujumbura, Burundi
| | - Anatole Nkeshimana
- National Institute of Public Health, Ministry of Health and Fight Against AIDS, Bujumbura, Burundi
| | - Abdi Roba
- National Public Health Laboratories, Ministry of Health, Nairobi, Kenya
| | | | - Mamo U Abudo
- National Public Health Laboratories, Ministry of Health, Nairobi, Kenya
| | - Alice Kabanda
- National Reference Laboratory Division, Rwanda Biomedical Centre, Ministry of Health, Kigali, Rwanda
| | - Etienne Mpabuka
- National Reference Laboratory Division, Rwanda Biomedical Centre, Ministry of Health, Kigali, Rwanda
| | - Emil Ivan Mwikarago
- National Reference Laboratory Division, Rwanda Biomedical Centre, Ministry of Health, Kigali, Rwanda
| | - Philip Ezekiel Kutjok
- Public Health Laboratory and National Blood Transfusion Centre, Ministry of Health, Juba, South Sudan
| | - Donald Duku Samson
- Public Health Laboratory and National Blood Transfusion Centre, Ministry of Health, Juba, South Sudan
| | - Lul Lojok Deng
- Public Health Laboratory and National Blood Transfusion Centre, Ministry of Health, Juba, South Sudan
| | - Nyambura Moremi
- Ministry of Health, Community Development, Gender, Elderly and Children, Dodoma, Tanzania.,National Health Laboratory, Quality Assurance and Training Centre, Dar es Salaam, Tanzania
| | - Maria Ezekiely Kelly
- Ministry of Health, Community Development, Gender, Elderly and Children, Dodoma, Tanzania.,National Health Laboratory, Quality Assurance and Training Centre, Dar es Salaam, Tanzania
| | - Peter Bernard Mtesigwa Mkama
- Ministry of Health, Community Development, Gender, Elderly and Children, Dodoma, Tanzania.,National Health Laboratory, Quality Assurance and Training Centre, Dar es Salaam, Tanzania
| | - Alex Magesa
- Ministry of Health, Community Development, Gender, Elderly and Children, Dodoma, Tanzania.,National Health Laboratory, Quality Assurance and Training Centre, Dar es Salaam, Tanzania
| | | | - Godfrey Pimundu
- National Health Laboratory and Diagnostic Services (NHLDS), Ministry of Health, Kampala, Uganda
| | - Susan Ndidde Nabadda
- National Health Laboratory and Diagnostic Services (NHLDS), Ministry of Health, Kampala, Uganda
| | - Dewi Ismajani Puradiredja
- Department for Infectious Disease Epidemiology, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, Germany
| | - Julia Hinzmann
- Virology Department, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, Germany.,German Center for Infection Research (DZIF), partner site Hamburg-Lübeck-Borstel-Riems, Hamburg, Germany
| | - Sophie Duraffour
- Virology Department, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, Germany.,German Center for Infection Research (DZIF), partner site Hamburg-Lübeck-Borstel-Riems, Hamburg, Germany
| | - Martin Gabriel
- Virology Department, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, Germany.,German Center for Infection Research (DZIF), partner site Hamburg-Lübeck-Borstel-Riems, Hamburg, Germany
| | - Gerd Ruge
- Department for Infectious Disease Epidemiology, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, Germany
| | - Wibke Loag
- Department for Infectious Disease Epidemiology, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, Germany
| | | | | | - Juergen May
- Department for Infectious Disease Epidemiology, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, Germany.,German Center for Infection Research (DZIF), partner site Hamburg-Lübeck-Borstel-Riems, Hamburg, Germany.,Tropical Medicine II, University Medical Center Hamburg-Eppendorf (UKE), Hamburg, Germany
| | | | - Florian Gehre
- Department for Infectious Disease Epidemiology, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, Germany. .,East African Community (EAC), Arusha, Tanzania.
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Njenge H, Copper F, Bell A, Charles D, Mullen L, de Vázquez CC, Wesonga T, Wakhungu JN, Katende M, Komba EA, Kituyi PNN, Mmbaga V, Nguvila T, Makata MA, Chinyuka H, de La Rocque S, Sreedharan R, Stephen M, Mayigane LN, Saguti GEB, Ganda N, Gachohi J, Nyaberi JM, Kabanda D, Marwa F, Mwatondo A, Mukora GG, Muinde JM, Komora S, Msangi C, Malinda BL, Uiso V, Mwaipopo C, Dulu TD, Gehre F, Affara M, Mutabazi F, Balikowa D, Kiarie SW, Kivuva J, Wambua C, Were W, Nyakundi PM, Makayotto L, Njoroge M, Kebaki GM, Swai ES, Mwakyusa EK, Kauki G, Fasina FO, Byoona K, Woldetsadik SF, Allan M, Wekesa J, Nanyunja M, Mutoka FB, Knaggs D, Nsenga N, Yahaya AA, Talisuna A, Omaar A, Ho ZJM, Kandel N, Chungong S. Lessons Learned From a Large Cross-Border Field Simulation Exercise to Strengthen Emergency Preparedness in East Africa, 2019. Health Secur 2021; 19:413-423. [PMID: 34339258 DOI: 10.1089/hs.2020.0162] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Field simulation exercises (FSXs) require substantial time, resources, and organizational experience to plan and implement and are less commonly undertaken than drills or tabletop exercises. Despite this, FSXs provide an opportunity to test the full scope of operational capacities, including coordination across sectors. From June 11 to 14, 2019, the East African Community Secretariat conducted a cross-border FSX at the Namanga One Stop Border Post between the Republic of Kenya and the United Republic of Tanzania. The World Health Organization Department of Health Security Preparedness was the technical lead responsible for developing and coordinating the exercise. The purpose of the FSX was to assess and further enhance multisectoral outbreak preparedness and response in the East Africa Region, using a One Health approach. Participants included staff from the transport, police and customs, public health, animal health, and food inspection sectors. This was the first FSX of this scale, magnitude, and complexity to be conducted in East Africa for the purpose of strengthening emergency preparedness capacities. The FSX provided an opportunity for individual learning and national capacity strengthening in emergency management and response coordination. In this article, we describe lessons learned and propose recommendations relevant to FSX design, management, and organization to inform future field exercises.
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Gehre F, Lagu H, Achol E, Katende M, May J, Affara M. Commentary: mobile laboratories for SARS-CoV-2 diagnostics: what Europe could learn from the East African Community to assure trade in times of border closures. Global Health 2021; 17:49. [PMID: 33892773 PMCID: PMC8063167 DOI: 10.1186/s12992-021-00700-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Accepted: 04/12/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The emergence of SARS-CoV-2 mutants might lead to European border closures, which impact on trade and result in serious economic losses. In April 2020, similar border closures were observed during the first SARS-CoV-2 wave in East Africa. MAIN BODY Since 2017 the East African Community EAC together with the Bernhard-Nocht-Institute for Tropical Medicine BNITM established a mobile laboratory network integrated into the National Public Health Laboratories of the six Partner States for molecular diagnosis of viral haemorrhagic fevers and SARS-CoV-2. Since May 2020, the National Public Health Laboratories of Kenya, Rwanda, Burundi, Uganda and South Sudan deployed these mobile laboratories to their respective borders, issuing a newly developed "Electronic EAC COVID-19 Digital Certificate" to SARS-CoV-2 PCR-negative truck drivers, thus assuring regional trade. CONCLUSION Considering the large financial damages of border closures, such a mobile laboratory network as demonstrated in East Africa is cost-effective, easy to implement and feasible. The East African Community mobile laboratory network could serve as a blueprint for Europe and other countries around the globe.
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Affiliation(s)
- Florian Gehre
- Department of Infectious Disease Epidemiology, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, Germany.
- East African Community Secretariat, Health Department, Arusha, Tanzania.
| | - Hakim Lagu
- East African Community Secretariat, Health Department, Arusha, Tanzania
| | - Emmanuel Achol
- East African Community Secretariat, Health Department, Arusha, Tanzania
| | - Michael Katende
- East African Community Secretariat, Health Department, Arusha, Tanzania
| | - Jürgen May
- Department of Infectious Disease Epidemiology, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, Germany
- Tropical Medicine II, University Medical Center Hamburg-Eppendorf (UKE), Hamburg, Germany
- German Center for Infection Research (DZIF), Hamburg-Borstel-Lübeck-Riems, Hamburg, Germany
| | - Muna Affara
- Department of Infectious Disease Epidemiology, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, Germany
- East African Community Secretariat, Health Department, Arusha, Tanzania
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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9
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Ejo M, Torrea G, Uwizeye C, Kassa M, Girma Y, Bekele T, Ademe Y, Diro E, Gehre F, Rigouts L, de Jong BC. Genetic diversity of the Mycobacterium tuberculosis complex strains from newly diagnosed tuberculosis patients in Northwest Ethiopia reveals a predominance of East-African-Indian and Euro-American lineages. Int J Infect Dis 2020; 103:72-80. [PMID: 33189940 DOI: 10.1016/j.ijid.2020.11.129] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Revised: 11/03/2020] [Accepted: 11/06/2020] [Indexed: 11/16/2022] Open
Abstract
OBJECTIVES This study described the population structure of M. tuberculosis complex (MTBc) strains among patients with pulmonary or lymph node tuberculosis (TB) in Northwest Ethiopia and tested the performance of culture isolation and MPT64-based speciation for Lineage 7 (L7). METHODS Patients were recruited between April 2017 and June 2019 in North Gondar, Ethiopia. The MPT64 assay was used to confirm MTBc, and spoligotyping was used to characterize mycobacterial lineages. Line probe assay (LPA) was used to detect resistance to rifampicin and isoniazid. RESULTS Among 274 MTBc genotyped isolates, there were five MTBc lineages: L1-L4 and L7 were identified, with predominant East-African-Indian (L3) (53.6%) and Euro-American (L4) (40.1%) strains, and low prevalence (2.6%) of Ethiopia L7. The genotypes were similarly distributed between pulmonary and lymph node TB, and all lineages were equally isolated by culture and recognized as MTBc by the MPT64 assay. Additionally, LPA showed that 259 (94.5%) MTBc were susceptible to both rifampicin and isoniazid, and one (0.4%) was multi-drug resistant (resistant to both rifampicin and isoniazid). CONCLUSION These findings show that TB in North Gondar, Ethiopia, is mainly caused by L3 and L4 strains, with low rates of L7, confirmed as MTBc by MPT64 assay and with limited resistance to rifampicin and isoniazid.
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Affiliation(s)
- Mebrat Ejo
- Institute of Tropical Medicine (ITM), Antwerp, Belgium; University of Gondar, Gondar, Ethiopia; Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium.
| | | | | | - Meseret Kassa
- TB Culture Laboratory, University of Gondar Comprehensive Specialized Hospital, Gondar, Ethiopia
| | - Yilak Girma
- TB Culture Laboratory, University of Gondar Comprehensive Specialized Hospital, Gondar, Ethiopia
| | - Tiruzer Bekele
- Department of Pathology, College of Medicine and Health Sciences, University of Gondar, Gondar, Ethiopia
| | - Yilkal Ademe
- Department of Pathology, College of Medicine and Health Sciences, University of Gondar, Gondar, Ethiopia
| | - Ermias Diro
- Department of Internal Medicine, College of Medicine and Health Sciences, University of Gondar, Gondar, Ethiopia
| | - Florian Gehre
- Institute of Tropical Medicine (ITM), Antwerp, Belgium; Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, Germany; East African Community Secretariat (EAC), Arusha, Tanzania
| | - Leen Rigouts
- Institute of Tropical Medicine (ITM), Antwerp, Belgium; Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
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10
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Tagbo BN, Bancroft RE, Fajolu I, Abdulkadir MB, Bashir MF, Okunola OP, Isiaka AH, Lawal NM, Edelu BO, Onyejiaka N, Ihuoma CJ, Ndu F, Ozumba UC, Udeinya F, Ogunsola F, Saka AO, Fadeyi A, Aderibigbe SA, Abdulraheem J, Yusuf AG, Sylvanus Ndow P, Ogbogu P, Kanu C, Emina V, Makinwa OJ, Gehre F, Yusuf K, Braka F, Mwenda JM, Ticha JM, Nwodo D, Worwui A, Biey JN, Kwambana-Adams BA, Antonio M. Pediatric Bacterial Meningitis Surveillance in Nigeria From 2010 to 2016, Prior to and During the Phased Introduction of the 10-Valent Pneumococcal Conjugate Vaccine. Clin Infect Dis 2020; 69:S81-S88. [PMID: 31505626 PMCID: PMC6736152 DOI: 10.1093/cid/ciz474] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Background Historically, Nigeria has experienced large bacterial meningitis outbreaks with high mortality in children. Streptococcus pneumoniae (pneumococcus), Neisseria meningitidis (meningococcus), and Haemophilus influenzae are major causes of this invasive disease. In collaboration with the World Health Organization, we conducted longitudinal surveillance in sentinel hospitals within Nigeria to establish the burden of pediatric bacterial meningitis (PBM). Methods From 2010 to 2016, cerebrospinal fluid was collected from children <5 years of age, admitted to 5 sentinel hospitals in 5 Nigerian states. Microbiological and latex agglutination techniques were performed to detect the presence of pneumococcus, meningococcus, and H. influenzae. Species-specific polymerase chain reaction and serotyping/grouping were conducted to determine specific causative agents of PBM. Results A total of 5134 children with suspected meningitis were enrolled at the participating hospitals; of these 153 (2.9%) were confirmed PBM cases. The mortality rate for those infected was 15.0% (23/153). The dominant pathogen was pneumococcus (46.4%: 71/153) followed by meningococcus (34.6%: 53/153) and H. influenzae (19.0%: 29/153). Nearly half the pneumococcal meningitis cases successfully serotyped (46.4%: 13/28) were caused by serotypes that are included in the 10-valent pneumococcal conjugate vaccine. The most prevalent meningococcal and H. influenzae strains were serogroup W and serotype b, respectively. Conclusions Vaccine-type bacterial meningitis continues to be common among children <5 years in Nigeria. Challenges with vaccine introduction and coverage may explain some of these finding. Continued surveillance is needed to determine the distribution of serotypes/groups of meningeal pathogens across Nigeria and help inform and sustain vaccination policies in the country.
