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Zhao J, Qian C, Jiang Y, He W, Wu W. Drug-Resistant Characteristics, Genetic Diversity, and Transmission Dynamics of Multidrug-Resistant Mycobacterium tuberculosis in Jiangxi, China. Infect Drug Resist 2024; 17:2213-2223. [PMID: 38840971 PMCID: PMC11152055 DOI: 10.2147/idr.s460267] [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: 01/18/2024] [Accepted: 05/21/2024] [Indexed: 06/07/2024] Open
Abstract
Purpose In this study, we aimed to determine the transmission pattern of multidrug-resistant tuberculosis (MDR-TB) isolates circulating in Jiangxi Province with whole-genome sequencing (WGS). In addition, we also sought to describe mutational resistome of MDR-TB isolates. Patients and Methods A total of 115 MDR-TB isolates determined by the phenotypic proportion method of drug susceptibility testing between January 2018 and December 2022 from provincial drug surveillance (DRS) in Jiangxi were included in our analysis. The demographic data and treatment history were extracted from the National TB Registry System. WGS was used to analyze the genotypic characteristics of drug resistance and transmissions. Results About 62.6% of MDR-TB strains were isolated from cases that received previous anti-tuberculosis treatment. According to the WGS results, 96.5% were genotypic MDR-TB, and more than half of MDR-TB isolates tested were also resistant to streptomycin (59.1%), ethambutol (56.5%), and fluroquinolones (53.0%), while resistance to cycloserine and linezolid was lowest, only in two (1.7%) and one (0.9%) isolate, respectively. Ser450Leu in rpoB (57.9%), Ser315Thr in katG (74.1%), Met306Val in embB (40.0%), Lys43Arg in rpsL (75.0%), Ala90Val in gyrA (32.8%) were predominant mutant types among the rifampin-, isoniazid-, ethambutol-, streptomycin-, fluoroquinolones-resistant isolates, respectively. Lineage 2 (East Asian genotype) occurred at the highest frequency with 97 cases (84.3%), followed by lineage 4 (Euro-American genotype) with 18 cases (15.7%). Additionally, 5 clusters consisting of 10 isolates were identified in the present study, demonstrating a clustering rate of 8.7%. Conclusion MDR/Rifampicin-Resistant (RR)-TB epidemic in this region is driven by lineage 2 clade that also show higher resistance to other anti-tuberculosis drugs. Lower cluster rates compared with a relatively higher proportion of new MDR-TB cases indicate that a considerable number of MDR-TB cases remain undiagnosed.
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Affiliation(s)
- Jingnan Zhao
- Tuberculosis Control Department, Jiangxi Provincial Center for Disease Control and Prevention, Nanchang, 330029, People’s Republic of China
| | - Chengyu Qian
- Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing Chest Hospital, Capital Medical University, Beijing, 101149, People’s Republic of China
| | - Youqiao Jiang
- Tuberculosis Control Department, Jiangxi Provincial Center for Disease Control and Prevention, Nanchang, 330029, People’s Republic of China
- Young Scientific Research and Innovation Team, Jiangxi Provincial Center for Disease Control and Prevention, Nanchang, Jiangxi, 330029, People’s Republic of China
| | - Wangrui He
- Tuberculosis Control Department, Jiangxi Provincial Center for Disease Control and Prevention, Nanchang, 330029, People’s Republic of China
| | - Wenhua Wu
- Tuberculosis Control Department, Jiangxi Provincial Center for Disease Control and Prevention, Nanchang, 330029, People’s Republic of China
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Valencia-Trujillo D, Avila-Trejo AM, García-Reyes RL, Narváez-Díaz L, Segura del Pilar M, Mújica-Sánchez MA, Becerril-Vargas E, León-Juárez M, Mata-Miranda MM, Rivera-Gutiérrez S, Cerna-Cortés JF. Genetic Diversity of Mycobacterium tuberculosis Strains Isolated from HIV-Infected Patients in Mexico. Pathogens 2024; 13:428. [PMID: 38787280 PMCID: PMC11124049 DOI: 10.3390/pathogens13050428] [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: 04/19/2024] [Revised: 05/14/2024] [Accepted: 05/17/2024] [Indexed: 05/25/2024] Open
Abstract
There has been very limited investigation regarding the genetic diversity of Mycobacterium tuberculosis (MTb) strains isolated from human immunodeficiency virus (HIV)-infected patients in Mexico. In this study, we isolated 93 MTb strains from pulmonary and extrapulmonary samples of HIV-infected patients treated in a public hospital in Mexico City to evaluate the genetic diversity using spoligotyping and mycobacterial interspersed repetitive unit-variable-number tandem-repeat (MIRU-VNTR) typing (based on 24 loci). The cohort comprised 80 male and 13 female individuals. There was a positive correlation between a high HIV viral load (>100,000 copies) and extrapulmonary tuberculosis (TB) (r = 0.306, p = 0.008). Lineage 4 was the most frequent lineage (79 strains). In this lineage, we found the H clade (n = 24), including the Haarlem, H3, and H1 families; the T clade (n = 22), including T1 and T2; the X clade (n = 15), including X1 and X3; the LAM clade (n = 14), including LAM1, LAM2, LAM3, LAM6, and LAM9; the S clade (n = 2); Uganda (n = 1); and Ghana (n = 1). We also found 12 strains in the EAI clade belonging to lineage 1, including the EAI2-Manila and EAI5 families. Interestingly, we identified one strain belonging to the Beijing family, which is part of lineage 2. One strain could not be identified. This study reports high genetic diversity among MTb strains, highlighting the need for a molecular epidemiological surveillance system that can help to monitor the spread of these strains, leading to more appropriate measures for TB control in HIV-infected patients.
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Affiliation(s)
- Daniel Valencia-Trujillo
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Ciudad de México 11340, Mexico; (D.V.-T.); (R.L.G.-R.); (S.R.-G.)
- Servicio de Microbiología Clínica, Instituto Nacional de Enfermedades Respiratorias, Ciudad de México 14080, Mexico; (L.N.-D.); (M.S.d.P.); (M.A.M.-S.); (E.B.-V.)
- Escuela Militar de Medicina, Centro Militar de Ciencias de la Salud, Secretaría de la Defensa Nacional, Ciudad de México 11200, Mexico; (A.M.A.-T.); (M.M.M.-M.)
| | - Amanda Marineth Avila-Trejo
- Escuela Militar de Medicina, Centro Militar de Ciencias de la Salud, Secretaría de la Defensa Nacional, Ciudad de México 11200, Mexico; (A.M.A.-T.); (M.M.M.-M.)
| | - Rocío Liliana García-Reyes
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Ciudad de México 11340, Mexico; (D.V.-T.); (R.L.G.-R.); (S.R.-G.)
| | - Luis Narváez-Díaz
- Servicio de Microbiología Clínica, Instituto Nacional de Enfermedades Respiratorias, Ciudad de México 14080, Mexico; (L.N.-D.); (M.S.d.P.); (M.A.M.-S.); (E.B.-V.)
| | - Mariela Segura del Pilar
- Servicio de Microbiología Clínica, Instituto Nacional de Enfermedades Respiratorias, Ciudad de México 14080, Mexico; (L.N.-D.); (M.S.d.P.); (M.A.M.-S.); (E.B.-V.)
| | - Mario Alberto Mújica-Sánchez
- Servicio de Microbiología Clínica, Instituto Nacional de Enfermedades Respiratorias, Ciudad de México 14080, Mexico; (L.N.-D.); (M.S.d.P.); (M.A.M.-S.); (E.B.-V.)
| | - Eduardo Becerril-Vargas
- Servicio de Microbiología Clínica, Instituto Nacional de Enfermedades Respiratorias, Ciudad de México 14080, Mexico; (L.N.-D.); (M.S.d.P.); (M.A.M.-S.); (E.B.-V.)
| | - Moises León-Juárez
- Departamento de Inmunobioquímica, Instituto Nacional de Perinatología Isidro Espinosa de los Reyes, Ciudad de México 11000, Mexico;
| | - Mónica Maribel Mata-Miranda
- Escuela Militar de Medicina, Centro Militar de Ciencias de la Salud, Secretaría de la Defensa Nacional, Ciudad de México 11200, Mexico; (A.M.A.-T.); (M.M.M.-M.)
| | - Sandra Rivera-Gutiérrez
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Ciudad de México 11340, Mexico; (D.V.-T.); (R.L.G.-R.); (S.R.-G.)
| | - Jorge Francisco Cerna-Cortés
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Ciudad de México 11340, Mexico; (D.V.-T.); (R.L.G.-R.); (S.R.-G.)
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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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Castro-Rodriguez B, Franco-Sotomayor G, Benitez-Medina JM, Cardenas-Franco G, Jiménez-Pizarro N, Cardenas-Franco C, Aguirre-Martinez JL, Orlando SA, Hermoso de Mendoza J, Garcia-Bereguiain MA. Prevalence, drug resistance, and genotypic diversity of the RD Rio subfamily of Mycobacterium tuberculosis in Ecuador: a retrospective analysis for years 2012-2016. Front Public Health 2024; 12:1337357. [PMID: 38689770 PMCID: PMC11060180 DOI: 10.3389/fpubh.2024.1337357] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2023] [Accepted: 03/15/2024] [Indexed: 05/02/2024] Open
Abstract
Introduction A major sublineage within the Mycobacterium tuberculosis (MTB) LAM family characterized by a new in-frame fusion gene Rv3346c/55c was discovered in Rio de Janeiro (Brazil) in 2007, called RDRio, associated to drug resistance. The few studies about prevalence of MTB RDRio strains in Latin America reported values ranging from 3% in Chile to 69.8% in Venezuela, although no information is available for countries like Ecuador. Methods A total of 814 MTB isolates from years 2012 to 2016 were screened by multiplex PCR for RDRio identification, followed by 24-loci MIRU-VNTR and spoligotyping. Results A total number of 17 MTB RDRio strains were identified, representing an overall prevalence of 2.09% among MTB strains in Ecuador. While 10.9% of the MTB isolates included in the study were multidrug resistance (MDR), 29.4% (5/17) of the RDRio strains were MDR. Discussion This is the first report of the prevalence of MTB RDRio in Ecuador, where a strong association with MDR was found, but also a very low prevalence compared to other countries in Latin America. It is important to improve molecular epidemiology tools as a part of MTB surveillance programs in Latin America to track the transmission of potentially dangerous MTB stains associated to MDR TB like MTB RDRio.
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Affiliation(s)
| | - Greta Franco-Sotomayor
- Instituto Nacional de Investigación en Salud Pública “Leopoldo Izquieta Pérez”, Guayaquil, Ecuador
- Universidad Católica Santiago de Guayaquil, Guayaquil, Ecuador
| | | | | | - Natalia Jiménez-Pizarro
- Departamento de Sanidad Animal, Facultad de Veterinaria, Universidad de Extremadura, Cáceres, Spain
| | | | | | - Solon Alberto Orlando
- Instituto Nacional de Investigación en Salud Pública “Leopoldo Izquieta Pérez”, Guayaquil, Ecuador
- Universidad Espiritu Santo, Guayaquil, Ecuador
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Castro-Rodriguez B, Franco-Sotomayor G, Rodriguez-Pazmiño ÁS, Cardenas-Franco GE, Orlando SA, Hermoso de Mendoza J, Parra-Vera H, García-Bereguiain MÁ. Rapid and accurate identification and differentiation of Mycobacterium tuberculosis and non-tuberculous mycobacteria using PCR kits available in a high-burden setting. Front Public Health 2024; 12:1358261. [PMID: 38628855 PMCID: PMC11018931 DOI: 10.3389/fpubh.2024.1358261] [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: 12/19/2023] [Accepted: 03/04/2024] [Indexed: 04/19/2024] Open
Abstract
Infections caused by mycobacteria, including Mycobacterium tuberculosis complex (MTBC) and non-tuberculous mycobacteria (NTM), are a major public health issue worldwide. An accurate diagnosis of mycobacterial species is a challenge for surveillance and treatment, particularly in high-burden settings usually associated with low- and middle-income countries. In this study, we analyzed the clinical performance of two commercial PCR kits designed for the identification and differentiation of MTBC and NTM, available in a high-burden setting such as Ecuador. A total of 109 mycobacteria isolates were included in the study, 59 of which were previously characterized as M. tuberculosis and the other 59 as NTM. Both kits displayed great clinical performance for the identification of M. tuberculosis, with 100% sensitivity. On the other hand, for NTM, one of the kits displayed a good clinical performance with a sensitivity of 94.9% (CI 95%: 89-100%), while the second kit had a reduced sensitivity of 77.1% (CI 95%: 65-89%). In conclusion, one of the kits is a fast and reliable tool for the identification and discrimination of MTBC and NTM from clinical isolates.
