Benin Population Diversity of Tuberculosis and Implications (BeniDiT)

Implications of the Population Structure of the Mycobacterium Tuberculosis Complex in Benin for Tuberculosis Presentation, Diagnosis and Outcome

Tuberculosis is a public health problem caused by a microbe. This microbe may differ from one patient to another. The purpose of this study is to know to which extent, each of these various microbes is involved in tuberculosis disease in Benin. This study will also find out whether the type that affects a patient, depends on patient characteristics and whether the difference affects the outcome of the treatment. Finally the study will also help to find out whether diagnostic tests are reliable for all types of the microbe. This information will be used after the study to inform decision making in order to improve tuberculosis control.

Study Overview

• Status: Completed
• Conditions: Tuberculosis
• Intervention / Treatment: Other: No intervention (observational study)

Detailed Description

The overall aim of this study is to determine the population structure of Mycobacterium tuberculosis complex in Benin, and implications for tuberculosis presentation, diagnosis and outcome The primary objective is to compare the characteristics of ancestral lineages of Mycobacterium tuberculosis complex, such as M. africanum West African 1 (Lineage 5), with modern M. tuberculosis in Benin.

This study will build on the system of nationwide surveillance already implemented for retreatment patients and recruit in addition a representative random sample of new patients. So for this study sputa from retreatment patients and from a sample of new patients, from the 24 tuberculosis (TB) clinics (Centres de Diagnostic et de Traitement de la Tuberculose) selected all over the country (Benin), will be shipped from TB clinics to the ''Laboratoire de Référence des Mycobactéries'' (LRM), Cotonou (National Reference Laboratory for Mycobacteria, Cotonou) if they consent. All retreatment patients will be recruited into the study and each 4 new patients detected after detection of a retreatment patient will also be recruited into the study.

At enrolment, a questionnaire will be used to collect from consenting participants information such as: Participant place of residence (rural or urban as determined by population density); ethnic group; age; sex; Human Immuno-deficiency Virus (HIV) status; Bacillus Calmette Guerin (BCG) vaccine scar...

Spoligotype analysis will be used to determine the population structure, as it allows the classification of most Mycobacterium tuberculosis complex isolates in lineages, including strains with single or few copies of IS6110.

The external quality evaluation (assurance quality) of the laboratory analyses to be performed at the LRM (National Reference Laboratory for Mycobacteria) in Cotonou, Benin during the study, will be performed by the Institute of Tropical Medicine of Antwerp in Belgium.

