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Welekidan LN, Yimer SA, Skjerve E, Dejene TA, Homberset H, Tønjum T, Brynildsrud O. Whole Genome Sequencing of Drug Resistant and Drug Susceptible Mycobacterium tuberculosis Isolates From Tigray Region, Ethiopia. Front Microbiol 2021; 12:743198. [PMID: 34938276 PMCID: PMC8685502 DOI: 10.3389/fmicb.2021.743198] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2021] [Accepted: 11/15/2021] [Indexed: 11/13/2022] Open
Abstract
Background: Tuberculosis, mainly caused by Mycobacterium tuberculosis (Mtb), is an ancient human disease that gravely affects millions of people annually. We wanted to explore the genetic diversity and lineage-specific association of Mtb with drug resistance among pulmonary tuberculosis patients. Methods: Sputum samples were collected from pulmonary tuberculosis patients at six different healthcare institutions in Tigray, Ethiopia, between July 2018 and August 2019. DNA was extracted from 74 Mtb complex isolates for whole-genome sequencing (WGS). All genomes were typed and screened for mutations with known associations with antimicrobial resistance using in silico methods, and results were cross-verified with wet lab methods. Results: Lineage (L) 4 (55.8%) was predominant, followed by L3 (41.2%); L1 (1.5%) and L2 (1.5%) occurred rarely. The most frequently detected sublineage was CAS (38.2%), followed by Ural (29.4%), and Haarlem (11.8%). The recent transmission index (RTI) was relatively low. L4 and Ural strains were more resistant than the other strains to any anti-TB drug (P < 0.05). The most frequent mutations to RIF, INH, EMB, SM, PZA, ETH, FLQs, and 2nd-line injectable drugs occurred at rpoB S450L, katG S315T, embB M306I/V, rpsL K43R, pncA V139A, ethA M1R, gyrA D94G, and rrs A1401G, respectively. Disputed rpoB mutations were also shown in four (16%) of RIF-resistant isolates. Conclusion: Our WGS analysis revealed the presence of diverse Mtb genotypes. The presence of a significant proportion of disputed rpoB mutations highlighted the need to establish a WGS facility at the regional level to monitor drug-resistant mutations. This will help control the transmission of DR-TB and ultimately contribute to the attainment of 100% DST coverage for TB patients as per the End TB strategy.
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Affiliation(s)
- Letemichael Negash Welekidan
- Department of Production Animal Medicine, Norwegian University of Life Sciences, Oslo, Norway.,Division of Biomedical Sciences, Department of Medical Microbiology and Immunology, College of Health Sciences, Mekelle University, Mekelle, Ethiopia
| | - Solomon Abebe Yimer
- Coalition for Epidemic Preparedness Innovations, Oslo, Norway.,Unit for Genome Dynamics, Department of Microbiology, University of Oslo, Oslo, Norway
| | - Eystein Skjerve
- Department of Production Animal Medicine, Norwegian University of Life Sciences, Oslo, Norway
| | - Tsehaye Asmelash Dejene
- Division of Biomedical Sciences, Department of Medical Microbiology and Immunology, College of Health Sciences, Mekelle University, Mekelle, Ethiopia
| | - Håvard Homberset
- Unit for Genome Dynamics, Department of Microbiology, University of Oslo, Oslo, Norway
| | - Tone Tønjum
- Unit for Genome Dynamics, Department of Microbiology, University of Oslo, Oslo, Norway.,Unit for Genome Dynamics, Department of Microbiology, Oslo University Hospital, Oslo, Norway
