1
|
Lugonzo GO, Njeru EM, Songock W, Okumu AA, Ndombi EM. Epidemiology of multi-drug resistant Tuberculosis in the western region of Kenya. AIMS Microbiol 2024; 10:273-287. [PMID: 38919722 PMCID: PMC11194625 DOI: 10.3934/microbiol.2024014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Revised: 04/08/2024] [Accepted: 04/10/2024] [Indexed: 06/27/2024] Open
Abstract
Multidrug-resistant tuberculosis (TB) (MDR-TB), or TB that is simultaneously resistant to both isoniazid (INH) and rifampicin (RIF), is a barrier to successful TB control and treatment. Stratified data on MDR-TB, particularly in the high-burden western Kenya region, remain unknown. This data is important to monitor the efficacy of TB control and treatment efforts. Herein, we determined the molecular epidemiology of drug-resistant TB and associated risk factors in western Kenya. This was a non-experimental, population-based, cross-sectional study conducted between January and August 2018. Morning sputum samples of individuals suspected of pulmonary TB were collected, processed, and screened for Mycobacterium tuberculosis (Mtb) and drug resistance using line probe assay (LPA) and Mycobacterium growth indicator tubes (MGIT) culture. MGIT-positive samples were cultured on brain heart infusion (BHII) agar media, and the presence of Mtb was validated using Immunochromatographic assay (ICA). Drug sensitivity was performed on MGIT and ICA-positive but BHI-negative samples. Statistical significance was set at P < 0.05. Of the 622 Mtb isolates, 536 (86.2%) were susceptible to RIF and INH. The rest, 86 (13.83%), were resistant to either drugs or both. A two-sample proportional equality test revealed that the MDR-TB prevalence in western Kenya (5%) did not vary significantly from the global MDR-TB estimate (3.9%) (P = 0.196). Men comprised the majority of susceptible and resistant TB (75.9% and 77.4%%, respectively). Also, compared with healthy individuals, the prevalence of HIV was significantly higher in MDR-TB patients (35.9% vs 5.6%). Finally, TB prevalence was highest in individuals aged 25-44 years, who accounted for 58.4% of the total TB cases. Evidently, the prevalence of MDRTB in western Kenya is high. Particular attention should be paid to men, young adults, and those with HIV, who bear the greatest burden of resistant TB. Overall, there is a need to refine TB control and treatment programs in the region to yield better outcomes.
Collapse
Affiliation(s)
- George O Lugonzo
- Department of Biochemistry, Microbiology, and Biotechnology, Kenyatta University, Nairobi, Kenya
| | - Ezekiel M. Njeru
- Department of Biochemistry, Microbiology, and Biotechnology, Kenyatta University, Nairobi, Kenya
| | - William Songock
- Department of Medical Microbiology and Parasitology, Kenyatta University, Nairobi, Kenya
| | - Albert A. Okumu
- Centre for Global Health Research, Kenya Medical Research Institute, Kisumu, Kenya
| | - Eric M. Ndombi
- Department of Medical Microbiology and Parasitology, Kenyatta University, Nairobi, Kenya
- Centre for Global Health Research, Kenya Medical Research Institute, Kisumu, Kenya
| |
Collapse
|
2
|
Mekonnen D, Munshea A, Nibret E, Adnew B, Getachew H, Kebede A, Gebrewahid A, Herrera-Leon S, Aramendia AA, Benito A, Abascal E, Jacqueline C, Aseffa A, Herrera-Leon L. Mycobacterium tuberculosis Sub-Lineage 4.2.2/SIT149 as Dominant Drug-Resistant Clade in Northwest Ethiopia 2020-2022: In-silico Whole-Genome Sequence Analysis. Infect Drug Resist 2023; 16:6859-6870. [PMID: 37908783 PMCID: PMC10614653 DOI: 10.2147/idr.s429001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2023] [Accepted: 10/09/2023] [Indexed: 11/02/2023] Open
Abstract
Introduction Drug resistance (DR) in Mycobacterium tuberculosis complex (MTBC) is mainly associated with certain lineages and varies across regions and countries. The Beijing genotype is the leading resistant lineage in Asia and western countries. M. tuberculosis (Mtb) (sub) lineages responsible for most drug resistance in Ethiopia are not well described. Hence, this study aimed to identify the leading drug resistance sub-lineages and characterize first-line anti-tuberculosis drug resistance-associated single nucleotide polymorphisms (SNPs). Methods A facility-based cross-sectional study was conducted in 2020-2022 among new and presumptive multidrug resistant-TB (MDR-TB) cases in Northwest Ethiopia. Whole-genome sequencing (WGS) was performed on 161 isolates using Illumina NovaSeq 6000 technology. The SNP mutations associated with drug resistance were identified using MtbSeq and TB profiler Bioinformatics softwares. Results Of the 146 Mtb isolates that were successfully genotyped, 20 (13.7%) harbored one or more resistance-associated SNPs. L4.2.2.ETH was the leading drug-resistant sub-lineage, accounting for 10/20 (50%) of the resistant Mtb. MDR-TB isolates showed extensive mutations against first-line anti-TB drugs. Ser450Leu/(tcg/tTg) for Rifampicin (RIF), Ser315Thr/(agc/aCc) for Isoniazid (INH), Met306Ile/(atg/atA(C)) for Ethambutol (EMB), and Gly69Asp for Streptomycin (STR) were the leading resistance associated mutations which accounted for 56.5%, 89.5%, 47%, and 29.4%, respectively. The presence of both clustered and non-clustered drug resistance (DR) isolates indicated that the epidemics is driven by both new DR development and acquired resistance. Conclusion The high prevalence of drug-resistant TB due to geographically restricted sub-lineages (L4.2.2.ETH) indicates the ongoing local micro epidemics. The Mtb drug resistance surveillance system must be improved. Further evolutionary analysis of L4.2.2.ETH strain is highly desirable to understand evolutionary forces that leads L4.2.2.ETH in to high level DR and transmissible sub-lineage.
