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Ayoubi S, Farnia P, Farnia P, Ghanavi J, Velayati AA. Prevalence and Temporal Trends of Multidrug-resistant Tuberculosis in Iran from 1981 to 2023: A Systematic Review and Meta-analysis. Int J Mycobacteriol 2024; 13:320-330. [PMID: 39277896 DOI: 10.4103/ijmy.ijmy_162_24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2024] [Accepted: 08/18/2024] [Indexed: 09/17/2024] Open
Abstract
BACKGROUND Multidrug-resistant tuberculosis (MDR-TB) is a serious threat to global tuberculosis (TB) control efforts. This study aims to investigate the trend of MDR-TB prevalence in Iran over 20 years. METHODS A systematic literature search was conducted in various databases, including PubMed, Embase, and Web of Science, from 1981 to 2023. Studies reporting the prevalence of MDR-TB in Iran were included in the meta-analysis. Statistical analysis was performed using Comprehensive Meta-Analysis software. RESULTS A total of 58 studies from different provinces of Iran were included in the meta-analysis. The majority of studies were from Tehran (n = 33), Kermanshah (n = 5), Mashhad (n = 4), and Tabriz (n = 4) provinces. Overall, 1885 cases of MDR-TB were reported in Iran during the study period. The highest number of MDR-TB cases was reported in 2000 (582 cases) and the lowest in 2001 (1 case). An increasing trend in MDR-TB prevalence was observed, particularly between 2018 and 2019. The pooled prevalence of MDR-TB in Iran was 12.31% (95% CI: 11.83-12.80) using the fixed-effects model and 20.21% (95% CI: 15.70-26.01) using the random-effects model. No evidence of publication bias was found. CONCLUSION The results of this comprehensive meta-analysis highlight the increasing trend of MDR-TB in Iran over the past two decades. This underscores the urgent need for strengthening TB control strategies, including improved surveillance, case detection, treatment, and management of MDR-TB in the country. Developing diagnostic and treatment approaches for MDR-TB should be prioritized by Iranian medical universities and public health authorities.
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Affiliation(s)
- Saman Ayoubi
- Mycobacteriology Research Center (MRC), National Research Institute of Tuberculosis and Lung Disease (NRITLD), Shahid Beheshti University of Medical Sciences, Tehran, Iran
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Mousavi-Sagharchi SMA, Afrazeh E, Seyyedian-Nikjeh SF, Meskini M, Doroud D, Siadat SD. New insight in molecular detection of Mycobacterium tuberculosis. AMB Express 2024; 14:74. [PMID: 38907086 PMCID: PMC11192714 DOI: 10.1186/s13568-024-01730-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Accepted: 06/06/2024] [Indexed: 06/23/2024] Open
Abstract
Mycobacterium tuberculosis, the causative agent of tuberculosis, is a pathogenic bacterium that has claimed millions of lives since the Middle Ages. According to the World Health Organization's report, tuberculosis ranks among the ten deadliest diseases worldwide. The presence of an extensive array of genes and diverse proteins within the cellular structure of this bacterium has provided us with a potent tool for diagnosis. While the culture method remains the gold standard for tuberculosis diagnosis, it is possible that molecular diagnostic methods, emphasis on the identification of mutation genes (e.g., rpoB and gyrA) and single nucleotide polymorphisms, could offer a safe and reliable alternative. Over the past few decades, as our understanding of molecular genetics has expanded, methods have been developed based on gene expansion and detection. These methods typically commence with DNA amplification through nucleic acid targeted techniques such as polymerase chain reaction. Various molecular compounds and diverse approaches have been employed in molecular assays. In this review, we endeavor to provide an overview of molecular assays for the diagnosis of tuberculosis with their properties (utilization, challenges, and functions). The ultimate goal is to explore the potential of replacing traditional bacterial methods with these advanced molecular diagnostic techniques.
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Affiliation(s)
| | - Elina Afrazeh
- Department of Marine Biology, Faculty of Marine Science, Khorramshahr University of Marine Science and Technology, Khorramshahr, Iran
| | | | - Maryam Meskini
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran.
- Microbiology Research Center (MRC), Pasteur Institute of Iran, Tehran, Iran.
- Department of Genetics, Faculty of Natural and Agricultural Sciences, University of the Free State, Bloemfontein, 9301, South Africa.
- Student Research Committee, Pasteur Institute of Iran, Tehran, Iran.
| | - Delaram Doroud
- Department of Immunotherapy and Leishmania Vaccine Research, Pasteur Institute of Iran, Tehran, Iran
| | - Seyed Davar Siadat
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran.
- Microbiology Research Center (MRC), Pasteur Institute of Iran, Tehran, Iran.
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Abbasian S, Heidari H, Abbasi Tadi D, Kardan-Yamchi J, Taji A, Darbandi A, Asadollahi P, Maleki A, Kazemian H. Epidemiology of first- and second-line drugs-resistant pulmonary tuberculosis in Iran: Systematic review and meta-analysis. J Clin Tuberc Other Mycobact Dis 2024; 35:100430. [PMID: 38560029 PMCID: PMC10981085 DOI: 10.1016/j.jctube.2024.100430] [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] [Indexed: 04/04/2024] Open
Abstract
Drug resistance among Mycobacterium tuberculosis (MTB) strains is a growing concern in developing countries. We conducted a comprehensive search for relevant studies in Iran on PubMed, Scopus, and Embase until June 12, 2020. Our study focused on determining the prevalence of antibiotic resistance in MTB isolates, with subgroup analyses based on year, location, and drug susceptibility testing (DST) methods. Statistical analyses were performed using STATA software. Our meta-analysis included a total of 47 articles. Among new TB cases, we found the following prevalence rates: Any-resistance to first-line drugs: 31 % (95 % CI, 24-38), mono-drug resistance: 15 % (95 % CI, 10-22), and multidrug resistance to first-line drugs: 6 % (95 % CI, 4-8). There was a significant variation in the rate of MDR among new TB cases based on the year of publication, location, and DST methods (P < 0.0001). We observed substantial variability in multidrug-resistant TB rates among new cases across the studies. Stratified analyses revealed that publication years and DST methods significantly affected resistance rates. Studies from southern and central Iran reported higher any-drug resistance rates, suggesting regional differences. Among retreatment cases, the prevalence rates were as follows: Any resistance: 68 % (95 % CI 58-78), mono-resistance: 19 % (95 % CI 7-34), multidrug resistance: 28 % (95 % CI 15-43). Our study revealed that the prevalence of drug-resistant TB (DR-TB) among TB cases in Iran is higher than the global average. Particularly, MDR-TB among retreatment TB cases is a significant public health issue.
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Affiliation(s)
- Sara Abbasian
- Laboratory Sciences Research Center, Golestan University of Medical Sciences, Gorgan, Iran
| | - Hamid Heidari
- Department of Microbiology, Faculty of Medicine, Shahid Sadoughi University of Medical Sciences, Yazd, Iran
| | - Danyal Abbasi Tadi
- Department of Veterinary, Azad University of Shahr-e Kord, Shahr-e Kord, Iran
| | - Jalil Kardan-Yamchi
- Quality Control and Screening Management Office, Deputy of Technical and New Technologies, Iranian Blood Transfusion Organization, Tehran, Iran
| | - Asieh Taji
- International Campus, Shahid Sadoughi University of Medical Sciences, Yazd, Iran
| | - Atieh Darbandi
- Department of Microbiology, Faculty of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Parisa Asadollahi
- Clinical Microbiology Research Center, Ilam University of Medical Sciences, Ilam, Iran
| | - Abbas Maleki
- Clinical Microbiology Research Center, Ilam University of Medical Sciences, Ilam, Iran
| | - Hossein Kazemian
- Clinical Microbiology Research Center, Ilam University of Medical Sciences, Ilam, Iran
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Madadi-Goli N, Ahmadi K, Kamakoli MK, Azizi M, Khanipour S, Dizaji SP, Nasehi M, Siadat SD, Fateh A, Vaziri F. The importance of heteroresistance and efflux pumps in bedaquiline-resistant Mycobacterium tuberculosis isolates from Iran. Ann Clin Microbiol Antimicrob 2024; 23:36. [PMID: 38664815 PMCID: PMC11046812 DOI: 10.1186/s12941-024-00694-3] [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: 11/09/2023] [Accepted: 04/04/2024] [Indexed: 04/28/2024] Open
Abstract
BACKGROUND Tuberculosis (TB) continues to pose a threat to communities worldwide and remains a significant public health issue in several countries. We assessed the role of heteroresistance and efflux pumps in bedaquiline (BDQ)-resistant Mycobacterium tuberculosis isolates. METHODS Nineteen clinical isolates were included in the study, of which fifteen isolates were classified as MDR or XDR, while four isolates were fully susceptible. To evaluate BDQ heteroresistance, the Microplate Alamar Blue Assay (MABA) method was employed. For screening mixed infections, MIRU-VNTR was performed on clinical isolates. Mutations in the atpE and Rv0678 genes were determined based on next-generation sequencing data. Additionally, real-time PCR was applied to assess the expression of efflux pump genes in the absence and presence of verapamil (VP). RESULTS All 15 drug-resistant isolates displayed resistance to BDQ. Among the 19 total isolates, 21.05% (4/19) exhibited a heteroresistance pattern to BDQ. None of the isolates carried a mutation of the atpE and Rv0678 genes associated with BDQ resistance. Regarding the MIRU-VNTR analysis, most isolates (94.73%) showed the Beijing genotype. Fifteen (78.9%) isolates showed a significant reduction in BDQ MIC after VP treatment. The efflux pump genes of Rv0676c, Rv1258c, Rv1410c, Rv1634, Rv1819, Rv2459, Rv2846, and Rv3065 were overexpressed in the presence of BDQ. CONCLUSIONS Our results clearly demonstrated the crucial role of heteroresistance and efflux pumps in BDQ resistance. Additionally, we established a direct link between the Rv0676c gene and BDQ resistance. The inclusion of VP significantly reduced the MIC of BDQ in both drug-susceptible and drug-resistant clinical isolates.