| | - Ola Brynildsrud
- Department of Production Animal Medicine, Norwegian University of Life Sciences, Oslo, Norway.,Norwegian Institute of Public Health, Oslo, Norway
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Welekidan LN, Skjerve E, Dejene TA, Gebremichael MW, Brynildsrud O, Agdestein A, Tessema GT, Tønjum T, Yimer SA. Correction: Characteristics of pulmonary multidrug-resistant tuberculosis patients in Tigray Region, Ethiopia: A cross-sectional study. PLoS One 2021; 16:e0258457. [PMID: 34614019 PMCID: PMC8494371 DOI: 10.1371/journal.pone.0258457] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
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Welekidan LN, Skjerve E, Dejene TA, Gebremichael MW, Brynildsrud O, Tønjum T, Yimer SA. Frequency and patterns of first- and second-line drug resistance-conferring mutations in Mycobacterium tuberculosis isolated from pulmonary tuberculosis patients in a cross-sectional study in Tigray Region, Ethiopia. J Glob Antimicrob Resist 2020; 24:6-13. [PMID: 33279682 DOI: 10.1016/j.jgar.2020.11.017] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [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: 05/09/2020] [Revised: 10/23/2020] [Accepted: 11/17/2020] [Indexed: 10/22/2022] Open
Abstract
OBJECTIVES Tuberculosis (TB) is a preventable and treatable infectious disease, but the continuing emergence and spread of multidrug-resistant TB is threatening global TB control efforts. This study aimed to describe the frequency and patterns of drug resistance-conferring mutations of Mycobacterium tuberculosis (MTB) isolates detected from pulmonary TB patients in Tigray Region, Ethiopia. METHODS A cross-sectional study design was employed to collect sputum samples from pulmonary TB patients between July 2018 to August 2019. Culture and identification tests were done at Tigray Health Research Institute (THRI). Mutations conferring rifampicin (RIF), isoniazid (INH) and fluoroquinolone (FQ) resistance were determined in 227 MTB isolates using GenoType MTBDRplus and GenoType MTBDRsl. RESULTS Mutations conferring resistance to RIF, INH and FQs were detected in 40/227 (17.6%), 41/227 (18.1%) and 2/38 (5.3%) MTB isolates, respectively. The majority of mutations for RIF, INH and FQs occurred at codons rpoB S531L (70%), katG S315T (78%) and gyrA D94Y/N (100%), respectively. This study revealed a significant number of unknown mutations in the rpoB, katG and inhA genes. CONCLUSION High rates of mutations conferring resistance to RIF, INH and FQs were observed in this study. A large number of isolates showed unknown mutations, which require further DNA sequencing analysis. Periodic drug resistance surveillance and scaling-up of drug resistance testing facilities are imperative to prevent the transmission of drug-resistant TB in the community.
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Affiliation(s)
- Letemichael Negash Welekidan
- Department of Para Clinical Sciences, Norwegian University of Life Sciences, P.O. Box 369, 0102 Oslo, Norway; Department of Production Animal Medicine, Norwegian University of Life Sciences, P.O. Box 369, 0102 Oslo, Norway; Department of Medical Microbiology and Immunology, Division of Biomedical Sciences, College of Health Sciences, Mekelle University, P.O. Box 1871, Mekelle, Ethiopia.