Collapse
Affiliation(s)
- Daniel Mekonnen
- Department of Medical Laboratory Sciences, School of Health Science, College of Medicine and Health Sciences, Bahir Dar University, Bahir Dar, Ethiopia
- Health Biotechnology Division, Institute of Biotechnology, Bahir Dar University, Bahir Dar, Ethiopia
| | - Abaineh Munshea
- Health Biotechnology Division, Institute of Biotechnology, Bahir Dar University, Bahir Dar, Ethiopia
- Department of Biology, Bahir Dar University, Bahir Dar, Ethiopia
| | - Endalkachew Nibret
- Health Biotechnology Division, Institute of Biotechnology, Bahir Dar University, Bahir Dar, Ethiopia
- Department of Biology, Bahir Dar University, Bahir Dar, Ethiopia
| | | | | | - Amiro Kebede
- Amhara Public Health Institute, Bahir Dar, Ethiopia
| | | | - Silvia Herrera-Leon
- National Centre for Microbiology, Instituto de Salud Carlos III, Madrid, Spain
| | | | - Agustín Benito
- National Center of Tropical Medicine, Institute of Health Carlos III, Centro de Investigación Biomédica En Red de Enfermedades Infecciosas, Madrid, Spain
| | - Estefanía Abascal
- National Centre for Microbiology, Instituto de Salud Carlos III, Madrid, Spain
| | - Camille Jacqueline
- National Centre for Microbiology, Instituto de Salud Carlos III, Madrid, Spain
- European Public Health Microbiology Training Programme, European Centre for Disease Prevention and Control, Stockholm, Sweden
| | - Abraham Aseffa
- Armauer Hansen Research Institute, Addis Ababa, Ethiopia
| | - Laura Herrera-Leon
- National Centre for Microbiology, Instituto de Salud Carlos III, Madrid, Spain
- CIBER Epidemiologia y Salud Publica, Madrid, Spain
| |
Collapse
|
3
|
Rostamian M, Kooti S, Abiri R, Khazayel S, Kadivarian S, Borji S, Alvandi A. Prevalence of Mycobacterium tuberculosis mutations associated with isoniazid and rifampicin resistance: A systematic review and meta-analysis. J Clin Tuberc Other Mycobact Dis 2023; 32:100379. [PMID: 37389010 PMCID: PMC10302537 DOI: 10.1016/j.jctube.2023.100379] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/01/2023] Open
Abstract
Tuberculosis (TB) is still one of the leading causes of worldwide death, especially following the emergence of strains resistant to isoniazid (INH) and rifampicin (RIF). This study aimed to systematically review published articles focusing on the prevalence of INH and/or RIF resistance-associated mutations of Mycobacterium tuberculosis isolates in recent years. Literature databases were searched using appropriate keywords. The data of the included studies were extracted and used for a random-effects model meta-analysis. Of the initial 1442 studies, 29 were finally eligible to be included in the review. The overall resistance to INH and RIF was about 17.2% and 7.3%, respectively. There was no difference between the frequency of INH and RIF resistance using different phenotypic or genotypic methods. The INH and/or RIF resistance was higher in Asia. The S315T mutation in KatG (23.7 %), C-15 T in InhA (10.7 %), and S531L in RpoB (13.5 %) were the most prevalent mutations. Altogether, the results showed that due to S531L in RpoB, S315T in KatG, and C-15 T in InhA mutations INH- and RIF-resistant M. tuberculosis isolates were widely distributed. Thus, it would be diagnostically and epidemiologically beneficial to track these gene mutations among resistant isolates.