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Affiliation(s)
| | - Greta Franco-Sotomayor
- Instituto Nacional de Investigación en Salud Pública "Leopoldo Izquieta Pérez", Guayaquil, Ecuador
- Universidad Católica Santiago de Guayaquil, Guayaquil, Ecuador
| | | | | | - Solón Alberto Orlando
- Instituto Nacional de Investigación en Salud Pública "Leopoldo Izquieta Pérez", Guayaquil, Ecuador
- Universidad Espíritu Santo, Samborondón, Ecuador
| | | | - Henry Parra-Vera
- Centro de Investigación Microbiológica (CIM), Guayaquil, Ecuador
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Rudeeaneksin J, Bunchoo S, Phetsuksiri B, Srisungngam S, Khummin R, Thapa J, Nakajima C, Suzuki Y. The first insight into Mycobacterium tuberculosis complex isolates in the lower northern region in Thailand. Trans R Soc Trop Med Hyg 2024:trae014. [PMID: 38554067 DOI: 10.1093/trstmh/trae014] [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: 11/19/2023] [Revised: 01/21/2024] [Accepted: 02/29/2024] [Indexed: 04/01/2024] Open
Abstract
BACKGROUND Tuberculosis (TB) remains an important infectious disease and different genotypes have been reported. This study aimed to investigate the genetic diversity and molecular epidemiology of TB in the lower northern region of Thailand, where genotyping data are limited. METHODS A total of 159 Mycobacterium tuberculosis complex (MTBC) isolates from this region were genotyped by spoligotyping and the major spoligotypes were further subdivided by the mycobacterial interspersed repetitive unit-variable number tandem repeat (MIRU-VNTR) method. RESULTS Spoligotyping identified 34 types and classified them into 14 clusters. East African-Indian (EAI) groups were the most frequent (44.7%), followed by Beijing (36.5%), with a higher prevalence of drug resistance. By 15-loci MIRU-VNTR typing, the major groups of the Beijing and EAI2_NTB were further differentiated into 44 and 21 subtypes forming 9 and 5 subclusters with cluster rates of 0.26 and 0.44, respectively. The Hunter-Gaston Discriminatory Index among the Beijing and EAI2_NTB groups were 0.987 and 0.931, respectively, indicating high diversity. CONCLUSIONS This is the first look at the MTBC genotypes in the lower northern region of Thailand, which could aid in understanding the distribution and potential spread of MTBC and Mycobacterium bovis in the target region to support TB control in Thailand.
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Affiliation(s)
- Janisara Rudeeaneksin
- National Institute of Health, Department of Medical Sciences, Ministry of Public Health, Nonthaburi 11000, Thailand
| | - Supranee Bunchoo
- National Institute of Health, Department of Medical Sciences, Ministry of Public Health, Nonthaburi 11000, Thailand
| | - Benjawan Phetsuksiri
- National Institute of Health, Department of Medical Sciences, Ministry of Public Health, Nonthaburi 11000, Thailand
- Medical Sciences Technical Office, Department of Medical Sciences, Ministry of Public Health, Nonthaburi 11000, Thailand
| | - Sopa Srisungngam
- National Institute of Health, Department of Medical Sciences, Ministry of Public Health, Nonthaburi 11000, Thailand
| | - Ratchaneeporn Khummin
- Office of Disease Prevention and Control Region 2 Phitsanulok, Department of Disease Control, Ministry of Public Health, Phitsanulok 65000, Thailand
| | - Jeewan Thapa
- Division of Bioresources, Hokkaido University International Institute for Zoonosis Control, Sapporo, Japan
| | - Chie Nakajima
- Division of Bioresources, Hokkaido University International Institute for Zoonosis Control, Sapporo, Japan
- International Collaboration Unit, Hokkaido University International Institute for Zoonosis Control, Sapporo, Japan
| | - Yasuhiko Suzuki
- Division of Bioresources, Hokkaido University International Institute for Zoonosis Control, Sapporo, Japan
- International Collaboration Unit, Hokkaido University International Institute for Zoonosis Control, Sapporo, Japan
- Hokkaido University Institute for Vaccine Research and Development, Sapporo, Japan
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Castro-Rodriguez B, León-Ordóñez K, Franco-Sotomayor G, Benítez-Medina JM, Jiménez-Pizarro N, Cárdenas-Franco G, Granda JC, Aguirre-Martínez JL, Orlando SA, Hermoso de Mendoza J, García-Bereguiain MÁ. Population structure of Mycobacterium tuberculosis in El Oro: A first insight into Ecuador-Peru tuberculosis transmission. J Infect Public Health 2024; 17:527-534. [PMID: 38310744 DOI: 10.1016/j.jiph.2024.01.015] [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: 11/13/2023] [Revised: 01/17/2024] [Accepted: 01/22/2024] [Indexed: 02/06/2024] Open
Abstract
BACKGROUND Tuberculosis (TB) is a major public health concern in Ecuador and Peru, both settings of high burden of drug resistance TB. Molecular epidemiology tools are important to understand the transmission dynamics of Mycobacterium tuberculosis Complex (MTBC) and to track active transmission clusters of regional importance. This study is the first to address the transmission of TB between Peru and Ecuador through the population structure of MTBC lineages circulating in the Ecuadorian border province of "El Oro". METHODS A total number of 56 MTBC strains from this province for years 2012-2015 were included in the study and analyzed by 24-loci MIRU-VNTR and spoligotyping. RESULTS Genotyping revealed a high degree of diversity for MTBC in "El Oro", without active transmission clusters. MTBC L4 was predominant, with less than 2% of strains belonging to MTBC L2-Beijing. CONCLUSIONS These results may suggest that TB dynamics in this rural and semi-urban area would not be linked to highly transmitted strains like MTBC L2-Beijing from Peru, but related to TB relapse; although further studies with larger MTBC cultures collection from recent years are needed. Nevertheless, we recommend to reinforce TB surveillance programs in remote rural settings and border regions in Ecuador.
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Affiliation(s)
| | - Kerly León-Ordóñez
- One Health Research Group. Universidad de las Américas, Quito, Ecuador; Yachay Tech University, Urcuquí, Ecuador
| | - Greta Franco-Sotomayor
- Instituto Nacional de Investigación en Salud Pública "Leopoldo Izquieta Pérez", Guayaquil, Ecuador; Universidad Católica Santiago de Guayaquil, Guayaquil, Ecuador
| | | | - Natalia Jiménez-Pizarro
- Departamento de Sanidad Animal. Facultad de Veterinaria, Universidad de Extremadura, Cáceres, Spain
| | | | - Juan Carlos Granda
- Instituto Nacional de Investigación en Salud Pública "Leopoldo Izquieta Pérez", Guayaquil, Ecuador
| | | | - Solon Alberto Orlando
- Instituto Nacional de Investigación en Salud Pública "Leopoldo Izquieta Pérez", Guayaquil, Ecuador; Universidad Espíritu Santo, Guayaquil, Ecuador
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Castro-Rodriguez B, Espinoza-Andrade S, Franco-Sotomayor G, Benítez-Medina JM, Jiménez-Pizarro N, Cárdenas-Franco C, Granda JC, Jouvin JL, Orlando SA, Hermoso de Mendoza J, García-Bereguiain MÁ. A first insight into tuberculosis transmission at the border of Ecuador and Colombia: a retrospective study of the population structure of Mycobacterium tuberculosis in Esmeraldas province. Front Public Health 2024; 12:1343350. [PMID: 38384875 PMCID: PMC10879341 DOI: 10.3389/fpubh.2024.1343350] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Accepted: 01/18/2024] [Indexed: 02/23/2024] Open
Abstract
Objective Tuberculosis (TB) is a major public health concern in Ecuador and Colombia, considering that both countries are high-burden TB settings. Molecular epidemiology is crucial to understand the transmission dynamics of Mycobacterium tuberculosis complex (MTBC) and to identify active transmission clusters of regional importance. Methods We studied the potential transmission of TB between Colombia and Ecuador through the analysis of the population structure of MTBC lineages circulating in the Ecuadorian province of Esmeraldas at the border with Colombia. A total of 105 MTBC strains were characterized by 24-loci MIRU-VNTR and spoligotyping. Results MTBC lineage 4 is only present in Esmeraldas; no MTBC strains belonging to Lineage 2-sublineage Beijing were found despite its presence in other provinces of Ecuador and, in Colombia. Genotyping results revealed a high degree of diversity for MTBC in Esmeraldas: Neither active transmission clusters within this province nor including MTBC strains from Colombia or other provinces of Ecuador were found. Conclusion Our data suggest that tuberculosis dynamics in this rural and isolated area may be not related to highly transmitted strains but could be influenced by other health determinants that favor TB relapse such as poverty and poor health system access. Further studies including a larger number of MTBC strains from Esmeraldas are necessary to test this hypothesis.
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Affiliation(s)
| | | | - Greta Franco-Sotomayor
- Instituto Nacional de Investigación en Salud Pública “Leopoldo Izquieta Pérez”, Guayaquil, Ecuador
- Facultad de Medicina, Universidad Católica Santiago de Guayaquil, Guayaquil, Ecuador
| | - José Manuel Benítez-Medina
- Departamento de Patología Infecciosa, Facultad de Veterinaria, Universidad de Extremadura, Cáceres, Spain
| | - Natalia Jiménez-Pizarro
- Departamento de Patología Infecciosa, Facultad de Veterinaria, Universidad de Extremadura, Cáceres, Spain
| | | | - Juan Carlos Granda
- Instituto Nacional de Investigación en Salud Pública “Leopoldo Izquieta Pérez”, Guayaquil, Ecuador
| | - Jose Luis Jouvin
- Facultad de Medicina, Universidad Católica Santiago de Guayaquil, Guayaquil, Ecuador
| | - Solon Alberto Orlando
- Instituto Nacional de Investigación en Salud Pública “Leopoldo Izquieta Pérez”, Guayaquil, Ecuador
- Universidad Espíritu Santo, Guayaquil, Ecuador
| | - Javier Hermoso de Mendoza
- Departamento de Patología Infecciosa, Facultad de Veterinaria, Universidad de Extremadura, Cáceres, Spain
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Liu B, Su P, Hu P, Yan M, Li W, Yi S, Chen Z, Zhang X, Guo J, Wan X, Wang J, Gong D, Bai H, Wan K, Liu H, Li G, Tan Y. Prevalence, Transmission and Genetic Diversity of Pyrazinamide Resistance Among Multidrug-Resistant Mycobacterium tuberculosis Isolates in Hunan, China. Infect Drug Resist 2024; 17:403-416. [PMID: 38328339 PMCID: PMC10849141 DOI: 10.2147/idr.s436161] [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: 09/14/2023] [Accepted: 01/15/2024] [Indexed: 02/09/2024] Open
Abstract
Background China is a country with a burden of high rates of both TB and multidrug-resistant TB (MDR-TB). However, published data on pyrazinamide (PZA) resistance are still limited in Hunan province, China. This study investigated the prevalence, transmission, and genetic diversity of PZA resistance among multidrug-resistant Mycobacterium tuberculosis isolates in Hunan province. Methods Drug susceptibility testing (DST) with the Bactec MGIT 960 PZA kit and pyrazinamidase (PZase) testing were conducted on all 298 MDR clinical isolates. Moreover, 24-locus MIRU-VNTR and DNA sequencing of pncA, rpsA, and panD genes were conducted on 180 PZA-resistant (PZA-R) isolates. Results The prevalence of PZA resistance among MDR-TB strains reached 60.4%. Newly diagnosed PZA-R TB patients and clustered isolates with identical pncA, rpsA, and panD mutations showed that transmission of PZA-R isolates played a significant role in the formation of PZA-R TB. Ninety-eight mutation patterns were observed in the pncA among 180 PZA-R isolates, and seventy-one (72.4%) were point mutations. Twenty-four of these mutations are new, including 2 base substitutions (V93G and T153S) and 22 nucleotide deletions or insertions. The W119C was found in PZA-S isolates, on the other hand, F94L and V155A mutations were found in both PZA resistant and susceptible isolates with positive PZase activity, indicating that they were not associated with PZA resistance. This is not entirely in line with the WHO catalogue. Ten novel rpsA mutations were found in 10 PZA-R isolates, which all combined with mutations in pncA. Thus, it is unpredictable whether these mutations in rpsA can impact PZA resistance. No panD mutation was found in all PZA-R isolates. Conclusion DNA sequencing of pncA and PZase activity testing have great potential in predicting PZA resistance.