| | - Eystein Skjerve
- Department of Production Animal Medicine, Norwegian University of Life Sciences, P.O. Box 369, 0102 Oslo, Norway
| | - Tsehaye Asmelash Dejene
- Department of Medical Microbiology and Immunology, Division of Biomedical Sciences, College of Health Sciences, Mekelle University, P.O. Box 1871, Mekelle, Ethiopia
| | | | - Ola Brynildsrud
- Department of Para Clinical Sciences, Norwegian University of Life Sciences, P.O. Box 369, 0102 Oslo, Norway; Department of Bacteriology and Immunology, Norwegian Institute of Public Health, P.O. Box 222, 0213 Oslo, Norway
| | - Tone Tønjum
- Department of Microbiology, Unit for Genome Dynamics, University of Oslo, P.O. Box 1072, 0316 Oslo, Norway; Department of Microbiology, Unit for Genome Dynamics, Oslo University Hospital, P.O. Box 4950, 0424 Oslo, Norway
| | - Solomon Abebe Yimer
- Department of Microbiology, Unit for Genome Dynamics, Oslo University Hospital, P.O. Box 4950, 0424 Oslo, Norway; Coalition for Epidemic Preparedness Innovations, Oslo, Norway
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Welekidan LN, Skjerve E, Dejene TA, Gebremichael MW, Brynildsrud O, Agdestein A, Tessema GT, Tønjum T, Yimer SA. Characteristics of pulmonary multidrug-resistant tuberculosis patients in Tigray Region, Ethiopia: A cross-sectional study. PLoS One 2020; 15:e0236362. [PMID: 32797053 PMCID: PMC7428183 DOI: 10.1371/journal.pone.0236362] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [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: 03/10/2020] [Accepted: 07/03/2020] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Tuberculosis (TB) is among the top 10 causes of mortality and the first killer among infectious diseases worldwide. One of the factors fuelling the TB epidemic is the global rise of multidrug resistant TB (MDR-TB). The aim of this study was to determine the magnitude and factors associated with MDR-TB in the Tigray Region, Ethiopia. METHOD This study employed a facility-based cross-sectional study design, which was conducted between July 2018 and August 2019. The inclusion criteria for the study participants were GeneXpert-positive who were not under treatment for TB, PTB patients' ≥15 years of age and who provided written informed consent. A total of 300 participants were enrolled in the study, with a structured questionnaire used to collect data on clinical, sociodemographic and behavioral factors. Sputum samples were collected and processed for acid-fast bacilli staining, culture and drug susceptibility testing. Drug susceptibility testing was performed using a line probe assay. Logistic regression was used to analyze associations between outcome and predictor variables. RESULTS The overall proportion of MDR-TB was 16.7% (11.6% and 32.7% for new and previously treated patients, respectively). Of the total MDR-TB isolates, 5.3% were pre-XDR-TB. The proportion of MDR-TB/HIV co-infection was 21.1%. A previous history of TB treatment AOR 3.75; 95% CI (0.7-2.24), cigarette smoking AOR 6.09; CI (1.65-2.50) and patients who had an intermittent fever (AOR = 2.54, 95% CI = 1.21-5.4) were strongly associated with MDR-TB development. CONCLUSIONS The magnitude of MDR-TB observed among new and previously treated patients is very alarming, which calls for an urgent need for intervention. The high proportion of MDR-TB among newly diagnosed cases indicates ongoing transmission, which suggests the need for enhanced TB control program performance to interrupt transmission. The increased proportion of MDR-TB among previously treated cases indicates a need for better patient management to prevent the evolution of drug resistance. Assessing the TB control program performance gaps and an optimal implementation of the WHO recommended priority actions for the management of drug-resistant TB, is imperative to help reduce the current high MDR-TB burden in the study region.