Collapse
Affiliation(s)
- Mosayeb Rostamian
- Infectious Diseases Research Center, Health Institute, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Sara Kooti
- Behbahan Faculty of Medical Sciences, Behbahan, Iran
| | - Ramin Abiri
- Fertility and Infertility Research Center, Research Institute for Health Technology, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Saeed Khazayel
- Deupty of Research and Technology Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Sepide Kadivarian
- Department of Microbiology, School of Medicine, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Soroush Borji
- Department of Microbiology, School of Medicine, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Amirhooshang Alvandi
- Medical Technology Research Center, Research Institute for Health Technology, Kermanshah University of Medical Sciences, Kermanshah, Iran
| |
Collapse
|
4
|
HIV Prevalence among Injury Patients Compared to Other High-Risk Groups in Tanzania. TRAUMA CARE 2022. [DOI: 10.3390/traumacare2030041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Sixty-eight percent of persons infected with HIV live in Africa, but as few as 67% of those know their infection status. The emergency department (ED) might be a critical access point to HIV testing. This study sought to measure and compare HIV prevalence in an ED injury population with other clinical and nonclinical populations across Tanzania. Adults (≥18 years) presenting to Kilimanjaro Christian Medical Center ED with acute injury of any severity were enrolled in a trauma registry. A systematic review and meta-analysis was conducted to compare HIV prevalence in the trauma registry with other population groups. Further, 759 injury patients were enrolled in the registry; 78.6% were men and 68.2% consented to HIV counseling and testing. The HIV prevalence was 5.02% (tested), 6.25% (self-report), and 5.31% (both). The systematic review identified 79 eligible studies reporting HIV prevalence (tested) in 33 clinical and 12 nonclinical population groups. Notable groups included ED injury patients (3.53%, 95% CI), multiple injury patients (10.67%, 95% CI), and people who inject drugs (17.43%, 95% CI). These findings suggest that ED injury patients might be at higher HIV risk compared to the general population, and the ED is a potential avenue to increasing HIV testing among young adults, particularly men.
Collapse
|
5
|
Mbelele PM, Utpatel C, Sauli E, Mpolya EA, Mutayoba BK, Barilar I, Dreyer V, Merker M, Sariko ML, Swema BM, Mmbaga BT, Gratz J, Addo KK, Pletschette M, Niemann S, Houpt ER, Mpagama SG, Heysell SK. OUP accepted manuscript. JAC Antimicrob Resist 2022; 4:dlac042. [PMID: 35465240 PMCID: PMC9021016 DOI: 10.1093/jacamr/dlac042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Accepted: 03/25/2022] [Indexed: 12/02/2022] Open
Abstract
Background Rifampicin- or multidrug-resistant (RR/MDR) Mycobacterium tuberculosis complex (MTBC) strains account for considerable morbidity and mortality globally. WGS-based prediction of drug resistance may guide clinical decisions, especially for the design of RR/MDR-TB therapies. Methods We compared WGS-based drug resistance-predictive mutations for 42 MTBC isolates from MDR-TB patients in Tanzania with the MICs of 14 antibiotics measured in the Sensititre™ MycoTB assay. An isolate was phenotypically categorized as resistant if it had an MIC above the epidemiological-cut-off (ECOFF) value, or as susceptible if it had an MIC below or equal to the ECOFF. Results Overall, genotypically non-wild-type MTBC isolates with high-level resistance mutations (gNWT-R) correlated with isolates with MIC values above the ECOFF. For instance, the median MIC value (mg/L) for rifampicin-gNWT-R strains was >4.0 (IQR 4.0–4.0) compared with 0.5 (IQR 0.38–0.50) in genotypically wild-type (gWT-S, P < 0.001); isoniazid-gNWT-R >4.0 (IQR 2.0–4.0) compared with 0.25 (IQR 0.12–1.00) among gWT-S (P = 0.001); ethionamide-gNWT-R 15.0 (IQR 10.0–20.0) compared with 2.50 (IQR; 2.50–5.00) among gWT-S (P < 0.001). WGS correctly predicted resistance in 95% (36/38) and 100% (38/38) of the rifampicin-resistant isolates with ECOFFs >0.5 and >0.125 mg/L, respectively. No known resistance-conferring mutations were present in genes associated with resistance to fluoroquinolones, aminoglycosides, capreomycin, bedaquiline, delamanid, linezolid, clofazimine, cycloserine, or p-amino salicylic acid. Conclusions WGS-based drug resistance prediction worked well to rule-in phenotypic drug resistance and the absence of second-line drug resistance-mediating mutations has the potential to guide the design of RR/MDR-TB regimens in the future.