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Affiliation(s)
- Nahid Madadi-Goli
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, No. 358, 12th Farvardin Ave., Jomhoori St, Tehran, 1316943551, Iran
- Microbiology Research Center (MRC), Pasteur Institute of Iran, Tehran, Iran
- Student Research Committee, Pasteur Institute of Iran, Tehran, Iran
| | - Kamal Ahmadi
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, No. 358, 12th Farvardin Ave., Jomhoori St, Tehran, 1316943551, Iran
- Microbiology Research Center (MRC), Pasteur Institute of Iran, Tehran, Iran
- Department of Microbiology, School of Medicine, Kermanshah University of Medical Sciences, Kermanshah, Iran
- Student Research Committee, Pasteur Institute of Iran, Tehran, Iran
| | - Mansour Kargarpour Kamakoli
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, No. 358, 12th Farvardin Ave., Jomhoori St, Tehran, 1316943551, Iran
- Microbiology Research Center (MRC), Pasteur Institute of Iran, Tehran, Iran
| | - Mohsen Azizi
- Department of Microbiology, School of Medicine, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Sharareh Khanipour
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, No. 358, 12th Farvardin Ave., Jomhoori St, Tehran, 1316943551, Iran
- Microbiology Research Center (MRC), Pasteur Institute of Iran, Tehran, Iran
| | - Shahin Pourazar Dizaji
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, No. 358, 12th Farvardin Ave., Jomhoori St, Tehran, 1316943551, Iran
- Microbiology Research Center (MRC), Pasteur Institute of Iran, Tehran, Iran
| | - Mahshid Nasehi
- Department of Epidemiology and Biostatistics, School of Public Health, Iran University of Medical Sciences, Tehran, Iran
- Center for Communicable Diseases Control, Ministry of Health and Medical Education, Tehran, Iran
| | - Seyed Davar Siadat
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, No. 358, 12th Farvardin Ave., Jomhoori St, Tehran, 1316943551, Iran
- Microbiology Research Center (MRC), Pasteur Institute of Iran, Tehran, Iran
| | - Abolfazl Fateh
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, No. 358, 12th Farvardin Ave., Jomhoori St, Tehran, 1316943551, Iran.
- Microbiology Research Center (MRC), Pasteur Institute of Iran, Tehran, Iran.
| | - Farzam Vaziri
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, No. 358, 12th Farvardin Ave., Jomhoori St, Tehran, 1316943551, Iran.
- Microbiology Research Center (MRC), Pasteur Institute of Iran, Tehran, Iran.
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Dheda K, Mirzayev F, Cirillo DM, Udwadia Z, Dooley KE, Chang KC, Omar SV, Reuter A, Perumal T, Horsburgh CR, Murray M, Lange C. Multidrug-resistant tuberculosis. Nat Rev Dis Primers 2024; 10:22. [PMID: 38523140 DOI: 10.1038/s41572-024-00504-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 02/16/2024] [Indexed: 03/26/2024]
Abstract
Tuberculosis (TB) remains the foremost cause of death by an infectious disease globally. Multidrug-resistant or rifampicin-resistant TB (MDR/RR-TB; resistance to rifampicin and isoniazid, or rifampicin alone) is a burgeoning public health challenge in several parts of the world, and especially Eastern Europe, Russia, Asia and sub-Saharan Africa. Pre-extensively drug-resistant TB (pre-XDR-TB) refers to MDR/RR-TB that is also resistant to a fluoroquinolone, and extensively drug-resistant TB (XDR-TB) isolates are additionally resistant to other key drugs such as bedaquiline and/or linezolid. Collectively, these subgroups are referred to as drug-resistant TB (DR-TB). All forms of DR-TB can be as transmissible as rifampicin-susceptible TB; however, it is more difficult to diagnose, is associated with higher mortality and morbidity, and higher rates of post-TB lung damage. The various forms of DR-TB often consume >50% of national TB budgets despite comprising <5-10% of the total TB case-load. The past decade has seen a dramatic change in the DR-TB treatment landscape with the introduction of new diagnostics and therapeutic agents. However, there is limited guidance on understanding and managing various aspects of this complex entity, including the pathogenesis, transmission, diagnosis, management and prevention of MDR-TB and XDR-TB, especially at the primary care physician level.
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Affiliation(s)
- Keertan Dheda
- Centre for Lung Infection and Immunity, Division of Pulmonology, Department of Medicine and UCT Lung Institute & South African MRC/UCT Centre for the Study of Antimicrobial Resistance, University of Cape Town, Cape Town, South Africa.
- Faculty of Infectious and Tropical Diseases, Department of Immunology and Infection, London School of Hygiene and Tropical Medicine, London, UK.
| | - Fuad Mirzayev
- Global Tuberculosis Programme, WHO, Geneva, Switzerland
| | - Daniela Maria Cirillo
- Emerging Bacterial Pathogens Unit, IRCCS San Raffaele Scientific Institute Milan, Milan, Italy
| | - Zarir Udwadia
- Department of Pulmonology, Hinduja Hospital & Research Center, Mumbai, India
| | - Kelly E Dooley
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Kwok-Chiu Chang
- Tuberculosis and Chest Service, Centre for Health Protection, Department of Health, Hong Kong, SAR, China
| | - Shaheed Vally Omar
- Centre for Tuberculosis, National & WHO Supranational TB Reference Laboratory, National Institute for Communicable Diseases, a division of the National Health Laboratory Service, Johannesburg, South Africa
- Department of Molecular Medicine & Haematology, School of Pathology, Faculty of Health Sciences, University of Witwatersrand, Johannesburg, South Africa
| | - Anja Reuter
- Sentinel Project on Paediatric Drug-Resistant Tuberculosis, Boston, MA, USA
| | - Tahlia Perumal
- Centre for Lung Infection and Immunity, Division of Pulmonology, Department of Medicine and UCT Lung Institute & South African MRC/UCT Centre for the Study of Antimicrobial Resistance, University of Cape Town, Cape Town, South Africa
- Faculty of Infectious and Tropical Diseases, Department of Immunology and Infection, London School of Hygiene and Tropical Medicine, London, UK
| | - C Robert Horsburgh
- Department of Epidemiology, Boston University Schools of Public Health and Medicine, Boston, MA, USA
| | - Megan Murray
- Department of Epidemiology, Harvard Medical School, Boston, MA, USA
| | - Christoph Lange
- Division of Clinical Infectious Diseases, Research Center Borstel, Borstel, Germany
- German Center for Infection Research (DZIF), TTU-TB, Borstel, Germany
- Respiratory Medicine & International Health, University of Lübeck, Lübeck, Germany
- Department of Paediatrics, Baylor College of Medicine and Texas Children's Hospital, Houston, TX, USA
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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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Abdolhamidi R, Haghighat S, Moshiri A, Fateh A, Siadat SD. Significance of genotypes and resistance status of Mycobacterium tuberculosis strains in gene expression of apoptosis cell death and inflammatory pathways in A549 lung epithelial cell line. IRANIAN JOURNAL OF BASIC MEDICAL SCIENCES 2024; 27:825-831. [PMID: 38800030 PMCID: PMC11127082 DOI: 10.22038/ijbms.2024.75195.16303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Accepted: 01/27/2024] [Indexed: 05/29/2024]
Abstract
Objectives Tuberculosis (TB) has been a major health issue throughout history. As part of TB infection, host-Mycobacterium tuberculosis (Mtb) interactions are important. Through immune pathology and cell death control processes, Mtb infection facilitates intracellular growth. The relationship between apoptosis and inflammation in Mtb infection remains unclear. In this study, the levels of related apoptosis and inflammatory genes were assessed in A549 cells infected with a variety of Mtb strains. Materials and Methods Mtb isolates with different phenotypes (sensitive, INHR, RifR, MDR, and XDR) were collected from the Pasteur Institute of Iran, during this study. Whole genome sequencing was previously performed on all strains, and the Beijing genotype was selected as sensitive. Also, for other resistant strains, the New-1 genotype was available and isolated for genotype comparison. A549 lung carcinoma cells were also grown and infected with selected Mtb strains. Genes involved in inflammation and apoptosis were detected using reverse transcription-PCR (RT-PCR). Results All sensitive strains and resistant strains were found to significantly up-regulate anti-apoptotic (bcl2 and rb1), chemokine (IL-8 and MCP-1), and pro-inflammatory cytokine (TNF-α and IFN-γ) expression, while significant down-regulation was observed after 24 and 48 hr of infection in anti-inflammatory genes (IL-10) and pro-apoptotic genes (bad and bax). Besides resistance strains, Mtb genotypes also affected gene expression. The Beijing genotype (sensitive isolate) influences inflammatory and apoptotic genes more sharply than the New-1 genotype (INHR, RifR, MDR, and XDR). Conclusion Gene expression differences related to apoptosis and inflammation examined in the current study may be attributed to genotypes rather than resistance status since the expression of most genes has been observed to be lower in resistant strains (INHR, RifR, MDR, and XDR belonging to the New-1 genotype) compared to sensitive strains (Beijing genotype).