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Affiliation(s)
- Binbin Liu
- Clinical Laboratory, Hunan Chest Hospital, Changsha, People’s Republic of China
| | - Pan Su
- Clinical Laboratory, Hunan Chest Hospital, Changsha, People’s Republic of China
| | - Peilei Hu
- Clinical Laboratory, Hunan Chest Hospital, Changsha, People’s Republic of China
| | - Mi Yan
- Clinical Laboratory, Hunan Chest Hospital, Changsha, People’s Republic of China
| | - Wenbin Li
- Clinical Laboratory, Hunan Chest Hospital, Changsha, People’s Republic of China
| | - Songlin Yi
- Clinical Laboratory, Hunan Chest Hospital, Changsha, People’s Republic of China
| | - Zhenhua Chen
- Clinical Laboratory, Hunan Chest Hospital, Changsha, People’s Republic of China
| | - Xiaoping Zhang
- Clinical Laboratory, Hunan Chest Hospital, Changsha, People’s Republic of China
| | - Jingwei Guo
- Clinical Laboratory, Hunan Chest Hospital, Changsha, People’s Republic of China
| | - Xiaojie Wan
- Clinical Laboratory, Hunan Chest Hospital, Changsha, People’s Republic of China
| | - Jue Wang
- Clinical Laboratory, Hunan Chest Hospital, Changsha, People’s Republic of China
| | - Daofang Gong
- Clinical Laboratory, Hunan Chest Hospital, Changsha, People’s Republic of China
| | - Hua Bai
- Clinical Laboratory, Hunan Chest Hospital, Changsha, People’s Republic of China
| | - Kanglin Wan
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, People’s Republic of China
| | - Haican Liu
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, People’s Republic of China
| | - Guilian Li
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, People’s Republic of China
| | - Yunhong Tan
- Clinical Laboratory, Hunan Chest Hospital, Changsha, People’s Republic of China
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10
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Akhmetova A, Bismilda V, Chingissova L, Filipenko M, Akilzhanova A, Kozhamkulov U. Prevalence of Beijing Central Asian/Russian Cluster 94-32 among Multidrug-Resistant M. tuberculosis in Kazakhstan. Antibiotics (Basel) 2023; 13:9. [PMID: 38275319 PMCID: PMC10812519 DOI: 10.3390/antibiotics13010009] [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: 11/15/2023] [Revised: 12/12/2023] [Accepted: 12/14/2023] [Indexed: 01/27/2024] Open
Abstract
The Beijing genotype is the most distributed M. tuberculosis family in Kazakhstan. In this study, we identified dominant Beijing clusters in Kazakhstan and assessed their drug susceptibility profiles and association with the most widely spread mutation Ser531Leu of the rpoB gene and the mutation Ser315Thr of the katG gene associated with resistance to rifampicin and isoniazid, respectively. M. tuberculosis isolates (n = 540) from new TB cases were included in the study. MIRU-VNTR genotyping was performed for 540 clinical isolates to determine M. tuberculosis families using 24 loci. RD analysis was additionally performed for the Beijing isolates. The identification of mutations in the drug-resistance genes of M. tuberculosis was performed with allele-specific real-time PCR and Sanger sequencing. The Beijing genotype was identified in 60% (324/540) of the clinical isolates. Central Asian/Russian cluster 94-32 was the most distributed cluster among the Beijing isolates (50.3%; 163/324). Three other dominant Beijing clusters were identified as 94-33 (3.4%; 11/324), 100-32 (3.1%; 10/324) and 99-32 (3.1%; 10/324). The Beijing genotype was associated with drug-resistant TB (p < 0.0001), including multidrug-resistant TB (p < 0.0001), in our study. An association of the mutation Ser531Leu of the rpoB gene with the Beijing genotype was found (p < 0.0001; OR = 16.0000; 95%CI: 4.9161-52.0740). Among the Beijing isolates, cluster 94-32 showed an association with MDR-TB (p = 0.021). This is why the evaluation of the Beijing genotype and its clusters is needed to control MDR-TB in Kazakhstan.
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Affiliation(s)
- Ainur Akhmetova
- Laboratory of Genomic and Personalized Medicine, Center for Life Sciences, National Laboratory Astana, Nazarbayev University, Astana 010000, Kazakhstan
- Department of General Biology and Genomics, L.N. Gumilyov Eurasian National University, Astana 010000, Kazakhstan
| | - Venera Bismilda
- National Scientific Center of Phthisiopulmonology of the Republic of Kazakhstan, Almaty 050000, Kazakhstan
| | - Lyailya Chingissova
- National Scientific Center of Phthisiopulmonology of the Republic of Kazakhstan, Almaty 050000, Kazakhstan
| | - Maxim Filipenko
- Laboratory of Pharmacogenomics, Institute of Chemical Biology and Fundamental Medicine, Novosibirsk 630000, Russia
- Faculty of Natural Sciences, Novosibirsk State University, Novosibirsk 630090, Russia
| | - Ainur Akilzhanova
- Laboratory of Genomic and Personalized Medicine, Center for Life Sciences, National Laboratory Astana, Nazarbayev University, Astana 010000, Kazakhstan
| | - Ulan Kozhamkulov
- Laboratory of Genomic and Personalized Medicine, Center for Life Sciences, National Laboratory Astana, Nazarbayev University, Astana 010000, Kazakhstan
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11
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Acosta F, Saldaña R, Miranda S, Candanedo D, Sambrano D, Morán M, Bejarano S, De Arriba Y, Reigosa A, De Dixon E, Atencio M, Castillo R, Goodridge A. Heterogeneity of Mycobacterium tuberculosis Strains Circulating in Panama's Western Region. Am J Trop Med Hyg 2023; 109:740-747. [PMID: 37604472 PMCID: PMC10551089 DOI: 10.4269/ajtmh.23-0039] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Accepted: 06/08/2023] [Indexed: 08/23/2023] Open
Abstract
Tuberculosis remains a challenge in both rural and urban areas. Although a majority of countries display a higher burden in urban areas compared with rural areas, Panama continues to report the highest mortality rate in Central America. Urban areas, such as Panama City, report a high tuberculosis burden, whereas Panama's western region, including the provinces of Chiriquí, Bocas del Toro (both semiurban) and Ngäbe-Bugle (rural), show a lower burden. We aimed to identify highly transmitted Mycobacterium tuberculosis strains within rural and semiurban settings of Panama's western region during a 3-year period (2017, 2019, 2021). We randomly selected 87 M. tuberculosis isolates from a biobank from Panama's western region and analyzed them using allele-specific oligonucleotide polymerase chain reaction and 24-mycobacterial interspersed repetitive unit-variable number tandem repeat (MIRU-VNTR). Our results show only 11.7% (10/85) of M. tuberculosis strains identified as prevalent A-Beijing, B-Haarlem, or C-LAM Strains. We found a low prevalence of A, B, and C M. tuberculosis strains in both rural and semirural settings compared with isolates collected from the Eastern Colon Province. MIRU-VNTR genotyping revealed a high degree of diversity with no clusters with single loci variation of ≥ 2 loci. These results support the notion that tuberculosis prevalence in the rural and semiurban western region of Panama are not due to previously described highly transmitted strains but is influenced instead by other health determinants, including poor health system access and a lack of systematic transmission chain monitoring. For remote rural and semiurban settings, we recommend allocating resources to reinforce efforts to prevent tuberculosis spread.
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Affiliation(s)
- Fermin Acosta
- Tuberculosis Biomarker Research Unit at Centro de Biologia Celular y Molecular de Enfermedades (CBCME) Instituto de Investigaciones Científicas y Servicios de Alta Tecnología (INDICASAT-AIP), City of Knowledge, Panama City, Panama
| | - Ricardo Saldaña
- Hospital Materno Infantil José Domingo de Obaldía, David City, Provincia de Chiriquí, Panama
| | - Sara Miranda
- Tuberculosis Biomarker Research Unit at Centro de Biologia Celular y Molecular de Enfermedades (CBCME) Instituto de Investigaciones Científicas y Servicios de Alta Tecnología (INDICASAT-AIP), City of Knowledge, Panama City, Panama
- Universidad Autónoma de Chiriqui (UNACHI), David City, Provincia de Chiriquí, Panama
| | - Daniela Candanedo
- Tuberculosis Biomarker Research Unit at Centro de Biologia Celular y Molecular de Enfermedades (CBCME) Instituto de Investigaciones Científicas y Servicios de Alta Tecnología (INDICASAT-AIP), City of Knowledge, Panama City, Panama
| | - Dilcia Sambrano
- Tuberculosis Biomarker Research Unit at Centro de Biologia Celular y Molecular de Enfermedades (CBCME) Instituto de Investigaciones Científicas y Servicios de Alta Tecnología (INDICASAT-AIP), City of Knowledge, Panama City, Panama
| | - Mitchelle Morán
- Tuberculosis Biomarker Research Unit at Centro de Biologia Celular y Molecular de Enfermedades (CBCME) Instituto de Investigaciones Científicas y Servicios de Alta Tecnología (INDICASAT-AIP), City of Knowledge, Panama City, Panama
| | - Saily Bejarano
- Hospital Materno Infantil José Domingo de Obaldía, David City, Provincia de Chiriquí, Panama
| | - Yeraldine De Arriba
- Hospital Materno Infantil José Domingo de Obaldía, David City, Provincia de Chiriquí, Panama
| | - Angel Reigosa
- Hospital Materno Infantil José Domingo de Obaldía, David City, Provincia de Chiriquí, Panama
| | - Elizabeth De Dixon
- Hospital Materno Infantil José Domingo de Obaldía, David City, Provincia de Chiriquí, Panama
| | - María Atencio
- Hospital Materno Infantil José Domingo de Obaldía, David City, Provincia de Chiriquí, Panama
| | - Ramón Castillo
- Programa Regional de Tuberculosis de la Provincia de Chiriquí, Ministerio de Salud, David City, Provincia de Chiriquí, Panama
| | - Amador Goodridge
- Tuberculosis Biomarker Research Unit at Centro de Biologia Celular y Molecular de Enfermedades (CBCME) Instituto de Investigaciones Científicas y Servicios de Alta Tecnología (INDICASAT-AIP), City of Knowledge, Panama City, Panama
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12
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Sahal MR, Senelle G, La K, Panda TW, Taura DW, Guyeux C, Cambau E, Sola C. Mycobacterium tuberculosis complex drug-resistance, phylogenetics, and evolution in Nigeria: Comparison with Ghana and Cameroon. PLoS Negl Trop Dis 2023; 17:e0011619. [PMID: 37824575 PMCID: PMC10597489 DOI: 10.1371/journal.pntd.0011619] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Revised: 10/24/2023] [Accepted: 08/24/2023] [Indexed: 10/14/2023] Open
Abstract
In this article, we provide an in-depth analysis on the drug-resistance phenotypic characteristics of a cohort of 325 tuberculosis and characterize by Whole Genome Sequencing 24 isolates from Nigeria belonging to L4, L5 and L6. Our results suggest an alarming rate of drug-resistance of the L4.6.2.2 Mycobacterium tuberculosis complex (MTBC) lineage and a high diversity of L5. We compiled these new Sequence Read Archives (SRAs) to previously published ones from available Bioprojects run in Nigeria. We performed RAxML phylogenetic reconstructions of larger samples that include public NCBI SRAs from some neighboring countries (Cameroon, Ghana). To confront phylogenetic reconstruction to metadata, we used a new proprietary database named TB-Annotator. We show that L5 genomes in Northern Nigeria belong to new clades as the ones described until now and allow an update of the taxonomy of L5. In addition, we describe the L4.6.2.2 lineage in Nigeria, Cameroon and Ghana. We provide computations on the likely divergence time of L4.6.2.2 and suggest a new hypothesis concerning its origin. Finally we provide a short overview on M. bovis diversity in Nigeria. This study constitutes a baseline knowledge on the global genomic diversity, phylogeography and phylodynamics of MTBC in Nigeria, as well as on the natural history of this largely ignored but densely populated country of Africa. These results highlight the need of sequencing additional MTBC genomes in Nigeria and more generally in West-Africa, both for public health and for academic reasons. The likelihood of replacement of L5-L6 by L4.6.2.2 isolates, leave potentially little time to gather historical knowledge informative on the ancient history of tuberculosis in West-Africa.
