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Hiebert M, Sharma MK, Rabb M, Karlowsky L, Bergman K, Soualhine H. Mutations in embB406 Are Associated with Low-Level Ethambutol Resistance in Canadian Mycobacterium tuberculosis Isolates. Antibiotics (Basel) 2024; 13:624. [PMID: 39061306 PMCID: PMC11273804 DOI: 10.3390/antibiotics13070624] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2024] [Revised: 06/28/2024] [Accepted: 06/30/2024] [Indexed: 07/28/2024] Open
Abstract
In Mycobacterium tuberculosis, molecular predictions of ethambutol resistance rely primarily on the detection of mutations within embB. However, discordance between embB406 mutations and gold standard phenotypic drug sensitivity testing (DST) questions the significance of embB406 mutations used in molecular DST. This study tabulates embB mutations found in Canadian M. tuberculosis isolates and evaluates the impact of specific mutations on ethambutol resistance. The National Reference Centre for Mycobacteriology culture collection (n = 2796) was screened for isolates with embB mutations. Phenotypic DST was performed on the BACTEC™ MGIT™ 960 at ethambutol concentrations of 2-5 μg/mL. Whole genome sequencing was used for drug resistance predictions, phylogenomics and single nucleotide polymorphism analysis. Detection of resistance-associated embB mutations corresponded to a positive predictive value of 64.3%, negative predictive value of 99.2%, 98.7% specificity, and 73.3% sensitivity compared to phenotypic DST. Two embB406 mutation subtypes (Gly406Asp, Gly406Ala) were found among 16 isolates, of which 12 were sensitive at 5 µg/mL ethambutol with variable resistance between 2-4 µg/mL. A novel frameshift mutation in regulator embR (Gln258fs) was found in nine isolates. Mutations in embB406 were associated with low-level ethambutol resistance undetectable at the recommended critical concentration (5 μg/mL). These novel mutations may exacerbate variability in ethambutol resistance.
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Affiliation(s)
- Morgan Hiebert
- National Reference Centre for Mycobacteriology, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB R3E 3R2, Canada; (M.H.); (M.K.S.); (M.R.); (L.K.); (K.B.)
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, MB R3E 0J9, Canada
| | - Meenu K. Sharma
- National Reference Centre for Mycobacteriology, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB R3E 3R2, Canada; (M.H.); (M.K.S.); (M.R.); (L.K.); (K.B.)
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, MB R3E 0J9, Canada
| | - Melissa Rabb
- National Reference Centre for Mycobacteriology, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB R3E 3R2, Canada; (M.H.); (M.K.S.); (M.R.); (L.K.); (K.B.)
| | - Lisa Karlowsky
- National Reference Centre for Mycobacteriology, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB R3E 3R2, Canada; (M.H.); (M.K.S.); (M.R.); (L.K.); (K.B.)
| | - Kiana Bergman
- National Reference Centre for Mycobacteriology, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB R3E 3R2, Canada; (M.H.); (M.K.S.); (M.R.); (L.K.); (K.B.)
| | - Hafid Soualhine
- National Reference Centre for Mycobacteriology, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB R3E 3R2, Canada; (M.H.); (M.K.S.); (M.R.); (L.K.); (K.B.)
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, MB R3E 0J9, Canada
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Ferdosnejad K, Sholeh M, Abdolhamidi R, Soroush E, Siadat SD, Tarashi S. The occurrence rate of Haarlem and Beijing genotypes among Middle Eastern isolates of multi drug resistant Mycobacterium tuberculosis: A systematic review and meta-analysis. Respir Investig 2024; 62:296-304. [PMID: 38295613 DOI: 10.1016/j.resinv.2024.01.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Revised: 12/04/2023] [Accepted: 01/19/2024] [Indexed: 02/02/2024]
Abstract
Antibiotic resistance is a serious problem that poses a major challenge to tuberculosis control worldwide. Many developing countries still struggle with this infection in term of various aspects as it remains a major health concern. A number of developing countries are located in the Middle East, one of the world's most important regions. The control of this infection remains largely suboptimal despite intensive research in the field, and the mechanisms that lead to its progression have not yet been fully understood. Therefore, TB control must be amended through the identification of new strategies. For this reason, monitoring genetic characterizations of TB strains by molecular typing methods in different geographical regions can be important to setting local programs and global strategies to control TB infection. It is important to know the genotype of Mycobacterium tuberculosis strains to evaluate the occurrence of outbreaks and the transmission of this disease. Beijing and Haarlem genotypes are the most prevalent and, in these families, there is greater association with drug resistance, resulting in more severe forms of TB and higher levels of treatment failure than in other families. The current study is planned to systematically conduct a review using a meta-analysis to show the prevalence of Beijing and Haarlem genotypes in the Middle Eastern MDR-TB cases. M. tuberculosis strains pose particular epidemiological and clinical concerns as they can endanger tuberculosis control programs.
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Affiliation(s)
| | - Mohammad Sholeh
- Microbiology Research Center (MRC), Pasteur Institute of Iran, Tehran, Iran; Department of Bacteriology, Pasture Institute of Iran, Tehran, Iran
| | | | - Erfan Soroush
- Microbiology Research Center (MRC), Pasteur Institute of Iran, Tehran, Iran
| | - Seyed Davar Siadat
- Microbiology Research Center (MRC), Pasteur Institute of Iran, Tehran, Iran; Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran
| | - Samira Tarashi
- Microbiology Research Center (MRC), Pasteur Institute of Iran, Tehran, Iran; Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran.