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Affiliation(s)
- Beckie N Tagbo
- Institute of Child Health, University of Nigeria Teaching Hospital, Ituku-Ozalla, and.,Department of Paediatrics University of Nigeria Teaching Hospital Ituku-Ozalla, Enugu State
| | - Rowan E Bancroft
- World Health Organization (WHO) Collaborating Centre for New Vaccines Surveillance, Medical Research Council Unit The Gambia at London School of Hygiene & Tropical Medicine, Banjul
| | - Iretiola Fajolu
- Department of Paediatrics, Lagos University Teaching Hospital.,Department of Paediatrics, College of Medicine, University of Lagos
| | | | - Muhammad F Bashir
- Department of Paediatrics, Abubakar Tafawa Balewa University Teaching Hospital, Bauchi
| | | | | | - Namadi M Lawal
- Department of Disease Control and Immunization, National Primary Health Care Development Agency, Abuja
| | - Benedict O Edelu
- Department of Paediatrics University of Nigeria Teaching Hospital Ituku-Ozalla, Enugu State
| | - Ngozi Onyejiaka
- Department of Medical Microbiology and Parasitology, Lagos University Teaching Hospital
| | - Chinonyerem J Ihuoma
- Department of Microbiology, University of Nigeria Teaching Hospital, Ituku-Ozalla, Enugu State
| | | | - Uchenna C Ozumba
- Department of Microbiology, University of Nigeria Teaching Hospital, Ituku-Ozalla, Enugu State
| | - Frances Udeinya
- Department of Microbiology, University of Nigeria Teaching Hospital, Ituku-Ozalla, Enugu State
| | - Folasade Ogunsola
- Department of Medical Microbiology and Parasitology, Lagos University Teaching Hospital
| | - Aishat O Saka
- Department of Paediatrics and Child Health, University of Ilorin Teaching Hospital
| | - Abayomi Fadeyi
- Department of Medical Microbiology and Parasitology, University of Ilorin Teaching Hospital, Kwara
| | - Sunday A Aderibigbe
- Department of Epidemiology and Community Health, University of Ilorin Teaching Hospital, Kwara
| | - Jimoh Abdulraheem
- Department of Medical Microbiology and Parasitology, University of Ilorin Teaching Hospital, Kwara
| | - Adamu G Yusuf
- Medical Microbiology Department, Abubakar Tafawa Balewa University Teaching Hospital, Bauchi
| | - Peter Sylvanus Ndow
- World Health Organization (WHO) Collaborating Centre for New Vaccines Surveillance, Medical Research Council Unit The Gambia at London School of Hygiene & Tropical Medicine, Banjul
| | - Philomena Ogbogu
- Department of Medical Microbiology, University of Benin Teaching Hospital
| | - Chinomnso Kanu
- Department of Community Health, University of Benin Teaching Hospital, and
| | - Velly Emina
- Department of Community Health and Primary Care, Lagos University Teaching Hospital, Nigeria
| | - Olajumoke J Makinwa
- Department of Medical Microbiology and Parasitology, Lagos University Teaching Hospital
| | - Florian Gehre
- Department of Paediatrics University of Nigeria Teaching Hospital Ituku-Ozalla, Enugu State.,Department of Infectious Disease Epidemiology, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, Germany
| | - Kabir Yusuf
- Department of Disease Control and Immunization, National Primary Health Care Development Agency, Abuja
| | | | - Jason M Mwenda
- WHO Regional Office for Africa WHO/AFRO, Republic of Congo, Brazzaville
| | | | | | - Archibald Worwui
- World Health Organization (WHO) Collaborating Centre for New Vaccines Surveillance, Medical Research Council Unit The Gambia at London School of Hygiene & Tropical Medicine, Banjul
| | - Joseph N Biey
- WHO Regional Office for Africa WHO/AFRO, Republic of Congo, Brazzaville
| | - Brenda A Kwambana-Adams
- World Health Organization (WHO) Collaborating Centre for New Vaccines Surveillance, Medical Research Council Unit The Gambia at London School of Hygiene & Tropical Medicine, Banjul
| | - Martin Antonio
- World Health Organization (WHO) Collaborating Centre for New Vaccines Surveillance, Medical Research Council Unit The Gambia at London School of Hygiene & Tropical Medicine, Banjul.,Microbiology and Infection Unit, Warwick Medical School, University of Warwick, Coventry, United Kingdom
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11
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Senghore M, Diarra B, Gehre F, Otu J, Worwui A, Muhammad AK, Kwambana-Adams B, Kay GL, Sanogo M, Baya B, Orsega S, Doumbia S, Diallo S, de Jong BC, Pallen MJ, Antonio M. Evolution of Mycobacterium tuberculosis complex lineages and their role in an emerging threat of multidrug resistant tuberculosis in Bamako, Mali. Sci Rep 2020; 10:327. [PMID: 31941887 PMCID: PMC6962199 DOI: 10.1038/s41598-019-56001-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2018] [Accepted: 09/30/2019] [Indexed: 11/10/2022] Open
Abstract
In recent years Bamako has been faced with an emerging threat from multidrug resistant TB (MDR-TB). Whole genome sequence analysis was performed on a subset of 76 isolates from a total of 208 isolates recovered from tuberculosis patients in Bamako, Mali between 2006 and 2012. Among the 76 patients, 61(80.3%) new cases and 15(19.7%) retreatment cases, 12 (16%) were infected by MDR-TB. The dominant lineage was the Euro-American lineage, Lineage 4. Within Lineage 4, the Cameroon genotype was the most prevalent genotype (n = 20, 26%), followed by the Ghana genotype (n = 16, 21%). A sub-clade of the Cameroon genotype, which emerged ~22 years ago was likely to be involved in community transmission. A sub-clade of the Ghana genotype that arose approximately 30 years ago was an important cause of MDR-TB in Bamako. The Ghana genotype isolates appeared more likely to be MDR than other genotypes after controlling for treatment history. We identified a clade of four related Beijing isolates that included one MDR-TB isolate. It is a major concern to find the Cameroon and Ghana genotypes involved in community transmission and MDR-TB respectively. The presence of the Beijing genotype in Bamako remains worrying, given its high transmissibility and virulence.
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Affiliation(s)
- Madikay Senghore
- Medical Research Council Unit The Gambia at The London School of Hygiene & Tropical Medicine, Atlantic Boulevard, Fajara, PO Box 273, Banjul, The Gambia
- Division of Microbiology & Immunity, Warwick Medical School, University of Warwick, Coventry, CV4 7AL, UK
| | - Bassirou Diarra
- University Clinical Research Center (UCRC)-SEREFO-Laboratory, University of Sciences, Techniques and Technologies of Bamako (USTTB), Bamako, Mali
| | - Florian Gehre
- Medical Research Council Unit The Gambia at The London School of Hygiene & Tropical Medicine, Atlantic Boulevard, Fajara, PO Box 273, Banjul, The Gambia
- Institute of Tropical Medicine, Antwerp, Belgium
| | - Jacob Otu
- Medical Research Council Unit The Gambia at The London School of Hygiene & Tropical Medicine, Atlantic Boulevard, Fajara, PO Box 273, Banjul, The Gambia
| | - Archibald Worwui
- Medical Research Council Unit The Gambia at The London School of Hygiene & Tropical Medicine, Atlantic Boulevard, Fajara, PO Box 273, Banjul, The Gambia
| | - Abdul Khalie Muhammad
- Medical Research Council Unit The Gambia at The London School of Hygiene & Tropical Medicine, Atlantic Boulevard, Fajara, PO Box 273, Banjul, The Gambia
| | - Brenda Kwambana-Adams
- Medical Research Council Unit The Gambia at The London School of Hygiene & Tropical Medicine, Atlantic Boulevard, Fajara, PO Box 273, Banjul, The Gambia
| | - Gemma L Kay
- Division of Microbiology & Immunity, Warwick Medical School, University of Warwick, Coventry, CV4 7AL, UK
- Norwich Medical School, University of East Anglia, Norwich, NR4 7TJ, UK
| | - 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
| | - Susan Orsega
- Collaborative Clinical Research Branch, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, Bethesda, Maryland, USA
| | - 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
| | | | - Mark J Pallen
- Division of Microbiology & Immunity, Warwick Medical School, University of Warwick, Coventry, CV4 7AL, UK
- Quadram Institute, Norwich Research Park, Norwich, Norfolk, NR4 7UA, UK
| | - Martin Antonio
- Medical Research Council Unit The Gambia at The London School of Hygiene & Tropical Medicine, Atlantic Boulevard, Fajara, PO Box 273, Banjul, The Gambia.
- Division of Microbiology & Immunity, Warwick Medical School, University of Warwick, Coventry, CV4 7AL, UK.
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12
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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13
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de Jong BC, Gaye BM, Luyten J, van Buitenen B, André E, Meehan CJ, O'Siochain C, Tomsu K, Urbain J, Grietens KP, Njue M, Pinxten W, Gehre F, Nyan O, Buvé A, Roca A, Ravinetto R, Antonio M. Ethical Considerations for Movement Mapping to Identify Disease Transmission Hotspots. Emerg Infect Dis 2019; 25. [PMID: 31211938 PMCID: PMC6590736 DOI: 10.3201/eid2507.181421] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022] Open
Abstract
Traditional public health methods for detecting infectious disease transmission, such as contact tracing and molecular epidemiology, are time-consuming and costly. Information and communication technologies, such as global positioning systems, smartphones, and mobile phones, offer opportunities for novel approaches to identifying transmission hotspots. However, mapping the movements of potentially infected persons comes with ethical challenges. During an interdisciplinary meeting of researchers, ethicists, data security specialists, information and communication technology experts, epidemiologists, microbiologists, and others, we arrived at suggestions to mitigate the ethical concerns of movement mapping. These suggestions include a template Data Protection Impact Assessment that follows European Union General Data Protection Regulations.
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14
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Faburay AK, Mendy FS, Gibba SA, Lamin M, Sambou B, Mendy A, Faal-Jawara TI, Gehre F, Sutherland J, Kampmann B, Secka O. PO 8414 EVALUATION OF MYCOBACTERIUM TUBERCULOSIS COMPLEX (MTBC) CULTURE METHODS IN MYCOBACTERIUM AFRICANUM-ENDEMIC REGION OF WEST AFRICA. BMJ Glob Health 2019. [DOI: 10.1136/bmjgh-2019-edc.88] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
Abstract
BackgroundWith the endemic Mycobacterium africanum (Maf), West African laboratories use glycerol and pyruvate in separate LJ cultures (LJG and LJP) for isolation of MTBC. The aim of this work is to evaluate if combining both glycerol and pyruvate in a single LJ medium (LJGP) will lead to comparable growth characteristics and time to detection in comparison to LJG, LJP and MGIT 960.MethodTotal of 118 smear-positive sputum samples were processed using 4% NaOH-NALC decontamination method. The decontaminated samples were inoculated parallel on LJG, LGP, MGIT 960 and LJGP. Positive cultures were confirmed using Ziehl-Neelsen staining method. MTBC identification was done using the Capilia TBNeo kit and spoligotyping used for speciation.ResultsThe recovery rate for LJG, LJP, LJPG and MGIT was found to be 73.7% (87/118), 82.2% (96/118), 83.9% (99/118) and 93.2% (110/118) respectively. No significant agreement was observed between the LJPG and MGIT 960 with Kappa values of −0.105 (p-value=0.199). However, there was significant agreement between LJGP and LJG and LJP with Kappa value of 0736 (p-value<0.001) and 0.756 (p-value<0.001), respectively. There were 70 Euro-American, 34 Maf, 9 East-Asian, 2Indo-Oceanic, 2 East-African-Indian and 1 M. Bovis. LJGP have better Maf recovery rate, 85.3% (29/34) in comparison to MGIT 960, 79.4% (27/34), LJP, 76.5% (26/34) and LJG, 61.8% (21/34). Seven of the 8 MGIT negatives that were LJPG positive were M. africanum and 1 M. bovis.ConclusionLJPG has a better detection rate and time to positivity compared to LJG and LJP and was shown to have a better Maf recovery than other LJ methods and MGIT 960. It is evident that LJGP is a promising culture tool for Maf-endemic West African countries that will not only increase MTBC recovery rate in combination with MGIT, but also leads to better detection of Maf.
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Meehan CJ, Moris P, Kohl TA, Pečerska J, Akter S, Merker M, Utpatel C, Beckert P, Gehre F, Lempens P, Stadler T, Kaswa MK, Kühnert D, Niemann S, de Jong BC. The relationship between transmission time and clustering methods in Mycobacterium tuberculosis epidemiology. EBioMedicine 2018; 37:410-416. [PMID: 30341041 PMCID: PMC6284411 DOI: 10.1016/j.ebiom.2018.10.013] [Citation(s) in RCA: 80] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Revised: 09/17/2018] [Accepted: 10/03/2018] [Indexed: 11/20/2022] Open
Abstract
BACKGROUND Tracking recent transmission is a vital part of controlling widespread pathogens such as Mycobacterium tuberculosis. Multiple methods with specific performance characteristics exist for detecting recent transmission chains, usually by clustering strains based on genotype similarities. With such a large variety of methods available, informed selection of an appropriate approach for determining transmissions within a given setting/time period is difficult. METHODS This study combines whole genome sequence (WGS) data derived from 324 isolates collected 2005-2010 in Kinshasa, Democratic Republic of Congo (DRC), a high endemic setting, with phylodynamics to unveil the timing of transmission events posited by a variety of standard genotyping methods. Clustering data based on Spoligotyping, 24-loci MIRU-VNTR typing, WGS based SNP (Single Nucleotide Polymorphism) and core genome multi locus sequence typing (cgMLST) typing were evaluated. FINDINGS Our results suggest that clusters based on Spoligotyping could encompass transmission events that occurred almost 200 years prior to sampling while 24-loci-MIRU-VNTR often represented three decades of transmission. Instead, WGS based genotyping applying low SNP or cgMLST allele thresholds allows for determination of recent transmission events, e.g. in timespans of up to 10 years for a 5 SNP/allele cut-off. INTERPRETATION With the rapid uptake of WGS methods in surveillance and outbreak tracking, the findings obtained in this study can guide the selection of appropriate clustering methods for uncovering relevant transmission chains within a given time-period. For high resolution cluster analyses, WGS-SNP and cgMLST based analyses have similar clustering/timing characteristics even for data obtained from a high incidence setting.