• Study Type: Observational
• Enrollment (Actual): 1490

Contacts and Locations

Study Locations

• Belgium
  • Antwerp, Belgium
    • Institute of Tropical Medicine
• Benin
  • Atacora/Donga
    • Djougou, Atacora/Donga, Benin
      • Centre de Diagnostic et de Traitement de la Tuberculose de Djougou
    • Matéri, Atacora/Donga, Benin
      • Centre de Diagnostic et de Traitement de la Tuberculose de Matéri
    • Natitingou, Atacora/Donga, Benin
      • Centre de Diagnostic et de Traitement de la Tuberculose de Natitingou
    • Tanguiéta, Atacora/Donga, Benin
      • Centre de Diagnostic et de Traitement de la Tuberculose de Tanguiéta
  • Atlantique/Littoral
    • Abomey-Calavi, Atlantique/Littoral, Benin
      • Centre de Diagnostic et de Traitement de la tuberculose d'Abomey-Calavi
    • Allada, Atlantique/Littoral, Benin
      • Centre de Diagnostic et de Traitement de la Tuberculose d'Allada
    • Cotonou, Atlantique/Littoral, Benin, 01BP321
      • Centre National Hospitalier Universitaire de Pneumo-Phtisiologie de Cotonou
    • Ouidah, Atlantique/Littoral, Benin
      • Centre de Diagnostic et de Traitement de la Tuberculose de Ouidah
  • Borgou/Alibori
    • Bembèrèkè, Borgou/Alibori, Benin
      • Centre de Diagnostic et de Traitement de la Tuberculose de Bembèrèkè HE
    • Kandi, Borgou/Alibori, Benin
      • Centre de Diagnostic et de Traitement de la Tuberculose de Kandi
    • Nikki, Borgou/Alibori, Benin
      • Centre de Diagnostic et de Traitement de la Tuberculose de Nikki Hopital Sounou-Séro
    • Parakou, Borgou/Alibori, Benin
      • Centre de Diagnostic et de Traitement de la Tuberculose de Parakou CSCom
  • Littoral
    • Cotonou, Littoral, Benin, 01BP321
      • Laboratoire de Référence des Mycobactéries
  • Mono/Couffo
    • Aplahoué, Mono/Couffo, Benin
      • Centre de Diagnostic et de Traitement de la Tuberculose d'Aplahoué
    • Bopa, Mono/Couffo, Benin
      • Centre de Diagnostic et de Traitement de la Tuberculose de Bopa
    • Comè, Mono/Couffo, Benin
      • Centre de Diagnostic et de Traitement de la Tuberculose de Comè
    • Houéyogbé, Mono/Couffo, Benin
      • Centre de Diagnostic et de Traitement de la Tuberculose de Houéyogbé
  • Oueme/Plateau
    • Avrankou, Oueme/Plateau, Benin
      • Centre de Diagnostic et de Traitement de la Tuberculose de Avrankou
    • Pobe, Oueme/Plateau, Benin
      • Centre de Diagnostic et de Traitement de la Tuberculose de Pobè
    • Porto-Novo, Oueme/Plateau, Benin
      • Centre de Pneumo-Phtisiologie d'Akron
    • Sakété, Oueme/Plateau, Benin
      • Centre de Diagnostic et de Traitement de la Tuberculose de Sakété
  • Zou/Collines
    • Abomey, Zou/Collines, Benin
      • Centre de Diagnostic et de Traitement de la Tuberculose d'Abomey
    • Bohicon, Zou/Collines, Benin
      • Centre de Diagnostic et de Traitement de la Tuberculose de Bohicon
    • Dassa-Zoumè, Zou/Collines, Benin
      • Centre de Diagnostic et de Traitement de la Tuberculose de Dassa-Zoumè
    • Zagnanado, Zou/Collines, Benin
      • Centre de Diagnostic et de Traitement de la Tuberculose de Zagnanado

Participation Criteria

Eligibility Criteria

• Ages Eligible for Study: 15 years and older (Child, Adult, Older Adult)
• Accepts Healthy Volunteers: No
• Genders Eligible for Study: All

• Sampling Method: Probability Sample

Study Population

There is a National Tuberculosis Program in Benin with a network of 57 TB (tuberculosis) 'diagnosis and treatment centers' (TB clinics). In order to be able to ensure a realistic (cost, time, personnel) strong quality control of data to record on fields in TB clinics, a smaller number of TB clinics where most of Benin TB patients are diagnosed is selected instead of including all the 57 TB clinics. Participants will be recruited from the 4 largest TB clinics of each of Benin's 6 (former) departments (Atlantique/Littoral, Oueme/Plateau, Mono/Couffo, Zou/Collines, Borgou/Alibori, Atacora/Donga), amounting to 24 TB clinics.

Description

Inclusion Criteria:

• New or retreatment tuberculosis patients with Acid Fast Bacilli-positive microscopy,
• Diagnosed in a participating TB clinic of Benin,
• Aged ≥15 years (Patients aged less than 15 years old will not be included in this study as acid-fast-bacilli microscopy is rarely positive in children)
• Who has given his/her informed consent (if adult potential participant:≥18 years old) OR who has given his/her assent in addition to the informed consent of his/her legal representative (if potential participant aged 15-<18 years)

Exclusion Criteria:

• Extra-pulmonary TB only,
• New patient who has started taking the TB treatment drugs.
• Retreatment patient who has started taking the TB retreatment drugs.
• Very low sputum quantity (at least 5 milliliters total sputum is acceptable) and potential participant refusing to give more sputum

Study Plan

How is the study designed?