Collapse
Affiliation(s)
- Peter M. Mbelele
- Kibong’oto Infectious Diseases Hospital (KIDH), Siha, Kilimanjaro, Tanzania
- Department of Global Health and Biomedical Sciences, School of Life Sciences and Bioengineering, Nelson Mandela African Institution of Science and Technology (NM-AIST), Arusha, Tanzania
- Corresponding author. E-mail:
| | - Christian Utpatel
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Germany
- German Center for Infection Research (DZIF) Tuberculosis Unit, Borstel, Germany
| | - Elingarami Sauli
- Department of Global Health and Biomedical Sciences, School of Life Sciences and Bioengineering, Nelson Mandela African Institution of Science and Technology (NM-AIST), Arusha, Tanzania
| | - Emmanuel A. Mpolya
- Department of Global Health and Biomedical Sciences, School of Life Sciences and Bioengineering, Nelson Mandela African Institution of Science and Technology (NM-AIST), Arusha, Tanzania
| | - Beatrice K. Mutayoba
- Ministry of Health, National AIDS Control Program, Department of Preventive Services, Dodoma, Tanzania
- CIHLMU Center for International Health, University Hospital, LMU Munich, Germany
| | - Ivan Barilar
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Germany
- German Center for Infection Research (DZIF) Tuberculosis Unit, Borstel, Germany
| | - Viola Dreyer
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Germany
- German Center for Infection Research (DZIF) Tuberculosis Unit, Borstel, Germany
| | - Matthias Merker
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Germany
- Evolution of the Resistome, Research Center Borstel, Borstel, Germany
| | | | | | - Blandina T. Mmbaga
- Kilimanjaro Clinical Research Institute, Moshi, Tanzania
- Kilimanjaro Christian Medical University College, Moshi, Tanzania
| | - Jean Gratz
- Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, Virginia, USA
| | - Kennedy K. Addo
- Department of Bacteriology, Noguchi Memorial Institute for Medical Research, University of Ghana, Accra, Ghana
| | - Michel Pletschette
- CIHLMU Center for International Health, University Hospital, LMU Munich, Germany
- Division of Infectious Diseases and Tropical Medicine, Medical Center of the University of Munich (LMU), Munich, Germany
| | - Stefan Niemann
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Germany
- German Center for Infection Research (DZIF) Tuberculosis Unit, Borstel, Germany
| | - Eric R. Houpt
- Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, Virginia, USA
| | - Stellah G. Mpagama
- Kibong’oto Infectious Diseases Hospital (KIDH), Siha, Kilimanjaro, Tanzania
- Department of Global Health and Biomedical Sciences, School of Life Sciences and Bioengineering, Nelson Mandela African Institution of Science and Technology (NM-AIST), Arusha, Tanzania
- Kilimanjaro Clinical Research Institute, Moshi, Tanzania
- Kilimanjaro Christian Medical University College, Moshi, Tanzania
| | - Scott K. Heysell
- Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, Virginia, USA
| |
Collapse
|
6
|
Monde N, Zulu M, Tembo M, Handema R, Munyeme M, Malama S. Drug Resistant Tuberculosis in the Northern Region of Zambia: A Retrospective Study. FRONTIERS IN TROPICAL DISEASES 2021. [DOI: 10.3389/fitd.2021.735028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
BackgroundZambia like many countries in sub-Saharan Africa is affected with drug resistant tuberculosis. However, the drug resistant tuberculosis situation over the years has not been described in various regions of the country. Consequently, this study aims to determine the drug resistant tuberculosis burden in northern regions of Zambia over a four-year period based on data generated from a Regional Tuberculosis Reference Laboratory.MethodTwo hundred and thirty two (232) Tuberculosis Drug Susceptibility Testing results over a four-year period (2016-2019) were reviewed. Data was collected from tuberculosis registers and patient request forms and entered into a pre-tested standardized checklist and later entered in Excel Computer software. Double blinded checking was done by two independent data clerks to minimize duplication of cases. Cleaned data was then imported in R programme for analysis. Bivariant and descriptive statistics were performed and reported.ResultsOf 232 Drug Susceptibility Testing results, 90.9% were drug resistant TB while 9% were drug susceptible. Fifty three percent (53%) of these were multi-drug resistant Tuberculosis and 32% were confirmed as Rifampicin Mono-resistance. Only 1.7% of the Multi-drug resistant Tuberculosis patients were Pre-extensively drug-resistant Tuberculosis. Copperbelt province had the largest proportion (46.0%) of multi-drug resistant tuberculosis patients followed by Luapula (8.1%) and North-Western (4.7%) provinces. In new and previously treated patients, the proportion of Multi-drug resistant tuberculosis was 71.8% and 28.7% respectively. History of previous anti-tuberculosis treatment and treatment failure were associated with multi-drug resistance TB.Conclusion and RecommendationThis study has shown a small increase in the proportions of drug resistant tuberculosis cases over the four years under review with high rates being recorded on the Copperbelt Province. Previous treatment to first line TB treatment and treatment failure were associated with development of Multi-drug resistance. We therefore recommend strengthened routine laboratory surveillance and improved case management of multi-drug resistant tuberculosis patients in the region.
Collapse
|
7
|
Cuevas-Córdoba B, Fresno C, Haase-Hernández JI, Barbosa-Amezcua M, Mata-Rocha M, Muñoz-Torrico M, Salazar-Lezama MA, Martínez-Orozco JA, Narváez-Díaz LA, Salas-Hernández J, González-Covarrubias V, Soberón X. A bioinformatics pipeline for Mycobacterium tuberculosis sequencing that cleans contaminant reads from sputum samples. PLoS One 2021; 16:e0258774. [PMID: 34699523 PMCID: PMC8547644 DOI: 10.1371/journal.pone.0258774] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Accepted: 10/06/2021] [Indexed: 12/30/2022] Open
Abstract
Next-Generation Sequencing (NGS) is widely used to investigate genomic variation. In several studies, the genetic variation of Mycobacterium tuberculosis has been analyzed in sputum samples without previous culture, using target enrichment methodologies for NGS. Alignments obtained by different programs generally map the sequences under default parameters, and from these results, it is assumed that only Mycobacterium reads will be obtained. However, variants of interest microorganism in clinical samples can be confused with a vast collection of reads from other bacteria, viruses, and human DNA. Currently, there are no standardized pipelines, and the cleaning success is never verified since there is a lack of rigorous controls to identify and remove reads from other sputum-microorganisms genetically similar to M. tuberculosis. Therefore, we designed a bioinformatic pipeline to process NGS data from sputum samples, including several filters and quality control points to identify and eliminate non-M. tuberculosis reads to obtain a reliable genetic variant report. Our proposal uses the SURPI software as a taxonomic classifier to filter input sequences and perform a mapping that provides the highest percentage of Mycobacterium reads, minimizing the reads from other microorganisms. We then use the filtered sequences to perform variant calling with the GATK software, ensuring the mapping quality, realignment, recalibration, hard-filtering, and post-filter to increase the reliability of the reported variants. Using default mapping parameters, we identified reads of contaminant bacteria, such as Streptococcus, Rhotia, Actinomyces, and Veillonella. Our final mapping strategy allowed a sequence identity of 97.8% between the input reads and the whole M. tuberculosis reference genome H37Rv using a genomic edit distance of three, thus removing 98.8% of the off-target sequences with a Mycobacterium reads loss of 1.7%. Finally, more than 200 unreliable genetic variants were removed during the variant calling, increasing the report’s reliability.
