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Seid A, Girma Y, Abebe A, Dereb E, Kassa M, Berhane N. Characteristics of TB/HIV Co-Infection and Patterns of Multidrug-Resistance Tuberculosis in the Northwest Amhara, Ethiopia. Infect Drug Resist 2023; 16:3829-3845. [PMID: 37346368 PMCID: PMC10281285 DOI: 10.2147/idr.s412951] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Accepted: 06/12/2023] [Indexed: 06/23/2023] Open
Abstract
Background Multidrug-resistant tuberculosis (MDR-TB) has continued to be a serious public health threat and significantly challenges global TB control and prevention efforts, where the TB/HIV co-infection epidemic makes the situation much worse. The aim of the study was to determine the determinant factors associated with patterns of MDR-TB among pulmonary TB patients in the Northwest Amhara, Ethiopia. Methods A hospital-based cross-sectional study was conducted from May 2022 to February 2023 in the Northwest Amhara, Ethiopia. Data on the participants' socio-demographics and clinical characteristics were obtained using a pre-tested checklist. Phenotypic susceptibility testing to first-line anti-TB drugs was performed on 180 isolates by automated BD BACTEC MGIT 960 system. Logistic regression analysis was performed to determine the association of risk factors with patterns of MDR-TB. A p-value ≤0.05 was considered statistically significant. Results The overall proportion of TB with HIV co-infected cases was 19.8% (50/252). Culture positivity was confirmed in 203/252 (80.6%) of sputum samples. Among 168 isolates, the DST showed that 119 (70.8%) isolates were pan-susceptible to all first-line drugs and prevalence of any resistance to first-line drugs was 49,168 (29.2%). Among the resistant isolates, 28 (16.7%) were any mono-resistance and 12 (7.1%) were determined to be resistant to MDR-TB. TB with a previous TB treatment (aOR = 6.73, 95% CI: 1.78-25.47, p = 0.005) and HIV co-infected (aOR = 0.252, 95% CI: 0.73-0.875, p = 0.03) were significantly associated with MDR-TB. Conclusion Higher prevalence of TB and MDR-TB was examined among TB patients in the study area. In the study, history of previous TB treatment was the strongest risk factor MDR-TB infection followed by TB with HIV co-infected cases. Therefore, there is a need of strengthening TB control and prevention programs to reduce the increase of TB incidence, further emergence and transmission of a public health threat of MDR-TB cases.
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Affiliation(s)
- Aynias Seid
- Department of Biology, College of Natural and Computational Science, Debre-Tabor University, Debre-Tabor, Ethiopia
- Department of Medical Biotechnology, Institute of Biotechnology, University of Gondar, Gondar, Ethiopia
| | - Yilak Girma
- TB Culture Laboratory, University of Gondar Comprehensive Specialized Hospital, Gondar, Ethiopia
| | - Ayenesh Abebe
- TB Culture Laboratory, University of Gondar Comprehensive Specialized Hospital, Gondar, Ethiopia
| | - Eseye Dereb
- TB Culture Laboratory, University of Gondar Comprehensive Specialized Hospital, Gondar, Ethiopia
| | - Meseret Kassa
- TB Culture Laboratory, University of Gondar Comprehensive Specialized Hospital, Gondar, Ethiopia
| | - Nega Berhane
- Department of Medical Biotechnology, Institute of Biotechnology, University of Gondar, Gondar, Ethiopia
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Genestet C, Refrégier G, Hodille E, Zein-Eddine R, Le Meur A, Hak F, Barbry A, Westeel E, Berland JL, Engelmann A, Verdier I, Lina G, Ader F, Dray S, Jacob L, Massol F, Venner S, Dumitrescu O. Mycobacterium tuberculosis genetic features associated with pulmonary tuberculosis severity. Int J Infect Dis 2022; 125:74-83. [PMID: 36273524 DOI: 10.1016/j.ijid.2022.10.026] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Revised: 10/13/2022] [Accepted: 10/15/2022] [Indexed: 11/06/2022] Open
Abstract
OBJECTIVES Mycobacterium tuberculosis (Mtb) infections result in a wide spectrum of clinical presentations but without proven Mtb genetic determinants. Herein, we hypothesized that the genetic features of Mtb clinical isolates, such as specific polymorphisms or microdiversity, may be linked to tuberculosis (TB) severity. METHODS A total of 234 patients with pulmonary TB (including 193 drug-susceptible and 14 monoresistant cases diagnosed between 2017 and 2020 and 27 multidrug-resistant cases diagnosed between 2010 and 2020) were stratified according to TB disease severity, and Mtb genetic features were explored using whole genome sequencing, including heterologous single-nucleotide polymorphism (SNP), calling to explore microdiversity. Finally, we performed a structural equation modeling analysis to relate TB severity to Mtb genetic features. RESULTS The clinical isolates from patients with mild TB carried mutations in genes associated with host-pathogen interaction, whereas those from patients with moderate/severe TB carried mutations associated with regulatory mechanisms. Genome-wide association study identified an SNP in the promoter of the gene coding for the virulence regulator espR, statistically associated with moderate/severe disease. Structural equation modeling and model comparisons indicated that TB severity was associated with the detection of Mtb microdiversity within clinical isolates and to the espR SNP. CONCLUSION Taken together, these results provide a new insight to better understand TB pathophysiology and could provide a new prognosis tool for pulmonary TB severity.