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Affiliation(s)
- Rouhollah Abdolhamidi
- Department of Microbiology, Faculty of Advanced Science and Technology, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
| | - Setareh Haghighat
- Department of Microbiology, Faculty of Advanced Science and Technology, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
| | - Arfa Moshiri
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran
- Microbiology Research Center (MRC), Pasteur Institute of Iran, Tehran, Iran
| | - Abolfazl Fateh
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran
- Microbiology Research Center (MRC), Pasteur Institute of Iran, Tehran, Iran
| | - Seyed Davar Siadat
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran
- Microbiology Research Center (MRC), Pasteur Institute of Iran, Tehran, Iran
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Wang J, Yu C, Xu Y, Chen Z, Qiu W, Chen S, Pei H, Zhong Y. Analysis of Drug-Resistance Characteristics and Genetic Diversity of Multidrug-Resistant Tuberculosis Based on Whole-Genome Sequencing on the Hainan Island, China. Infect Drug Resist 2023; 16:5783-5798. [PMID: 37692467 PMCID: PMC10487742 DOI: 10.2147/idr.s423955] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Accepted: 08/22/2023] [Indexed: 09/12/2023] Open
Abstract
Purpose Given the high burden of Tuberculosis (TB) in China, the prevalence of multidrug-resistant tuberculosis (MDR-TB) is significant. Whole-genome sequencing (WGS) of Mycobacterium tuberculosis (MTB) enables the identification of lineages, drug-resistant mutations, and transmission patterns, offering valuable insights for TB control, clinical diagnosis, and treatment. Methods We collected 202 MDR-MTB strains from 3519 suspected pulmonary TB patients treated at The Second Affiliated Hospital of Hainan Medical University between July 2019 and June 2021. Proportional drug-susceptibility testing was performed using 8 common anti-tuberculosis drugs. Subsequently, the genotypic drug resistance and genetic characteristics were analyzed by the WGS. Results Lineages are identified by TB-profiler revealed 202 MDR-MTB strains, showcasing three predominant lineages, with lineage 2 being the most prevalent. Close genomic relatedness analysis and evidence of MTB transmission led to the formation of 15 clusters comprising 42 isolates, resulting in a clustering rate of 20.8%. Novelty, lineage 2.1 (non-Beijing) accounted for 27.2% of the MDR-MTB strains, which is rare in China and Neighboring countries. Regarding first-line anti-TB drugs, genes associated with rifampicin resistance, primarily the rpoB gene, were detected in 200 strains (99.0%). Genes conferring resistance to isoniazid, ethambutol, and streptomycin were identified in 191 (94.5%), 125 (61.9%), and 100 (49.5%) strains, respectively. Among the second-line drugs, 97 (48.0%) strains exhibited genes encoding resistance to fluoroquinolones. Comparing the results to phenotypic drug susceptibility-based testing, the sensitivity of WGS for detecting resistance to each of the six drugs (rifampicin, isoniazid, ethambutol, ofloxacin, kanamycin, capreomycin) was 90% or higher. With the exception of ethambutol, the specificity of WGS prediction for the remaining drugs exceeded 88%. Conclusion Our study provides crucial insights into genetic mutation types, genetic diversity, and transmission of MDR-MTB on Hainan Island, serving as a significant reference for MDR-MTB surveillance and clinical decision-making.
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Affiliation(s)
- Jieying Wang
- Department of Clinical Laboratory, The Second Affiliated Hospital of Hainan Medical University, Haikou, 570216, People’s Republic of China
| | - Chunchun Yu
- Department of Clinical Laboratory, The Second Affiliated Hospital of Hainan Medical University, Haikou, 570216, People’s Republic of China
| | - Yuni Xu
- Department of Clinical Laboratory, The Second Affiliated Hospital of Hainan Medical University, Haikou, 570216, People’s Republic of China
| | - Zhuolin Chen
- Department of Clinical Laboratory, The Second Affiliated Hospital of Hainan Medical University, Haikou, 570216, People’s Republic of China
| | - Wenhua Qiu
- Department of Clinical Laboratory, The Second Affiliated Hospital of Hainan Medical University, Haikou, 570216, People’s Republic of China
| | - Shaowen Chen
- Department of Clinical Laboratory, The Second Affiliated Hospital of Hainan Medical University, Haikou, 570216, People’s Republic of China
| | - Hua Pei
- Department of Clinical Laboratory, The Second Affiliated Hospital of Hainan Medical University, Haikou, 570216, People’s Republic of China
| | - Yeteng Zhong
- Department of Clinical Laboratory, The Second Affiliated Hospital of Hainan Medical University, Haikou, 570216, People’s Republic of China
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Liang D, Song Z, Liang X, Qin H, Huang L, Ye J, Lan R, Luo D, Zhao Y, Lin M. Whole Genomic Analysis Revealed High Genetic Diversity and Drug-Resistant Characteristics of Mycobacterium tuberculosis in Guangxi, China. Infect Drug Resist 2023; 16:5021-5031. [PMID: 37554542 PMCID: PMC10405913 DOI: 10.2147/idr.s410828] [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: 03/27/2023] [Accepted: 06/21/2023] [Indexed: 08/10/2023] Open
Abstract
Background Tuberculosis (TB), caused by Mycobacterium tuberculosis (Mtb), is a major public health issue in China. Nevertheless, the prevalence and drug resistance characteristics of isolates vary in different regions and provinces. In this study, we investigated the population structure, transmission dynamics and drug-resistant profiles of Mtb in Guangxi, located on the border of China. Methods From February 2016 to April 2017, 462 clinical M. tuberculosis isolates were selected from 5 locations in Guangxi. Drug-susceptibility testing was performed using 6 common anti-tuberculosis drugs. The genotypic drug resistance and transmission dynamics were analyzed by the whole genome sequence. Results Our data showed that the Mtb in Guangxi has high genetic diversity including Lineage 1 to Lineage 4, and mostly belong to Lineage 2 and Lineage 4. Novelty, 9.6% of Lineage 2 isolates were proto-Beijing genotype (L2.1), which is rare in China. About 12.6% of isolates were phylogenetically clustered and formed into 28 transmission clusters. We observed that the isolates with the high resistant rate of isoniazid (INH, 21.2%), followed by rifampicin (RIF, 13.2%), and 6.7%, 12.1%, 6.7% and 1.9% isolates were resistant to ethambutol (EMB), streptomycin (SM), ofloxacin (OFL) and kanamycin (KAN), respectively. Among these, 6.5% and 3.3% of isolates belong to MDR-TB and Pre-XDR, respectively, with a high drug-resistant burden. Genetic analysis identified the most frequently encountered mutations of INH, RIF, EMB, SM, OFL and KAN were katG_Ser315Thr (62.2%), rpoB_Ser450Leu (42.6%), embB_Met306Vol (45.2%), rpsL_Lys43Arg (53.6%), gyrA_Asp94Gly (29.0%) and rrs_A1401G (66.7%), respectively. Additionally, we discovered that isolates from border cities are more likely to be drug-resistant than isolates from non-border cities. Conclusion Our findings provide a deep analysis of the genomic population characteristics and drug-resistant of M. tuberculosis in Guangxi, which could contribute to developing effective TB prevention and control strategies.