Collapse
Affiliation(s)
- Betzaida Cuevas-Córdoba
- Laboratorio de Farmacogenómica, Instituto Nacional de Medicina Genómica (INMEGEN), Ciudad de México, México
- Instituto de Investigaciones Biológicas, Universidad Veracruzana, Xalapa, Veracruz, México
| | - Cristóbal Fresno
- Departamento de Desarrollo Tecnológico, Instituto Nacional de Medicina Genómica (INMEGEN), Ciudad de México, México
| | - Joshua I. Haase-Hernández
- Departamento de Desarrollo Tecnológico, Instituto Nacional de Medicina Genómica (INMEGEN), Ciudad de México, México
| | - Martín Barbosa-Amezcua
- Laboratorio de Farmacogenómica, Instituto Nacional de Medicina Genómica (INMEGEN), Ciudad de México, México
| | - Minerva Mata-Rocha
- Laboratorio de Farmacogenómica, Instituto Nacional de Medicina Genómica (INMEGEN), Ciudad de México, México
| | - Marcela Muñoz-Torrico
- Clínica de Tuberculosis y Enfermedades Pleurales, Instituto Nacional de Enfermedades Respiratorias (INER), Ciudad de México, México
| | - Miguel A. Salazar-Lezama
- Clínica de Tuberculosis y Enfermedades Pleurales, Instituto Nacional de Enfermedades Respiratorias (INER), Ciudad de México, México
| | - José A. Martínez-Orozco
- Clínica de Tuberculosis y Enfermedades Pleurales, Instituto Nacional de Enfermedades Respiratorias (INER), Ciudad de México, México
| | - Luis A. Narváez-Díaz
- Clínica de Tuberculosis y Enfermedades Pleurales, Instituto Nacional de Enfermedades Respiratorias (INER), Ciudad de México, México
| | - Jorge Salas-Hernández
- Clínica de Tuberculosis y Enfermedades Pleurales, Instituto Nacional de Enfermedades Respiratorias (INER), Ciudad de México, México
| | - Vanessa González-Covarrubias
- Laboratorio de Farmacogenómica, Instituto Nacional de Medicina Genómica (INMEGEN), Ciudad de México, México
- * E-mail: (XS); (VGC)
| | - Xavier Soberón
- Laboratorio de Farmacogenómica, Instituto Nacional de Medicina Genómica (INMEGEN), Ciudad de México, México
- * E-mail: (XS); (VGC)
| |
Collapse
|
8
|
Munir A, Wilson MT, Hardwick SW, Chirgadze DY, Worrall JAR, Blundell TL, Chaplin AK. Using cryo-EM to understand antimycobacterial resistance in the catalase-peroxidase (KatG) from Mycobacterium tuberculosis. Structure 2021; 29:899-912.e4. [PMID: 33444527 PMCID: PMC8355310 DOI: 10.1016/j.str.2020.12.008] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Revised: 11/27/2020] [Accepted: 12/16/2020] [Indexed: 12/12/2022]
Abstract
Resolution advances in cryoelectron microscopy (cryo-EM) now offer the possibility to visualize structural effects of naturally occurring resistance mutations in proteins and also of understanding the binding mechanisms of small drug molecules. In Mycobacterium tuberculosis the multifunctional heme enzyme KatG is indispensable for activation of isoniazid (INH), a first-line pro-drug for treatment of tuberculosis. We present a cryo-EM methodology for structural and functional characterization of KatG and INH resistance variants. The cryo-EM structure of the 161 kDa KatG dimer in the presence of INH is reported to 2.7 Å resolution allowing the observation of potential INH binding sites. In addition, cryo-EM structures of two INH resistance variants, identified from clinical isolates, W107R and T275P, are reported. In combination with electronic absorbance spectroscopy our cryo-EM approach reveals how these resistance variants cause disorder in the heme environment preventing heme uptake and retention, providing insight into INH resistance. A cryo-EM structure to 2.7 Å resolution of M. tuberculosis KatG with isoniazid Cryo-EM is able to visualize multiple dynamic binding modes of isoniazid to KatG Structural disorder in isoniazid resistance mutations is observed Structural disorder of the resistance mutations results in the lack of heme retention
Collapse
Affiliation(s)
- Asma Munir
- Department of Biochemistry, University of Cambridge, Cambridge, CB2 1GA, UK
| | - Michael T Wilson
- School of Life Sciences, University of Essex, Wivenhoe Park, Colchester CO4 3SQ, UK
| | - Steven W Hardwick
- CryoEM Facility, Department of Biochemistry, University of Cambridge, Cambridge, CB2 1GA, UK
| | - Dimitri Y Chirgadze
- CryoEM Facility, Department of Biochemistry, University of Cambridge, Cambridge, CB2 1GA, UK
| | - Jonathan A R Worrall
- School of Life Sciences, University of Essex, Wivenhoe Park, Colchester CO4 3SQ, UK
| | - Tom L Blundell
- Department of Biochemistry, University of Cambridge, Cambridge, CB2 1GA, UK.