Number of groups / cohorts

2

Cohorts and Interventions

Group / Cohort	Intervention / Treatment
New patients; ''New tuberculosis patients'' are patients just diagnosed for tuberculosis, and who were never treated for tuberculosis or who are treated for less than 1 month. In total, 1192 new patients will be recruited.	Other: No intervention (observational study)
Retreatment patients; ''Retreatment tuberculosis patients'' are patients just diagnosed for tuberculosis and who were previously treated for tuberculosis (for a duration of 1 month at least). This group includes: patients with treatment relapse, failure and patients who return after default. In total, 298 retreatment patients will be recruited.	Other: No intervention (observational study)

What is the study measuring?

Primary Outcome Measures

Outcome Measure	Measure Description	Time Frame
Lineage	Mycobacterium tuberculosis lineage as determined by the spoligotyping pattern. The lineage will be determined using the specimen collected at participant enrolment. Spoligotyping will be done on sputum, or on culture isolate if failed on sputum and culture is positive.	At enrollment

Secondary Outcome Measures

Outcome Measure	Measure Description	Time Frame
Spoligotype (family)	Mycobacterium tuberculosis spoligotype (family) as determined by the spoligotyping pattern. The lineage will be determined using the specimen collected at participant enrolment.	At enrollment
Treatment failure or success as evidenced by microscopy result (for new and retreatment patients)	Treatment failure will be ascertained at the end of the treatment period using microscopy for detection of acid-fast bacilli in participant' sputa. Treatment failure or success will be measured using microscopy, only for new and retreatment patients.	At Month 6 for new patient; at Month 8 for retreatment patients
Treatment failure or success as evidenced by culture result (for rifampicin resistant patients)	Treatment failure will be ascertained at the end of the 20 months treatment period by culturing sputa from rifampicin resistant participants.	At Month 20 for rifampicin resistant patients
Relapse ascertainment (by questioning and retrospective check of microscopy evidence in TB clinics)	Participants will be called and will be asked whether they have experienced another episode of tuberculosis. This will be retrospectively confirmed in the TB clinic by checking microscopy results for the new episode of tuberculosis.	At Month 18 for new patients; at Month 20 for retreatment patients; at Month 32 for rifampicin resistant patients
Chest X-ray findings	Chest X-ray will be performed in participants to be enrolled in Cotonou and Porto-Novo, the 2 biggest TB clinics and where X-ray is available.	At enrollment
Culture positivity	Isolation of mycobacteria (in vitro mycobacterial growth) in culture	At enrollment
Phenotypic Drug-resistance or susceptibility	Drug resistance as determined using phenotypic drug susceptibility testing on 1st and 2nd line anti-tuberculous drugs	At enrollment (if positive culture)
Genotypic resistance to rifampin (GeneXpert)	Resistance of Mycobacterium tuberculosis to rifampin as determined using the GeneXpert Mtb/Rif test.	At enrollment
(Phenotypic)Type of Mycobacteria (tuberculous or non-tuberculous)	Group of Mycobacteria (tuberculous or non-tuberculous) as determined by the result of phenotypic drug sensitivity testing on para-nitro-benzoic acid	At enrollment (if positive culture)
(Mpt64's)Type of Mycobacteria (tuberculous or non-tuberculous)	Group of Mycobacteria (tuberculous or non-tuberculous) as determined using the Mpt64 antigen test	At enrollment (if positive culture)

Other Outcome Measures

Outcome Measure	Measure Description	Time Frame
Acid-Fast Bacilli microcopy result	Acid-Fast Bacilli microcopy result on patients' sputa determined using the Ziehl-Neelsen method or the auramine method depending on which of these methods is used at the various tuberculosis clinics where participants will be enrolled.	1 Day
Acid-Fast Bacilli microcopy on pooled sputum	Acid-Fast Bacilli microcopy result on the pooled sputum of each participant. The pooled sputum results from the addition of the 2 leftover routine sputa of a participant to the third sputum given after informed consent. This Acid-Fast Bacilli microcopy on pooled sputum will be done after shipment of the pooled sputum to the Reference Laboratory (LRM), using auramine method.	At enrollment
Drug resistance or susceptibility (Novel diagnostic tests)	Drug resistance pattern for 1st and 2nd lines drugs using novel diagnostic tests.	At enrollment