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Babiker HA, Al-Jardani A, Al-Azri S, Petit RA, Saad E, Al-Mahrouqi S, Mohamed RA, Al-Hamidhi S, Balkhair AA, Al Kharusi N, Al Balushi L, Al Zadjali S, Pérez-Pardal L, Beja-Pereira A, Babiker A. Mycobacterium tuberculosis epidemiology in Oman: whole-genome sequencing uncovers transmission pathways. Microbiol Spectr 2023; 11:e0242023. [PMID: 37768070 PMCID: PMC10581073 DOI: 10.1128/spectrum.02420-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Accepted: 08/07/2023] [Indexed: 09/29/2023] Open
Abstract
Tuberculosis (TB) originating from expatriates that hail from high TB-burden countries is hypothesized to play a role in continued TB transmission in Oman. Here, we used whole-genome sequencing (WGS) to assess national TB transmission dynamics. The annual incidence per 100,000 population per year was calculated for nationals and expatriates. A convenience sample of Mycobacterium tuberculosis (MTB) isolates from 2018 to 2019 was sequenced and analyzed with publicly available TB sequences from Bangladesh, Tanzania, the Philippines, India, and Pakistan. Relatedness was assessed by generating core-genome single nucleotide polymorphism (SNP) distances. The incidence of TB was five cases per 100,000 persons in 2018 and seven cases per 100,000 persons in 2020 (R2 = 0.34, P = 0.60). Incidence among nationals was 3.9 per 100,000 persons in 2018 and 3.5 per 100,000 persons in 2020 (R2 = 0.20, P = 0.70), and incidence among expatriates was 7.2 per 100,000 persons in 2018 and 12.7 per 100,000 persons in 2020 (R2 = 0.74, P = 0.34). Sixty-eight local MTB isolates were sequenced and analyzed with 393 global isolates. Isolates belonged to nine distinct spoligotypes. Two isolates, originating from an expatriate and an Omani national, were grouped into a WGS-based cluster (SNP distance < 12), which was corroborated by an epidemiological investigation. Relatedness of local and global isolates (SNP distance < 100) was also seen. The relatedness between MTB strains in Oman and those in expatriate countries of origin can aid inform TB control policy. Our results provide evidence that WGS can complement epidemiological analysis to achieve the End TB strategy goal in Oman. IMPORTANCE Tuberculosis (TB) incidence in Oman remains above national program control targets. TB transmission originating from expatriates from high TB-burden countries has been hypothesized to play a role. We used whole-genome sequencing (WGS) to assess TB transmission dynamics between expatriates and Omani nationals to inform TB control efforts. Available Mycobacterium tuberculosis isolates from 2018 to 2019 underwent WGS and analysis with publicly available TB sequences from Bangladesh, the Philippines, India, and Pakistan to assess for genetic relatedness. Our analysis revealed evidence of previously unrecognized transmission between an expatriate and an Omani national, which was corroborated by epidemiological investigation. Analysis of local and global isolates revealed evidence of distant relatedness between local and global isolates. Our results provide evidence that WGS can complement classic public health surveillance to inform targeted interventions to achieve the End TB strategy goal in Oman.
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Affiliation(s)
- Hamza A Babiker
- Biochemistry Department, College of Medicine and Health Sciences, Sultan Qaboos University, Muscat, Oman
- Institute of Immunology and Infection Research, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Amina Al-Jardani
- Central Public Health Laboratories, National Tuberculosis Reference Laboratory, Directorate General for Disease Surveillance and Control, Ministry of Health, Muscat, Oman
| | - Saleh Al-Azri
- Central Public Health Laboratories, National Tuberculosis Reference Laboratory, Directorate General for Disease Surveillance and Control, Ministry of Health, Muscat, Oman
| | - Robert A. Petit
- Wyoming Department of Health, Wyoming Public Health Laboratory, Cheyenne, Wyoming, USA
| | - Eltaib Saad
- Department of Medicine, Ascension Saint Francis Hospital, Evanston, Illinois, USA
| | - Sarah Al-Mahrouqi
- Central Public Health Laboratories, National Tuberculosis Reference Laboratory, Directorate General for Disease Surveillance and Control, Ministry of Health, Muscat, Oman
| | - Reham A.H. Mohamed
- Biochemistry Department, College of Medicine and Health Sciences, Sultan Qaboos University, Muscat, Oman
| | - Salama Al-Hamidhi
- Biochemistry Department, College of Medicine and Health Sciences, Sultan Qaboos University, Muscat, Oman
| | - Abdullah A. Balkhair
- Department of Medicine, College of Medicine and Health Sciences, Sultan Qaboos University, Muscat, Oman
| | - Najma Al Kharusi
- Central Public Health Laboratories, National Tuberculosis Reference Laboratory, Directorate General for Disease Surveillance and Control, Ministry of Health, Muscat, Oman
| | - Laila Al Balushi
- Central Public Health Laboratories, National Tuberculosis Reference Laboratory, Directorate General for Disease Surveillance and Control, Ministry of Health, Muscat, Oman
| | - Samiya Al Zadjali
- Central Public Health Laboratories, National Tuberculosis Reference Laboratory, Directorate General for Disease Surveillance and Control, Ministry of Health, Muscat, Oman
| | - Lucía Pérez-Pardal
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Labora tório Associado, Campus de Vairão, Universidade do Porto, Vairão, Portugal, Vairão, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, Vairão, Portugal
| | - Albano Beja-Pereira
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Labora tório Associado, Campus de Vairão, Universidade do Porto, Vairão, Portugal, Vairão, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, Vairão, Portugal
- DGAOT, Faculty of Sciences, Universidade do Porto, Porto, Portugal
| | - Ahmed Babiker
- Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine, Atlanta, Georgia, USA
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, Georgia, USA
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