| | - Amanda K Chaplin
- Department of Biochemistry, University of Cambridge, Cambridge, CB2 1GA, UK.
| |
Collapse
|
9
|
Bhattacharyya K, Nemaysh V, Joon M, Pratap R, Varma-Basil M, Bose M, Brahmachari V. Correlation of drug resistance with single nucleotide variations through genome analysis and experimental validation in a multi-drug resistant clinical isolate of M. tuberculosis. BMC Microbiol 2020; 20:223. [PMID: 32711461 PMCID: PMC7382824 DOI: 10.1186/s12866-020-01912-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Accepted: 07/19/2020] [Indexed: 01/02/2023] Open
Abstract
BACKGROUND Genome sequencing and genetic polymorphism analysis of clinical isolates of M. tuberculosis is carried out to gain further insight into molecular pathogenesis and host-pathogen interaction. Therefore the functional evaluation of the effect of single nucleotide variation (SNV) is essential. At the same time, the identification of invariant sequences unique to M. tuberculosis contributes to infection detection by sensitive methods. In the present study, genome analysis is accompanied by evaluation of the functional implication of the SNVs in a MDR clinical isolate VPCI591. RESULT By sequencing and comparative analysis of VPCI591 genome with 1553 global clinical isolates of M. tuberculosis (GMTV and tbVar databases), we identified 141 unique strain specific SNVs. A novel intergenic variation in VPCI591 in the putative promoter/regulatory region mapping between embC (Rv3793) and embA (Rv3794) genes was found to enhance the expression of embAB, which correlates with the high resistance of the VPCI591 to ethambutol. Similarly, the unique combination of three genic SNVs in RNA polymerase β gene (rpoB) in VPCI591 was evaluated for its effect on rifampicin resistance through molecular docking analysis. The comparative genomics also showed that along with variations, there are genes that remain invariant. 173 such genes were identified in our analysis. CONCLUSION The genetic variation in M. tuberculosis clinical isolate VPCI591 is found in almost all functional classes of genes. We have shown that SNV in rpoB gene mapping outside the drug binding site along with two SNVs in the binding site can contribute to quantitative change in MIC for rifampicin. Our results show the collective effect of SNVs on the structure of the protein, impacting the interaction between the target protein and the drug molecule in rpoB as an example. The study shows that intergenic variations bring about quantitative changes in transcription in embAB and in turn can lead to drug resistance.
Collapse
Affiliation(s)
- Kausik Bhattacharyya
- Dr. B. R. Ambedkar Center for Biomedical Research (ACBR), University of Delhi, 110007, New Delhi, India.,Department of Microbiology, Vallabhbhai Patel Chest Institute, University of Delhi, New Delhi, India
| | - Vishal Nemaysh
- Department of Chemistry, University of Delhi, New Delhi, India
| | - Monika Joon
- Dr. B. R. Ambedkar Center for Biomedical Research (ACBR), University of Delhi, 110007, New Delhi, India
| | - Ramendra Pratap
- Department of Chemistry, University of Delhi, New Delhi, India
| | - Mandira Varma-Basil
- Department of Microbiology, Vallabhbhai Patel Chest Institute, University of Delhi, New Delhi, India
| | - Mridula Bose
- Department of Microbiology, Vallabhbhai Patel Chest Institute, University of Delhi, New Delhi, India
| | - Vani Brahmachari
- Dr. B. R. Ambedkar Center for Biomedical Research (ACBR), University of Delhi, 110007, New Delhi, India.
| |
Collapse
|
10
|
Bitar I, Medvecky M, Amlerova J, Papagiannitsis CC, Hrabak J. Frequency of mutations associated with resistance to first- and second-line drugs in multidrug-resistant Mycobacterium tuberculosis isolates. J Glob Antimicrob Resist 2020; 22:275-282. [PMID: 32247078 DOI: 10.1016/j.jgar.2020.03.013] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Revised: 02/27/2020] [Accepted: 03/14/2020] [Indexed: 01/19/2023] Open
Abstract
INTRODUCTION Tuberculosis is considered one of the most fatal diseases worldwide, with an estimation of 10.1 million cases. In this study, whole-genome sequencing was used to determine the genomic characterisation of 40 Mycobacterium tuberculosis isolates from patients with different nationalities hospitalised in the Czech Republic. MATERIALS AND METHODS Susceptibility testing for first-line drugs was performed. DNA was sequenced using the Illumina MiSeq platform. Spoligotype single-nucleotide polymorphisms and mutations in antibiotic-resistant genes were detected, and phylogenetic analysis was performed. RESULTS Samples showing phenotypic resistance to at least one drug were 12 to streptomycin, 11 to isoniazid, 7 to rifampicin, 6 to ethambutol and 5 to pyrazinamide. Phenotypic and genotypic profiles did not match in all cases, suggesting the presence of a novel mutation in some cases and a low expression of resistant genes in others. The presented phylogeny enables the correct assignation of M. tuberculosis lineages and sublineages. Our results suggest that the most dominant lineage in our samples was lineage 4 (33/40). CONCLUSION To our knowledge, this is the first study using this approach to be done in the Czech Republic. Lineage 4 was the predominant lineage identified among our samples. Nevertheless, the dominance of Lineage 4 along with other lineages suggests that infections can originate from different sources.