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Affiliation(s)
- Conor J Meehan
- Unit of Mycobacteriology, Biomedical Sciences, Institute of Tropical Medicine, Antwerp 2000, Belgium.
| | - Pieter Moris
- Unit of Mycobacteriology, Biomedical Sciences, Institute of Tropical Medicine, Antwerp 2000, Belgium; Adrem Data Lab (Adrem), Department of Mathematics and Computer Science, University of Antwerp, Antwerp 2020, Belgium; Biomedical Informatics Research Network Antwerp (biomina), University of Antwerp, Antwerp 2020, Belgium
| | - Thomas A Kohl
- German Center for Infection Research, Partner Site Hamburg-Lübeck-Borstel-Riems, D-23845 Borstel, Germany; Molecular and Experimental Mycobacteriology, Priority Area Infections, Research Center Borstel, D-23845 Borstel, Germany
| | - Jūlija Pečerska
- Swiss Institute of Bioinformatics (SIB), 1015 Lausanne, Switzerland
| | - Suriya Akter
- Unit of Mycobacteriology, Biomedical Sciences, Institute of Tropical Medicine, Antwerp 2000, Belgium
| | - Matthias Merker
- German Center for Infection Research, Partner Site Hamburg-Lübeck-Borstel-Riems, D-23845 Borstel, Germany; Molecular and Experimental Mycobacteriology, Priority Area Infections, Research Center Borstel, D-23845 Borstel, Germany
| | - Christian Utpatel
- German Center for Infection Research, Partner Site Hamburg-Lübeck-Borstel-Riems, D-23845 Borstel, Germany; Molecular and Experimental Mycobacteriology, Priority Area Infections, Research Center Borstel, D-23845 Borstel, Germany
| | - Patrick Beckert
- German Center for Infection Research, Partner Site Hamburg-Lübeck-Borstel-Riems, D-23845 Borstel, Germany; Molecular and Experimental Mycobacteriology, Priority Area Infections, Research Center Borstel, D-23845 Borstel, Germany
| | - Florian Gehre
- Unit of Mycobacteriology, Biomedical Sciences, Institute of Tropical Medicine, Antwerp 2000, Belgium; Vaccines and Immunity Theme, Medical Research Council Unit The Gambia, Serekunda, Gambia; Department Infectious Diseases Epidemiology, Bernhard Nocht Institute for Tropical Medicine, Hamburg 20359, Germany
| | - Pauline Lempens
- Unit of Mycobacteriology, Biomedical Sciences, Institute of Tropical Medicine, Antwerp 2000, Belgium
| | - Tanja Stadler
- Swiss Institute of Bioinformatics (SIB), 1015 Lausanne, Switzerland
| | - Michel K Kaswa
- Unit of Mycobacteriology, Biomedical Sciences, Institute of Tropical Medicine, Antwerp 2000, Belgium; National Tuberculosis Program, Kinshasa, DR Congo
| | - Denise Kühnert
- Max Planck Institute for the Science of Human History, 07745 JENA, Germany
| | - Stefan Niemann
- German Center for Infection Research, Partner Site Hamburg-Lübeck-Borstel-Riems, D-23845 Borstel, Germany; Molecular and Experimental Mycobacteriology, Priority Area Infections, Research Center Borstel, D-23845 Borstel, Germany
| | - Bouke C de Jong
- Unit of Mycobacteriology, Biomedical Sciences, Institute of Tropical Medicine, Antwerp 2000, Belgium
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Senghore M, Diarra B, Gehre F, Otu J, Worwui A, Muhammad A, Sanogo M, Baya B, Orsega S, Doumbia S, Diallo S, de Jong B, Pallen M, Antonio M. Evolution of virulent genotypes and an emerging threat of multidrug resistant tuberculosis in Bamako, Mali. Int J Infect Dis 2018. [DOI: 10.1016/j.ijid.2018.04.3573] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022] Open
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Morter R, Adetifa I, Antonio M, Touray F, de Jong BC, Gower CM, Gehre F. Examining human paragonimiasis as a differential diagnosis to tuberculosis in The Gambia. BMC Res Notes 2018; 11:31. [PMID: 29334998 PMCID: PMC5769439 DOI: 10.1186/s13104-018-3134-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2017] [Accepted: 01/06/2018] [Indexed: 11/10/2022] Open
Abstract
OBJECTIVE Paragonimiasis is a foodborne trematode infection of the lungs caused by Paragonimus spp., presenting clinically with similar symptoms to active tuberculosis (TB). Worldwide, an estimated 20.7 million people are infected with paragonimiasis, but relatively little epidemiological data exists for Africa. Given a recently reported case, we sought to establish whether paragonimiasis should be considered as an important differential diagnosis for human TB in The Gambia, West Africa. RESULTS We developed a novel PCR-based diagnostic test for Paragonimus species known to be found in West Africa, which we used to examine archived TB negative sputum samples from a cross-sectional study of volunteers with tuberculosis-like symptoms from communities in the Western coastal region of The Gambia. Based on a "zero patient" design for detection of rare diseases, 300 anonymised AFB smear negative sputum samples, randomly selected from 25 villages, were screened for active paragonimiasis by molecular detection of Paragonimus spp. DNA. No parasite DNA was found in any of the sputa of our patient group. Despite the recent case report, we found no evidence of active paragonimiasis infection masking as TB in the Western region of The Gambia.
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Affiliation(s)
- Richard Morter
- Vaccines and Immunity Theme, Medical Research Council (MRC) Unit The Gambia, Fajara, The Gambia
- School of Biological Sciences, The University of Manchester, Manchester, UK
| | - Ifedayo Adetifa
- Disease Control and Elimination Theme, Medical Research Council (MRC) Unit The Gambia, Fajara, The Gambia
- Department of Infectious Disease Epidemiology, London School of Hygiene and Tropical Medicine, London, UK
| | - Martin Antonio
- Vaccines and Immunity Theme, Medical Research Council (MRC) Unit The Gambia, Fajara, The Gambia
- Microbiology and Infection Unit, Warwick Medical School, University of Warwick, Coventry, UK
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, UK
| | - Fatima Touray
- Vaccines and Immunity Theme, Medical Research Council (MRC) Unit The Gambia, Fajara, The Gambia
| | - Bouke C. de Jong
- Vaccines and Immunity Theme, Medical Research Council (MRC) Unit The Gambia, Fajara, The Gambia
- Department of Medicine, New York University, New York, USA
- Mycobacteriology Unit, Institute of Tropical Medicine, Antwerp, Belgium
| | - Charlotte M. Gower
- Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - Florian Gehre
- Vaccines and Immunity Theme, Medical Research Council (MRC) Unit The Gambia, Fajara, The Gambia
- Mycobacteriology Unit, Institute of Tropical Medicine, Antwerp, Belgium
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Gower CM, Gehre F, Marques SR, Lamberton PHL, Lwambo NJ, Webster JP. Phenotypic and genotypic monitoring of Schistosoma mansoni in Tanzanian schoolchildren five years into a preventative chemotherapy national control programme. Parasit Vectors 2017; 10:593. [PMID: 29197426 PMCID: PMC5712074 DOI: 10.1186/s13071-017-2533-6] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2017] [Accepted: 11/13/2017] [Indexed: 01/06/2023] Open
Abstract
BACKGROUND Schistosoma mansoni is a parasite of profound medical importance. Current control focusses on mass praziquantel (PZQ) treatment of populations in endemic areas, termed Preventative Chemotherapy (PC). Large-scale PC programmes exert prolonged selection pressures on parasites with the potential for, direct and/or indirect, emergence of drug resistance. Molecular methods can help monitor genetic changes of schistosome populations over time and in response to drug treatment, as well as estimate adult worm burdens through parentage analysis. Furthermore, methods such as in vitro drug sensitivity assays help phenotype in vivo parasite genotypic drug efficacy. METHODS We conducted combined in vitro PZQ efficacy testing with population genetic analyses of S. mansoni collected from children from two schools in 2010, five years after the introduction of a National Control Programme. Children at one school had received four annual PZQ treatments and the other school had received two mass treatments in total. We compared genetic differentiation, indices of genetic diversity, and estimated adult worm burden from parasites collected in 2010 with samples collected in 2005 (before the control programme began) and in 2006 (six months after the first PZQ treatment). Using 2010 larval samples, we also compared the genetic similarity of those with high and low in vitro sensitivity to PZQ. RESULTS We demonstrated that there were individual parasites with reduced PZQ susceptibility in the 2010 collections, as evidenced by our in vitro larval behavioural phenotypic assay. There was no evidence, however, that miracidia showing phenotypically reduced susceptibility clustered together genetically. Molecular analysis also demonstrated a significant reduction of adult worm load over time, despite little evidence of reduction in parasite infection intensity, as measured by egg output. Genetic diversity of infections did not reduce over time, despite changes in the genetic composition of the parasite populations. CONCLUSIONS Genotypic and phenotypic monitoring did not indicate a selective sweep, as may be expected if PZQ treatment was selecting a small number of related "resistant" parasites, but there was evidence of genetic changes at the population level over time. Genetic data were used to estimate adult worm burdens, which unlike parasite infection intensity, showed reductions over time, suggesting the relaxation of negative density-dependent constraints on parasite fecundity with PZQ treatment. We thereby demonstrated that density-dependence in schistosome populations may complicate evaluation and monitoring of control programmes.
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Affiliation(s)
- Charlotte M. Gower
- Centre for Endemic, Emerging and Exotic Diseases, The Royal Veterinary College, University of London, London, AL9 7TA UK
- Department of Infectious Disease Epidemiology, Imperial College, Faculty of Medicine, W2 1PG, London, UK
| | - Florian Gehre
- Department of Infectious Disease Epidemiology, Imperial College, Faculty of Medicine, W2 1PG, London, UK
- Mycobacteriology Unit, Institute of Tropical Medicine, Antwerp, Belgium
| | - Sara R. Marques
- Department of Life Sciences, Imperial College, Faculty of Medicine, London, UK
| | - Poppy H. L. Lamberton
- Department of Infectious Disease Epidemiology, Imperial College, Faculty of Medicine, W2 1PG, London, UK
- Institute of Biodiversity, Animal Health & Comparative Medicine & Wellcome Centre for Molecular Parasitology, University of Glasgow, G12 8QQ, Glasgow, UK
| | - Nicholas J. Lwambo
- Mwanza Research Centre, National Institute for Medical Research, Mwanza, Tanzania
| | - Joanne P. Webster
- Centre for Endemic, Emerging and Exotic Diseases, The Royal Veterinary College, University of London, London, AL9 7TA UK
- Department of Infectious Disease Epidemiology, Imperial College, Faculty of Medicine, W2 1PG, London, UK
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Okoi C, Anderson STB, Antonio M, Mulwa SN, Gehre F, Adetifa IMO. Non-tuberculous Mycobacteria isolated from Pulmonary samples in sub-Saharan Africa - A Systematic Review and Meta Analyses. Sci Rep 2017; 7:12002. [PMID: 28931915 PMCID: PMC5607231 DOI: 10.1038/s41598-017-12175-z] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2017] [Accepted: 09/05/2017] [Indexed: 01/29/2023] Open
Abstract
Pulmonary non-tuberculous mycobacterial (NTM) disease epidemiology in sub-Saharan Africa is not as well described as for pulmonary tuberculosis. Earlier reviews of global NTM epidemiology only included subject-level data from one sub-Saharan Africa country. We systematically reviewed the literature and searched PubMed, Embase, Popline, OVID and Africa Wide Information for articles on prevalence and clinical relevance of NTM detection in pulmonary samples in sub-Saharan Africa. We applied the American Thoracic Society/Infectious Disease Society of America criteria to differentiate between colonisation and disease. Only 37 articles from 373 citations met our inclusion criteria. The prevalence of pulmonary NTM colonization was 7.5% (95% CI: 7.2%–7.8%), and 75.0% (2325 of 3096) occurred in males, 16.5% (512 of 3096) in those previously treated for tuberculosis and Mycobacterium avium complex predominated (27.7% [95% CI: 27.2–28.9%]). In seven eligible studies, 27.9% (266 of 952) of participants had pulmonary NTM disease and M. kansasii with a prevalence of 69.2% [95% CI: 63.2–74.7%] was the most common cause of pulmonary NTM disease. NTM species were unidentifiable in 29.2% [2,623 of 8,980] of isolates. In conclusion, pulmonary NTM disease is a neglected and emerging public health disease and enhanced surveillance is required.
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Affiliation(s)
- Catherine Okoi
- Vaccines and Immunity Theme, Medical Research Council Unit, Fajara, The Gambia
| | | | - Martin Antonio
- Vaccines and Immunity Theme, Medical Research Council Unit, Fajara, The Gambia.,Microbiology and Infection Unit, Warwick Medical School, University of Warwick, Coventry, United Kingdom.,Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, United Kingdom
| | - Sarah N Mulwa
- Disease Control and Elimination Theme, Medical Research Council Unit The Gambia, Fajara, The Gambia
| | - Florian Gehre
- Vaccines and Immunity Theme, Medical Research Council Unit, Fajara, The Gambia.,Institute of Tropical Medicine, Antwerp, Belgium
| | - Ifedayo M O Adetifa
- Department of Infectious Diseases Epidemiology, London School of Hygiene and Tropical Medicine, London, United Kingdom. .,Epidemiology and Demography Department, KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya. .,College of Medicine University of Lagos, Lagos, Nigeria.