Collaborators and Investigators

• Sponsor: Laboratoire de Référence des Mycobactéries
• Collaborators: Institute of Tropical Medicine, Belgium; Universiteit Antwerpen; Direction Générale de la Coopération au Développement, Belgique; Laboratoire de Référence des Mycobactéries, Benin republic; Centre National Hospitalier Universitaire de Pneumo-Phtisiologie de Cotonou, Benin; Centres de Diagnostic et de Traitement de la tuberculose, National Tuberculosis Programme, Benin
• Investigators: Principal Investigator: Dissou Affolabi, MD PhD Prof, Laboratoire de Référence des Mycobactéries, Benin; Principal Investigator: Bouke de Jong, MD PhD Prof, Institute of Tropical Medicine, Belgium

Publications and helpful links

General Publications

• Affolabi D, Anyo G, Faihun F, Sanoussi N, Shamputa IC, Rigouts L, Kestens L, Anagonou S, Portaels F. First molecular epidemiological study of tuberculosis in Benin. Int J Tuberc Lung Dis. 2009 Mar;13(3):317-22.
• Brudey K, Driscoll JR, Rigouts L, Prodinger WM, Gori A, Al-Hajoj SA, Allix C, Aristimuno L, Arora J, Baumanis V, Binder L, Cafrune P, Cataldi A, Cheong S, Diel R, Ellermeier C, Evans JT, Fauville-Dufaux M, Ferdinand S, Garcia de Viedma D, Garzelli C, Gazzola L, Gomes HM, Guttierez MC, Hawkey PM, van Helden PD, Kadival GV, Kreiswirth BN, Kremer K, Kubin M, Kulkarni SP, Liens B, Lillebaek T, Ho ML, Martin C, Martin C, Mokrousov I, Narvskaia O, Ngeow YF, Naumann L, Niemann S, Parwati I, Rahim Z, Rasolofo-Razanamparany V, Rasolonavalona T, Rossetti ML, Rusch-Gerdes S, Sajduda A, Samper S, Shemyakin IG, Singh UB, Somoskovi A, Skuce RA, van Soolingen D, Streicher EM, Suffys PN, Tortoli E, Tracevska T, Vincent V, Victor TC, Warren RM, Yap SF, Zaman K, Portaels F, Rastogi N, Sola C. Mycobacterium tuberculosis complex genetic diversity: mining the fourth international spoligotyping database (SpolDB4) for classification, population genetics and epidemiology. BMC Microbiol. 2006 Mar 6;6:23. doi: 10.1186/1471-2180-6-23.
• de Jong BC, Antonio M, Gagneux S. Mycobacterium africanum--review of an important cause of human tuberculosis in West Africa. PLoS Negl Trop Dis. 2010 Sep 28;4(9):e744. doi: 10.1371/journal.pntd.0000744.
• de Jong BC, Hill PC, Aiken A, Awine T, Antonio M, Adetifa IM, Jackson-Sillah DJ, Fox A, Deriemer K, Gagneux S, Borgdorff MW, McAdam KP, Corrah T, Small PM, Adegbola RA. Progression to active tuberculosis, but not transmission, varies by Mycobacterium tuberculosis lineage in The Gambia. J Infect Dis. 2008 Oct 1;198(7):1037-43. doi: 10.1086/591504.
• de Jong BC, Hill PC, Brookes RH, Otu JK, Peterson KL, Small PM, Adegbola RA. Mycobacterium africanum: a new opportunistic pathogen in HIV infection? AIDS. 2005 Oct 14;19(15):1714-5. doi: 10.1097/01.aids.0000185991.54595.41. No abstract available.
• Gehre F, Antonio M, Faihun 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 Oct 15;8(10):e77000. doi: 10.1371/journal.pone.0077000. eCollection 2013.
• Affolabi D, Faihun F, Sanoussi N, Anyo G, Shamputa IC, Rigouts L, Kestens L, Anagonou S, Portaels F. Possible outbreak of streptomycin-resistant Mycobacterium tuberculosis Beijing in Benin. Emerg Infect Dis. 2009 Jul;15(7):1123-5. doi: 10.3201/eid1507.080697.
• Kamerbeek J, Schouls L, Kolk A, van Agterveld M, van Soolingen D, Kuijper S, Bunschoten A, Molhuizen H, Shaw R, Goyal M, van Embden J. Simultaneous detection and strain differentiation of Mycobacterium tuberculosis for diagnosis and epidemiology. J Clin Microbiol. 1997 Apr;35(4):907-14. doi: 10.1128/jcm.35.4.907-914.1997.
• Gagneux S, Small PM. Global phylogeography of Mycobacterium tuberculosis and implications for tuberculosis product development. Lancet Infect Dis. 2007 May;7(5):328-37. doi: 10.1016/S1473-3099(07)70108-1.
• Castets M. [Mycobacterium africanum (author's transl)]. Med Trop (Mars). 1979 Mar-Apr;39(2):145-8. French.
• Parwati I, van Crevel R, van Soolingen D, van der Zanden A. Application of spoligotyping to noncultured Mycobacterium tuberculosis bacteria requires an optimized approach. J Clin Microbiol. 2003 Nov;41(11):5350-1. doi: 10.1128/JCM.41.11.5350-5351.2003. No abstract available.
• Asante-Poku A, Yeboah-Manu D, Otchere ID, Aboagye SY, Stucki D, Hattendorf J, Borrell S, Feldmann J, Danso E, Gagneux S. Mycobacterium africanum is associated with patient ethnicity in Ghana. PLoS Negl Trop Dis. 2015 Jan 8;9(1):e3370. doi: 10.1371/journal.pntd.0003370. eCollection 2015 Jan.
• Yin X, Zheng L, Lin L, Hu Y, Zheng F, Hu Y, Wang Q. Commercial MPT64-based tests for rapid identification of Mycobacterium tuberculosis complex: a meta-analysis. J Infect. 2013 Nov;67(5):369-77. doi: 10.1016/j.jinf.2013.06.009. Epub 2013 Jun 22.
• Sanoussi CN, de Jong BC, Affolabi D, Meehan CJ, Odoun M, Rigouts L. Storage of Sputum in Cetylpyridinium Chloride, OMNIgene.SPUTUM, and Ethanol Is Compatible with Molecular Tuberculosis Diagnostic Testing. J Clin Microbiol. 2019 Jun 25;57(7):e00275-19. doi: 10.1128/JCM.00275-19. Print 2019 Jul.
• Sanoussi CN, Affolabi D, Rigouts L, Anagonou S, de Jong B. Genotypic characterization directly applied to sputum improves the detection of Mycobacterium africanum West African 1, under-represented in positive cultures. PLoS Negl Trop Dis. 2017 Sep 1;11(9):e0005900. doi: 10.1371/journal.pntd.0005900. eCollection 2017 Sep.