Collapse
Affiliation(s)
- Ibrahim Bitar
- Department of Microbiology, Faculty of Medicine in Pilsen, Charles University, Plzen, Czech Republic; Biomedical Center, Faculty of Medicine in Pilsen, Charles University, Plzen, Czech Republic.
| | - Matej Medvecky
- Biomedical Center, Faculty of Medicine in Pilsen, Charles University, Plzen, Czech Republic; CEITEC VFU, University of Veterinary and Pharmaceutical Sciences Brno, Brno, Czech Republic
| | - Jana Amlerova
- Department of Microbiology, Faculty of Medicine in Pilsen, Charles University, Plzen, Czech Republic; Biomedical Center, Faculty of Medicine in Pilsen, Charles University, Plzen, Czech Republic
| | - Costas C Papagiannitsis
- Department of Microbiology, Faculty of Medicine in Pilsen, Charles University, Plzen, Czech Republic; Biomedical Center, Faculty of Medicine in Pilsen, Charles University, Plzen, Czech Republic
| | - Jaroslav Hrabak
- Department of Microbiology, Faculty of Medicine in Pilsen, Charles University, Plzen, Czech Republic; Biomedical Center, Faculty of Medicine in Pilsen, Charles University, Plzen, Czech Republic
| |
Collapse
|
11
|
Katale BZ, Mbelele PM, Lema NA, Campino S, Mshana SE, Rweyemamu MM, Phelan JE, Keyyu JD, Majigo M, Mbugi EV, Dockrell HM, Clark TG, Matee MI, Mpagama S. Whole genome sequencing of Mycobacterium tuberculosis isolates and clinical outcomes of patients treated for multidrug-resistant tuberculosis in Tanzania. BMC Genomics 2020; 21:174. [PMID: 32085703 PMCID: PMC7035673 DOI: 10.1186/s12864-020-6577-1] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Accepted: 02/12/2020] [Indexed: 11/17/2022] Open
Abstract
BACKGROUND Tuberculosis (TB), particularly multi- and or extensive drug resistant TB, is still a global medical emergency. Whole genome sequencing (WGS) is a current alternative to the WHO-approved probe-based methods for TB diagnosis and detection of drug resistance, genetic diversity and transmission dynamics of Mycobacterium tuberculosis complex (MTBC). This study compared WGS and clinical data in participants with TB. RESULTS This cohort study performed WGS on 87 from MTBC DNA isolates, 57 (66%) and 30 (34%) patients with drug resistant and susceptible TB, respectively. Drug resistance was determined by Xpert® MTB/RIF assay and phenotypic culture-based drug-susceptibility-testing (DST). WGS and bioinformatics data that predict phenotypic resistance to anti-TB drugs were compared with participant's clinical outcomes. They were 47 female participants (54%) and the median age was 35 years (IQR): 29-44). Twenty (23%) and 26 (30%) of participants had TB/HIV co-infection BMI < 18 kg/m2 respectively. MDR-TB participants had MTBC with multiple mutant genes, compared to those with mono or polyresistant TB, and the majority belonged to lineage 3 Central Asian Strain (CAS). Also, MDR-TB was associated with delayed culture-conversion (median: IQR (83: 60-180 vs. 51:30-66) days). WGS had high concordance with both culture-based DST and Xpert® MTB/RIF assay in detecting drug resistance (kappa = 1.00). CONCLUSION This study offers comparison of mutations detected by Xpert and WGS with phenotypic DST of M. tuberculosis isolates in Tanzania. The high concordance between the different methods and further insights provided by WGS such as PZA-DST, which is not routinely performed in most resource-limited-settings, provides an avenue for inclusion of WGS into diagnostic matrix of TB including drug-resistant TB.