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Senghore M, Otu J, Witney A, Gehre F, Doughty EL, Kay GL, Butcher P, Salako K, Kehinde A, Onyejepu N, Idigbe E, Corrah T, de Jong B, Pallen MJ, Antonio M. Whole-genome sequencing illuminates the evolution and spread of multidrug-resistant tuberculosis in Southwest Nigeria. PLoS One 2017; 12:e0184510. [PMID: 28926571 PMCID: PMC5604961 DOI: 10.1371/journal.pone.0184510] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2017] [Accepted: 08/27/2017] [Indexed: 11/18/2022] Open
Abstract
Nigeria has an emerging problem with multidrug-resistant tuberculosis (MDR-TB). Whole-genome sequencing was used to understand the epidemiology of tuberculosis and genetics of multi-drug resistance among patients from two tertiary referral centers in Southwest Nigeria. In line with previous molecular epidemiology studies, most isolates of Mycobacterium tuberculosis from this dataset belonged to the Cameroon clade within the Euro-American lineage. Phylogenetic analysis showed this clade was undergoing clonal expansion in this region, and suggests that it was involved in community transmission of sensitive and multidrug-resistant tuberculosis. Five patients enrolled for retreatment were infected with pre-extensively drug resistant (pre-XDR) due to fluoroquinolone resistance in isolates from the Cameroon clade. In all five cases resistance was conferred through a mutation in the gyrA gene. In some patients, genomic changes occurred in bacterial isolates during the course of treatment that potentially led to decreased drug susceptibility. We conclude that inter-patient transmission of resistant isolates, principally from the Cameroon clade, contributes to the spread of MDR-TB in this setting, underscoring the urgent need to curb the spread of multi-drug resistance in this region.
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MESH Headings
- Adolescent
- Adult
- Antitubercular Agents/pharmacology
- Bacterial Proteins/genetics
- Cameroon/epidemiology
- Child
- Child, Preschool
- DNA Gyrase/genetics
- Drug Resistance, Multiple, Bacterial/drug effects
- Drug Resistance, Multiple, Bacterial/genetics
- Female
- Genome, Bacterial
- Humans
- Infant
- Infant, Newborn
- Male
- Mutation
- Mycobacterium tuberculosis/classification
- Mycobacterium tuberculosis/drug effects
- Mycobacterium tuberculosis/genetics
- Mycobacterium tuberculosis/isolation & purification
- Nigeria/epidemiology
- Phylogeny
- Sequence Analysis, DNA
- Tuberculosis, Multidrug-Resistant/diagnosis
- Tuberculosis, Multidrug-Resistant/epidemiology
- Tuberculosis, Multidrug-Resistant/microbiology
- Young Adult
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Affiliation(s)
- Madikay Senghore
- Vaccines and Immunity Theme, Medical Research Council Unit The Gambia, Fajara, The Gambia
- Microbiology and Infection Unit, The University of Warwick, Coventry, United Kingdom
| | - Jacob Otu
- Vaccines and Immunity Theme, Medical Research Council Unit The Gambia, Fajara, The Gambia
| | - Adam Witney
- Institute of Infection and Immunity, St George’s University of London, London, United Kingdom
| | - Florian Gehre
- Vaccines and Immunity Theme, Medical Research Council Unit The Gambia, Fajara, The Gambia
- Institute of Tropical Medicine, Antwerp, Belgium
| | - Emma L. Doughty
- Microbiology and Infection Unit, The University of Warwick, Coventry, United Kingdom
| | - Gemma L. Kay
- Microbiology and Infection Unit, The University of Warwick, Coventry, United Kingdom
| | - Phillip Butcher
- Institute of Infection and Immunity, St George’s University of London, London, United Kingdom
| | - Kayode Salako
- Department of Medical Microbiology & Parasitology, University College Hospital, Ibadan, Nigeria
| | - Aderemi Kehinde
- Department of Medical Microbiology & Parasitology, University College Hospital, Ibadan, Nigeria
| | - Nneka Onyejepu
- National Tuberculosis Reference Laboratory, Nigeria Institute of Medical Research, Lagos, Nigeria
| | - Emmanuel Idigbe
- National Tuberculosis Reference Laboratory, Nigeria Institute of Medical Research, Lagos, Nigeria
| | - Tumani Corrah
- Vaccines and Immunity Theme, Medical Research Council Unit The Gambia, Fajara, The Gambia
| | | | - Mark J. Pallen
- Microbiology and Infection Unit, The University of Warwick, Coventry, United Kingdom
- Quadram Institute, Norwich Research Park, Norwich, Norfolk, NR4 7UA
| | - Martin Antonio
- Vaccines and Immunity Theme, Medical Research Council Unit The Gambia, Fajara, The Gambia
- Microbiology and Infection Unit, The University of Warwick, Coventry, United Kingdom
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, United Kingdom
- * E-mail:
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Ba Diallo A, Ossoga GW, Daneau G, Lo S, Ngandolo R, Djaibé CD, Djouater B, Mboup S, de Jong BC, Diallo AG, Gehre F. Emergence and clonal transmission of multi-drug-resistant tuberculosis among patients in Chad. BMC Infect Dis 2017; 17:579. [PMID: 28830384 PMCID: PMC5567628 DOI: 10.1186/s12879-017-2671-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2016] [Accepted: 08/07/2017] [Indexed: 11/10/2022] Open
Abstract
Background Emergence of Multidrug-resistant (MDR) strains constitutes a significant public health problem worldwide. Prevalence of MDR tuberculosis from Chad is unavailable to date. Methods We collected samples from consecutive TB patients nationwide in the seven major cities of Chad between 2007 and 2012 to characterize drug resistance and the population structure of circulating Mycobacterium tuberculosis complex (MTBC) strains. We tested drug sensitivity using Line Probe Assays and phenotypic drug susceptibility testing (DST) were used for second line drugs. We genotyped the isolates using spoligotype analysis and MIRU-VNTR. Results A total of 311 cultures were isolated from 593 patients. The MDR prevalence was 0.9% among new patients and 3.5% among retreatment patients, and no second line drug resistance was identified. The distribution of genotypes suggests a dissemination of MDR strains in the Southern city of Moundou, bordering Cameroon and Central African Republic. Conclusion Emerging MDR isolates pose a public health threat to Southern Chad, with risk to neighboring countries. This study informs public health practitioners, justifying the implementation of continuous surveillance with DST for all retreatment cases as well as contacts of MDR patients, in parallel with provision of adequate 2nd line regimens in the region. Electronic supplementary material The online version of this article (doi:10.1186/s12879-017-2671-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Awa Ba Diallo
- Mycobacteria Unit, Bacteriology- Virology Laboratory, CHU Aristide Le Dantec, 30 Avenue Pasteur, BP 7325, Dakar, Senegal.
| | - Gedeon W Ossoga
- Institut de Recherche en Elevage pour le Developpement, N'Djamena, Chad
| | - Geraldine Daneau
- Mycobacteriology Unit, Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | - Seynabou Lo
- Faculty of Health Sciences, Gaston Berger University, Saint Louis, Senegal
| | - Richard Ngandolo
- Institut de Recherche en Elevage pour le Developpement, N'Djamena, Chad
| | | | - Barou Djouater
- Institut de Recherche en Elevage pour le Developpement, N'Djamena, Chad
| | - Souleymane Mboup
- Institut de Recherche en Santé, de Surveillance Epidemiologique et de Formation, Diamniadio, Senegal
| | - Bouke C de Jong
- Mycobacteriology Unit, Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | - Aissatou G Diallo
- Mycobacteria Unit, Bacteriology- Virology Laboratory, CHU Aristide Le Dantec, 30 Avenue Pasteur, BP 7325, Dakar, Senegal
| | - Florian Gehre
- Mycobacteriology Unit, Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium.,Medical Reserach Council (MRC) Unit, Fajara, Gambia
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Zumla A, Otchere ID, Mensah GI, Asante-Poku A, Gehre F, Maeurer M, Bates M, Mwaba P, Ntoumi F, Yeboah-Manu D. Learning from epidemiological, clinical, and immunological studies on Mycobacterium africanum for improving current understanding of host–pathogen interactions, and for the development and evaluation of diagnostics, host-directed therapies, and vaccines for tuberculosis. Int J Infect Dis 2017; 56:126-129. [DOI: 10.1016/j.ijid.2016.12.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2016] [Revised: 12/01/2016] [Accepted: 12/05/2016] [Indexed: 11/25/2022] Open
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25
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Otu J, Gehre F, Zingue D, Kudzawu S, Forson A, Mane M, Rabna P, Diarra B, Kayede S, Adebiyi E, Kehinde A, Onyejepu N, Onubogu C, Idigbe E, Ba A, Diallo A, Mboup S, Disse K, Kadanga G, Dagnra Y, Baldeh I, Corrah T, Jong BD, Antonio M. MULTIDRUG-RESISTANT TUBERCULOSIS (MDR-TB): AN EMERGING PROBLEM IN WEST AFRICA. BMJ Glob Health 2017. [DOI: 10.1136/bmjgh-2016-000260.85] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
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26
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Jobarteh T, Otu J, Gitteh E, Mendy F, Faal-Jawara TI, Ofori-Anyinam B, Ayorinde A, Secka O, Antonio M, Gehre F. Evaluation of the Kudoh method for mycobacterial culture: Gambia experience. Int J Mycobacteriol 2017; 5 Suppl 1:S166. [PMID: 28043531 DOI: 10.1016/j.ijmyco.2016.09.049] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2016] [Accepted: 09/20/2016] [Indexed: 11/19/2022] Open
Abstract
OBJECTIVE/BACKGROUND To evaluate the Kudoh swab method for improving laboratory diagnosis of tuberculosis (TB) in Gambia. METHODS A total of 75 sputa (50 smear positive and 25 smear negative) were examined. Sputum samples were collected from leftover routine samples from the Medical Research Council Unit, Gambia TB Diagnostic Laboratory. The samples were processed using the standard N-acetyl-l-cysteine-NaOH (NALC-NaOH) methods currently used and Kudoh swab method. These were cultured on standard Lowenstein Jensen (LJ) and Modified Ogawa media, respectively, and incubated aerobically at 36±1°C for mycobacterial growth. To determine if the decontamination and culture methods compared could equally detect the Mycobacterium tuberculosis complex (MTBC) highly commonly isolated in Gambia, spoligotyping was done. RESULTS In total, 72% (54/75) of MTBC were recovered by both LJ and Modified Ogawa methods. The LJ method recovered 52% (39/75) and Modified Ogawa recovered 56% (42/75) of the MTBC, respectively. Spoligotyping showed Euro-American 35% (19/54), Indo-Oceanic 35% (19/54), Mycobacterium africanum (West African type 2) 26% (14/54), Beijing 2% (1/54), and M. africanum (West African type 1) 2% (1/54). CONCLUSION The Kudoh method is simpler and cheaper than the NALC-NaOH method. There was no significant difference in recovery between the methods. The Kudoh method is ideal in overburdened TB laboratories with poor resources in developing countries. The predominant lineages were Euro-American and Indo-Oceanic, followed by M. africanum (West African type 2).
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Affiliation(s)
| | - Jacob Otu
- Medical Research Council Unit, Gambia
| | | | | | | | | | | | | | | | - Florian Gehre
- Medical Research Council Unit, Gambia; Institute of Tropical Medicine, Antwerp, Belgium
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27
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Faburay AK, Mendy FS, Otu JK, Faal-Jawara TI, Gehre F, Secka O. Performance comparison of a pair of Lowenstein-Jensen media supplemented with pyruvate or glycerol, and the combination of both supplements in a single Lowenstein-Jensen medium for the growth support of the Mycobacterium Tuberculosis complex. Int J Mycobacteriol 2017; 5 Suppl 1:S169. [PMID: 28043533 DOI: 10.1016/j.ijmyco.2016.09.019] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2016] [Accepted: 09/23/2016] [Indexed: 11/17/2022] Open
Abstract
OBJECTIVE/BACKGROUND To evaluate the performance of Lowenstein-Jensen medium (LJ) supplemented with pyruvate and glycerol (LJPG), compared with LJ supplemented with pyruvate (LJP) or glycerol (LJG) for the support of mycobacterial growth. METHOD This study used 100 Ziehl-Neelsen-confirmed positive mycobacterium growth indicator tube 960 culture samples that were obtained from clinical samples during routine diagnosis. All cultures were inoculated in parallel on LJG/LJP and on LJGP, which were incubated and read weekly for the evidence of growth. The mycobacterial recovery rate, contamination rate, and time to detection were compared. RESULT The recovery rate for LJG/LJP and for LJPG was 90% (90 samples) and 88% (88 samples), respectively (kappa p-value, 0.9). There was no significant difference in the contamination rate, which was 8% (8 samples) for LJG/LJP and 9% (9 samples) for LJPG. Mycobacterial growth was faster in LJPG (1.6weeks) than in LJG/LJP (2weeks). CONCLUSION A single LJPG slope was not significantly different, compared with the usual pair of LJG or LJP slopes. This is a promising new culturing approach that could be used in Mycobacterium africanum-endemic in West African countries. It significantly reduces labor time and consumable costs and more quickly detects the M. tuberculosis complex.