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Affiliation(s)
- Dabin Liang
- Guangxi Zhuang Autonomous Region Center for Disease Control and Prevention, Nanning, Guangxi, People’s Republic of China
- Guangxi Key Laboratory of Major Infectious Disease Prevention and Control and Biosafety Emergency Response, Nanning, Guangxi, People’s Republic of China
| | - Zexuan Song
- National Tuberculosis Reference Laboratory, Chinese Center for Disease Control and Prevention, Beijing, People’s Republic of China
| | - Xiaoyan Liang
- Guangxi Zhuang Autonomous Region Center for Disease Control and Prevention, Nanning, Guangxi, People’s Republic of China
- Guangxi Key Laboratory of Major Infectious Disease Prevention and Control and Biosafety Emergency Response, Nanning, Guangxi, People’s Republic of China
| | - Huifang Qin
- Guangxi Zhuang Autonomous Region Center for Disease Control and Prevention, Nanning, Guangxi, People’s Republic of China
- Guangxi Key Laboratory of Major Infectious Disease Prevention and Control and Biosafety Emergency Response, Nanning, Guangxi, People’s Republic of China
| | - Liwen Huang
- Guangxi Zhuang Autonomous Region Center for Disease Control and Prevention, Nanning, Guangxi, People’s Republic of China
- Guangxi Key Laboratory of Major Infectious Disease Prevention and Control and Biosafety Emergency Response, Nanning, Guangxi, People’s Republic of China
| | - Jing Ye
- Guangxi Zhuang Autonomous Region Center for Disease Control and Prevention, Nanning, Guangxi, People’s Republic of China
- Guangxi Key Laboratory of Major Infectious Disease Prevention and Control and Biosafety Emergency Response, Nanning, Guangxi, People’s Republic of China
| | - Rushu Lan
- Department of Clinical Laboratory, Jiangbin Hospital of Guangxi Zhuang Autonomous Region, Nanning, Guangxi, People’s Republic of China
| | - Dan Luo
- School of Public Health and Management, Guangxi University of Chinese Medicine, Nanning, Guangxi, People’s Republic of China
| | - Yanlin Zhao
- National Tuberculosis Reference Laboratory, Chinese Center for Disease Control and Prevention, Beijing, People’s Republic of China
| | - Mei Lin
- Guangxi Zhuang Autonomous Region Center for Disease Control and Prevention, Nanning, Guangxi, People’s Republic of China
- Guangxi Key Laboratory of Major Infectious Disease Prevention and Control and Biosafety Emergency Response, Nanning, Guangxi, People’s Republic of China
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10
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Hall MB, Lima L, Coin LJM, Iqbal Z. Drug resistance prediction for Mycobacterium tuberculosis with reference graphs. Microb Genom 2023; 9:mgen001081. [PMID: 37552534 PMCID: PMC10483414 DOI: 10.1099/mgen.0.001081] [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: 05/09/2023] [Accepted: 07/14/2023] [Indexed: 08/09/2023] Open
Abstract
Tuberculosis is a global pandemic disease with a rising burden of antimicrobial resistance. As a result, the World Health Organization (WHO) has a goal of enabling universal access to drug susceptibility testing (DST). Given the slowness of and infrastructure requirements for phenotypic DST, whole-genome sequencing, followed by genotype-based prediction of DST, now provides a route to achieving this. Since a central component of genotypic DST is to detect the presence of any known resistance-causing mutations, a natural approach is to use a reference graph that allows encoding of known variation. We have developed DrPRG (Drug resistance Prediction with Reference Graphs) using the bacterial reference graph method Pandora. First, we outline the construction of a Mycobacterium tuberculosis drug resistance reference graph. The graph is built from a global dataset of isolates with varying drug susceptibility profiles, thus capturing common and rare resistance- and susceptible-associated haplotypes. We benchmark DrPRG against the existing graph-based tool Mykrobe and the haplotype-based approach of TBProfiler using 44 709 and 138 publicly available Illumina and Nanopore samples with associated phenotypes. We find that DrPRG has significantly improved sensitivity and specificity for some drugs compared to these tools, with no significant decreases. It uses significantly less computational memory than both tools, and provides significantly faster runtimes, except when runtime is compared to Mykrobe with Nanopore data. We discover and discuss novel insights into resistance-conferring variation for M. tuberculosis - including deletion of genes katG and pncA - and suggest mutations that may warrant reclassification as associated with resistance.
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Affiliation(s)
- Michael B. Hall
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, Cambridgeshire, UK
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Australia
| | - Leandro Lima
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, Cambridgeshire, UK
| | - Lachlan J. M. Coin
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Australia
| | - Zamin Iqbal
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, Cambridgeshire, UK
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11
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Cao B, Mijiti X, Deng LL, Wang Q, Yu JJ, Anwaierjiang A, Qian C, Li M, Fang DA, Jiang Y, Zhao LL, Zhao X, Wan K, Liu H, Li G, Yuan X. Genetic Characterization Conferred Co-Resistance to Isoniazid and Ethionamide in Mycobacterium tuberculosis Isolates from Southern Xinjiang, China. Infect Drug Resist 2023; 16:3117-3135. [PMID: 37228658 PMCID: PMC10204763 DOI: 10.2147/idr.s407525] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Accepted: 05/02/2023] [Indexed: 05/27/2023] Open
Abstract
Background Ethionamide (ETH), a structural analogue of isoniazid (INH), is used for treating multidrug-resistant tuberculosis (MDR-TB). Due to the common target InhA, INH and ETH showed cross-resistance in M. tuberculosis. This study aimed to explore the INH and ETH resistant profiles and genetic mutations conferring independent INH- or ETH-resistance and INH-ETH cross-resistance in M. tuberculosis circulating in south of Xinjiang, China. Methods From Sep 2017 to Dec 2018, 312 isolates were included using drug susceptibility testing (DST), spoligotyping, and whole genome sequencing (WGS) to analyze the resistance characteristics for INH and/or ETH. Results Among the 312 isolates, 185 (58.3%) and 127 (40.7%) belonged to the Beijing family and non-Beijing family, respectively; 90 (28.9%) were INH-resistant (INHR) with mutation rates of 74.4% in katG, 13.3% in inhA and its promoter, 11.1% in ahpC and its upstream region, 2.2% in ndh, 0.0% in mshA, whilst 34 (10.9%) were ETH-resistant (ETHR) with mutation rates of 38.2% in ethA, 26.2% in inhA and its promoter, and 5.9% in ndh, 0.0% in ethR or mshA; and 25 (8.0%) were INH-ETH co-resistant (INHRETHR) with mutation rates of 40.0% in inhA and its promoter, and 8% in ndh. katG mutants tended to display high-level resistant to INH; and more inhA and its promoter mutants showed low-level of INH and ETH resistance. The optimal gene combinations by WGS for the prediction of INHR, ETHR, and INHRETHR were, respectively, katG+inhA and its promoter (sensitivity: 81.11%, specificity: 90.54%), ethA+inhA and its promoter+ndh (sensitivity: 61.76%, specificity: 76.62%), and inhA and its promoter+ndh (sensitivity: 48.00%, specificity: 97.65%). Conclusion This study revealed the high diversity of genetic mutations conferring INH and/or ETH resistance among M. tuberculosis isolates, which would facilitate the study on INHR and/or ETHR mechanisms and provide clues for choosing ETH for MDR treatment and molecular DST methods in south of Xinjiang, China.
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Affiliation(s)
- Bin Cao
- School of Public Health, University of South China, Hengyang, 421001, People’s Republic of China
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, People’s Republic of China
| | - Xiaokaiti Mijiti
- The Eighth Affiliated Hospital of Xinjiang Medical University, Urumqi, 830000, People’s Republic of China
| | - Le-Le Deng
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, People’s Republic of China
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, People’s Republic of China
| | - Quan Wang
- The Eighth Affiliated Hospital of Xinjiang Medical University, Urumqi, 830000, People’s Republic of China
| | - Jin-Jie Yu
- School of Public Health, University of South China, Hengyang, 421001, People’s Republic of China
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, People’s Republic of China
| | | | - Chengyu Qian
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, People’s Republic of China
- Wenzhou Key Laboratory of Sanitary Microbiology, Key Laboratory of Laboratory Medicine, Ministry of Education, China, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, 325035, People’s Republic of China
| | - Machao Li
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, People’s Republic of China
| | - Dan-Ang Fang
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, People’s Republic of China
- Wenzhou Key Laboratory of Sanitary Microbiology, Key Laboratory of Laboratory Medicine, Ministry of Education, China, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, 325035, People’s Republic of China
| | - Yi Jiang
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, People’s Republic of China
| | - Li-Li Zhao
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, People’s Republic of China
| | - Xiuqin Zhao
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, People’s Republic of China
| | - Kanglin Wan
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, People’s Republic of China
| | - Haican Liu
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, People’s Republic of China
| | - Guilian Li
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, People’s Republic of China
| | - Xiuqin Yuan
- School of Public Health, University of South China, Hengyang, 421001, People’s Republic of China
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12
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Hadifar S, Kargarpour Kamakoli M, Eybpoosh S, Nakhaeizadeh M, Kargarpour Kamakoli MA, Ebrahimifard N, Fateh A, Siadat SD, Vaziri F. The shortcut of mycobacterial interspersed repetitive unit-variable number tandem repeat typing for Mycobacterium tuberculosis differentiation. Front Microbiol 2022; 13:978355. [PMID: 36160200 PMCID: PMC9493315 DOI: 10.3389/fmicb.2022.978355] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2022] [Accepted: 08/18/2022] [Indexed: 11/16/2022] Open
Abstract
The 24-loci mycobacterial interspersed repetitive unit-variable number tandem repeat (MIRU-VNTR) genotyping has been used as an international standard method for Mycobacterium tuberculosis (Mtb) genotyping. However, different optimized VNTR loci sets for improving the discrimination of specific Mtb genotypes have been proposed. In this regard, we investigated the efficacy of accumulation of the percentage differences (APDs) compared with the least absolute shrinkage and selection operator (LASSO) regression strategy to identify a customized genotype-specific VNTR loci set which provides a resolution comparable to 24-loci MIRU-VNTR in divergent Mtb populations. We utilized Spoligotyping and 24-loci MIRU-VNTR typing for genotyping 306 Mtb isolates. The APD and LASSO regression approaches were used to identify a customized VNTR set in our studied isolates. Besides, the Hunter-Gaston discriminatory index (HGDI), sensitivity, and specificity of each selected loci set were calculated based on both strategies. The selected loci based on LASSO regression compared with APD-based loci showed a better discriminatory power for identifying all studied genotypes except for T genotype, which APD-based loci showed promising discriminative power. Our findings suggested the LASSO regression rather than the APD approach is more effective in the determination of possible discriminative VNTR loci set to precise discrimination of our studied Mtb population and may be beneficial to be used in finding reduced number loci sets in other Mtb genotypes or sublineages. Moreover, we proposed customized genotype-specific MIRU-VNTR loci sets based on the LASSO regression and APD approaches for precise Mtb strains identification. As the proposed VNTR sets offered a comparable discriminatory power to the standard 24 MIRU-VNTR loci set could be promising alternatives to the standard genotyping for using in resource-limited settings.