Collapse
Affiliation(s)
- Bugwesa Z Katale
- Department of Microbiology and Immunology, School of Medicine, Muhimbili University of Health and Allied Sciences (MUHAS), Dar es Salaam, Tanzania
- Tanzania Wildlife Research Institute (TAWIRI), Arusha, Tanzania
| | - Peter M Mbelele
- Kibong'oto Infectious Disease Hospital (KIDH), Sanya Juu, Tanzania
- Department of Global Health and Biomedical Sciences, School of Life Sciences and Bioengineering, Nelson Mandela African Institution of Science and Technology (NM-AIST), Arusha, Tanzania
| | - Nsiande A Lema
- Field Epidemiology and Laboratory Training Programme, Dar es Salaam, Tanzania
| | - Susana Campino
- Faculty of Infectious and Tropical Diseases, London School of Hygiene &Tropical Medicine (LSHTM), Keppel Street, London, WC1E 7HT, UK
| | - Stephen E Mshana
- Department of Medical Microbiology, Catholic University of Health and Allied Sciences, Mwanza, Tanzania
| | - Mark M Rweyemamu
- Southern African Centre for Infectious Diseases Surveillance (SACIDS), Sokoine University of Agriculture (SUA), Morogoro, Tanzania
| | - Jody E Phelan
- Faculty of Infectious and Tropical Diseases, London School of Hygiene &Tropical Medicine (LSHTM), Keppel Street, London, WC1E 7HT, UK
| | - Julius D Keyyu
- Tanzania Wildlife Research Institute (TAWIRI), Arusha, Tanzania
| | - Mtebe Majigo
- Department of Microbiology and Immunology, School of Medicine, Muhimbili University of Health and Allied Sciences (MUHAS), Dar es Salaam, Tanzania
| | - Erasto V Mbugi
- Department of Biochemistry, Muhimbili University of Health and Allied Sciences (MUHAS), Dar es Salaam, Tanzania
| | - Hazel M Dockrell
- Faculty of Infectious and Tropical Diseases, London School of Hygiene &Tropical Medicine (LSHTM), Keppel Street, London, WC1E 7HT, UK
| | - Taane G Clark
- Faculty of Infectious and Tropical Diseases, London School of Hygiene &Tropical Medicine (LSHTM), Keppel Street, London, WC1E 7HT, UK
- Faculty of Epidemiology and Population Health, London School of Hygiene &Tropical Medicine (LSHTM), Keppel Street, London, WC1E 7HT, UK
| | - Mecky I Matee
- Department of Microbiology and Immunology, School of Medicine, Muhimbili University of Health and Allied Sciences (MUHAS), Dar es Salaam, Tanzania.
| | - Stellah Mpagama
- Kibong'oto Infectious Disease Hospital (KIDH), Sanya Juu, Tanzania
| |
Collapse
|
12
|
Antibiotic resistance of Mycobacterium tuberculosis complex in Africa: A systematic review of current reports of molecular epidemiology, mechanisms and diagnostics. J Infect 2019; 79:550-571. [DOI: 10.1016/j.jinf.2019.10.006] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2019] [Accepted: 10/13/2019] [Indexed: 12/11/2022]
|
13
|
Ogari CO, Nyamache AK, Nonoh J, Amukoye E. Prevalence and detection of drug resistant mutations in Mycobacterium tuberculosis among drug naïve patients in Nairobi, Kenya. BMC Infect Dis 2019; 19:279. [PMID: 30909867 PMCID: PMC6434623 DOI: 10.1186/s12879-019-3911-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2018] [Accepted: 03/17/2019] [Indexed: 11/12/2022] Open
Abstract
Background Tuberculosis (TB), an ancient scourge of humanity known for several thousands of years, is still a significant public health challenge in many countries today even though some progress has been made in recent years in controlling the disease. The study’s aim was to determine the prevalence of mutations responsible for drug resistance in Mycobacterium tuberculosis among patients visiting selected health centers in Nairobi, Kenya. Methods The cross-sectional study involved 132 TB positive patients visiting Mbagathi and Chandaria hospitals between September 2015 and August 2016. Sputum samples were collected from the participants and handled in a biosafety level 3 laboratory at the Kenya Medical Research Institute (KEMRI). Samples were decontaminated using N-Acetyl-L-Cysteine (NALC) – Sodium Hydroxide (NALC-NaOH), stained using Zeihl–Neelsen (ZN), and cultured in Mycobacterium Growth Indicator Tube (MGIT). DNA extracted from cultured isolates using Genolyse™ technique was subjected to Multiplex PCR amplification and reverse hybridization for detection of drug resistance mutations on rpoB, katG, inhA, gyrA, gyrB, rrs and eis genes using Hain Genotype MTBDRplus and MTBDRsl. Results All 132 (100%) patients included in the study were culture positive for M. tuberculosis. Among them, 72 (54%) were male while the remaining 60 (46%) were female. The mean age of the patients was 26.4 ± 19.4 (SD) with a range of 18 to 60 years. Overall, the prevalence of the resistance to first and second-line TB drugs was 1.5% (2/132). Resistance to isoniazid (INH) was observed in 1 of 132 patients (0.8%), as was multi-drug resistant tuberculosis (MDR-TB), also at 0.8%. No resistance to fluoroquinolones (FQ) or kanamycin (KAN) was observed. The INH resistant strain had the katG mutations S315 T, while mutations detected for the MDR-TB were katG S513 T for INH, rpoB S531 L for rifampicin (RIF) and rrs G1484 T for cross-resistance to aminoglycosides/capreomycin (AG/CP). Conclusions Molecular analysis confirms transmission of the drug-resistant M. tuberculosis strains. The data suggested that there is homogeneity when it comes to the type of drug resistance and mutation that occurs in the region. This calls for intensified drug resistance surveillance and drug adherence among patients infected with TB.
Collapse
Affiliation(s)
| | | | - James Nonoh
- Microbiology Department, Kenyatta University, Nairobi, Kenya
| | - Evans Amukoye
- Kenya Medical Research Institute, Centre for Respiratory Disease and Research, Nairobi, Kenya
| |
Collapse
|