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Affiliation(s)
- Alieu K Faburay
- Medical Research Council Unit, Serrekunda, the Gambia, Serrekunda, Gambia; Institute of Tropical Medicine, Antwerp, Belgium.
| | - Francis S Mendy
- Medical Research Council Unit, Serrekunda, the Gambia, Serrekunda, Gambia
| | - Jacob K Otu
- Medical Research Council Unit, Serrekunda, the Gambia, Serrekunda, Gambia
| | | | - F Gehre
- Medical Research Council Unit, Serrekunda, the Gambia, Serrekunda, Gambia; Institute of Tropical Medicine, Antwerp, Belgium
| | - Ousman Secka
- Medical Research Council Unit, Serrekunda, the Gambia, Serrekunda, Gambia
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28
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Abstract
West Africa is the only region in the world where six out of seven mycobacterial lineages of human importance are endemic. In particular, two evolutionary ancient lineages, Mycobacterium africanum West Africa 1 (MTBC Lineage 5) and M. africanum West Africa 2 (MTBC Lineage 6) are of interest as they cause up to 40% of all pulmonary TB cases in some West African countries. Although these M. africanum lineages are closely related to M. tuberculosis sensu stricto lineages, they differ significantly in respect to biology, epidemiology and in their potential to cause disease in humans. Most importantly the M. africanum lineages are exclusive to West Africa. Although the exact mechanisms underlying this geographical restriction are still not understood, it is increasingly suspected that this is due to an adaptation of the bacteria to West African host populations. In this chapter, we summarize the geographical distribution of the M. africanum lineages within the region, describe biological and clinical differences and the consequent implications for TB control in West Africa. We also try to shed light on the geographical restriction, based on recently published analyses on whole genomes of M. africanum isolates.
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Affiliation(s)
- Dorothy Yeboah-Manu
- Noguchi Memorial Institute for Medical Research, University of Ghana, Accra, Ghana.
| | | | - Florian Gehre
- Institute for Tropical Medicine, Antwerp, Belgium
- Medical Research Council (MRC) Unit, The Gambia Serrekunda, Gambia
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29
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Gitteh E, Kweku Otu J, Jobarteh T, Mendy F, Faal-Jawara IT, Ofori-Anyinam NB, Ayorinde A, Secka O, Gehre F. Evaluation of sodium hydroxide–N-acetyl-l-cysteine and 0.7% chlorhexidine decontamination methods for recovering Mycobacterium tuberculosis from sputum samples: A comparative analysis (The Gambia Experience). Int J Mycobacteriol 2016; 5 Suppl 1:S167-S168. [DOI: 10.1016/j.ijmyco.2016.09.020] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2016] [Accepted: 09/23/2016] [Indexed: 11/30/2022] Open
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30
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Diarra B, Goita D, Tounkara S, Sanogo M, Baya B, Togo ACG, Maiga M, Sarro YS, Kone A, Kone B, M'Baye O, Coulibaly N, Kassambara H, Cisse A, Belson M, Polis MA, Otu J, Gehre F, Antonio M, Dao S, Siddiqui S, Murphy RL, de Jong BC, Diallo S. Tuberculosis drug resistance in Bamako, Mali, from 2006 to 2014. BMC Infect Dis 2016; 16:714. [PMID: 27894266 PMCID: PMC5126865 DOI: 10.1186/s12879-016-2060-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2016] [Accepted: 11/22/2016] [Indexed: 12/02/2022] Open
Abstract
Background Although Drug resistance tuberculosis is not a new phenomenon, Mali remains one of the “blank” countries without systematic data. Methods Between 2006 and 2014, we enrolled pulmonary TB patients from local TB diagnostics centers and a university referral hospital in several observational cohort studies. These consecutive patients had first line drug susceptibility testing (DST) performed on their isolates. A subset of MDR was subsequently tested for second line drug resistance. Results A total of 1186 mycobacterial cultures were performed on samples from 522 patients, including 1105 sputa and 81 blood samples, yielding one or more Mycobacterium tuberculosis complex (Mtbc) positive cultures for 343 patients. Phenotypic DST was performed on 337 (98.3%) unique Mtbc isolates, of which 127 (37.7%) were resistant to at least one drug, including 75 (22.3%) with multidrug resistance (MDR). The overall prevalence of MDR-TB was 3.4% among new patients and 66.3% among retreatment patients. Second line DST was available for 38 (50.7%) of MDR patients and seven (18.4%) had resistance to either fluoroquinolones or second-line injectable drugs. Conclusion The drug resistance levels, including MDR, found in this study are relatively high, likely related to the selected referral population. While worrisome, the numbers remained stable over the study period. These findings prompt a nationwide drug resistance survey, as well as continuous surveillance of all retreatment patients, which will provide more accurate results on countrywide drug resistance rates and ensure that MDR patients access appropriate second line treatment. Electronic supplementary material The online version of this article (doi:10.1186/s12879-016-2060-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- B Diarra
- SEREFO Program, University of Sciences, Techniques and Technologies of Bamako (USTTB), Bamako, Mali. .,Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium.
| | - D Goita
- SEREFO Program, University of Sciences, Techniques and Technologies of Bamako (USTTB), Bamako, Mali
| | - S Tounkara
- SEREFO Program, University of Sciences, Techniques and Technologies of Bamako (USTTB), Bamako, Mali
| | - M Sanogo
- SEREFO Program, University of Sciences, Techniques and Technologies of Bamako (USTTB), Bamako, Mali
| | - B Baya
- SEREFO Program, University of Sciences, Techniques and Technologies of Bamako (USTTB), Bamako, Mali
| | - A C G Togo
- SEREFO Program, University of Sciences, Techniques and Technologies of Bamako (USTTB), Bamako, Mali
| | - M Maiga
- SEREFO Program, University of Sciences, Techniques and Technologies of Bamako (USTTB), Bamako, Mali
| | - Y S Sarro
- SEREFO Program, University of Sciences, Techniques and Technologies of Bamako (USTTB), Bamako, Mali
| | - A Kone
- SEREFO Program, University of Sciences, Techniques and Technologies of Bamako (USTTB), Bamako, Mali
| | - B Kone
- SEREFO Program, University of Sciences, Techniques and Technologies of Bamako (USTTB), Bamako, Mali
| | - O M'Baye
- SEREFO Program, University of Sciences, Techniques and Technologies of Bamako (USTTB), Bamako, Mali
| | - N Coulibaly
- SEREFO Program, University of Sciences, Techniques and Technologies of Bamako (USTTB), Bamako, Mali
| | - H Kassambara
- SEREFO Program, University of Sciences, Techniques and Technologies of Bamako (USTTB), Bamako, Mali
| | - A Cisse
- Laboratoire National de Référence des Mycobactéries (LNR), Institut National de Recherche en Santé publique (INRSP), Bamako, Mali
| | - M Belson
- CCRB, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, Bethesda, MD, USA
| | - M A Polis
- CCRB, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, Bethesda, MD, USA
| | - J Otu
- Vaccines and Immunity Theme, Atlantic Boulevard, Medical Research Council (MRC), Fajara, Banjul, The Gambia
| | - F Gehre
- Vaccines and Immunity Theme, Atlantic Boulevard, Medical Research Council (MRC), Fajara, Banjul, The Gambia.,Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | - M Antonio
- Vaccines and Immunity Theme, Atlantic Boulevard, Medical Research Council (MRC), Fajara, Banjul, The Gambia.,Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, UK.,Microbiology and Infection Unit, Warwick Medical School, University of Warwick, Coventry, UK
| | - S Dao
- SEREFO Program, University of Sciences, Techniques and Technologies of Bamako (USTTB), Bamako, Mali
| | - S Siddiqui
- CCRB, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, Bethesda, MD, USA
| | - R L Murphy
- Global Health, Northwestern University, Chicago, IL, USA
| | - B C de Jong
- Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | - S Diallo
- SEREFO Program, University of Sciences, Techniques and Technologies of Bamako (USTTB), Bamako, Mali
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31
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Gehre F, Otu J, Kendall L, Forson A, Kwara A, Kudzawu S, Kehinde AO, Adebiyi O, Salako K, Baldeh I, Jallow A, Jallow M, Dagnra A, Dissé K, Kadanga EA, Idigbe EO, Onubogu C, Onyejepu N, Gaye-Diallo A, Ba-Diallo A, Rabna P, Mane M, Sanogo M, Diarra B, Dezemon Z, Sanou A, Senghore M, Kwambana-Adams BA, Demba E, Faal-Jawara T, Kumar S, Tientcheu LD, Jallow A, Ceesay S, Adetifa I, Jaye A, Pallen MJ, D'Alessandro U, Kampmann B, Adegbola RA, Mboup S, Corrah T, de Jong BC, Antonio M. The emerging threat of pre-extensively drug-resistant tuberculosis in West Africa: preparing for large-scale tuberculosis research and drug resistance surveillance. BMC Med 2016; 14:160. [PMID: 27806714 PMCID: PMC5094099 DOI: 10.1186/s12916-016-0704-5] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/06/2016] [Accepted: 09/28/2016] [Indexed: 11/22/2022] Open
Abstract
BACKGROUND Drug-resistant tuberculosis (TB) is a global public health problem. Adequate management requires baseline drug-resistance prevalence data. In West Africa, due to a poor laboratory infrastructure and inadequate capacity, such data are scarce. Therefore, the true extent of drug-resistant TB was hitherto undetermined. In 2008, a new research network, the West African Network of Excellence for Tuberculosis, AIDS and Malaria (WANETAM), was founded, comprising nine study sites from eight West African countries (Burkina Faso, The Gambia, Ghana, Guinea-Bissau, Mali, Nigeria, Senegal and Togo). The goal was to establish Good Clinical Laboratory Practice (GCLP) principles and build capacity in standardised smear microscopy and mycobacterial culture across partnering laboratories to generate the first comprehensive West African drug-resistance data. METHODS Following GCLP and laboratory training sessions, TB isolates were collected at sentinel referral sites between 2009-2013 and tested for first- and second-line drug resistance. RESULTS From the analysis of 974 isolates, an unexpectedly high prevalence of multi-drug-resistant (MDR) strains was found in new (6 %) and retreatment patients (35 %) across all sentinel sites, with the highest prevalence amongst retreatment patients in Bamako, Mali (59 %) and the two Nigerian sites in Ibadan and Lagos (39 % and 66 %). In Lagos, MDR is already spreading actively amongst 32 % of new patients. Pre-extensively drug-resistant (pre-XDR) isolates are present in all sites, with Ghana showing the highest proportion (35 % of MDR). In Ghana and Togo, pre-XDR isolates are circulating amongst new patients. CONCLUSIONS West African drug-resistance prevalence poses a previously underestimated, yet serious public health threat, and our estimates obtained differ significantly from previous World Health Organisation (WHO) estimates. Therefore, our data are reshaping current concepts and are essential in informing WHO and public health strategists to implement urgently needed surveillance and control interventions in West Africa.
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Affiliation(s)
- Florian Gehre
- Vaccines and Immunity Theme, Medical Research Council Unit The Gambia, Banjul, The Gambia.,Institute of Tropical Medicine, Antwerp, Belgium
| | - Jacob Otu
- Vaccines and Immunity Theme, Medical Research Council Unit The Gambia, Banjul, The Gambia
| | - Lindsay Kendall
- Vaccines and Immunity Theme, Medical Research Council Unit The Gambia, Banjul, The Gambia
| | - Audrey Forson
- University of Ghana Medical School, Accra, Ghana.,Korle-Bu Teaching Hospital, Accra, Ghana
| | - Awewura Kwara
- Warren Alpert Medical School of Brown University, Providence, RI, USA.,The Miriam Hospital, Providence, RI, USA
| | | | - Aderemi O Kehinde
- College of Medicine, University of Ibadan, Ibadan, Nigeria.,University College Hospital, Ibadan, Oyo, 23402, Nigeria
| | | | - Kayode Salako
- University College Hospital, Ibadan, Oyo, 23402, Nigeria
| | - Ignatius Baldeh
- National Public Health Laboratory Services, Banjul, The Gambia
| | - Aisha Jallow
- National Public Health Laboratory Services, Banjul, The Gambia
| | - Mamadou Jallow
- National Public Health Laboratory Services, Banjul, The Gambia
| | - Anoumou Dagnra
- Laboratoire National de Reference Mycobacteria, Lome, Togo
| | - Kodjo Dissé
- Laboratoire National de Reference Mycobacteria, Lome, Togo
| | | | | | | | | | | | - Awa Ba-Diallo
- Laboratoire Bactériologie Virologie Aristide Le Dantec Sénégal, Dakar, Senegal
| | - Paulo Rabna
- National Institute of Public Health, Bissau, Guinea-Bissau
| | - Morto Mane
- National Institute of Public Health, Bissau, Guinea-Bissau
| | - Moumine Sanogo
- SEREFO Program, University of Sciences, Techniques and Technologies of Bamako, Bamako, Mali
| | - Bassirou Diarra
- SEREFO Program, University of Sciences, Techniques and Technologies of Bamako, Bamako, Mali
| | - Zingue Dezemon
- Centre Muraz and the National TB Program, Ouagadougou, Burkina Faso
| | - Adama Sanou
- Centre Muraz and the National TB Program, Ouagadougou, Burkina Faso
| | - Madikay Senghore
- Vaccines and Immunity Theme, Medical Research Council Unit The Gambia, Banjul, The Gambia.,Microbiology and Infection Unit, Warwick Medical School, University of Warwick, Coventry, UK
| | - Brenda A Kwambana-Adams
- Vaccines and Immunity Theme, Medical Research Council Unit The Gambia, Banjul, The Gambia.,Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
| | - Edward Demba
- Vaccines and Immunity Theme, Medical Research Council Unit The Gambia, Banjul, The Gambia
| | - Tutty Faal-Jawara
- Vaccines and Immunity Theme, Medical Research Council Unit The Gambia, Banjul, The Gambia
| | - Samrat Kumar
- Institute of Tropical Medicine, Antwerp, Belgium
| | - 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
| | - Adama Jallow
- National Tuberculosis/Leprosy Control Program, Banjul, The Gambia
| | - Samba Ceesay
- Health Services, Ministry of Health and Social Welfare, Banjul, The Gambia
| | - Ifedayo Adetifa
- Department of Infectious Diseases Epidemiology, London School of Hygiene and Tropical Medicine, London, UK.,Disease Control and Elimination, Medical Research Council Unit, Serrekunda, The Gambia
| | - Assan Jaye
- Vaccines and Immunity Theme, Medical Research Council Unit The Gambia, Banjul, The Gambia
| | - Mark J Pallen
- Microbiology and Infection Unit, Warwick Medical School, University of Warwick, Coventry, UK
| | - Umberto D'Alessandro
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK.,Disease Control and Elimination, Medical Research Council Unit, Serrekunda, The Gambia.,Institute of Tropical Medicine, Antwerp, Belgium
| | - Beate Kampmann
- Vaccines and Immunity Theme, Medical Research Council Unit The Gambia, Banjul, The Gambia.,Department of Paediatrics, Imperial College London, London, UK
| | | | - Souleymane Mboup
- Laboratoire Bactériologie Virologie Aristide Le Dantec Sénégal, Dakar, Senegal
| | - Tumani Corrah
- 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. .,Microbiology and Infection Unit, Warwick Medical School, University of Warwick, Coventry, UK. .,Department of Infectious Diseases Epidemiology, London School of Hygiene and Tropical Medicine, London, UK.