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Affiliation(s)
- Shima Hadifar
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran
- Microbiology Research Center, Pasteur Institute of Iran, Tehran, Iran
| | - Mansour Kargarpour Kamakoli
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran
- Microbiology Research Center, Pasteur Institute of Iran, Tehran, Iran
| | - Sana Eybpoosh
- Department of Epidemiology and Biostatistics, Research Centre for Emerging and Reemerging Infectious Diseases, Pasteur Institute of Iran, Tehran, Iran
| | - Mehran Nakhaeizadeh
- Modeling in Health Research Center, Institute for Futures Studies in Health, Kerman University of Medical Sciences, Kerman, Iran
- Department of Biostatistics and Epidemiology, School of Public Health, Kerman University of Medical Sciences, Kerman, Iran
| | | | - Nasim Ebrahimifard
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran
- Microbiology Research Center, Pasteur Institute of Iran, Tehran, Iran
| | - Abolfazl Fateh
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran
- Microbiology Research Center, Pasteur Institute of Iran, Tehran, Iran
| | - Seyed Davar Siadat
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran
- Microbiology Research Center, Pasteur Institute of Iran, Tehran, Iran
| | - Farzam Vaziri
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran
- Microbiology Research Center, Pasteur Institute of Iran, Tehran, Iran
- *Correspondence: Farzam Vaziri, ,
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13
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Menardo F. Understanding drivers of phylogenetic clustering and terminal branch lengths distribution in epidemics of Mycobacterium tuberculosis. eLife 2022; 11:76780. [PMID: 35762734 PMCID: PMC9239681 DOI: 10.7554/elife.76780] [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] [Received: 01/04/2022] [Accepted: 06/15/2022] [Indexed: 11/13/2022] Open
Abstract
Detecting factors associated with transmission is important to understand disease epidemics, and to design effective public health measures. Clustering and terminal branch lengths (TBL) analyses are commonly applied to genomic data sets of Mycobacterium tuberculosis (MTB) to identify sub-populations with increased transmission. Here, I used a simulation-based approach to investigate what epidemiological processes influence the results of clustering and TBL analyses, and whether differences in transmission can be detected with these methods. I simulated MTB epidemics with different dynamics (latency, infectious period, transmission rate, basic reproductive number R0, sampling proportion, sampling period, and molecular clock), and found that all considered factors, except for the length of the infectious period, affect the results of clustering and TBL distributions. I show that standard interpretations of this type of analyses ignore two main caveats: (1) clustering results and TBL depend on many factors that have nothing to do with transmission, (2) clustering results and TBL do not tell anything about whether the epidemic is stable, growing, or shrinking, unless all the additional parameters that influence these metrics are known, or assumed identical between sub-populations. An important consequence is that the optimal SNP threshold for clustering depends on the epidemiological conditions, and that sub-populations with different epidemiological characteristics should not be analyzed with the same threshold. Finally, these results suggest that different clustering rates and TBL distributions, that are found consistently between different MTB lineages, are probably due to intrinsic bacterial factors, and do not indicate necessarily differences in transmission or evolutionary success.
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Affiliation(s)
- Fabrizio Menardo
- Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland
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14
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Oostvogels S, Ley SD, Heupink TH, Dippenaar A, Streicher EM, De Vos E, Meehan CJ, Dheda K, Warren R, Van Rie A. Transmission, distribution and drug resistance-conferring mutations of extensively drug-resistant tuberculosis in the Western Cape Province, South Africa. Microb Genom 2022; 8. [PMID: 35471145 PMCID: PMC9453078 DOI: 10.1099/mgen.0.000815] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Extensively drug-resistant tuberculosis (XDR-TB), defined as resistance to at least isoniazid (INH), rifampicin (RIF), a fluoroquinolone (FQ) and a second-line injectable drug (SLID), is difficult to treat and poses a major threat to TB control. The transmission dynamics and distribution of XDR Mycobacterium tuberculosis (Mtb) strains have not been thoroughly investigated. Using whole genome sequencing data on 461 XDR-Mtb strains, we aimed to investigate the geographical distribution of XDR-Mtb strains in the Western Cape Province of South Africa over a 10 year period (2006–2017) and assess the association between Mtb sub-lineage, age, gender, geographical patient location and membership or size of XDR-TB clusters. First, we identified transmission clusters by excluding drug resistance-conferring mutations and using the 5 SNP cutoff, followed by merging clusters based on their most recent common ancestor. We then consecutively included variants conferring resistance to INH, RIF, ethambutol (EMB), pyrazinamide (PZA), SLIDs and FQs in the cluster definition. Cluster sizes were classified as small (2–4 isolates), medium (5–20 isolates), large (21–100 isolates) or very large (>100 isolates) to reflect the success of individual strains. We found that most XDR-TB strains were clustered and that including variants conferring resistance to INH, RIF, EMB, PZA and SLIDs in the cluster definition did not significantly reduce the proportion of clustered isolates (85.5–82.2 %) but increased the number of patients belonging to small clusters (4.3–12.4 %, P=0.56). Inclusion of FQ resistance-conferring variants had the greatest effect, with 11 clustered isolates reclassified as unique while the number of clusters increased from 17 to 37. Lineage 2 strains (lineage 2.2.1 typical Beijing or lineage 2.2.2 atypical Beijing) showed the large clusters which were spread across all health districts of the Western Cape Province. We identified a significant association between residence in the Cape Town metropole and cluster membership (P=0.016) but no association between gender, age and cluster membership or cluster size (P=0.39). Our data suggest that the XDR-TB epidemic in South Africa probably has its origin in the endemic spread of MDR Mtb and pre-XDR Mtb strains followed by acquisition of FQ resistance, with more limited transmission of XDR Mtb strains. This only became apparent with the inclusion of drug resistance-conferring variants in the definition of a cluster. In addition to the prevention of amplification of resistance, rapid diagnosis of MDR, pre-XDR and XDR-TB and timely initiation of appropriate treatment is needed to reduce transmission of difficult-to-treat TB.