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Affiliation(s)
- Muhammed Rabiu Sahal
- Université Paris-Cité, IAME, Inserm, Paris, France
- Université Paris-Saclay, Gif-sur-Yvette, France
| | - Gaetan Senelle
- FEMTO-ST Institute, UMR 6174 CNRS, DISC Computer Science Department, Univ. Franche-Comté (UFC), 16 Route de Gray, 25000 Besançon, France
| | - Kevin La
- Université Paris-Cité, IAME, Inserm, Paris, France
| | | | | | - Christophe Guyeux
- FEMTO-ST Institute, UMR 6174 CNRS, DISC Computer Science Department, Univ. Franche-Comté (UFC), 16 Route de Gray, 25000 Besançon, France
| | - Emmanuelle Cambau
- Université Paris-Cité, IAME, Inserm, Paris, France
- APHP, GHU Nord site Bichat, Service de Mycobactériologie Spécialisée et de Référence, Paris, France
| | - Christophe Sola
- Université Paris-Cité, IAME, Inserm, Paris, France
- Université Paris-Saclay, Gif-sur-Yvette, France
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13
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Jeon SM, Park S, Lim NR, Lee N, Jung J, Sung N, Kim S. Molecular Analysis of Anti-Tuberculosis Drug Resistance of Mycobacterium tuberculosis Isolated in the Republic of Korea. Antibiotics (Basel) 2023; 12:1324. [PMID: 37627744 PMCID: PMC10451913 DOI: 10.3390/antibiotics12081324] [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: 06/20/2023] [Revised: 08/03/2023] [Accepted: 08/15/2023] [Indexed: 08/27/2023] Open
Abstract
Rapid and accurate detection of tuberculosis (TB) drug resistance is critical for the successful treatment and control of TB. Here, we investigated resistance to anti-TB drugs and genetic variations in 215 drug-resistant Mycobacterium tuberculosis isolates in Korea. Genetic variations were observed in rpoB Ser531Leu, katG Ser315Thr, and gyrA Asp94Gly; however, the minimum inhibitory concentrations varied, which can be attributed to other resistance mechanisms. Examination of genetic relatedness among drug-resistant isolates revealed that the cluster size of resistant bacteria was less than six strains, suggesting no evidence of a large-scale epidemic caused by a specific strain. However, rpoC mutants of the rifampicin-resistant isolates were composed of five types of clusters, suggesting that these compensatory mutations advance propagation. In the present study, more than 90% of the resistance mechanisms to major anti-TB drugs were identified, and the effect of each mutation on drug resistance was estimated. With the clinical application of recent next-generation sequencing-based susceptibility testing, the present study is expected to improve the clinical utilization of genotype-based drug susceptibility testing for the diagnosis and treatment of patients with drug-resistant TB.
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Affiliation(s)
- Se-Mi Jeon
- Division of Bacterial Disease Research, Korea National Institute of Health, Korea Disease Control and Prevention Agency, Cheongju-si 28159, Republic of Korea; (S.-M.J.); (S.P.); (N.-R.L.)
| | - Sanghee Park
- Division of Bacterial Disease Research, Korea National Institute of Health, Korea Disease Control and Prevention Agency, Cheongju-si 28159, Republic of Korea; (S.-M.J.); (S.P.); (N.-R.L.)
| | - Na-Ra Lim
- Division of Bacterial Disease Research, Korea National Institute of Health, Korea Disease Control and Prevention Agency, Cheongju-si 28159, Republic of Korea; (S.-M.J.); (S.P.); (N.-R.L.)
| | - Noori Lee
- Clinical Research Center, Masan National Tuberculosis Hospital, Changwon-si 51755, Republic of Korea; (N.L.); (J.J.); (N.S.)
| | - Jihee Jung
- Clinical Research Center, Masan National Tuberculosis Hospital, Changwon-si 51755, Republic of Korea; (N.L.); (J.J.); (N.S.)
| | - Nackmoon Sung
- Clinical Research Center, Masan National Tuberculosis Hospital, Changwon-si 51755, Republic of Korea; (N.L.); (J.J.); (N.S.)
| | - Seonghan Kim
- Division of Bacterial Disease Research, Korea National Institute of Health, Korea Disease Control and Prevention Agency, Cheongju-si 28159, Republic of Korea; (S.-M.J.); (S.P.); (N.-R.L.)
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14
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Damina SM, Barnes DA, Inuwa B, Ularamu GH, Bello M, Okaiyeto OS, Kudi AC, Thapa J, Nakajima C, Suzuki Y. Molecular Characterisation of Mycobacterium bovis Isolates from Cattle Slaughtered in Adamawa and Gombe States, North-Eastern Nigeria. Curr Issues Mol Biol 2023; 45:6055-6066. [PMID: 37504298 PMCID: PMC10377879 DOI: 10.3390/cimb45070382] [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: 06/13/2023] [Revised: 07/12/2023] [Accepted: 07/15/2023] [Indexed: 07/29/2023] Open
Abstract
Bovine tuberculosis is endemic in Nigeria with control measures as provided by the laws of the country being minimally enforced mostly at the abattoirs only. This study focused on bovine tuberculosis in Adamawa and Gombe States. Tuberculosis lesions were observed in 183 of 13,688 slaughtered cattle in the regions between June and December 2020. Analysis of tissue samples resulted in 17 Mycobacterium bovis isolates, predominantly from Gombe State. Spoligotyping identified four spoligotypes, including SB0944, SB1025, SB1104, and one novel pattern. MIRU-VNTR analysis further differentiated these spoligotypes into eight profiles. All isolates belonged to the Af1 clonal complex. The study emphasises the need for broader coverage and more isolates to comprehensively understand the molecular epidemiology of bovine tuberculosis in Nigeria. To enhance research and surveillance, a cost-effective approach is proposed, utilising a discriminatory VNTR panel comprising five or nine loci. The five-locus panel consists of ETR-C, QUB26, QUB11b, MIRU04, and QUB323. Alternatively, the nine-locus panel includes ETR-A, ETR-B, QUB11a, and MIRU26. Implementing this approach would provide valuable insights into the genetic diversity of M. bovis strains in Nigeria. These findings are crucial for developing effective control measures and minimising the impact of bovine tuberculosis on both animal and human health.
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Affiliation(s)
| | - David Atomanyi Barnes
- Division of Bioresources, Hokkaido University International Institute for Zoonosis Control, Kita 20 Nishi 10, Kita-ku, Hokkaido 001-0020, Japan
| | - Bitrus Inuwa
- National Veterinary Research Institute, P.M.B.01, Vom 930103, Nigeria
| | | | - Mohammed Bello
- Department of Veterinary, Medicine, Faculty of Veterinary Medicine, Ahmadu Bello University, Zaria 810211, Nigeria
| | - Olu Solomon Okaiyeto
- Department of Veterinary, Medicine, Faculty of Veterinary Medicine, Ahmadu Bello University, Zaria 810211, Nigeria
| | - Ayuba Caleb Kudi
- Department of Veterinary, Medicine, Faculty of Veterinary Medicine, Ahmadu Bello University, Zaria 810211, Nigeria
| | - Jeewan Thapa
- Division of Bioresources, Hokkaido University International Institute for Zoonosis Control, Kita 20 Nishi 10, Kita-ku, Hokkaido 001-0020, Japan
| | - Chie Nakajima
- Division of Bioresources, Hokkaido University International Institute for Zoonosis Control, Kita 20 Nishi 10, Kita-ku, Hokkaido 001-0020, Japan
- International Collaboration Unit, Hokkaido University International Institute for Zoonosis Control, Kita 20 Nishi 10, Kita-ku, Hokkaido 001-0020, Japan
- Division of Research Support, Hokkaido University Institute for Vaccine Research and Development, Kita 20 Nishi 10, Kita-ku, Hokkaido 001-0020, Japan
| | - Yasuhiko Suzuki
- Division of Bioresources, Hokkaido University International Institute for Zoonosis Control, Kita 20 Nishi 10, Kita-ku, Hokkaido 001-0020, Japan
- International Collaboration Unit, Hokkaido University International Institute for Zoonosis Control, Kita 20 Nishi 10, Kita-ku, Hokkaido 001-0020, Japan
- Division of Research Support, Hokkaido University Institute for Vaccine Research and Development, Kita 20 Nishi 10, Kita-ku, Hokkaido 001-0020, Japan
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15
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Mokrousov I, Vyazovaya A, Shitikov E, Badleeva M, Belopolskaya O, Bespiatykh D, Gerasimova A, Ioannidis P, Jiao W, Khromova P, Masharsky A, Naizabayeva D, Papaventsis D, Pasechnik O, Perdigão J, Rastogi N, Shen A, Sinkov V, Skiba Y, Solovieva N, Tafaj S, Valcheva V, Kostyukova I, Zhdanova S, Zhuravlev V, Ogarkov O. Insight into pathogenomics and phylogeography of hypervirulent and highly-lethal Mycobacterium tuberculosis strain cluster. BMC Infect Dis 2023; 23:426. [PMID: 37353765 DOI: 10.1186/s12879-023-08413-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2023] [Accepted: 06/21/2023] [Indexed: 06/25/2023] Open
Abstract
BACKGROUND . The Mycobacterium tuberculosis Beijing genotype is globally spread lineage with important medical properties that however vary among its subtypes. M. tuberculosis Beijing 14717-15-cluster was recently discovered as both multidrug-resistant, hypervirulent, and highly-lethal strain circulating in the Far Eastern region of Russia. Here, we aimed to analyze its pathogenomic features and phylogeographic pattern. RESULTS . The study collection included M. tuberculosis DNA collected between 1996 and 2020 in different world regions. The bacterial DNA was subjected to genotyping and whole genome sequencing followed by bioinformatics and phylogenetic analysis. The PCR-based assay to detect specific SNPs of the Beijing 14717-15-cluster was developed and used for its screening in the global collections. Phylogenomic and phylogeographic analysis confirmed endemic prevalence of the Beijing 14717-15-cluster in the Asian part of Russia, and distant common ancestor with isolates from Korea (> 115 SNPs). The Beijing 14717-15-cluster isolates had two common resistance mutations RpsL Lys88Arg and KatG Ser315Thr and belonged to spoligotype SIT269. The Russian isolates of this cluster were from the Asian Russia while 4 isolates were from the Netherlands and Spain. The cluster-specific SNPs that significantly affect the protein function were identified in silico in genes within different categories (lipid metabolism, regulatory proteins, intermediary metabolism and respiration, PE/PPE, cell wall and cell processes). CONCLUSIONS . We developed a simple method based on real-time PCR to detect clinically significant MDR and hypervirulent Beijing 14717-15-cluster. Most of the identified cluster-specific mutations were previously unreported and could potentially be associated with increased pathogenic properties of this hypervirulent M. tuberculosis strain. Further experimental study to assess the pathobiological role of these mutations is warranted.
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Affiliation(s)
- Igor Mokrousov
- Laboratory of Molecular Epidemiology and Evolutionary Genetics, St. Petersburg Pasteur Institute, St. Petersburg, Russia.
- Henan International Joint Laboratory of Children's Infectious Diseases, Henan Children's Hospital, Children's Hospital, Zhengzhou University, Zhengzhou Children's Hospital, Zhengzhou, China.