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Stucki D, Brites D, Jeljeli L, Coscolla M, Liu Q, Trauner A, Fenner L, Rutaihwa L, Borrell S, Luo T, Gao Q, Kato-Maeda M, Ballif M, Egger M, Macedo R, Mardassi H, Moreno M, Tudo Vilanova G, Fyfe J, Globan M, Thomas J, Jamieson F, Guthrie JL, Asante-Poku A, Yeboah-Manu D, Wampande E, Ssengooba W, Joloba M, Henry Boom W, Basu I, Bower J, Saraiva M, Vaconcellos SEG, Suffys P, Koch A, Wilkinson R, Gail-Bekker L, Malla B, Ley SD, Beck HP, de Jong BC, Toit K, Sanchez-Padilla E, Bonnet M, Gil-Brusola A, Frank M, Penlap Beng VN, Eisenach K, Alani I, Wangui Ndung'u P, Revathi G, Gehre F, Akter S, Ntoumi F, Stewart-Isherwood L, Ntinginya NE, Rachow A, Hoelscher M, Cirillo DM, Skenders G, Hoffner S, Bakonyte D, Stakenas P, Diel R, Crudu V, Moldovan O, Al-Hajoj S, Otero L, Barletta F, Jane Carter E, Diero L, Supply P, Comas I, Niemann S, Gagneux S. Mycobacterium tuberculosis lineage 4 comprises globally distributed and geographically restricted sublineages. Nat Genet 2016; 48:1535-1543. [PMID: 27798628 PMCID: PMC5238942 DOI: 10.1038/ng.3704] [Citation(s) in RCA: 239] [Impact Index Per Article: 29.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2016] [Accepted: 09/27/2016] [Indexed: 12/30/2022]
Abstract
Generalist and specialist species differ in the breadth of their ecological niches. Little is known about the niche width of obligate human pathogens. Here we analyzed a global collection of Mycobacterium tuberculosis lineage 4 clinical isolates, the most geographically widespread cause of human tuberculosis. We show that lineage 4 comprises globally distributed and geographically restricted sublineages, suggesting a distinction between generalists and specialists. Population genomic analyses showed that, whereas the majority of human T cell epitopes were conserved in all sublineages, the proportion of variable epitopes was higher in generalists. Our data further support a European origin for the most common generalist sublineage. Hence, the global success of lineage 4 reflects distinct strategies adopted by different sublineages and the influence of human migration.
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Affiliation(s)
- David Stucki
- Swiss Tropical and Public Health Institute, Basel, Switzerland.,University of Basel, Switzerland
| | - Daniela Brites
- Swiss Tropical and Public Health Institute, Basel, Switzerland.,University of Basel, Switzerland
| | - Leïla Jeljeli
- Forschungszentrum Borstel, Germany.,Institut Pasteur de Tunis, Université de Tunis El Manar, Tunis, Tunisia
| | - Mireia Coscolla
- Swiss Tropical and Public Health Institute, Basel, Switzerland.,University of Basel, Switzerland
| | - Qingyun Liu
- The Key Laboratory of Medical Molecular Virology of Ministries of Education and Health, Institutes of Biomedical Sciences and Institute of Medical Microbiology, School of Basic Medical Science of Fudan University, Shanghai, China
| | - Andrej Trauner
- Swiss Tropical and Public Health Institute, Basel, Switzerland.,University of Basel, Switzerland
| | - Lukas Fenner
- Swiss Tropical and Public Health Institute, Basel, Switzerland.,University of Basel, Switzerland.,Institute for Social and Preventive Medicine, University of Bern, Switzerland
| | - Liliana Rutaihwa
- Swiss Tropical and Public Health Institute, Basel, Switzerland.,University of Basel, Switzerland
| | - Sonia Borrell
- Swiss Tropical and Public Health Institute, Basel, Switzerland.,University of Basel, Switzerland
| | - Tao Luo
- Laboratory of Infection and Immunity, School of Basic Medical Science, West China Center of Medical Sciences, Sichuan University, Chengdu, Sichuan 610041, China
| | - Qian Gao
- The Key Laboratory of Medical Molecular Virology of Ministries of Education and Health, Institutes of Biomedical Sciences and Institute of Medical Microbiology, School of Basic Medical Science of Fudan University, Shanghai, China
| | | | - Marie Ballif
- Swiss Tropical and Public Health Institute, Basel, Switzerland.,University of Basel, Switzerland.,Institute for Social and Preventive Medicine, University of Bern, Switzerland
| | - Matthias Egger
- Institute for Social and Preventive Medicine, University of Bern, Switzerland
| | - Rita Macedo
- Laboratòrio de Saùde Publica, Lisbon, Portugal
| | - Helmi Mardassi
- Institut Pasteur de Tunis, Université de Tunis El Manar, Tunis, Tunisia
| | | | | | - Janet Fyfe
- Victorian Infectious Diseases Reference Laboratory, Victoria, Australia
| | - Maria Globan
- Victorian Infectious Diseases Reference Laboratory, Victoria, Australia
| | | | | | | | - Adwoa Asante-Poku
- Noguchi Memorial Institute for Medical Research, University of Ghana, Accra, Ghana
| | - Dorothy Yeboah-Manu
- Noguchi Memorial Institute for Medical Research, University of Ghana, Accra, Ghana
| | - Eddie Wampande
- Department of Medical Microbiology, Makerere University, Kampala, Uganda
| | - Willy Ssengooba
- Department of Medical Microbiology, Makerere University, Kampala, Uganda.,Department of Global Health, University of Amsterdam, Amsterdam, the Netherlands
| | - Moses Joloba
- Department of Medical Microbiology, Makerere University, Kampala, Uganda
| | - W Henry Boom
- Department of Molecular Biology and Microbiology, Case Western Reserve University, Cleveland, USA
| | - Indira Basu
- LabPlus, Auckland City Hospital, Auckland, New Zealand
| | - James Bower
- LabPlus, Auckland City Hospital, Auckland, New Zealand
| | - Margarida Saraiva
- Life and Health Sciences Research Institute (ICVS), School of Health Sciences, University of Minho, Braga, Portugal.,ICVS/3B's - PT Government Associate Laboratory, Braga/Guimarães, Portugal
| | | | | | - Anastasia Koch
- Institute of Infectious Disease and Molecular Medicine and Department of Clinical Laboratory Sciences, University of Cape Town, South Africa
| | - Robert Wilkinson
- Institute of Infectious Disease and Molecular Medicine and Department of Clinical Laboratory Sciences, University of Cape Town, South Africa.,Department of Medicine, Imperial College London, UK.,The Francis Crick Institute Mill Hill Laboratory, London, UK
| | - Linda Gail-Bekker
- Institute of Infectious Disease and Molecular Medicine and Department of Clinical Laboratory Sciences, University of Cape Town, South Africa
| | - Bijaya Malla
- Swiss Tropical and Public Health Institute, Basel, Switzerland.,University of Basel, Switzerland
| | - Serej D Ley
- Swiss Tropical and Public Health Institute, Basel, Switzerland.,University of Basel, Switzerland.,Papua New Guinea Institute of Medical Research, Goroka, PNG
| | - Hans-Peter Beck
- Swiss Tropical and Public Health Institute, Basel, Switzerland.,University of Basel, Switzerland
| | | | - Kadri Toit
- Tartu University Hospital United Laboratories, Mycobacteriology, Tartu, Estonia
| | | | | | - Ana Gil-Brusola
- Department of Microbiology, University Hospital La Fe, Valencia, Spain
| | - Matthias Frank
- Institute of Tropical Medicine, University of Tübingen, Tübingen, Germany
| | - Veronique N Penlap Beng
- Institute Laboratory for Tuberculosis Research (LTR), Biotechnology Center (BTC), University of Yaoundé I, Yaoundé, Cameroon
| | - Kathleen Eisenach
- Department of Pathology, University of Arkansas for Medical Sciences, Little Rock, Arkansas, USA
| | - Issam Alani
- Department of Medical Laboratory Technology, Faculty of Medical Technology, Baghdad, Iraq
| | - Perpetual Wangui Ndung'u
- Institute of Tropical Medicine and Infectious Diseases (ITROMID), Jomo Kenyatta University of Agriculture and Technology (JKUAT), Nairobi, Kenya
| | - Gunturu Revathi
- Department of Pathology, Aga Khan University Hospital (AKUH), Nairobi, Kenya
| | - Florian Gehre
- Insitute of Tropical Medicine, Antwerp, Belgium.,Medical Research Council, Fajara, the Gambia
| | | | - Francine Ntoumi
- Institute of Tropical Medicine, University of Tübingen, Tübingen, Germany.,Fondation Congolaise pour la Recherche Médicale, Université Marien Gouabi, Brazzaville, Congo
| | - Lynsey Stewart-Isherwood
- Right to Care and the Clinical HIV Research Unit, University of the Witwatersrand, Johannesburg, South Africa
| | - Nyanda E Ntinginya
- National Institute of Medical Research, Mbeya Medical Research Centre (NIMR-MMRC), Mbeya, Tanzania
| | - Andrea Rachow
- Division of Infectious Diseases and Tropical Medicine, Medical Centre of the University of Munich, Munich, Germany; German Centre for Infection Research (DZIF), partner site Munich, Germany
| | - Michael Hoelscher
- Division of Infectious Diseases and Tropical Medicine, Medical Centre of the University of Munich, Munich, Germany; German Centre for Infection Research (DZIF), partner site Munich, Germany
| | - Daniela Maria Cirillo
- Emerging Bacterial Pathogens Unit, IRCCS, San Raffaele Scientific Institute, Milan, Italy
| | - Girts Skenders
- Riga East University Hospital, Centre of Tuberculosis and Lung Diseases, Riga, Latvia
| | - Sven Hoffner
- WHO Supranational TB Reference Laboratory, Department of Microbiology, The Public Health Agency of Sweden, Solna, Sweden
| | - Daiva Bakonyte
- Department of Immunology and Cell Biology, Institute of Biotechnology, Vilnius University, Vilnius, Lithuania
| | - Petras Stakenas
- Department of Immunology and Cell Biology, Institute of Biotechnology, Vilnius University, Vilnius, Lithuania
| | - Roland Diel
- Institute for Epidemiology, Schleswig-Holstein University Hospital, Kiel, Germany
| | - Valeriu Crudu
- National Tuberculosis Reference Laboratory, Phthysiopneumology Institute, Chisinau, Republic of Moldova
| | - Olga Moldovan
- 'Marius Nasta' Pneumophtisiology Institute, Bucharest, Romania
| | - Sahal Al-Hajoj
- Department of Infection and Immunity, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
| | - Larissa Otero
- Instituto de Medicina Tropical Alexander von Humboldt, Molecular Epidemiology Unit-Tuberculosis, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Francesca Barletta
- Instituto de Medicina Tropical Alexander von Humboldt, Molecular Epidemiology Unit-Tuberculosis, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - E Jane Carter
- Alpert School of Medicine at Brown University, Providence, Rhode Island, USA.,Moi University School of Medicine, Eldoret, Kenya
| | - Lameck Diero
- Moi University School of Medicine, Eldoret, Kenya
| | - Philip Supply
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019 - UMR 8204 - CIIL - Centre d'Infection et d'Immunité de Lille, F-59000 Lille, France
| | - Iñaki Comas
- Institute of Biomedicine of Valencia (IBV-CSIC), 46010, Valencia, Spain.,CIBER Epidemiology and Public Health, Madrid, Spain
| | - Stefan Niemann
- Forschungszentrum Borstel, Germany.,German Center for Infection Research, Borstel Site, Borstel, Germany
| | - Sebastien Gagneux
- Swiss Tropical and Public Health Institute, Basel, Switzerland.,University of Basel, Switzerland
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Coscolla M, Copin R, Sutherland J, Gehre F, de Jong B, Owolabi O, Mbayo G, Giardina F, Ernst JD, Gagneux S. M. tuberculosis T Cell Epitope Analysis Reveals Paucity of Antigenic Variation and Identifies Rare Variable TB Antigens. Cell Host Microbe 2016; 18:538-48. [PMID: 26607161 DOI: 10.1016/j.chom.2015.10.008] [Citation(s) in RCA: 104] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2015] [Revised: 08/10/2015] [Accepted: 10/07/2015] [Indexed: 11/25/2022]
Abstract
Pathogens that evade adaptive immunity typically exhibit antigenic variation. By contrast, it appears that although the chronic human tuberculosis (TB)-causing pathogen Mycobacterium tuberculosis needs to counter host T cell responses, its T cell epitopes are hyperconserved. Here we present an extensive analysis of the T cell epitopes of M. tuberculosis. We combined population genomics with experimental immunology to determine the number and identity of T cell epitope sequence variants in 216 phylogenetically diverse strains of M. tuberculosis. Antigen conservation is indeed a hallmark of M. tuberculosis. However, our analysis revealed a set of seven variable antigens that were immunogenic in subjects with active TB. These findings suggest that M. tuberculosis uses mechanisms other than antigenic variation to evade T cells. T cell epitopes that exhibit sequence variation may not be subject to the same evasion mechanisms, and hence vaccines that include such variable epitopes may be more efficacious.