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Affiliation(s)
- Charlotte Genestet
- CIRI - Centre International de Recherche en Infectiologie, Ecole Normale Supérieure de Lyon, Université Claude Bernard Lyon-1, Rhône-Alpes, Lyon, France; Hospices Civils de Lyon, Institut des Agents Infectieux, Laboratoire de bactériologie, Rhône-Alpes, Lyon, France.
| | - Guislaine Refrégier
- Université Paris-Saclay, CNRS, AgroParisTech, Ecologie Systématique et Evolution, Île-de-France, Orsay, France.; Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris Sud, Université Paris-Saclay, Île-de-France, Gif-sur-Yvette, France
| | - Elisabeth Hodille
- CIRI - Centre International de Recherche en Infectiologie, Ecole Normale Supérieure de Lyon, Université Claude Bernard Lyon-1, Rhône-Alpes, Lyon, France; Hospices Civils de Lyon, Institut des Agents Infectieux, Laboratoire de bactériologie, Rhône-Alpes, Lyon, France
| | - Rima Zein-Eddine
- Université Paris-Saclay, CNRS, AgroParisTech, Ecologie Systématique et Evolution, Île-de-France, Orsay, France.; Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris Sud, Université Paris-Saclay, Île-de-France, Gif-sur-Yvette, France; Laboratory of Optics and Biosciences, CNRS-INSERM-Ecole Polytechnique, Île-de-France, Palaiseau, France
| | - Adrien Le Meur
- Université Paris-Saclay, CNRS, AgroParisTech, Ecologie Systématique et Evolution, Île-de-France, Orsay, France.; Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris Sud, Université Paris-Saclay, Île-de-France, Gif-sur-Yvette, France
| | - Fiona Hak
- Université Paris-Saclay, CNRS, AgroParisTech, Ecologie Systématique et Evolution, Île-de-France, Orsay, France.; Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris Sud, Université Paris-Saclay, Île-de-France, Gif-sur-Yvette, France
| | - Alexia Barbry
- CIRI - Centre International de Recherche en Infectiologie, Ecole Normale Supérieure de Lyon, Université Claude Bernard Lyon-1, Rhône-Alpes, Lyon, France; Hospices Civils de Lyon, Institut des Agents Infectieux, Laboratoire de bactériologie, Rhône-Alpes, Lyon, France
| | - Emilie Westeel
- Fondation Mérieux, Emerging Pathogens Laboratory, Rhône-Alpes, Lyon, France
| | - Jean-Luc Berland
- Fondation Mérieux, Emerging Pathogens Laboratory, Rhône-Alpes, Lyon, France
| | - Astrid Engelmann
- Centre Hospitalier Fleyriat, Rhône-Alpes, Bourg-en-Bresse, France
| | - Isabelle Verdier
- Centre Hospitalier Fleyriat, Rhône-Alpes, Bourg-en-Bresse, France
| | - Gérard Lina
- CIRI - Centre International de Recherche en Infectiologie, Ecole Normale Supérieure de Lyon, Université Claude Bernard Lyon-1, Rhône-Alpes, Lyon, France; Hospices Civils de Lyon, Institut des Agents Infectieux, Laboratoire de bactériologie, Rhône-Alpes, Lyon, France; Université Lyon 1, Facultés de Médecine et de Pharmacie de Lyon, Rhône-Alpes, Lyon, France
| | - Florence Ader
- CIRI - Centre International de Recherche en Infectiologie, Ecole Normale Supérieure de Lyon, Université Claude Bernard Lyon-1, Rhône-Alpes, Lyon, France; Hospices Civils de Lyon, Service des Maladies infectieuses et tropicales, Rhône-Alpes, Lyon, France
| | - Stéphane Dray
- Biometrics and Evolutionary Biology Laboratory, CNRS UMR 5558, Université Lyon 1, Rhône-Alpes, Villeurbanne, France
| | - Laurent Jacob
- Biometrics and Evolutionary Biology Laboratory, CNRS UMR 5558, Université Lyon 1, Rhône-Alpes, Villeurbanne, France
| | - François Massol
- UMR 8198 Evo-Eco-Paleo, SPICI Group, University of Lille, Hauts-de-France, Lille, France; CNRS, CHU Lille, Institut Pasteur de Lille, U1019-UMR 9017-CIIL-Center for Infection and Immunity of Lille, University of Lille, Hauts-de-France, Lille, France
| | - Samuel Venner
- Biometrics and Evolutionary Biology Laboratory, CNRS UMR 5558, Université Lyon 1, Rhône-Alpes, Villeurbanne, France
| | - Oana Dumitrescu
- CIRI - Centre International de Recherche en Infectiologie, Ecole Normale Supérieure de Lyon, Université Claude Bernard Lyon-1, Rhône-Alpes, Lyon, France; Hospices Civils de Lyon, Institut des Agents Infectieux, Laboratoire de bactériologie, Rhône-Alpes, Lyon, France; Université Lyon 1, Facultés de Médecine et de Pharmacie de Lyon, Rhône-Alpes, Lyon, France