| | - Anna Vyazovaya
- Laboratory of Molecular Epidemiology and Evolutionary Genetics, St. Petersburg Pasteur Institute, St. Petersburg, Russia
| | - Egor Shitikov
- Department of Biomedicine and Genomics, Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, 119435, Russia
| | - Maria Badleeva
- Department of Infectious Diseases, Dorji Banzarov Buryat State University, Ulan-Ude, Buryatia, Russia
| | - Olesya Belopolskaya
- Resource Center Bio-bank Center, Research Park of St. Petersburg State University, St. Petersburg, Russia
- Laboratory of Genogeography, Vavilov Institute of General Genetics Russian Academy of Sciences Moscow, Moscow, Russia
| | - Dmitry Bespiatykh
- Department of Biomedicine and Genomics, Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, 119435, Russia
| | - Alena Gerasimova
- Laboratory of Molecular Epidemiology and Evolutionary Genetics, St. Petersburg Pasteur Institute, St. Petersburg, Russia
| | - Panayotis Ioannidis
- National Reference Laboratory for Mycobacteria, Sotiria Chest Diseases Hospital, Athens, Greece
| | - Weiwei Jiao
- National Clinical Research Center for Respiratory Diseases, Beijing Key Laboratory of Pediatric Respiratory Infection Disease, Beijing Children's Hospital, Beijing Pediatric Research Institute, Capital Medical University, National Center for Children's Health, Beijing, China
| | - Polina Khromova
- Department of Epidemiology and Microbiology, Scientific Centre of the Family Health and Human Reproduction Problems, Irkutsk, Russia
| | - Aleksey Masharsky
- Resource Center Bio-bank Center, Research Park of St. Petersburg State University, St. Petersburg, Russia
| | - Dinara Naizabayeva
- Laboratory of Molecular Biology, Almaty Branch of National Center for Biotechnology in Central Reference Laboratory, Almaty, Kazakhstan
- Department of Biotechnology, Al-Farabi Kazakh National University, Almaty, Kazakhstan
| | - Dimitrios Papaventsis
- National Reference Laboratory for Mycobacteria, Sotiria Chest Diseases Hospital, Athens, Greece
| | - Oksana Pasechnik
- Department of Public Health, Omsk State Medical University, Omsk, Russia
| | - João Perdigão
- iMed.ULisboa - Instituto de Investigação do Medicamento, Faculdade de Farmácia, Universidade de Lisboa, Lisbon, Portugal
| | - Nalin Rastogi
- WHO Supranational TB Reference Laboratory, Unité de la Tuberculose et des Mycobactéries, Institut Pasteur de la Guadeloupe, Abymes, Guadeloupe, France
| | - Adong Shen
- National Clinical Research Center for Respiratory Diseases, Beijing Key Laboratory of Pediatric Respiratory Infection Disease, Beijing Children's Hospital, Beijing Pediatric Research Institute, Capital Medical University, National Center for Children's Health, Beijing, China
- Henan Children's Hospital, Children's Hospital Affiliated to Zhengzhou University, Zhengzhou Children's Hospital, Zhengzhou, China
| | - Viacheslav Sinkov
- Department of Epidemiology and Microbiology, Scientific Centre of the Family Health and Human Reproduction Problems, Irkutsk, Russia
| | - Yuriy Skiba
- Laboratory of Molecular Biology, Almaty Branch of National Center for Biotechnology in Central Reference Laboratory, Almaty, Kazakhstan
| | - Natalia Solovieva
- St. Petersburg Research Institute of Phthisiopulmonology, St. Petersburg, Russia
| | - Silva Tafaj
- National Mycobacteria Reference Laboratory, University Hospital Shefqet Ndroqi, Tirana, Albania
| | - Violeta Valcheva
- Laboratory of Molecular Genetics of Mycobacteria, The Stephan Angeloff Institute of Microbiology, Bulgarian Academy of Sciences, Sofia, Bulgaria
| | - Irina Kostyukova
- Bacteriology laboratory, Clinical Tuberculosis Dispensary, Omsk, Russia
| | - Svetlana Zhdanova
- Department of Epidemiology and Microbiology, Scientific Centre of the Family Health and Human Reproduction Problems, Irkutsk, Russia
| | - Viacheslav Zhuravlev
- St. Petersburg Research Institute of Phthisiopulmonology, St. Petersburg, Russia
| | - Oleg Ogarkov
- Department of Epidemiology and Microbiology, Scientific Centre of the Family Health and Human Reproduction Problems, Irkutsk, Russia
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Pérez-Llanos FJ, Dreyer V, Barilar I, Utpatel C, Kohl TA, Murcia MI, Homolka S, Merker M, Niemann S. Transmission Dynamics of a Mycobacterium tuberculosis Complex Outbreak in an Indigenous Population in the Colombian Amazon Region. Microbiol Spectr 2023; 11:e0501322. [PMID: 37222610 PMCID: PMC10269451 DOI: 10.1128/spectrum.05013-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Accepted: 05/04/2023] [Indexed: 05/25/2023] Open
Abstract
Whole genome sequencing (WGS) has become the main tool for studying the transmission of Mycobacterium tuberculosis complex (MTBC) strains; however, the clonal expansion of one strain often limits its application in local MTBC outbreaks. The use of an alternative reference genome and the inclusion of repetitive regions in the analysis could potentially increase the resolution, but the added value has not yet been defined. Here, we leveraged short and long WGS read data of a previously reported MTBC outbreak in the Colombian Amazon Region to analyze possible transmission chains among 74 patients in the indigenous setting of Puerto Nariño (March to October 2016). In total, 90.5% (67/74) of the patients were infected with one distinct MTBC strain belonging to lineage 4.3.3. Employing a reference genome from an outbreak strain and highly confident single nucleotide polymorphisms (SNPs) in repetitive genomic regions, e.g., the proline-glutamic acid/proline-proline-glutamic-acid (PE/PPE) gene family, increased the phylogenetic resolution compared to a classical H37Rv reference mapping approach. Specifically, the number of differentiating SNPs increased from 890 to 1,094, which resulted in a more granular transmission network as judged by an increasing number of individual nodes in a maximum parsimony tree, i.e., 5 versus 9 nodes. We also found in 29.9% (20/67) of the outbreak isolates, heterogenous alleles at phylogenetically informative sites, suggesting that these patients are infected with more than one clone. In conclusion, customized SNP calling thresholds and employment of a local reference genome for a mapping approach can improve the phylogenetic resolution in highly clonal MTBC populations and help elucidate within-host MTBC diversity. IMPORTANCE The Colombian Amazon around Puerto Nariño has a high tuberculosis burden with a prevalence of 1,267/100,000 people in 2016. Recently, an outbreak of Mycobacterium tuberculosis complex (MTBC) bacteria among the indigenous populations was identified with classical MTBC genotyping methods. Here, we employed a whole-genome sequencing-based outbreak investigation in order to improve the phylogenetic resolution and gain new insights into the transmission dynamics in this remote Colombian Amazon Region. The inclusion of well-supported single nucleotide polymorphisms in repetitive regions and a de novo-assembled local reference genome provided a more granular picture of the circulating outbreak strain and revealed new transmission chains. Multiple patients from different settlements were possibly infected with at least two different clones in this high-incidence setting. Thus, our results have the potential to improve molecular surveillance studies in other high-burden settings, especially regions with few clonal multidrug-resistant (MDR) MTBC lineages/clades.
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Affiliation(s)
| | - Viola Dreyer
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Germany
- German Center for Infection Research, Hamburg-Lübeck-Borstel-Riems, Germany
| | - Ivan Barilar
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Germany
- German Center for Infection Research, Hamburg-Lübeck-Borstel-Riems, Germany
| | - Christian Utpatel
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Germany
- German Center for Infection Research, Hamburg-Lübeck-Borstel-Riems, Germany
| | - Thomas A. Kohl
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Germany
- German Center for Infection Research, Hamburg-Lübeck-Borstel-Riems, Germany
| | - Martha Isabel Murcia
- Grupo MICOBAC-UN, Departamento de Microbiología, Facultad de Medicina, Universidad Nacional de Colombia, Bogotá, Colombia
| | - Susanne Homolka
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Germany
| | - Matthias Merker
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Germany
- German Center for Infection Research, Hamburg-Lübeck-Borstel-Riems, Germany
- Evolution of the Resistome, Research Center Borstel, Borstel, Germany
| | - Stefan Niemann
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Germany
- German Center for Infection Research, Hamburg-Lübeck-Borstel-Riems, Germany
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17
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Naseri-Nezhad M, Asadian M, Khalifeh Gholi M, Yaseri M, Douraghi M. Mycobacterium tuberculosis genotypes in an ethnically diverse area with millions of pilgrims and thousands of immigrants. BMC Infect Dis 2023; 23:354. [PMID: 37231348 DOI: 10.1186/s12879-023-08325-6] [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: 01/05/2023] [Accepted: 05/12/2023] [Indexed: 05/27/2023] Open
Abstract
BACKGROUND Immigration is considered as a risk factor of tuberculosis (TB). Qom province receives millions of pilgrims and significant numbers of immigrants each year. Most of the immigrants to Qom, arrive from neighboring TB-endemic countries. This study aimed to identify the current circulating Mycobacterium tuberculosis genotypes in Qom province using 24-locus MIRU-VNTR genotyping. METHODS Eighty six M. tuberculosis isolates were collected during 2018-2022 from patients referring to Qom TB reference laboratory. The DNA of isolates was extracted and followed by 24 loci MIRU-VNTR genotyping which performed using the web tools available on MIRU-VNTRplus. RESULTS Of 86 isolates, 39 (45.3%) were of Delhi/CAS genotype, 24 (27.9%) of NEW-1, 6 (7%) of LAM, 6 (7%) of Beijing, 2 (2.3%) of UgandaII, 2 (2.3%) of EAI, 1 of S (1.2%) and 6 (7%) did not match with profiles present in MIRUVNTRplus database. CONCLUSIONS About half of the isolates belong to Afghan immigrants; which warns health policy makers about the future situation of TB in Qom. Also, the similarity of Afghan and Iranian genotypes provides evidence that immigrants partake in the circulation of M. tuberculosis. This study underpin the studies about the circulating M. tuberculosis genotypes, their geographical distribution, the association of TB risk factors with these genotypes and the impact of immigration on the situation of TB in Qom province.
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Affiliation(s)
- Mostafa Naseri-Nezhad
- Division of Microbiology, Department of Pathobiology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Mahla Asadian
- Division of Microbiology, Department of Pathobiology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Mohammad Khalifeh Gholi
- Department of Microbiology and Immunology, Faculty of Medicine, Qom University of Medical Sciences, Qom, Iran
| | - Mehdi Yaseri
- Department of Epidemiology and Biostatistics, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Masoumeh Douraghi
- Division of Microbiology, Department of Pathobiology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran.
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Rossi G, Shih BBJ, Egbe NF, Motta P, Duchatel F, Kelly RF, Ndip L, Sander M, Tanya VN, Lycett SJ, Bronsvoort BM, Muwonge A. Unraveling the epidemiology of Mycobacterium bovis using whole-genome sequencing combined with environmental and demographic data. Front Vet Sci 2023; 10:1086001. [PMID: 37266384 PMCID: PMC10230100 DOI: 10.3389/fvets.2023.1086001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Accepted: 04/14/2023] [Indexed: 06/03/2023] Open
Abstract
When studying the dynamics of a pathogen in a host population, one crucial question is whether it transitioned from an epidemic (i.e., the pathogen population and the number of infected hosts are increasing) to an endemic stable state (i.e., the pathogen population reached an equilibrium). For slow-growing and slow-evolving clonal pathogens such as Mycobacterium bovis, the causative agent of bovine (or animal) and zoonotic tuberculosis, it can be challenging to discriminate between these two states. This is a result of the combination of suboptimal detection tests so that the actual extent of the pathogen prevalence is often unknown, as well as of the low genetic diversity, which can hide the temporal signal provided by the accumulation of mutations in the bacterial DNA. In recent years, the increased availability, efficiency, and reliability of genomic reading techniques, such as whole-genome sequencing (WGS), have significantly increased the amount of information we can use to study infectious diseases, and therefore, it has improved the precision of epidemiological inferences for pathogens such as M. bovis. In this study, we use WGS to gain insights into the epidemiology of M. bovis in Cameroon, a developing country where the pathogen has been reported for decades. A total of 91 high-quality sequences were obtained from tissue samples collected in four abattoirs, 64 of which were with complete metadata. We combined these with environmental, demographic, ecological, and cattle movement data to generate inferences using phylodynamic models. Our findings suggest M. bovis in Cameroon is slowly expanding its epidemiological range over time; therefore, endemic stability is unlikely. This suggests that animal movement plays an important role in transmission. The simultaneous prevalence of M. bovis in co-located cattle and humans highlights the risk of such transmission being zoonotic. Therefore, using genomic tools as part of surveillance would vastly improve our understanding of disease ecology and control strategies.