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Kehinde AO, Adebiyi EO, Salako AO, Ogunleye VO, Oni AA, Bakare RA, Eltayeb O, Dairo G, Out J, Gehre F, Corrah T, Deun AV, Gumusoboga M, Declercq E, Demeulenaere T, deJong BC, Antonio M. Drug resistance profiles of new- and previously treated patients with pulmonary tuberculosis in Ibadan, Nigeria. Afr J Med Med Sci 2016; 45:67-73. [PMID: 28686829] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
BACKGROUND Information on TB drug resistance profiles and its' associated risk factors are scarce in Nigeria despite the large burden of disease in the country. The study was designed to report drug resistance profiles of new- and previously treated patients with pulmonary tuberculosis (TB) in Ibadan, Nigeria. METHOD Sputum from consenting pulmonary TB patients were collected and cultured for Mycobacterium tuberculosis (Mtb) at the TB laboratory of the University College Hospital, Ibadan, Nigeria using standard method. Mtb were stored and sent for drug susceptibility testing against first and second-line anti-TB drugs at the MRC Unit, The Gambia and at the Institute of Tropical Medicine, Antwerp, Belgium using BACTEC MGIT 960 and proportion method on solid medium respectively. RESULTS Of 238 Mtb collected, 124 (52.1%) were viable, 102 (59.65%) non-viable while 12 (7.02%) were contaminated. About half (58.87%) of the Mtb were from previously treated patients, 40 (32.26%) were from new patients while treatment history of 1.1 (8.87%) were unknown. Forty-seven (37.90%) of the 124 Mtb. tested were multidrug resistant (MDR) out of which, 40 (85.10%) were from previously treated patients.. HIV prevalence was 8.69%. Of the 17 MDR-TB from previously treated cases tested for second-line drugs, four (23.53%) were resistant to fluoroquinolones or injectable agents, 13 (76.47%) were susceptible while none was resistant to both of these classes of drugs. CONCLUSION MDR-TB in Ibadan already demonstrates resistance to second line anti-TB drugs hence management of MDR-TB patients should be strengthened to prevent emergence of extensively drug-resistant TB (XDR-TB).
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Gehre F, Kumar S, Kendall L, Ejo M, Secka O, Ofori-Anyinam B, Abatih E, Antonio M, Berkvens D, de Jong BC. A Mycobacterial Perspective on Tuberculosis in West Africa: Significant Geographical Variation of M. africanum and Other M. tuberculosis Complex Lineages. PLoS Negl Trop Dis 2016; 10:e0004408. [PMID: 26964059 PMCID: PMC4786107 DOI: 10.1371/journal.pntd.0004408] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2015] [Accepted: 01/05/2016] [Indexed: 01/25/2023] Open
Abstract
BACKGROUND Phylogenetically distinct Mycobacterium tuberculosis lineages differ in their phenotypes and pathogenicity. Consequently, understanding mycobacterial population structures phylogeographically is essential for design, interpretation and generalizability of clinical trials. Comprehensive efforts are lacking to date to establish the West African mycobacterial population structure on a sub-continental scale, which has diagnostic implications and can inform the design of clinical TB trials. METHODOLOGY/PRINCIPAL FINDINGS We collated novel and published genotyping (spoligotyping) data and classified spoligotypes into mycobacterial lineages/families using TBLineage and Spotclust, followed by phylogeographic analyses using statistics (logistic regression) and lineage axis plot analysis in GenGIS, in which a phylogenetic tree constructed in MIRU-VNTRplus was analysed. Combining spoligotyping data from 16 previously published studies with novel data from The Gambia, we obtained a total of 3580 isolates from 12 countries and identified 6 lineages comprising 32 families. By using stringent analytical tools we demonstrate for the first time a significant phylogeographic separation between western and eastern West Africa not only of the two M. africanum (West Africa 1 and 2) but also of several major M. tuberculosis sensu stricto families, such as LAM10 and Haarlem 3. Moreover, in a longitudinal logistic regression analysis for grouped data we showed that M. africanum West Africa 2 remains a persistent health concern. CONCLUSIONS/SIGNIFICANCE Because of the geographical divide of the mycobacterial populations in West Africa, individual research findings from one country cannot be generalized across the whole region. The unequal geographical family distribution should be considered in placement and design of future clinical trials in West Africa.
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Affiliation(s)
- Florian Gehre
- Mycobacterial Unit, Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
- Vaccines and Immunity Theme, Medical Research Council (MRC) Unit, Fajara, The Gambia
| | - Samrat Kumar
- Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | - Lindsay Kendall
- Statistics and Bioinformatics Department, Medical Research Council (MRC) Unit, Fajara, The Gambia
| | - Mebrat Ejo
- Mycobacterial Unit, Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
- University of Gondar, Gondar, Ethiopia
| | - Oumie Secka
- Vaccines and Immunity Theme, Medical Research Council (MRC) Unit, Fajara, The Gambia
| | - Boatema Ofori-Anyinam
- Mycobacterial Unit, Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
- Vaccines and Immunity Theme, Medical Research Council (MRC) Unit, Fajara, The Gambia
| | - Emmanuel Abatih
- Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | - Martin Antonio
- Vaccines and Immunity Theme, Medical Research Council (MRC) Unit, Fajara, The Gambia
| | - Dirk Berkvens
- Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | - Bouke C. de Jong
- Mycobacterial Unit, Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
- Vaccines and Immunity Theme, Medical Research Council (MRC) Unit, Fajara, The Gambia
- Division of Infectious Diseases, Department of Medicine, New York University (NYU), New York, New York, United States of America
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37
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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. Infect Genet Evol 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] [What about the content of this article? (0)] [Affiliation(s)] [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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Gehre F, Ejo M, Fissette K, de Rijk P, Uwizeye C, Nduwamahoro E, Goovaerts O, Affolabi D, Gninafon M, Lingoupou FM, Barry MD, Sow O, Merle C, Olliaro P, Ba F, Sarr M, Piubello A, Noeske J, Antonio M, Rigouts L, de Jong BC. Shifts in Mycobacterial Populations and Emerging Drug-Resistance in West and Central Africa. PLoS One 2014; 9:e110393. [PMID: 25493429 PMCID: PMC4262193 DOI: 10.1371/journal.pone.0110393] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2014] [Accepted: 09/13/2014] [Indexed: 11/18/2022] Open
Abstract
In this study, we retrospectively analysed a total of 605 clinical isolates from six West or Central African countries (Benin, Cameroon, Central African Republic, Guinea-Conakry, Niger and Senegal). Besides spoligotyping to assign isolates to ancient and modern mycobacterial lineages, we conducted phenotypic drug-susceptibility-testing for each isolate for the four first-line drugs. We showed that phylogenetically modern Mycobacterium tuberculosis strains are more likely associated with drug resistance than ancient strains and predict that the currently ongoing replacement of the endemic ancient by a modern mycobacterial population in West/Central Africa might result in increased drug resistance in the sub-region.
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Affiliation(s)
- Florian Gehre
- Institute of Tropical Medicine (ITM), Antwerp, Belgium
- Medical Research Council (MRC), The Gambia Unit, Fajara, The Gambia
- * E-mail:
| | - Mebrat Ejo
- Institute of Tropical Medicine (ITM), Antwerp, Belgium
| | | | - Pim de Rijk
- Institute of Tropical Medicine (ITM), Antwerp, Belgium
| | | | | | | | | | | | - Fanny M. Lingoupou
- Laboratoire des Mycobactéries, Institut Pasteur de Bangui, Bangui, Central African Republic
| | | | - Oumou Sow
- Laboratoire de Reference des Mycobactéries, Conakry, Guinea-Conakry
| | - Corinne Merle
- London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Piero Olliaro
- UNICEF/UNDP/World Bank/WHO Special Programme for Research and Training in Tropical Diseases (TDR), Geneva, Switzerland
| | - Fatoumata Ba
- Laboratoire de Reference des Mycobactéries, Dakar, Senegal
| | | | | | | | - Martin Antonio
- Medical Research Council (MRC), The Gambia Unit, Fajara, The Gambia
| | - Leen Rigouts
- Institute of Tropical Medicine (ITM), Antwerp, Belgium
| | - Bouke C de Jong
- Institute of Tropical Medicine (ITM), Antwerp, Belgium
- New York University, New York, United States of America
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Gehre F, Antonio M, Otu JK, Sallah N, Secka O, Faal T, Owiafe P, Sutherland JS, Adetifa IM, Ota MO, Kampmann B, Corrah T, de Jong BC. Immunogenic Mycobacterium africanum strains associated with ongoing transmission in The Gambia. Emerg Infect Dis 2014; 19:1598-1604. [PMID: 24050158 PMCID: PMC3810728 DOI: 10.3201/eid1910.121023] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
In West Africa, Mycobacterium tuberculosis strains co-circulate with M. africanum, and both pathogens cause pulmonary tuberculosis in humans. Given recent findings that M. tuberculosis T-cell epitopes are hyperconserved, we hypothesized that more immunogenic strains have increased capacity to spread within the human host population. We investigated the relationship between the composition of the mycobacterial population in The Gambia, as measured by spoligotype analysis, and the immunogenicity of these strains as measured by purified protein derivative–induced interferon-γ release in ELISPOT assays of peripheral blood mononuclear cells. We found a positive correlation between strains with superior spreading capacity and their relative immunogenicity. Although our observation is true for M. tuberculosis and M. africanum strains, the association was especially pronounced in 1 M. africanum sublineage, characterized by spoligotype shared international type 181, which is responsible for 20% of all tuberculosis cases in the region and therefore poses a major public health threat in The Gambia.
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Gehre F, Antonio M, Faïhun F, Odoun M, Uwizeye C, de Rijk P, de Jong BC, Affolabi D. The first phylogeographic population structure and analysis of transmission dynamics of M. africanum West African 1--combining molecular data from Benin, Nigeria and Sierra Leone. PLoS One 2013; 8:e77000. [PMID: 24143198 PMCID: PMC3797137 DOI: 10.1371/journal.pone.0077000] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2013] [Accepted: 09/06/2013] [Indexed: 11/18/2022] Open
Abstract
Mycobacterium africanum is an important cause of tuberculosis (TB) in West Africa. So far, two lineages called M. africanum West African 1 (MAF1) and M. africanum West African 2 (MAF2) have been defined. Although several molecular studies on MAF2 have been conducted to date, little is known about MAF1. As MAF1 is mainly present in countries around the Gulf of Guinea we aimed to estimate its prevalence in Cotonou, the biggest city in Benin. Between 2005–06 we collected strains in Cotonou/Benin and genotyped them using spoligo- and 12-loci-MIRU-VNTR-typing. Analyzing 194 isolates, we found that 31% and 6% were MAF1 and MAF2, respectively. Therefore Benin is one of the countries with the highest prevalence (37%) of M. africanum in general and MAF1 in particular. Moreover, we combined our data from Benin with publicly available genotyping information from Nigeria and Sierra Leone, and determined the phylogeographic population structure and genotypic clustering of MAF1. Within the MAF1 lineage, we identified an unexpected great genetic variability with the presence of at least 10 sub-lineages. Interestingly, 8 out of 10 of the discovered sub-lineages not only clustered genetically but also geographically. Besides showing a remarkable local restriction to certain regions in Benin and Nigeria, the sub-lineages differed dramatically in their capacity to transmit within the human host population. While identifying Benin as one of the countries with the highest overall prevalence of M. africanum, this study also contains the first detailed description of the transmission dynamics and phylogenetic composition of the MAF1 lineage.
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Affiliation(s)
- Florian Gehre
- Medical Research Council (MRC) Unit, Fajara, The Gambia
- Institute for Tropical Medicine (ITM), Antwerp, Belgium
- * E-mail:
| | | | - Frank Faïhun
- Laboratoire de Reference des Mycobacteries, Cotonou, Benin
| | - Mathieu Odoun
- Laboratoire de Reference des Mycobacteries, Cotonou, Benin
| | | | - Pim de Rijk
- Institute for Tropical Medicine (ITM), Antwerp, Belgium
| | - Bouke C. de Jong
- Medical Research Council (MRC) Unit, Fajara, The Gambia
- Institute for Tropical Medicine (ITM), Antwerp, Belgium
- New York University (NYU), New York, New York, United States of America
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Gehre F, Otu J, DeRiemer K, de Sessions PF, Hibberd ML, Mulders W, Corrah T, de Jong BC, Antonio M. Deciphering the growth behaviour of Mycobacterium africanum. PLoS Negl Trop Dis 2013; 7:e2220. [PMID: 23696911 PMCID: PMC3656116 DOI: 10.1371/journal.pntd.0002220] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2012] [Accepted: 04/05/2013] [Indexed: 12/27/2022] Open
Abstract
BACKGROUND Human tuberculosis (TB) in West Africa is not only caused by M. tuberculosis but also by bacteria of the two lineages of M. africanum. For instance, in The Gambia, 40% of TB is due to infections with M. africanum West African 2. This bacterial lineage is associated with HIV infection, reduced ESAT-6 immunogenicity and slower progression to active disease. Although these characteristics suggest an attenuated phenotype of M. africanum, no underlying mechanism has been described. From the first descriptions of M. africanum in the literature in 1969, the time to a positive culture of M. africanum on solid medium was known to be longer than the time to a positive culture of M. tuberculosis. However, the delayed growth of M. africanum, which may correlate with the less virulent phenotype in the human host, has not previously been studied in detail. METHODOLOGY/PRINCIPAL FINDINGS We compared the growth rates of M. tuberculosis and M. africanum isolates from The Gambia in two liquid culture systems. M. africanum grows significantly slower than M. tuberculosis, not only when grown directly from sputa, but also in growth experiments under defined laboratory conditions. We also sequenced four M. africanum isolates and compared their whole genomes with the published M. tuberculosis H37Rv genome. M. africanum strains have several non-synonymous SNPs or frameshift mutations in genes that were previously associated with growth-attenuation. M. africanum strains also have a higher mutation frequency in genes crucial for transport of sulphur, ions and lipids/fatty acids across the cell membrane into the bacterial cell. Surprisingly, 5 of 7 operons, recently described as essential for intracellular survival of H37Rv in the host macrophage, showed at least one non-synonymously mutated gene in M. africanum. CONCLUSIONS/SIGNIFICANCE The altered growth behaviour of M. africanum might indicate a different survival strategy within host cells.