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Genestet C, Hodille E, Barbry A, Berland JL, Hoffmann J, Westeel E, Bastian F, Guichardant M, Venner S, Lina G, Ginevra C, Ader F, Goutelle S, Dumitrescu O. Rifampicin exposure reveals within-host Mycobacterium tuberculosis diversity in patients with delayed culture conversion. PLoS Pathog 2021; 17:e1009643. [PMID: 34166469 PMCID: PMC8224949 DOI: 10.1371/journal.ppat.1009643] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Accepted: 05/13/2021] [Indexed: 12/21/2022] Open
Abstract
Mycobacterium tuberculosis (Mtb) genetic micro-diversity in clinical isolates may underline mycobacterial adaptation to tuberculosis (TB) infection and provide insights to anti-TB treatment response and emergence of resistance. Herein we followed within-host evolution of Mtb clinical isolates in two cohorts of TB patients, either with delayed Mtb culture conversion (> 2 months), or with fast culture conversion (< 2 months). We captured the genetic diversity of Mtb isolates obtained in each patient, by focusing on minor variants detected as unfixed single nucleotide polymorphisms (SNPs). To unmask antibiotic tolerant sub-populations, we exposed these isolates to rifampicin (RIF) prior to whole genome sequencing (WGS) analysis. Thanks to WGS, we detected at least 1 unfixed SNP within the Mtb isolates for 9/15 patients with delayed culture conversion, and non-synonymous (ns) SNPs for 8/15 patients. Furthermore, RIF exposure revealed 9 additional unfixed nsSNP from 6/15 isolates unlinked to drug resistance. By contrast, in the fast culture conversion cohort, RIF exposure only revealed 2 unfixed nsSNP from 2/20 patients. To better understand the dynamics of Mtb micro-diversity, we investigated the variant composition of a persistent Mtb clinical isolate before and after controlled stress experiments mimicking the course of TB disease. A minor variant, featuring a particular mycocerosates profile, became enriched during both RIF exposure and macrophage infection. The variant was associated with drug tolerance and intracellular persistence, consistent with the pharmacological modeling predicting increased risk of treatment failure. A thorough study of such variants not necessarily linked to canonical drug-resistance, but which are prone to promote anti-TB drug tolerance, may be crucial to prevent the subsequent emergence of resistance. Taken together, the present findings support the further exploration of Mtb micro-diversity as a promising tool to detect patients at risk of poorly responding to anti-TB treatment, ultimately allowing improved and personalized TB management. Tuberculosis (TB) is caused by Mycobacterium tuberculosis (Mtb), bacteria that are able to persist inside the patient for many months or years, thus requiring long antibiotic treatments. Here we focused on TB patients with delayed response to treatment and we performed genetic characterization of Mtb isolates to search for sub-populations that may tolerate anti-TB drugs. We found that Mtb cultured from 9/15 patients contained different sub-populations, and in vitro drug exposure revealed Mtb sub-populations in 6/15 isolates, none related to known drug-resistance mechanisms. By contrast, drug exposure revealed Mtb sup-populations in 2/20 isolates in the control cohort of patients with fast culture conversion. Furthermore, we characterized a Mtb variant isolated from a sub-population growing in the presence of rifampicin (RIF), a major anti-TB drug. We found that this variant featured a modified lipidic envelope, and that it was able to develop in the presence of RIF and inside human macrophage cells. We performed pharmacological modelling and found that this kind of variant may be related to a poor response to treatment. In conclusion, searching for particular Mtb sub-populations may help to detect patients at risk of treatment failure and provide additional guidance for TB management.