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Affiliation(s)
- Gianluigi Rossi
- The Roslin Institute, R(D)SVS, University of Edinburgh – Easter Bush Campus, Midlothian, United Kingdom
- Centre of Expertise on Animal Diseases Outbreaks, EPIC, Edinburgh, United Kingdom
| | - Barbara Bo-Ju Shih
- The Roslin Institute, R(D)SVS, University of Edinburgh – Easter Bush Campus, Midlothian, United Kingdom
| | - Nkongho Franklyn Egbe
- School of Life Sciences, University of Lincoln, Brayford Pool, Lincoln, United Kingdom
| | - Paolo Motta
- The Food and Agriculture Organization of the United Nations, Regional Office for Asia and the Pacific, Bangkok, Thailand
| | - Florian Duchatel
- The Roslin Institute, R(D)SVS, University of Edinburgh – Easter Bush Campus, Midlothian, United Kingdom
| | - Robert Francis Kelly
- Royal (Dick) School of Veterinary Studies and the Roslin Institute, University of Edinburgh, Easter Bush, Midlothian, United Kingdom
| | - Lucy Ndip
- Laboratory for Emerging Infectious Diseases, University of Buea, Buea, Cameroon
- Department of Biomedical Sciences, Faculty of Health Sciences, University of Buea, Buea, Cameroon
| | | | | | - Samantha J. Lycett
- The Roslin Institute, R(D)SVS, University of Edinburgh – Easter Bush Campus, Midlothian, United Kingdom
- Centre of Expertise on Animal Diseases Outbreaks, EPIC, Edinburgh, United Kingdom
| | - Barend Mark Bronsvoort
- The Roslin Institute, R(D)SVS, University of Edinburgh – Easter Bush Campus, Midlothian, United Kingdom
- Centre of Expertise on Animal Diseases Outbreaks, EPIC, Edinburgh, United Kingdom
| | - Adrian Muwonge
- The Roslin Institute, R(D)SVS, University of Edinburgh – Easter Bush Campus, Midlothian, United Kingdom
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Ghazvini K, Khoshbakht R, Tadayon K, Mosavari N, BahramiTaghanaki HR, Mohammadi GR, Rashti Baf M, Nourian K, Samiei A, Ghavidel M. Genotyping of Mycobacterium tuberculosis complex isolated from humans and animals in northeastern Iran. Sci Rep 2023; 13:6746. [PMID: 37185604 PMCID: PMC10127167 DOI: 10.1038/s41598-023-33740-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Accepted: 04/18/2023] [Indexed: 05/17/2023] Open
Abstract
The objective of this study was to genotype Mycobacterium tuberculosis complex isolated from humans and cattle in northern Iran. Over the course of one year, a total of 120 human and 21 cattle isolates were tested using region of difference (RD)-based polymerase chain reaction (PCR) and mycobacterial interspersed repetitive unites-variable number tandem repeats (MIRU-VNTR). In M. tuberculosis, out of 120 isolates investigated, the most common genotype detected was NEW-1 (53.3%), followed by CAS/ Delhi (24.1%), Haarlem (5%), Beijing (4.16%), Uganda I (4.16%), S (3.3%), Ural (0.83%), TUR (0.83%), Uganda II (0.83%), Lam (0.83%) and Cameroon (0.83%). The HGDI rate was 0.9981 and the clustering rate was 10.83. Of the isolates, QUB26 had the highest allele diversity (h: 0.76), while the loci Mtub29 and MIRU24 had the lowest (h: 0). In M. Bovis, out of 123 collected tissue samples, 21 (17%) grew on culture media. The HGDI rate was 0.71 and clustering rate was 85.7%. The locus ETRC had the highest allele diversity (h: 0.45). The findings of this study suggest that there is high genetic diversity among M. tuberculosis isolates in Khorasan Razavi Province, which is consistent with similar results from other studies in other provinces in Iran and neighboring countries. This indicates that the prevalent genotypes in this study are spreading in the Middle East region. Furthermore, considering that M. Bovis isolates were identified in two clusters, it seems that all of them have a common origin and are circulating among the livestock farms in the province.
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Affiliation(s)
- Kiarash Ghazvini
- Antimicrobial Resistance Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
- Department of Microbiology and Virology, School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Reza Khoshbakht
- Department of Laboratory Sciences, School of Paramedical Sciences, Mashhad University of Medical Sciences, Mashhad, Iran
- Student Research Committee, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Keyvan Tadayon
- Department of Microbiology, Razi Vaccine and Serum Research Institute (RVSRI), Agricultural Research, Education and Extension Organization (AREEO), Karaj, Iran
| | - Nader Mosavari
- PPD Tuberculin Department, Razi Vaccine and Serum Research Institute, (RVSRI), Agricultural Research, Education and Extension Organization (AREEO), Karaj, Iran
| | | | - Gholam Reza Mohammadi
- Department of Clinical Sciences, School of Veterinary Medicine, Ferdowsi University of Mashhad, Mashhad, Iran
| | - Mohammad Rashti Baf
- Deputy of Veterinary Administration of Khorasan Razavi Province, Mashhad, Iran
| | - Kimiya Nourian
- Department of Veterinary Medicine, Ferdowsi University of Mashhad, Mashhad, Iran
| | - Amin Samiei
- Tuberculosis and Leprosy Coordinator at Health Chancellor, Health Center of Khorasan State, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Mahdis Ghavidel
- Shahid Hasheminejad Hospital, Mashhad University of Medical Sciences, Mashhad, Iran.
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Heffernan C, Egedahl ML, Barrie J, Winter C, Armstrong G, Doroshenko A, Tyrrell G, Paulsen C, Lau A, Long R. The prevalence, risk factors, and public health consequences of peripheral lymph node-associated clinical and subclinical pulmonary tuberculosis. Int J Infect Dis 2023; 129:165-174. [PMID: 36736990 DOI: 10.1016/j.ijid.2023.01.026] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Revised: 01/13/2023] [Accepted: 01/18/2023] [Indexed: 02/04/2023] Open
Abstract
OBJECTIVES Relatively little is known about the prevalence, risk factors, and public health consequences of peripheral lymph node (PLN)-associated pulmonary tuberculosis (PTB). METHODS We developed a 10-year (2010-2019) population-based cohort of PLNTB patients in Canada. We used systematically collected primary source data and expert reader chest radiograph interpretations in a multivariable logistic regression to determine associations between sputum culture positivity and demographic, clinical, and radiographic features. Public health risks were estimated among contacts of PLNTB patients. RESULTS There were 306 patients with PLNTB, among whom 283 (92.5%) were 15-64 years of age, 159 (52.0%) were female, and 293 (95.8%) were foreign-born. Respiratory symptoms were present in 21.6%, and abnormal chest radiograph in 23.2%. Sputum culture positivity ranged from 12.9% in patients with no symptoms and normal lung parenchyma to 66.7% in patients with both. Respiratory symptoms, abnormal lung parenchyma, and HIV-coinfection (borderline) were independent predictors of sputum culture positivity (odds ratio [OR] 2.24 [95% confidence interval [CI] 1.15-4.39], P = 0.01, OR 4.78 [95% CI 2.41-9.48], P < 0.001, and OR 2.54 [95% CI 0.99-6.52], P = 0.05), respectively. Among contacts of sputum culture-positive PLNTB patients, one secondary case and 16 new infections were identified. CONCLUSION Isochronous PTB is common in PLNTB patients. Routine screening of PLNTB patients for PTB is strongly recommended.
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Affiliation(s)
- Courtney Heffernan
- Department of Medicine, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, Canada
| | - Mary Lou Egedahl
- Department of Medicine, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, Canada
| | - James Barrie
- Department of Radiology and Diagnostic Imaging, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, Canada
| | - Christopher Winter
- Department of Radiology and Diagnostic Imaging, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, Canada
| | - Gavin Armstrong
- Department of Radiology and Diagnostic Imaging, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, Canada
| | - Alexander Doroshenko
- Department of Medicine, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, Canada
| | - Gregory Tyrrell
- Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, Canada
| | - Catherine Paulsen
- Department of Medicine, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, Canada
| | - Angela Lau
- Department of Medicine, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, Canada
| | - Richard Long
- Department of Medicine, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, Canada.
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Bakuła Z, Marczak M, Bluszcz A, Proboszcz M, Kościuch J, Krenke R, Stakėnas P, Mokrousov I, Jagielski T. Phylogenetic relationships of Mycobacterium tuberculosis isolates in Poland: The emergence of Beijing genotype among multidrug-resistant cases. Front Cell Infect Microbiol 2023; 13:1161905. [PMID: 37009494 PMCID: PMC10061152 DOI: 10.3389/fcimb.2023.1161905] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Accepted: 02/28/2023] [Indexed: 03/18/2023] Open
Abstract
IntroductionThe epidemiological situation of tuberculosis (TB) in Poland urges for its continuous and scrupulous monitoring. The objective of this study was to explore the genetic diversity of multidrug-resistant (MDR) and drug-susceptible (DS) Mycobacterium tuberculosis isolates from Poland with a combination of spoligotyping and high-resolution mycobacterial interspersed repetitive unit-variable number tandem repeat (MIRU-VNTR) analysis. The results were placed in the Northern and Eastern Europe context.MethodsThe study included 89 (39 MDR and 50 DS) M. tuberculosis isolates collected from as many patients between 2018 and 2021 in Poland. The analysis was done using spoligotyping, and MIRU-VNTR typing at 24 standard loci. The data were compared to those available on Poland and neighbors and global M. tuberculosis datasets.ResultsThe main identified families were Beijing (28.1%) and Haarlem (16.8%) while 34.8% of isolates were in the heterogeneous L4-unclassified group. Although the Beijing family was the most prevalent (61.5%) among MDR-TB cases, it accounted for only 2% of DS isolates. Among foreign-born patients, a higher ratio of MDR isolates were observed when compared with those who Poland-born (64.3% vs. 40%). Furthermore, all patients from the Former Soviet Union (FSU) countries were infected with MDR-TB.DiscussionWhereas DS M. tuberculosis population in Poland is dominated by L4 isolates, MDR isolates are mostly of the Beijing genotype. The rise in the prevalence of the Beijing isolates in Poland, coupled with high proportion of the Beijing genotype among foreign-born TB patients may reflect an ongoing transmission of this family, imported to Poland mainly from FSU countries.
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Affiliation(s)
- Zofia Bakuła
- Department of Medical Microbiology, Institute of Microbiology, University of Warsaw, Faculty of Biology, Warsaw, Poland
| | - Mateusz Marczak
- Department of Medical Microbiology, Institute of Microbiology, University of Warsaw, Faculty of Biology, Warsaw, Poland
| | - Agata Bluszcz
- Department of Medical Microbiology, Institute of Microbiology, University of Warsaw, Faculty of Biology, Warsaw, Poland
| | - Małgorzata Proboszcz
- Department of Internal Medicine, Pulmonary Diseases & Allergy, Medical University of Warsaw, Warsaw, Poland
| | - Justyna Kościuch
- Department of Internal Medicine, Pulmonary Diseases & Allergy, Medical University of Warsaw, Warsaw, Poland
| | - Rafał Krenke
- Department of Internal Medicine, Pulmonary Diseases & Allergy, Medical University of Warsaw, Warsaw, Poland
| | - Petras Stakėnas
- Department of Immunology and Cell Biology, Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Igor Mokrousov
- Laboratory of Molecular Epidemiology and Evolutionary Genetics, St. Petersburg Pasteur Institute, St. Petersburg, Russia
- Henan International Joint Laboratory of Children’s Infectious Diseases, Henan Children’s Hospital, Zhengzhou Children’s Hospital, Zhengzhou, China
- *Correspondence: Tomasz Jagielski, ; Igor Mokrousov,
| | - Tomasz Jagielski
- Department of Medical Microbiology, Institute of Microbiology, University of Warsaw, Faculty of Biology, Warsaw, Poland
- *Correspondence: Tomasz Jagielski, ; Igor Mokrousov,
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Perchlozone Resistance in Clinical Isolates of Mycobacterium tuberculosis. Antibiotics (Basel) 2023; 12:antibiotics12030590. [PMID: 36978456 PMCID: PMC10044601 DOI: 10.3390/antibiotics12030590] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Revised: 02/28/2023] [Accepted: 03/13/2023] [Indexed: 03/18/2023] Open
Abstract
The emergence of drug-resistant tuberculosis forced the development of new drugs and the screening of more effective or less toxic analogues. Mycolic acid biosynthesis is targeted by several antituberculosis drugs, isoniazid being one of the most important in tuberculosis therapy. Recently, perchlozone, acting on another step in the FAS-II cycle, was officially approved for tuberculosis treatment in the Russian Federation and was included in the Russian national clinical guidelines. Using the serial dilution method on 7H10 agar plates for perchlozone and a Sensititre MYCOTB microdilution plate, we analyzed the phenotypic properties of primary clinical isolates of M. tuberculosis and analyzed the molecular determinants of resistance to isoniazid, ethionamide, and perchlozone. We found a wide variation in the MIC of perchlozone from 2 to 64 mg/L, correlating with the overall resistance profile: the MIC was higher for MDR and pre-XDR isolates. The cross-resistance between ethionamide and perchlozone was driven by mutations in the ethA gene encoding monooxygenase responsible for the activation of both drugs. The presumably susceptible to perchlozone and wild-type strains had MICs ranging from 2 to 4 mg/L, and the breakpoint was estimated to be 4 or 8 mg/L. In conclusion, susceptibility to perchlozone is retained for a part of the MDR strains, as is susceptibility to ethionamide, providing the possibility of therapy for such cases based on phenotypic or molecular analysis.
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Busatto C, Possuelo LG, Bierhals D, de Oliveira CL, de Souza MQ, Fanfa D, Barreto É, Schwarzbold P, Von Groll A, Portugal I, Perdigão J, Croda J, Andrews JR, da Silva PA, Ramis IB. Spread of Mycobacterium tuberculosis in Southern Brazilian persons deprived of liberty: a molecular epidemiology study. Eur J Clin Microbiol Infect Dis 2023; 42:297-304. [PMID: 36701032 DOI: 10.1007/s10096-023-04546-4] [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: 08/16/2022] [Accepted: 01/10/2023] [Indexed: 01/27/2023]
Abstract
To evaluate the genetic diversity and clustering rates of M. tuberculosis strains to better understand transmission among persons deprived of liberty (PDL) in Rio Grande do Sul (RS), southern Brazil. This is a cross-sectional study, including strains of M. tuberculosis isolated from PDL, stored at the Central Laboratory of RS, in the period from 2013 to 2018. The molecular characterization was performed using the MIRU-VNTR 15 loci method. A total of 598 M. tuberculosis strains were genotyped, and 37.5% were grouped into 53 clusters. Cluster sizes ranged from 2 to 34 strains. The largest cluster of the study had strains from 34 PDL, and 58.8% of the PDL of this cluster were in P01. Among the clusters formed, in 60.3%, there was at least one strain from P01. The most common strains in RS were LAM (53.2%) and Haarlem (31.1%). The LAM strain was the most likely to form clusters, and Haarlem was associated with anti-TB drug resistance. This was translational research, and the results can collaborate with the TB control programs, leading to improved strategies that allow the reduction of the TB burden in prisons.