Study record dates

Study Major Dates

• Study Start (Actual): April 12, 2016
• Primary Completion (Actual): January 8, 2018
• Study Completion (Actual): December 12, 2019

Study Registration Dates

• First Submitted: April 4, 2016
• First Submitted That Met QC Criteria: April 19, 2016
• First Posted (Estimate): April 20, 2016

Study Record Updates

• Last Update Posted (Actual): February 23, 2021
• Last Update Submitted That Met QC Criteria: February 21, 2021
• Last Verified: February 1, 2021

More Information

Terms related to this study

• Keywords: outcome; Tuberculosis; sputum; diagnostics; resistance; culture; population structure; implications; lineages; spoligotyping; new/retreatment patient
• Additional Relevant MeSH Terms: Infections; Bacterial Infections; Bacterial Infections and Mycoses; Gram-Positive Bacterial Infections; Actinomycetales Infections; Mycobacterium Infections; Tuberculosis
• Other Study ID Numbers: LRM-N°030-15/12/2015; CNERS N°030 of 15th/12/2015 (Other Identifier: Comité National d'Ethique et de Recherche en Santé du Benin); ITM- N°1040/15 (Other Identifier: IRB of Institute of Tropical Medicine Belgium); EC UZA 15/49/532 (Other Identifier: University of Antwerp, Belgium; Ethics Committee); Belg registN°:B300201526865 (Other Identifier: University of Antwerp, Belgium; Ethics Committee)