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Affiliation(s)
- Charlotte Genestet
- CIRI—Centre International de Recherche en Infectiologie, Ecole Normale Supérieure de Lyon, Université Claude Bernard Lyon-1, Inserm U1111, CNRS UMR5308, Lyon, France
- Hospices Civils de Lyon, Institut des Agents Infectieux, Laboratoire de bactériologie, Lyon, France
- * E-mail:
| | - Elisabeth Hodille
- CIRI—Centre International de Recherche en Infectiologie, Ecole Normale Supérieure de Lyon, Université Claude Bernard Lyon-1, Inserm U1111, CNRS UMR5308, Lyon, France
- Hospices Civils de Lyon, Institut des Agents Infectieux, Laboratoire de bactériologie, Lyon, France
| | - Alexia Barbry
- CIRI—Centre International de Recherche en Infectiologie, Ecole Normale Supérieure de Lyon, Université Claude Bernard Lyon-1, Inserm U1111, CNRS UMR5308, Lyon, France
- Hospices Civils de Lyon, Institut des Agents Infectieux, Laboratoire de bactériologie, Lyon, France
| | - Jean-Luc Berland
- CIRI—Centre International de Recherche en Infectiologie, Ecole Normale Supérieure de Lyon, Université Claude Bernard Lyon-1, Inserm U1111, CNRS UMR5308, Lyon, France
- Fondation Mérieux, Emerging Pathogens Laboratory, Lyon, France
| | - Jonathan Hoffmann
- CIRI—Centre International de Recherche en Infectiologie, Ecole Normale Supérieure de Lyon, Université Claude Bernard Lyon-1, Inserm U1111, CNRS UMR5308, Lyon, France
- Fondation Mérieux, Emerging Pathogens Laboratory, Lyon, France
| | - Emilie Westeel
- CIRI—Centre International de Recherche en Infectiologie, Ecole Normale Supérieure de Lyon, Université Claude Bernard Lyon-1, Inserm U1111, CNRS UMR5308, Lyon, France
- Fondation Mérieux, Emerging Pathogens Laboratory, Lyon, France
| | - Fabiola Bastian
- Plateforme DTAMB, CNRS, Université Lyon 1, Villeurbanne, France
| | - Michel Guichardant
- CarMeN laboratory, INSA Lyon, INSERM U1060, INRA U1397, Université Lyon 1, Villeurbanne, France
| | - Samuel Venner
- Laboratoire de Biométrie et Biologie Évolutive, CNRS UMR 5558, Université Lyon 1, Villeurbanne, France
| | - Gérard Lina
- CIRI—Centre International de Recherche en Infectiologie, Ecole Normale Supérieure de Lyon, Université Claude Bernard Lyon-1, Inserm U1111, CNRS UMR5308, Lyon, France
- Hospices Civils de Lyon, Institut des Agents Infectieux, Laboratoire de bactériologie, Lyon, France
- Université Lyon 1, Facultés de Médecine et de Pharmacie de Lyon, Lyon, France
| | - Christophe Ginevra
- CIRI—Centre International de Recherche en Infectiologie, Ecole Normale Supérieure de Lyon, Université Claude Bernard Lyon-1, Inserm U1111, CNRS UMR5308, Lyon, France
- Hospices Civils de Lyon, Institut des Agents Infectieux, Laboratoire de bactériologie, Lyon, France
| | - Florence Ader
- CIRI—Centre International de Recherche en Infectiologie, Ecole Normale Supérieure de Lyon, Université Claude Bernard Lyon-1, Inserm U1111, CNRS UMR5308, Lyon, France
- Hospices Civils de Lyon, Service des Maladies infectieuses et tropicales, Lyon, France
| | - Sylvain Goutelle
- Laboratoire de Biométrie et Biologie Évolutive, CNRS UMR 5558, Université Lyon 1, Villeurbanne, France
- Université Lyon 1, Facultés de Médecine et de Pharmacie de Lyon, Lyon, France
- Hospices Civils de Lyon, Groupement Hospitalier Nord, Service pharmaceutique, Lyon, France
| | - Oana Dumitrescu
- CIRI—Centre International de Recherche en Infectiologie, Ecole Normale Supérieure de Lyon, Université Claude Bernard Lyon-1, Inserm U1111, CNRS UMR5308, Lyon, France
- Hospices Civils de Lyon, Institut des Agents Infectieux, Laboratoire de bactériologie, Lyon, France
- Université Lyon 1, Facultés de Médecine et de Pharmacie de Lyon, Lyon, France
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