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Affiliation(s)
- Selien Oostvogels
- Family Medicine and Population Health (FAMPOP), Faculty of Medicine and Health Sciences, University of Antwerp, Antwerp, Belgium
- *Correspondence: Selien Oostvogels,
| | - Serej D. Ley
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, SAMRC Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Stellenbosch University, Cape Town, South Africa
- Present address: Sefunda AG, Muttenz, Switzerland
| | - Tim H. Heupink
- Family Medicine and Population Health (FAMPOP), Faculty of Medicine and Health Sciences, University of Antwerp, Antwerp, Belgium
| | - Anzaan Dippenaar
- Family Medicine and Population Health (FAMPOP), Faculty of Medicine and Health Sciences, University of Antwerp, Antwerp, Belgium
- Unit of Mycobacteriology, Institute of Tropical Medicine, Antwerp, Belgium
| | - Elizabeth M. Streicher
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, SAMRC Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Stellenbosch University, Cape Town, South Africa
| | - Elise De Vos
- Family Medicine and Population Health (FAMPOP), Faculty of Medicine and Health Sciences, University of Antwerp, Antwerp, Belgium
| | - Conor J. Meehan
- Unit of Mycobacteriology, Institute of Tropical Medicine, Antwerp, Belgium
- Department of Biosciences, Nottingham Trent University, Nottingham, UK
| | - Keertan Dheda
- Centre for Lung Infection and Immunity, Division of Pulmonology, Department of Medicine and UCT Lung Institute, South Africa
- South African MRC Centre for the Study of Antimicrobial Resistance, University of Cape Town, Cape Town, South Africa
- Faculty of Infectious and Tropical Diseases, Department of Infection Biology, London School of Hygiene and Tropical Medicine, London, UK
| | - Rob Warren
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, SAMRC Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Stellenbosch University, Cape Town, South Africa
| | - Annelies Van Rie
- Family Medicine and Population Health (FAMPOP), Faculty of Medicine and Health Sciences, University of Antwerp, Antwerp, Belgium
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15
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Drug-Resistant Characteristics, Genetic Diversity, and Transmission Dynamics of Rifampicin-Resistant Mycobacterium tuberculosis in Hunan, China, Revealed by Whole-Genome Sequencing. Microbiol Spectr 2022; 10:e0154321. [PMID: 35171016 PMCID: PMC8849054 DOI: 10.1128/spectrum.01543-21] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
To gain a deep insight into the additional drug-resistant profiles, genetic diversity, and transmission dynamics of rifampicin-resistant tuberculosis (RR-TB) circulating in Hunan province, drug susceptibility testing and whole-genome-sequencing were performed among RR-TB strains collected from Jan. 2013 to Jun. 2018 in Hunan province. A total of 124 RR-TB strains were recovered successfully and included into the final analysis. Lineage 2.2.1 was the dominant sublineage, accounting for 72.6% (90/124), followed by lineage 4.5 (11.3%, 14/124), lineage 4.4 (8.1%, 10/124), lineage 4.2 (6.5%, 8/124) and lineage 2.2.2 (1.6%, 2/124). Overall, 83.1% (103/124) and 3.2% (4/124) of RR-TB were MDR-TB and XDR-TB, respectively. Nearly 30% of RR-TB isolates were resistant to fluoroquinolones, and 26.6% (33/124) were pre-XDR-TB. Moreover, 30.6% (38/124) of RR-TB strains were identified as phenotypically resistance to pyrazinamide. Totally, 17 clusters containing 48 (38.7%, 48/124) RR-TB strains were identified, ranging in size from 2 to 10 isolates. No significant difference was detected in clustering rate between lineage 2 and lineage 4 (χ2 = 0.027, P = 0.870). Our study revealed the complexity of RR-TB strains circulating in Hunan province with complex additional drug-resistant profile and relatively higher clustering rates. Comprehensive information based on WGS should be used to guide the design of treatment regimens and tailor public interventions. IMPORTANCE Comprehensive information such as genetic background and drug-resistant profile of MTB strains could help to tailor public interventions. However, these data are limited in Hunan province, one of the provinces with high-TB burden in China. So, this study aimed to provide us with deep insight into the molecular epidemiology of RR-TB isolates circulating in Hunan province by combining phenotypic drug susceptibility testing and whole-genome sequencing. To our knowledge, this is the first study to use whole-genome sequencing data of RR-TB strains spanning more than 5 years for molecular epidemiology analysis in Hunan province, which allows us to identify genetic background information and clustered strains more accurately. Our study revealed the complexity of RR-TB strains circulating in Hunan province with complex additional drug-resistant profile and relatively higher clustering rates. Comprehensive information based on WGS should be used to guide the design of treatment regimens and tailor public interventions.
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16
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Shafipour M, Shirzad-Aski H, Ghaemi EA, Sohrabi A, Babaii Kochaksaraei M, Taziki M, Rahimi S, Ghazvini K, Baei B. Mycobacterium tuberculosis typing using Allele-specific oligonucleotide multiplex PCR (ASO-PCR) method. Curr Microbiol 2021; 78:4009-4013. [PMID: 34570276 DOI: 10.1007/s00284-021-02659-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Accepted: 09/07/2021] [Indexed: 11/29/2022]
Abstract
Mycobacterium tuberculosis (M. tuberculosis) genotyping provides valuable information related to the origin and the evolution of the isolates. This study aimed to evaluate the applicability of single-nucleotide polymorphisms (SNPs) technique for lineages identification of M. tuberculosis and compare it with mycobacterial interspersed repetitive units-variable number of tandem repeats (MIRU-VNTR) method. The lineages of 162 clinically isolates were evaluated using six pair primers by Multiplex-PCR based on SNPs. Among 162 isolates, 70 (43.2%) isolates were lineage 4, following that 62 (38.3%) and 22 (13.6%) isolates were lineage 3 and 2, respectively. The method could not type 8 (4.9%) isolates. Moreover, we could identify 71 out of 79 unknown isolates resulted from the MIRU-VNTR method. The results showed that the SNP typing method has the potential to determine the lineages of M. tuberculosis as a rapid laboratory screening test.
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Affiliation(s)
- Maryam Shafipour
- Infectious Diseases Research Center, Golestan University of Medical Sciences, 49178-67439, Gorgan, Iran.,Department of Pathobiology, Faculty of Veterinary Science, Bu-Ali Sina University, Hamedan, Iran
| | - Hesamaddin Shirzad-Aski
- Infectious Diseases Research Center, Golestan University of Medical Sciences, 49178-67439, Gorgan, Iran.
| | - Ezzat Allah Ghaemi
- Infectious Diseases Research Center, Golestan University of Medical Sciences, 49178-67439, Gorgan, Iran
| | - Ahmad Sohrabi
- Infectious Diseases Research Center, Golestan University of Medical Sciences, 49178-67439, Gorgan, Iran.,Cancer Control Research Center, Cancer Control Foundation, Iran University of Medical Sciences, Tehran, Iran
| | - Maya Babaii Kochaksaraei
- Infectious Diseases Research Center, Golestan University of Medical Sciences, 49178-67439, Gorgan, Iran
| | - Masoume Taziki
- Tuberculosis Laboratory of Health Care Center, Golestan University of Medical Sciences, Gorgan, Iran
| | - Somayeh Rahimi
- Tuberculosis Laboratory of Health Care Center, Golestan University of Medical Sciences, Gorgan, Iran
| | - Kiarash Ghazvini
- Department of Microbiology and Virology, School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Basireh Baei
- Infectious Diseases Research Center, Golestan University of Medical Sciences, 49178-67439, Gorgan, Iran
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17
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Evaluating the Frequency of Resistance to Pyrazinamide Among Drug-resistant Strains of Mycobacterium tuberculosis in Isfahan, Iran. ARCHIVES OF CLINICAL INFECTIOUS DISEASES 2021. [DOI: 10.5812/archcid.101092] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Background: Pyrazinamide is one of the most important first-line medications for the treatment of tuberculosis and an alternative intake for MDR-TB and XDR-TB patients. Objectives: The purpose of this study was to evaluate resistance to pyrazinamide in the isolates resistant to the Mycobacterium tuberculosis drug in patients in the city of Isfahan. Methods: In this study, the drug susceptibility test was performed with pyrazinamide using the proportion method and PZA assay on 47 isolates resistant to Mycobacterium tuberculosis. Then, the mutations of the pncA and rpsA genes of the isolates resistant to pyrazinamide were evaluated by the sequencing method. Results: According to the proportion method, 19 cases were resistant to pyrazinamide, 16 of which had mutations in their pncA and rpsA genes. Besides, five new mutations were recorded, and three isolates lacked mutations in the mentioned genes. Conclusions: Pyrazinamide resistance is high in MDR-TB and INH mono-resistant isolates. Therefore, evaluating the susceptibility to pyrazinamide in patients with MDR-TB before the initiation of treatment with pyrazinamide is considered essential.
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Norouzi F, Moghim S, Farzaneh S, Fazeli H, Salehi M, Nasr Esfahani B. Significance of the coexistence of non-codon 315 katG, inhA, and oxyR-ahpC intergenic gene mutations among isoniazid-resistant and multidrug-resistant isolates of Mycobacterium tuberculosis: a report of novel mutations. Pathog Glob Health 2021; 116:22-29. [PMID: 34086544 DOI: 10.1080/20477724.2021.1928870] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
Abstract
Tuberculosis (TB) is a global threat due to the emergence and spread of drug-resistant Mycobacterium tuberculosis (MTB). Isoniazid (INH) is the main antibiotic used for prevention and treatment of TB. Evidence shows that accumulated mutations can produce INH resistant (INHR) strains, resulting in the progression of multidrug-resistant (MDR) TB. Since point mutations in katG gene, inhA gene, and oxyR-ahpC region correlated with the INH resistance, in this study, we aimed to identify mutations in these three genes in INHR and MDR clinical isolates of MTB by Sanger DNA sequencing analysis. Thirty-three out of 438 isolates were resistant, including 66.7% INHR and 30.3% MDR isolates. In the katG gene, 68.2% INHR isolates had non-synonymous point mutations, mainly R463L (63.6%), and non-synonymous point mutation KatG L587P was seen in one of the MDR isolate. A novel silent substitution L649L was identified in the inhA gene of the MDR isolates. The oxyR-ahpC intergenic region g-88a common mutations (63.6%) in INHR and two distinct novel mutations were found at positions -76 and -77 of the oxyR-ahpC intergenic region. The coexistence of katG non-codon 315 with oxyR-ahpC intergenic region mutations was highly frequent in INHR 59.1% and MDR isolates 70%. Since mutations of all three genes 95.5% lead to the detection of INHR, they might be useful for molecular detection. Our results indicated the continuous evolution and region-specific prevalence of INH resistance. Overall, identification of new mutations in INH resistance can improve the available strategies for diagnosis and control of TB.