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Affiliation(s)
- Caroline Busatto
- Núcleo de Pesquisa Em Microbiologia Medica, Faculdade de Medicina, Universidade Federal Do Rio Grande, Rio Grande, Rio Grande Do Sul, Brazil
| | - Lia Gonçalves Possuelo
- Programa de Pós-Graduação Em Promoção da Saúde, Universidade de Santa Cruz Do Sul, Santa Cruz Do Sul, Rio Grande Do Sul, Brazil
| | - Dienefer Bierhals
- Núcleo de Pesquisa Em Microbiologia Medica, Faculdade de Medicina, Universidade Federal Do Rio Grande, Rio Grande, Rio Grande Do Sul, Brazil
| | - Carolina Larrosa de Oliveira
- Núcleo de Pesquisa Em Microbiologia Medica, Faculdade de Medicina, Universidade Federal Do Rio Grande, Rio Grande, Rio Grande Do Sul, Brazil
| | - Mariana Quaresma de Souza
- Núcleo de Pesquisa Em Microbiologia Medica, Faculdade de Medicina, Universidade Federal Do Rio Grande, Rio Grande, Rio Grande Do Sul, Brazil
| | - Dandara Fanfa
- Programa de Pós-Graduação Em Promoção da Saúde, Universidade de Santa Cruz Do Sul, Santa Cruz Do Sul, Rio Grande Do Sul, Brazil
| | - Érika Barreto
- Programa de Pós-Graduação Em Promoção da Saúde, Universidade de Santa Cruz Do Sul, Santa Cruz Do Sul, Rio Grande Do Sul, Brazil
| | - Pauline Schwarzbold
- 8ª Delegacia Penitenciária Regional, Superintendência Dos Serviços Penitenciários, Santa Cruz Do Sul, RS, Brazil
| | - Andrea Von Groll
- Núcleo de Pesquisa Em Microbiologia Medica, Faculdade de Medicina, Universidade Federal Do Rio Grande, Rio Grande, Rio Grande Do Sul, Brazil
| | - Isabel Portugal
- Research Institute for Medicines - iMed.ULisboa, Faculdade de Farmácia, Universidade de Lisboa, Lisbon, Portugal
| | - João Perdigão
- Research Institute for Medicines - iMed.ULisboa, Faculdade de Farmácia, Universidade de Lisboa, Lisbon, Portugal
| | - Julio Croda
- Faculdade de Medicina, Universidade Federal Do Mato Grosso Do Sul, Campo Grande, Mato Grosso Do Sul, Brazil
| | - Jason R Andrews
- Division of Infectious Diseases and Geographic Medicine, Stanford University School of Medicine, Stanford, Palo Alto, CA, US
| | - Pedro Almeida da Silva
- Núcleo de Pesquisa Em Microbiologia Medica, Faculdade de Medicina, Universidade Federal Do Rio Grande, Rio Grande, Rio Grande Do Sul, Brazil.
- Rua General Osório S/N, Centro, Rio Grande Do Sul, Rio Grande, 96200190, Brazil.
| | - Ivy Bastos Ramis
- Núcleo de Pesquisa Em Microbiologia Medica, Faculdade de Medicina, Universidade Federal Do Rio Grande, Rio Grande, Rio Grande Do Sul, Brazil
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First Insight into Diversity of Minisatellite Loci in Mycobacterium bovis/ M. caprae in Bulgaria. Diagnostics (Basel) 2023; 13:diagnostics13040771. [PMID: 36832259 PMCID: PMC9955489 DOI: 10.3390/diagnostics13040771] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 02/13/2023] [Accepted: 02/15/2023] [Indexed: 02/22/2023] Open
Abstract
The aim of this study was to assess the diversity of minisatellite VNTR loci in Mycobacterium bovis/M. caprae isolates in Bulgaria and view their position within global M. bovis diversity. Forty-three M. bovis/M. caprae isolates from cattle in different farms in Bulgaria were collected in 2015-2021 and typed in 13 VNTR loci. The M. bovis and M. caprae branches were clearly separated on the VNTR phylogenetic tree. The larger and more geographically dispersed M. caprae group was more diverse than M. bovis group was (HGI 0.67 vs. 0.60). Overall, six clusters were identified (from 2 to 19 isolates) and nine orphans (all loci-based HGI 0.79). Locus QUB3232 was the most discriminatory one (HGI 0.64). MIRU4 and MIRU40 were monomorphic, and MIRU26 was almost monomorphic. Four loci (ETRA, ETRB, Mtub21, and MIRU16) discriminated only between M. bovis and M. caprae. The comparison with published VNTR datasets from 11 countries showed both overall heterogeneity between the settings and predominantly local evolution of the clonal complexes. To conclude, six loci may be recommended for primary genotyping of M. bovis/M. caprae isolates in Bulgaria: ETRC, QUB11b, QUB11a, QUB26, QUB3232, and MIRU10 (HGI 0.77). VNTR typing based on a limited number of loci appears to be useful for primary bTB surveillance.
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Genetic Diversity and Primary Drug Resistance of Mycobacterium tuberculosis Beijing Genotype Strains in Northwestern Russia. Microorganisms 2023; 11:microorganisms11020255. [PMID: 36838219 PMCID: PMC9966048 DOI: 10.3390/microorganisms11020255] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Revised: 01/12/2023] [Accepted: 01/17/2023] [Indexed: 01/21/2023] Open
Abstract
The Beijing genotype is the main family of Mycobacterium tuberculosis in Russia. We analyzed its diversity and drug resistance in provinces across Northwestern Russia to identify the epidemiologically relevant Beijing strains. The study collection included 497 isolates from newly-diagnosed tuberculosis (TB) patients. Bacterial isolates were subjected to drug-susceptibility testing and genotyping. The Beijing genotype was detected in 57.5% (286/497); 50% of the Beijing strains were multidrug-resistant (MDR). Central Asian/Russian and B0/W148 groups included 176 and 77 isolates, respectively. MDR was more frequent among B0/W148 strains compared to Central Asian/Russian strains (85.7% vs. 40.3%, p < 0.0001). Typing of 24 minisatellite loci of Beijing strains revealed 82 profiles; 230 isolates were in 23 clusters. The largest Central Asian/Russian types were 94-32 (n = 75), 1065-32 (n = 17), and 95-32 (n = 12). B0/W148 types were 100-32 (n = 59) and 4737-32 (n = 5). MDR was more frequent in types 1065-32 (88.2%), 100-32 (83.1%), and 4737-32 (100%). In contrast, type 9391-32 (n = 9) included only drug-susceptible strains. To conclude, M. tuberculosis Beijing genotype is dominant in Northwestern Russia, and an active transmission of overwhelmingly MDR B0/W148 types explains the reported increase of MDR-TB. The presence of MDR-associated minor variants (type 1071-32/ancient Beijing and Central Asia Outbreak strain) in some of the studied provinces also requires attention.
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Features of Mycobacterium bovis Complete Genomes Belonging to 5 Different Lineages. Microorganisms 2023; 11:microorganisms11010177. [PMID: 36677470 PMCID: PMC9865570 DOI: 10.3390/microorganisms11010177] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Revised: 01/06/2023] [Accepted: 01/07/2023] [Indexed: 01/12/2023] Open
Abstract
Mammalian tuberculosis (TB) is a zoonotic disease mainly due to Mycobacterium bovis (M. bovis). A current challenge for its eradication is understanding its transmission within multi-host systems. Improvements in long-read sequencing technologies have made it possible to obtain complete bacterial genomes that provide a comprehensive view of species-specific genomic features. In the context of TB, new genomic references based on complete genomes genetically close to field strains are also essential to perform precise field molecular epidemiological studies. A total of 10 M. bovis strains representing each genetic lineage identified in France and in other countries were selected for performing complete assembly of their genomes. Pangenome analysis revealed a "closed" pangenome composed of 3900 core genes and only 96 accessory genes. Whole genomes-based alignment using progressive Mauve showed remarkable conservation of the genomic synteny except that the genomes have a variable number of copies of IS6110. Characteristic genomic traits of each lineage were identified through the discovery of specific indels. Altogether, these results provide new genetic features that improve the description of M. bovis lineages. The availability of new complete representative genomes of M. bovis will be useful to epidemiological studies and better understand the transmission of this clonal-evolving pathogen.
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Zdziarski P, Paściak M, Chudzik A, Kozińska M, Augustynowicz-Kopeć E, Gamian A. Cutaneous tuberculosis-ambiguous transmission, bacterial diversity with biofilm formation in humoral abnormality: case report illustration. Front Public Health 2023; 11:1091373. [PMID: 37213612 PMCID: PMC10194659 DOI: 10.3389/fpubh.2023.1091373] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Accepted: 03/27/2023] [Indexed: 05/23/2023] Open
Abstract
Background Cutaneous tuberculosis (CTB) and its paucibacillary forms are rare and difficult to diagnose, especially in immunocompromised patients with significant comorbidity. The aim of the study was to introduce the modern concept of the microbiome and diagnostic chain into clinical practice (patient-centered care) with the presentation of an atypical form of cutaneous tuberculosis with necrotizing non-healing ulcers leading to polymicrobial infection. Methods The study material included samples from sputum, broncho-alveolar lavage and skin ulcer, taken from a patient developing cutaneous tuberculosis. The microbiological investigation was performed, and identification of the isolates was carried out using genotyping and the matrix-assisted laser desorption ionization-time of flight mass spectrometry. Results The immunocompromised patient with humoral abnormality (plasma cell dyscrasia) and severe paraproteinemia developed multiorgan tuberculosis. Although cutaneous manifestation preceded systemic and pulmonary symptoms (approximately half a year), the mycobacterial genotyping confirmed the same MTB strain existence in skin ulcers and the respiratory system. Therefore, the infectious chain: transmission, the portal of entry, and bacterial spreading in vivo, were unclear. Microbial diversity found in wound microbiota (among others Gordonia bronchialis, Corynebacterium tuberculostearicum, Staphylococcus haemolyticus, and Pseudomonas oryzihabitans) was associated with the spread of a skin lesion. The in vitro biofilm-forming capacity of strains isolated from the wound may represent the potential virulence of these strains. Thus, the role of polymicrobial biofilm may be crucial in ulcer formation and CTB manifestation. Conclusions Severe wound healing as a unique biofilm-forming niche should be tested for Mycobacterium (on species and strain levels) and coexisting microorganisms using a wide range of microbiological techniques. In immunodeficient patients with non-typical CTB presentation, the chain of transmission and MTB spread is still an open issue for further research.
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Affiliation(s)
- Przemysław Zdziarski
- Department of Clinical Immunology, Tuberculosis and Pulmonary Disease, Lower Silesian Oncology Center, Wroclaw, Poland
- *Correspondence: Przemysław Zdziarski
| | - Mariola Paściak
- Department of Immunology of Infectious Diseases, Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Wroclaw, Poland
| | - Anna Chudzik
- Department of Immunology of Infectious Diseases, Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Wroclaw, Poland
| | - Monika Kozińska
- Department of Microbiology, National Tuberculosis and Lung Diseases Research Institute, Warsaw, Poland
| | - Ewa Augustynowicz-Kopeć
- Department of Microbiology, National Tuberculosis and Lung Diseases Research Institute, Warsaw, Poland
| | - Andrzej Gamian
- Department of Immunology of Infectious Diseases, Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Wroclaw, Poland
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Finardi AJ, de Oliveira NG, de Moraes EB, Batista LCF, Bortolomai BE, Suffys PN, Baptista IMFD. Genetic diversity of Mycobacterium leprae in the state of São Paulo, an area of low-leprosy incidence in Brazil. Rev Soc Bras Med Trop 2023; 56:S0037-86822023000100607. [PMID: 36995787 PMCID: PMC10042472 DOI: 10.1590/0037-8682-0612-2022] [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: 12/15/2022] [Accepted: 02/02/2023] [Indexed: 03/29/2023] Open
Abstract
Background: Brazil has the second largest number of leprosy cases worldwide, and the state of São Paulo has been considered non-endemic since 2006. Methods: We analyzed 16 variable number tandem repeats loci and three single nucleotide polymorphisms loci of Mycobacterium leprae (M. leprae) in 125 clinical isolates from patients in different municipalities in the state. Results: The clustering pattern of M. leprae indicated that the transmission of leprosy persisted in the state and included scenarios of intra-extra-familial transmission in areas with low endemicity. Conclusions: A significantly active circulation of M. leprae was observed. Therefore, surveillance and control measures must be implemented.