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Affiliation(s)
- Letemichael Negash Welekidan
- Department of Para Clinical Sciences, Norwegian University of Life Sciences, Oslo, Norway
- Department of Production Animal Medicine, Norwegian University of Life Sciences, Oslo, Norway
- Department of Medical Microbiology and Immunology, Division of Biomedical Sciences, College of Health Sciences, Mekelle University, Mekelle, Ethiopia
| | - Eystein Skjerve
- Department of Production Animal Medicine, Norwegian University of Life Sciences, Oslo, Norway
| | - Tsehaye Asmelash Dejene
- Department of Medical Microbiology and Immunology, Division of Biomedical Sciences, College of Health Sciences, Mekelle University, Mekelle, Ethiopia
| | | | - Ola Brynildsrud
- Department of Para Clinical Sciences, Norwegian University of Life Sciences, Oslo, Norway
- Department of Bacteriology and Immunology, Norwegian Institute of Public Health, Oslo, Norway
| | | | | | - Tone Tønjum
- Department of Microbiology, Unit for Genome Dynamics, University of Oslo, Oslo, Norway
- Department of Microbiology, Unit for Genome Dynamics, Oslo University Hospital, Oslo, Norway
| | - Solomon Abebe Yimer
- Department of Bacteriology and Immunology, Norwegian Institute of Public Health, Oslo, Norway
- Department of Microbiology, Unit for Genome Dynamics, University of Oslo, Oslo, Norway
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Welekidan LN, Bahta YW, Teklehaimanot MG, Abay GK, Wasihun AG, Dejene TA, Muthupandian S, Mezgebo TA, Hagos AK. Prevalence and drug resistance pattern of Listeria monocytogenes among pregnant women in Tigray region, Northern Ethiopia: a cross-sectional study. BMC Res Notes 2019; 12:538. [PMID: 31443675 PMCID: PMC6708214 DOI: 10.1186/s13104-019-4566-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [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: 07/09/2019] [Accepted: 08/13/2019] [Indexed: 01/30/2023] Open
Abstract
Objective The aim of this study was to determine the prevalence and antimicrobial susceptibility test of Listeria monocytogenes among pregnant women in Tigray region, Ethiopia. Results The overall prevalence of L. monocytogenes among pregnant women was found to be (8.5%; 12/141). With regard to the socio-demographic characteristics, a high prevalence of L. monocytogenes was observed in the age group of 20–24 years (18.6%; 8/43), rural dwellers (10%; 3/30), secondary school (9.6%; 5/52), and housewives (11.4%;10/88). A high drug resistance rate was observed to penicillin G (66.7%), clindamycin (66.7%), amoxicillin (50%) and vancomycin (50%). However, isolates were relatively sensitive to ciprofloxacin (75%), erythromycin (75%), trimethoprim/sulphamethaxazole (66.7%) and chloramphenicol (60%).
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Affiliation(s)
- Letemichael Negash Welekidan
- Department of Medical Microbiology and Immunology, Division of Biomedical Sciences, College of Health Science, Mekelle University, P.O.Box:1871, Mekelle, Tigray, Ethiopia.
| | - Yemane Weldu Bahta
- Department of Medical Microbiology and Immunology, Division of Biomedical Sciences, College of Health Science, Mekelle University, P.O.Box:1871, Mekelle, Tigray, Ethiopia
| | - Mebrihit Gebremeskel Teklehaimanot
- Department of Obstetrics and Gynaecology, School of Medicine, College of Health Sciences, Mekelle University, P.O.Box:1871, Mekelle, Tigray, Ethiopia
| | - Getahun Kahsay Abay
- Department of Medical Microbiology and Immunology, Division of Biomedical Sciences, College of Health Science, Mekelle University, P.O.Box:1871, Mekelle, Tigray, Ethiopia
| | - Araya Gebreyesus Wasihun
- Department of Medical Microbiology and Immunology, Division of Biomedical Sciences, College of Health Science, Mekelle University, P.O.Box:1871, Mekelle, Tigray, Ethiopia
| | - Tsehaye Asmelash Dejene
- Department of Medical Microbiology and Immunology, Division of Biomedical Sciences, College of Health Science, Mekelle University, P.O.Box:1871, Mekelle, Tigray, Ethiopia.,College of Health Sciences, Environmental Microbiology, Aksum University, Axsum, Ethiopia
| | - Saravanan Muthupandian
- Department of Medical Microbiology and Immunology, Division of Biomedical Sciences, College of Health Science, Mekelle University, P.O.Box:1871, Mekelle, Tigray, Ethiopia
| | - Tadele Araya Mezgebo
- Department of Medical Microbiology and Immunology, Division of Biomedical Sciences, College of Health Science, Mekelle University, P.O.Box:1871, Mekelle, Tigray, Ethiopia
| | - Amlsha Kahsay Hagos
- Department of Medical Microbiology and Immunology, Division of Biomedical Sciences, College of Health Science, Mekelle University, P.O.Box:1871, Mekelle, Tigray, Ethiopia
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