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Affiliation(s)
- Fatemeh Norouzi
- Department of Microbiology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Sharareh Moghim
- Department of Microbiology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - ShimaSadat Farzaneh
- Department of Microbiology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Hossein Fazeli
- Department of Microbiology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Mahshid Salehi
- Regional Tuberculosis Reference Laboratories in Isfahan, Isfahan, Iran
| | - Bahram Nasr Esfahani
- Department of Microbiology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
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19
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Cheng B, Behr MA, Howden BP, Cohen T, Lee RS. Reporting practices for genomic epidemiology of tuberculosis: a systematic review of the literature using STROME-ID guidelines as a benchmark. THE LANCET. MICROBE 2021; 2:e115-e129. [PMID: 33842904 PMCID: PMC8034592 DOI: 10.1016/s2666-5247(20)30201-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
BACKGROUND Pathogen genomics have become increasingly important in infectious disease epidemiology and public health. The Strengthening the Reporting of Molecular Epidemiology for Infectious Diseases (STROME-ID) guidelines were developed to outline a minimum set of criteria that should be reported in genomic epidemiology studies to facilitate assessment of study quality. We evaluate such reporting practices, using tuberculosis as an example. METHODS For this systematic review, we initially searched MEDLINE, Embase Classic, and Embase on May 3, 2017, using the search terms "tuberculosis" and "genom* sequencing". We updated this initial search on April 23, 2019, and also included a search of bioRxiv at this time. We included studies in English, French, or Spanish that recruited patients with microbiologically confirmed tuberculosis and used whole genome sequencing for typing of strains. Non-human studies, conference abstracts, and literature reviews were excluded. For each included study, the number and proportion of fulfilled STROME-ID criteria were recorded by two reviewers. A comparison of the mean proportion of fulfilled STROME-ID criteria before and after publication of the STROME-ID guidelines (in 2014) was done using a two-tailed t test. Quasi-Poisson regression and tobit regression were used to examine associations between study characteristics and the number and proportion of fulfilled STROME-ID criteria. This study was registered with PROSPERO, CRD42017064395. FINDINGS 976 titles and abstracts were identified by our primary search, with an additional 16 studies identified in bioRxiv. 114 full texts (published between 2009 and 2019) were eligible for inclusion. The mean proportion of STROME-ID criteria fulfilled was 50% (SD 12; range 16-75). The proportion of criteria fulfilled was similar before and after STROME-ID publication (51% [SD 11] vs 46% [14], p=0·26). The number of criteria reported (among those applicable to all studies) was not associated with impact factor, h-index, country of affiliation of senior author, or sample size of isolates. Similarly, the proportion of criteria fulfilled was not associated with these characteristics, with the exception of a sample size of isolates of 277 or more (the highest quartile). In terms of reproducibility, 100 (88%) studies reported which bioinformatic tools were used, but only 33 (33%) reported corresponding version numbers. Sequencing data were available for 86 (75%) studies. INTERPRETATION The reporting of STROME-ID criteria in genomic epidemiology studies of tuberculosis between 2009 and 2019 was low, with implications for assessment of study quality. The considerable proportion of studies without bioinformatics version numbers or sequencing data available highlights a key concern for reproducibility.
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Affiliation(s)
- Brianna Cheng
- Department of Epidemiology, Biostatistics and Occupational Health, McGill University, Montreal, QC, Canada
| | - Marcel A Behr
- Department of Epidemiology, Biostatistics and Occupational Health, McGill University, Montreal, QC, Canada
| | - Benjamin P Howden
- The Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | | | - Robyn S Lee
- Epidemiology Division, Dalla Lana School of Public Health, University of Toronto, Toronto, ON, Canada
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20
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Hadifar S, Fateh A, Pourbarkhordar V, Siadat SD, Mostafaei S, Vaziri F. Variation in Mycobacterium tuberculosis population structure in Iran: a systemic review and meta-analysis. BMC Infect Dis 2021; 21:2. [PMID: 33397308 PMCID: PMC7784266 DOI: 10.1186/s12879-020-05639-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Accepted: 11/19/2020] [Indexed: 01/30/2023] Open
Abstract
Background Acquiring comprehensive insight into the dynamics of Mycobacterium tuberculosis (Mtb) population structure is an essential step to adopt effective tuberculosis (TB) control strategies and improve therapeutic methods and vaccines. Accordingly, we performed this systematic review and meta-analysis to determine the overall prevalence of Mtb genotypes/ sublineages in Iran. Methods We carried out a comprehensive literature search using the international databases of MEDLINE and Scopus as well as Iranian databases. Articles published until April 2020 were selected based on the PRISMA flow diagram. The overall prevalence of the Mtb genotypes/sublineage in Iran was determined using the random effects or fixed effect model. The metafor R package and MedCalc software were employed for performing this meta-analysis. Results We identified 34 studies for inclusion in this study, containing 8329 clinical samples. Based on the pooled prevalence of the Mtb genotypes, NEW1 (21.94, 95% CI: 16.41–28.05%), CAS (19.21, 95% CI: 14.95–23.86%), EAI (12.95, 95% CI: 7.58–19.47%), and T (12.16, 95% CI: 9.18–15.50%) were characterized as the dominant circulating genotypes in Iran. West African (L 5/6), Cameroon, TUR and H37Rv were identified as genotypes with the lowest prevalence in Iran (< 2%). The highest pooled prevalence rates of multidrug-resistant strains were related to Beijing (2.52, 95% CI) and CAS (1.21, 95% CI). Conclusions This systematic review showed that Mtb populations are genetically diverse in Iran, and further studies are needed to gain a better insight into the national diversity of Mtb populations and their drug resistance pattern.
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Affiliation(s)
- Shima Hadifar
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran.,Microbiology Research Centre (MRC), Pasteur Institute of Iran, Tehran, Iran
| | - Abolfazl Fateh
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran.,Microbiology Research Centre (MRC), Pasteur Institute of Iran, Tehran, Iran
| | - Vahid Pourbarkhordar
- Department of Pharmacology and Toxicology, School of Pharmacy and Pharmaceutical Science, Isfahan University of Medical Science, Isfahan, Iran
| | - Seyed Davar Siadat
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran.,Microbiology Research Centre (MRC), Pasteur Institute of Iran, Tehran, Iran
| | - Shayan Mostafaei
- Department of Biostatistics, School of Health, Kermanshah University of Medical Sciences, Kermanshah, Iran. .,Epidemiology and Biostatistics Unit, Rheumatology Research Centre, Tehran University of Medical Sciences, Tehran, Iran.
| | - Farzam Vaziri
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran. .,Microbiology Research Centre (MRC), Pasteur Institute of Iran, Tehran, Iran.
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21
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Keikha M. There is significant relationship between Beijing genotype family strains and resistance to the first-line anti-tuberculosis drugs in the Iranian population. J Clin Tuberc Other Mycobact Dis 2020; 19:100161. [PMID: 32368621 PMCID: PMC7186555 DOI: 10.1016/j.jctube.2020.100161] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Affiliation(s)
- Masoud Keikha
- Antimicrobial Resistance Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
- Department of Microbiology and Virology, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
- Student Research Committee, Mashhad University of Medical Sciences, Mashhad, Iran
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22
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Kargarpour Kamakoli M, Farmanfarmaei G, Masoumi M, Khanipour S, Gharibzadeh S, Sola C, Fateh A, Siadat SD, Refregier G, Vaziri F. Prediction of the hidden genotype of mixed infection strains in Iranian tuberculosis patients. Int J Infect Dis 2020; 95:22-27. [PMID: 32251801 DOI: 10.1016/j.ijid.2020.03.056] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2020] [Revised: 03/19/2020] [Accepted: 03/24/2020] [Indexed: 01/06/2023] Open
Abstract
BACKGROUND Patients with mixed-strain Mycobacterium tuberculosis infections may be at a high risk of poor treatment outcomes. However, the mechanisms through which mixed infections affect the clinical manifestations are not well recognized. Evidence suggests that failure to detect the pathogen diversity within the host can influence the clinical results. We aimed to investigate the effects of different genotypes in mixed infections and determine their relationship with heteroresistance in the treatment of Iranian tuberculosis patients. METHODS One of the genotypes was identified in the culture and another genotype pattern in the mixed infection was predicted by comparing the pattern of MIRU-VNTR between the clinical specimens and their respective cultures in each patient. For all patients, the drug susceptibility testing was carried out on three single colonies from each clinical sample. The follow-up of patients was carried out during six months of treatment. RESULTS Based on MIRU-VNTR profiles of clinical samples, we showed that 55.6% (25/45) of the Iranian patients included in the study had mixed infections. Patients with mixed infections had a higher rate of treatment failure, compared to others (P=0.03). By comparing clinical sample profiles to profiles obtained after culture, we were able to distinguish between major and hidden genotypes. Among hidden genotypes, Haarlem (L4.1.2) and Beijing (L2) were associated to treatment failure (6/8 patients). CONCLUSIONS To conclude, we propose a procedure using the MIRU-VNTR method to identify the different genotypes in mixed infections. The present findings suggest that genotypes with potentially higher pathogenicity may not be detected when performing experimental culture in patients with mixed infections.