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Affiliation(s)
- Florian Gehre
- Institute of Tropical Medicine, Antwerp, Belgium
- Medical Research Council Unit, Fajara, The Gambia
- * E-mail:
| | - Jacob Otu
- Medical Research Council Unit, Fajara, The Gambia
| | - Kathryn DeRiemer
- University of California, Davis, Davis, California, United States of America
| | | | | | - Wim Mulders
- Institute of Tropical Medicine, Antwerp, Belgium
| | | | - Bouke C. de Jong
- Institute of Tropical Medicine, Antwerp, Belgium
- Medical Research Council Unit, Fajara, The Gambia
- New York University, New York, New York, United States of America
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Bentley SD, Comas I, Bryant JM, Walker D, Smith NH, Harris SR, Thurston S, Gagneux S, Wood J, Antonio M, Quail MA, Gehre F, Adegbola RA, Parkhill J, de Jong BC. The genome of Mycobacterium africanum West African 2 reveals a lineage-specific locus and genome erosion common to the M. tuberculosis complex. PLoS Negl Trop Dis 2012; 6:e1552. [PMID: 22389744 PMCID: PMC3289620 DOI: 10.1371/journal.pntd.0001552] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2011] [Accepted: 01/17/2012] [Indexed: 01/16/2023] Open
Abstract
Background M. africanum West African 2 constitutes an ancient lineage of the M. tuberculosis complex that commonly causes human tuberculosis in West Africa and has an attenuated phenotype relative to M. tuberculosis. Methodology/Principal Findings In search of candidate genes underlying these differences, the genome of M. africanum West African 2 was sequenced using classical capillary sequencing techniques. Our findings reveal a unique sequence, RD900, that was independently lost during the evolution of two important lineages within the complex: the “modern” M. tuberculosis group and the lineage leading to M. bovis. Closely related to M. bovis and other animal strains within the M. tuberculosis complex, M. africanum West African 2 shares an abundance of pseudogenes with M. bovis but also with M. africanum West African clade 1. Comparison with other strains of the M. tuberculosis complex revealed pseudogenes events in all the known lineages pointing toward ongoing genome erosion likely due to increased genetic drift and relaxed selection linked to serial transmission-bottlenecks and an intracellular lifestyle. Conclusions/Significance The genomic differences identified between M. africanum West African 2 and the other strains of the Mycobacterium tuberculosis complex may explain its attenuated phenotype, and pave the way for targeted experiments to elucidate the phenotypic characteristic of M. africanum. Moreover, availability of the whole genome data allows for verification of conservation of targets used for the next generation of diagnostics and vaccines, in order to ensure similar efficacy in West Africa. Mycobacterium africanum, a close relative of M. tuberculosis, is studied for the following reasons: M. africanum is commonly isolated from West African patients with tuberculosis yet has not spread beyond this region, it is more common in HIV infected patients, and it is less likely to lead to tuberculosis after one is exposed to an infectious case. Understanding this organism's unique biology gets a boost from the decoding of its genome, reported in this issue. For example, genome analysis reveals that M. africanum contains a region shared with “ancient” lineages in the M. tuberculosis complex and other mycobacterial species, which was lost independently from both M. tuberculosis and M. bovis. This region encodes a protein involved in transmembrane transport. Furthermore, M. africanum has lost genes, including a known virulence gene and genes for vitamin synthesis, in addition to an intact copy of a gene that may increase its susceptibility to antibiotics that are insufficiently active against M. tuberculosis. Finally, the genome sequence and analysis reported here will aid in the development of new diagnostics and vaccines against tuberculosis, which need to take into account the differences between M. africanum and other species in order to be effective worldwide.
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Affiliation(s)
- Stephen D. Bentley
- Wellcome Trust Genome Campus, Wellcome Trust Sanger Institute, Hinxton, United Kingdom
| | - Iñaki Comas
- Genomics and Health Unit, Centre for Public Health Research, Valencia, Spain
- Division of Mycobacterial Research, MRC National Institute for Medical Research, The Ridgeway, Mill Hill, London, United Kingdom
| | - Josephine M. Bryant
- Wellcome Trust Genome Campus, Wellcome Trust Sanger Institute, Hinxton, United Kingdom
| | - Danielle Walker
- Wellcome Trust Genome Campus, Wellcome Trust Sanger Institute, Hinxton, United Kingdom
| | - Noel H. Smith
- TB Research Group, Veterinary Laboratories Agency (VLA), Weybridge, New Haw, Addlestone, Surrey, United Kingdom and The Centre for the Study of Evolution, University of Sussex, Brighton, United Kingdom
| | - Simon R. Harris
- Wellcome Trust Genome Campus, Wellcome Trust Sanger Institute, Hinxton, United Kingdom
| | - Scott Thurston
- Wellcome Trust Genome Campus, Wellcome Trust Sanger Institute, Hinxton, United Kingdom
| | - Sebastien Gagneux
- Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Jonathan Wood
- Wellcome Trust Genome Campus, Wellcome Trust Sanger Institute, Hinxton, United Kingdom
| | | | - Michael A. Quail
- Wellcome Trust Genome Campus, Wellcome Trust Sanger Institute, Hinxton, United Kingdom
| | - Florian Gehre
- Vaccinology Theme, MRC Unit, Banjul, The Gambia
- Institute of Tropical Medicine, Antwerp, Belgium
| | | | - Julian Parkhill
- Wellcome Trust Genome Campus, Wellcome Trust Sanger Institute, Hinxton, United Kingdom
| | - Bouke C. de Jong
- Vaccinology Theme, MRC Unit, Banjul, The Gambia
- Institute of Tropical Medicine, Antwerp, Belgium
- New York University, New York, New York, United States of America
- * E-mail:
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Gehre F, Leib SL, Grandgirard D, Kummer J, Bühlmann A, Simon F, Gäumann R, Kharat AS, Täuber MG, Tomasz A. Essential role of choline for pneumococcal virulence in an experimental model of meningitis. J Intern Med 2008; 264:143-54. [PMID: 18331292 DOI: 10.1111/j.1365-2796.2008.01930.x] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
OBJECTIVES The goal of the present study was to elucidate the contribution of the newly recognized virulence factor choline to the pathogenesis of Streptococcus pneumoniae in an animal model of meningitis. RESULTS The choline containing strain D39Cho(-) and its isogenic choline-free derivative D39Cho(-)licA64--each expressing the capsule polysaccharide 2--were introduced intracisternally at an inoculum size of 10(3) CFU into 11 days old Wistar rats. During the first 8 h post infection both strains multiplied and stimulated a similar immune response that involved expression of high levels of proinflammatory cytokines, the matrix metalloproteinase 9 (MMP-9), IL-10, and the influx of white blood cells into the CSF. Virtually identical immune response was also elicited by intracisternal inoculation of 10(7) CFU equivalents of either choline-containing or choline-free cell walls. At sampling times past 8 h strain D39Cho(-) continued to replicate accompanied by an intense inflammatory response and strong granulocytic pleiocytosis. Animals infected with D39Cho(-) died within 20 h and histopathology revealed brain damage in the cerebral cortex and hippocampus. In contrast, the initial immune response generated by the choline-free strain D39Cho(-)licA64 began to decline after the first 8 h accompanied by elimination of the bacteria from the CSF in parallel with a strong WBC response peaking at 8 h after infection. All animals survived and there was no evidence for brain damage. CONCLUSION Choline in the cell wall is essential for pneumococci to remain highly virulent and survive within the host and establish pneumococcal meningitis.
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Affiliation(s)
- F Gehre
- Laboratory of Microbiology, The Rockefeller University, New York, NY 10021, USA
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Klotz C, Gehre F, Lucius R, Pogonka T. Identification of Eimeria tenella genes encoding for secretory proteins and evaluation of candidates by DNA immunisation studies in chickens. Vaccine 2007; 25:6625-34. [PMID: 17675183 DOI: 10.1016/j.vaccine.2007.06.048] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2007] [Revised: 06/15/2007] [Accepted: 06/19/2007] [Indexed: 11/21/2022]
Abstract
In order to identify secretory proteins as possible new vaccine candidates, a cDNA-library from E. tenella sporozoites was generated in yeast and was used to select secreted and surface proteins. Herein 191 clones were isolated and analysis of the nucleic acid sequences revealed 162 deduced open reading frames with a prediction for signal peptides. These sequences are characterized by high redundancy, comprising 25 unique protein fragments with a high degree of stage specificity. Only three sequences showed identical homology to already known E. tenella proteins. The majority, 16 fragments, revealed homology to known or hypothetical proteins, and six fragments had no sequence homologues in protein databases. In order to obtain optimised conditions for a DNA vaccination trial in chickens, with which our selected new sequences could be tested, we performed variant DNA immunisations with the well-characterized E. tenella antigen SO7. The cDNA of the SO7 antigen was subcloned into two different eucaryotic expression vectors, i.e. pcDNA3 and pVR1012. In addition, the SO7 sequence was fused to the stabilizing sequence of the enhanced green fluorescence protein (EGFP). All SO7 constructs induced a SO7 specific immune response after intramuscular application and no significant differences were found on using constructs with or without the EGFP fusion or with different vector systems. Full-length open reading frames from six selected Eimeria sequences were introduced into the eucaryotic expression vector pcDNA3. Subsequent immunisation trials revealed a decrease in parasite excretion for three constructs after challenge infection in comparison to the control animals. Our approach represents a rapid screening to identify and test putative new vaccine candidates from E. tenella sporozoites that could also be adopted to other apicomplexan parasites.
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MESH Headings
- Animals
- Antibodies, Protozoan/immunology
- Antigens, Protozoan/genetics
- Antigens, Protozoan/immunology
- Antigens, Protozoan/metabolism
- Blotting, Western
- COS Cells
- Cell Line
- Chickens
- Chlorocebus aethiops
- Cloning, Molecular
- DNA, Protozoan/genetics
- DNA, Protozoan/immunology
- Eimeria tenella/genetics
- Eimeria tenella/immunology
- Eimeria tenella/metabolism
- Enzyme-Linked Immunosorbent Assay
- Gene Library
- Humans
- Immunization/methods
- Immunoglobulin G/immunology
- Molecular Sequence Data
- Protozoan Proteins/genetics
- Protozoan Proteins/immunology
- Protozoan Proteins/metabolism
- Protozoan Vaccines/genetics
- Protozoan Vaccines/immunology
- Reverse Transcriptase Polymerase Chain Reaction
- Sequence Analysis, DNA
- Vaccines, DNA/genetics
- Vaccines, DNA/immunology
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Affiliation(s)
- Christian Klotz
- Department of Molecular Parasitology, Humboldt University Berlin, Philippstrasse 13, 10115 Berlin, Germany
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Crisóstomo MI, Vollmer W, Kharat AS, Inhülsen S, Gehre F, Buckenmaier S, Tomasz A. Attenuation of penicillin resistance in a peptidoglycan O-acetyl transferase mutant of Streptococcus pneumoniae. Mol Microbiol 2006; 61:1497-509. [PMID: 16968223 DOI: 10.1111/j.1365-2958.2006.05340.x] [Citation(s) in RCA: 85] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The level of penicillin resistance in clinical isolates of Streptococcus pneumoniae depends not only on the reduced affinity of penicillin binding proteins (PBPs) but also on the functioning of enzymes that modify the stem peptide structure of cell wall precursors. We used mariner mutagenesis in search of additional genetic determinants that may further attenuate the level of penicillin resistance in the bacteria. A mariner mutant of the highly penicillin-resistant S. pneumoniae strain Pen6 showed reduction of the penicillin minimum inhibitory concentration (MIC) from 6 to 0.75 microg ml(-1). Decrease in penicillin MIC was also observed upon introduction of the mutation (named provisionally adr, for attenuator of drug resistance) into representatives of major epidemic clones of penicillin-resistant pneumococci. Attenuation of resistance levels was specific for beta-lactams. The adr mutant has retained unchanged (low affinity) PBPs, unaltered murM gene and unchanged cell wall stem peptide composition, but the mutant became hypersensitive to exogenous lysozyme and complementation experiments showed that both phenotypes--reduced resistance and lysozyme sensitivity--were linked to the defective adr gene. DNA sequence comparison and chemical analysis of the cell wall identified adr as the structural gene of the pneumococcal peptidoglycan O-acetylase.
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Affiliation(s)
- M Inês Crisóstomo
- Laboratory of Microbiology, The Rockefeller University, New York, NY, USA
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Schwenkenbecher JM, Fröhlich C, Gehre F, Schnur LF, Schönian G. Evolution and conservation of microsatellite markers for Leishmania tropica. Infect Genet Evol 2004; 4:99-105. [PMID: 15157627 DOI: 10.1016/j.meegid.2004.01.005] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2003] [Revised: 01/12/2004] [Accepted: 01/19/2004] [Indexed: 11/15/2022]
Abstract
Sixteen polymorphic microsatellite markers were developed for phylogenetic analysis of Leishmania tropica. The phylogenetic tests done demonstrated that they do provide a powerful tool for epidemiological studies. They were also tested for their ability to differentiate strains of other species of Leishmania, confirming that microsatellite markers developed for one leishmanial species cannot generally be used for other leishmanial species. In addition to length variation, a high degree of allelic heterozygosity was seen among the strains investigated, suggestive of sexual recombination within the species L. tropica.
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Affiliation(s)
- Jan M Schwenkenbecher
- Institute of Microbiology and Hygiene, Humboldt University, Charité, Berlin, Germany.
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