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Affiliation(s)
- Mansour Kargarpour Kamakoli
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran; Microbiology Research Center (MRC), Pasteur Institute of Iran, Tehran, Iran
| | - Ghazaleh Farmanfarmaei
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran; Microbiology Research Center (MRC), Pasteur Institute of Iran, Tehran, Iran
| | - Morteza Masoumi
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran; Microbiology Research Center (MRC), Pasteur Institute of Iran, Tehran, Iran
| | - Sharareh Khanipour
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran; Microbiology Research Center (MRC), Pasteur Institute of Iran, Tehran, Iran
| | - Safoora Gharibzadeh
- Department of Epidemiology and Biostatistics, Research Center for Emerging and Reemerging Infectious Diseases, Pasteur Institute of Iran, Tehran, Iran
| | - Christophe Sola
- Institut for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris Sud, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Abolfazl Fateh
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran; Microbiology Research Center (MRC), Pasteur Institute of Iran, Tehran, Iran
| | - Seyed Davar Siadat
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran; Microbiology Research Center (MRC), Pasteur Institute of Iran, Tehran, Iran
| | - Guislaine Refregier
- Institut for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris Sud, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Farzam Vaziri
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran; Microbiology Research Center (MRC), Pasteur Institute of Iran, Tehran, Iran.
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23
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Ghajavand H, Kargarpour Kamakoli M, Khanipour S, Pourazar Dizaji S, Masoumi M, Rahimi Jamnani F, Fateh A, Yaseri M, Siadat SD, Vaziri F. Scrutinizing the drug resistance mechanism of multi- and extensively-drug resistant Mycobacterium tuberculosis: mutations versus efflux pumps. Antimicrob Resist Infect Control 2019; 8:70. [PMID: 31073401 PMCID: PMC6498538 DOI: 10.1186/s13756-019-0516-4] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Accepted: 03/29/2019] [Indexed: 02/03/2023] Open
Abstract
Background In order to shorten the course of treatment and its effectiveness, it is essential to gain an in-depth insight into the drug resistance mechanisms of Mycobacterium tuberculosis (M. tuberculosis). Methods In this study, we evaluated the contribution of 26 drug efflux pumps plus target gene mutations to the drug resistance levels in multi-drug resistant (MDR)/pre-extensively drug-resistant (pre-XDR)/extensively drug-resistant (XDR) and mono-drug resistant clinical isolates of M. tuberculosis. The panels of 25 M. tuberculosis clinical strains were characterized for drug resistance-associated mutations with whole-genome sequencing and antibiotic profiles in the presence and absence of efflux inhibitor verapamil (VP). Results Different MICs were observed for the same target gene mutations. Out of the 16 MDR/pre-XDR/XDR isolates, 6 (37.5%) and 3 (18.8%) isolates demonstrated a significant decrease in rifampicin (RIF) MIC and isoniazid (INH) MIC due to the VP exposure (64 μg/mL), respectively. Susceptibility to RIF was fully restored in two isolates after VP exposure. Moreover, the efflux pump genes of Rv2938, Rv2936, Rv1145, Rv1146, Rv933, Rv1250, Rv876, Rv2333, Rv2459, Rv849, and Rv1819 were overexpressed in the presence of anti-TB drugs, showing the contribution of these efflux pumps to the overall resistance phenotype. Conclusions Our results clearly showed that efflux systems, besides spontaneous mutations, play a role in the development of INH/RIF resistance. In addition, although VP was effective in reducing the expression of some efflux pumps, it was not very successful at the phenotypic level.
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Affiliation(s)
- Hasan Ghajavand
- 1Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran.,2Microbiology Research Center (MRC), Pasteur Institute of Iran, No. 358, 12th Farvardin Ave, Jomhoori St, Tehran, 1316943551 Iran
| | - Mansour Kargarpour Kamakoli
- 1Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran.,2Microbiology Research Center (MRC), Pasteur Institute of Iran, No. 358, 12th Farvardin Ave, Jomhoori St, Tehran, 1316943551 Iran
| | - Sharareh Khanipour
- 1Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran.,2Microbiology Research Center (MRC), Pasteur Institute of Iran, No. 358, 12th Farvardin Ave, Jomhoori St, Tehran, 1316943551 Iran
| | - Shahin Pourazar Dizaji
- 1Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran.,2Microbiology Research Center (MRC), Pasteur Institute of Iran, No. 358, 12th Farvardin Ave, Jomhoori St, Tehran, 1316943551 Iran
| | - Morteza Masoumi
- 1Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran.,2Microbiology Research Center (MRC), Pasteur Institute of Iran, No. 358, 12th Farvardin Ave, Jomhoori St, Tehran, 1316943551 Iran
| | - Fatemeh Rahimi Jamnani
- 1Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran.,2Microbiology Research Center (MRC), Pasteur Institute of Iran, No. 358, 12th Farvardin Ave, Jomhoori St, Tehran, 1316943551 Iran
| | - Abolfazl Fateh
- 1Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran.,2Microbiology Research Center (MRC), Pasteur Institute of Iran, No. 358, 12th Farvardin Ave, Jomhoori St, Tehran, 1316943551 Iran
| | - Mehdi Yaseri
- 3Department of Epidemiology and Biostatistics, Tehran University of Medical Sciences, Tehran, Iran
| | - Seyed Davar Siadat
- 1Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran.,2Microbiology Research Center (MRC), Pasteur Institute of Iran, No. 358, 12th Farvardin Ave, Jomhoori St, Tehran, 1316943551 Iran
| | - Farzam Vaziri
- 1Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran.,2Microbiology Research Center (MRC), Pasteur Institute of Iran, No. 358, 12th Farvardin Ave, Jomhoori St, Tehran, 1316943551 Iran
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24
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High Prevalence of Bedaquiline Resistance in Treatment-Naive Tuberculosis Patients and Verapamil Effectiveness. Antimicrob Agents Chemother 2019; 63:AAC.02530-18. [PMID: 30602521 DOI: 10.1128/aac.02530-18] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Accepted: 12/15/2018] [Indexed: 11/20/2022] Open
Abstract
In the regions where bedaquiline (BDQ) is introduced into the regimen, analysis of MIC and screening for preexisting resistance mutations could be crucial. The high prevalence of isolates with high BDQ MICs without prior exposure to BDQ was worrisome. It was also concluded that efflux pumps play a pivotal role in intrinsic BDQ resistance; therefore, the potential of verapamil as an adjunctive therapy to combat BDQ resistance should be investigated.
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25
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Ravan P, Nejad Sattari T, Siadat SD, Vaziri F. Evaluation of the expression of cytokines and chemokines in macrophages in response to rifampin-monoresistant Mycobacterium tuberculosis and H37Rv strain. Cytokine 2018; 115:127-134. [PMID: 30594437 DOI: 10.1016/j.cyto.2018.12.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2018] [Revised: 11/17/2018] [Accepted: 12/02/2018] [Indexed: 01/02/2023]
Abstract
Macrophages are the primary phagocytes in the lungs and a part of the host defense system against Mycobacterium tuberculosis (Mtb), involved in the primary immune response. While several studies have assessed the effects of resistance to rifampin on Mtb physiology, the consequences of mutations in genes encoding the beta subunit of RNA polymerase (rpoB) for host-pathogen interactions remain poorly understood. In this study, rifampin-monoresistant (RMR) Mtb and H37Rv strains were used to infect the THP-1-derived macrophages. Real-time quantitative reverse transcription PCR assay was carried out to determine mRNA expression in 84 cytokine and chemokine genes. Production of specific cytokines and chemokines was measured by ELISA assay. In conclusion, the current study shed more light on the fitness cost of RMR strain and the potential effects of rpoB gene mutations on Mtb-host interactions. These results initially demonstrate that the Mtb carrying the rpoB-S450L can modulate macrophage responses to mediate bacterial survival.
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Affiliation(s)
- Parvaneh Ravan
- Department of Biology, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | - Taher Nejad Sattari
- Department of Biology, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | - Seyed Davar Siadat
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran; Microbiology Research Center (MRC), Pasteur Institute of Iran, Tehran, Iran
| | - Farzam Vaziri
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran; Microbiology Research Center (MRC), Pasteur Institute of Iran, Tehran, Iran.
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