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Affiliation(s)
- Amanda Juliane Finardi
- Instituto Lauro de Souza Lima, Bauru, SP, Brasil
- Universidade Estadual Paulista, Faculdade de Medicina, Botucatu, SP, Brasil
| | - Nathan Guilherme de Oliveira
- Instituto Lauro de Souza Lima, Bauru, SP, Brasil
- Universidade Estadual Paulista, Faculdade de Medicina, Botucatu, SP, Brasil
| | - Eloise Brasil de Moraes
- Instituto Lauro de Souza Lima, Bauru, SP, Brasil
- Universidade Estadual Paulista, Faculdade de Medicina, Botucatu, SP, Brasil
| | | | - Bruna Eduarda Bortolomai
- Instituto Lauro de Souza Lima, Bauru, SP, Brasil
- Universidade Estadual Paulista, Faculdade de Medicina, Botucatu, SP, Brasil
| | - Philip Noel Suffys
- Fundação Oswaldo Cruz, Laboratório de Biologia Molecular Aplicada a Micobactérias, Rio de Janeiro, RJ, Brasil
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Yin C, Mijiti X, Liu H, Wang Q, Cao B, Anwaierjiang A, Li M, Liu M, Jiang Y, Xu M, Wan K, Zhao X, Li G, Xiao H. Molecular Epidemiology of Clinical Mycobacterium tuberculosis Isolates from Southern Xinjiang, China Using Spoligotyping and 15-Locus MIRU-VNTR Typing. Infect Drug Resist 2023; 16:1313-1326. [PMID: 36919034 PMCID: PMC10008323 DOI: 10.2147/idr.s393192] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Accepted: 02/21/2023] [Indexed: 03/11/2023] Open
Abstract
Background In the last decades, the molecular epidemiological investigation of Mycobacterium tuberculosis has significantly increased our understanding of tuberculosis epidemiology. However, few such studies have been done in southern Xinjiang, China. We aimed to clarify the molecular epidemic characteristics and their association with drug resistance in the M. tuberculosis isolates circulating in this area. Methods A total of 347 isolates obtained from southern Xinjiang, China between Sep, 2017 and Sep, 2019 were included to characterize using a 15-locus MIRU-VNTR (VNTR-15China) typing and spoligotyping, and test for drug susceptibility profiles. Then the lineages and clustering of the isolates were analyzed, as well as their association with drug resistance. Results Spoligotyping results showed that 60 spoligotype international types (SITs) containing 35 predefined SITs and 25 Orphan or New patterns, and 12 definite genotypes were found, and the top three prevalent genotypes were Beijing genotype (207, 59.7%), followed by CAS1-Delhi (46, 13.6%), and Ural-2 (30, 8.6%). The prevalence of Beijing genotype infection in the younger age group (≤30) was more frequent than the two older groups (30~59 and ≥60 years old, both P values <0.05). The Beijing genotype showed significantly higher prevalence of resistance to isoniazid, rifampicin, ethambutol, multi-drug or at least one drug than the non-Beijing genotype (All P values ≤0.05). The estimated proportion of tuberculosis cases due to transmission was 18.4% according to the cluster rate acquired by VNTR-15China typing, and the Beijing genotype was the risk factor for the clustering (OR 9.15, 95% CI: 4.18-20.05). Conclusion Our data demonstrated that the Beijing genotype is the dominant lineage, associated with drug resistance, and was more likely to infect young people and contributed to tuberculosis transmission in southern Xinjiang, China. These findings will contribute to a better understanding of tuberculosis epidemiology in this area.
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Affiliation(s)
- Chunjie Yin
- School of Public Health, Xinjiang Medical University, Urumqi, People's Republic of China
| | - Xiaokaiti Mijiti
- The Eighth Affiliated Hospital of Xinjiang Medical University, Urumqi, 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, People's Republic of China
| | - Quan Wang
- The Eighth Affiliated Hospital of Xinjiang Medical University, Urumqi, People's Republic of China
| | - Bin Cao
- 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, People's Republic of China.,School of Public Health, University of South China, Hengyang, 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, People's Republic of China
| | - Mengwen Liu
- School of Public Health, Xinjiang Medical University, Urumqi, 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, People's Republic of China
| | - Miao Xu
- The Eighth Affiliated Hospital of Xinjiang Medical University, Urumqi, 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, 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, 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, People's Republic of China
| | - Hui Xiao
- School of Public Health, Xinjiang Medical University, Urumqi, People's Republic of China
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Mokrousov I, Vyazovaya A, Badleeva M, Gerasimova A, Belopolskaya O, Masharsky A, Kostyukova I, Zhdanova S, Mudarisova R, Avadenii I, Solovieva N, Skiba Y, Zhuravlev V, Pasechnik O, Ogarkov O. Molecular detection and phylogeography of the hypervirulent subtype of Mycobacterium tuberculosis Beijing 14717-15. RUSSIAN JOURNAL OF INFECTION AND IMMUNITY 2022. [DOI: 10.15789/2220-7619-mda-2082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/09/2023]
Abstract
Aim. To develop a method for the detection of Mycobacterium tuberculosis strains of the highly lethal, hypervirulent, and multidrug-resistant Beijing 14717-15-cluster and its application for screening retrospective collections of M. tuberculosis from regions of Russia. The collection included M. tuberculosis DNA samples collected within population studies. Spoligotyping and genotyping of 24 variable number of tandem repeats loci were performed according to standard protocols. Phylogenetic analysis was based on the whole genome sequencing data. Polymorphism at the genomic position 2423040 AG, specific for the Beijing 14717-15 cluster, was detected using PCR-RFLP and HhaI restriction enzyme. The bioinformatic and phylogenetic analysis of whole genome sequencing data of 205 strains of the early ancient sublineage of the M. tuberculosis Beijing genotype showed that strains with the VNTR 14717-15 profile (according to MIRU-VNTRplus.org) and those close to it were grouped into one monophyletic cluster of related strains, which we defined as Beijing 14717-15-cluster. Among the SNPs specific for the 14717-15 cluster, we chose a functionally neutral SNP at the genomic position 2423040 AG (Rv2161c Val33Ala) and developed a method for its detection in the PCR-RFLP format. Next, we applied this method to screening DNA collections from the regions of the European and Asian parts of Russia and Asian countries. The results demonstrate the presence of strains of the Beijing 14717-15 cluster only in the Asian part of Russia, with a peak in Buryatia (18%). We have developed a method for the detection of the hypervirulent and highly lethal genetic cluster M. tuberculosis Beijing 14717-15 based on the detection of a specific mutation in the Rv2161c gene using PCR followed by HhaI restriction of the PCR product and agarose gel electrophoresis to discriminate between wild-type and mutant alleles. The advantages of the proposed method are the speed, simple and unambiguous interpretation of the results, the ability to detect contamination and mixed infection, suitability for efficient analysis of large collections of M. tuberculosis strains.
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Zheng MQ, Li XX, Xu R, Liu S, Rui ZY, Guo ZY, Chen D. Bibliometric analysis of tuberculosis molecular epidemiology based on CiteSpace. Front Public Health 2022; 10:1040176. [PMID: 36483245 PMCID: PMC9723223 DOI: 10.3389/fpubh.2022.1040176] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Accepted: 10/24/2022] [Indexed: 12/13/2022] Open
Abstract
Background Tuberculosis is a communicable disease that is a major cause of ill health. Bibliometrics is an important statistical methodology used to analyze articles and other publications in the literature study. In this study, publications on molecular epidemiology were analyzed using bibliometric analysis. The statistical analysis of influential publications, journals, countries and authors was first conducted. Methods The Web of Science database was searched for publications on the molecular epidemiology of tuberculosis with the keywords "tuberculosis" and "molecular epidemiology" in the title. The number of publications, citation analysis, co-authorship of the author, institution and country, keyword co-occurrence, and reference co-citations were analyzed. Results A total of 225 journal articles were retrieved. The mean citation was 37.72 per article and 292.69 per year. The annual publications on molecular epidemiology fluctuated within a certain range in the past. Journal of Clinical Microbiology is the most published journal with 33 articles. RASTOGI N is the most prolific author with 11 articles. The top 1 research institution is Inst Pasteur Guadeloupe. Stratified by the number of publications, the USA was the most prolific country. It also cooperates closely with other countries. Burstness analysis of references and keywords showed that the developing research trends in this field mainly focused on "genetic diversity" and "lineage" during the past decade. Conclusion The annual publications on tuberculosis molecular epidemiology fluctuated within a specific range in the past decade. The USA continues to dominate research output and funding. The exchange of expertise, ideas, and technology is of paramount importance in this field. More frequent and deeper cooperation among countries or institutions will be essential in the future.
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Affiliation(s)
- Mei-qin Zheng
- Department of Pharmacy, Beijing Chest Hospital, Capital Medical University, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing, China,Department of Pharmacy, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China
| | - Xi-xi Li
- Department of Pharmacy, Beijing Chest Hospital, Capital Medical University, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing, China,Department of Pharmacy, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China
| | - Rui Xu
- Department of Pharmacy, Beijing Chest Hospital, Capital Medical University, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing, China
| | - Shuo Liu
- Department of Pharmacy, Beijing Chest Hospital, Capital Medical University, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing, China
| | - Zhi-yong Rui
- Department of Pharmacy, Beijing Chest Hospital, Capital Medical University, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing, China
| | - Zhen-yong Guo
- Department of Pharmacy, Beijing Chest Hospital, Capital Medical University, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing, China,*Correspondence: Zhen-yong Guo
| | - Di Chen
- Department of Pharmacy, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China,Di Chen
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Analysis of the twenty-six largest outbreaks of tuberculosis in Aragon using whole-genome sequencing for surveillance purposes. Sci Rep 2022; 12:18766. [PMID: 36335223 PMCID: PMC9637126 DOI: 10.1038/s41598-022-23343-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Accepted: 10/30/2022] [Indexed: 11/08/2022] Open
Abstract
The incidence of tuberculosis in Aragon, Spain, is around ten cases per 100,000 inhabitants. Since 2004, a molecular surveillance protocol has been carried out; therefore, all M. tuberculosis strains are genotyped. Recently, whole-genome sequencing has been implemented for relevant isolates. The aim of this work is to characterise at the molecular level the causative strains of the 26 largest outbreaks of the community (including ten or more cases), genotyped by IS6110-RFLP and causing 26% of tuberculosis cases. To achieve this objective, two or three isolates of each IS6110-cluster belonging to different years were selected for sequencing. We found that strains of lineages L4.8, L4.3 and L4.1.2 were the most frequent. The threshold of 12 SNPs as the maximum distance for confirming the belonging to an outbreak was met for 18 of the 26 IS6110-clusters. Four pairs of isolates with more than 90 SNPs were identified as not belonging to the same strain, and four other pairs were kept in doubt as the number of SNPs was close to 12, between 14 and 35. The study of Regions of Difference revealed that they are lineage conserved. Moreover, we could analyse the IS6110 locations for all genome-sequenced isolates, finding some frequent locations in isolates belonging to the same lineage and certain IS6110 movements between the paired isolates. In the vast majority, these movements were not captured by the IS6110-RFLP pattern. After classifying the genes containing SNP by their functional category, we could confirm that the number of SNPs detected in genes considered as virulence factors and the number of cases the strain produced were not related, suggesting that a particular SNP is more relevant than the number. The characteristics found in the most successful strains in our community could be useful for other researchers in epidemiology, virulence and pathogenesis.
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Gaballah A, Ghazal A, Almiry R, Hussein S, Emad R, El-Sherbini E. Fingerprinting of Mycobacterium tuberculosis isolates by MIRU-VNTR genotyping and detection of isoniazid resistance by real-time PCR. J Med Microbiol 2022; 71. [DOI: 10.1099/jmm.0.001603] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Introduction. Tuberculosis (TB) is a great public health problem in developing countries such as Egypt. Genotyping of
Mycobacterium tuberculosis
isolates has a prominent role in the field of TB prevention.
Aim. This study aimed to evaluate real-time PCR using Minor Groove Binder (MGB) probes and to identify circulating lineages/sub-lineages of
M. tuberculosis
and their transmission patterns.
Hypothesis. We hypothesize that MIRU-VNTR technique is efficient in identifying circulating
M. tuberculosis
lineages in Egypt.
Methodology. Fifty sputum specimens positive for acid-fast bacilli were included. Isoniazid (INH) resistance was detected using the 1 % proportion method. Real-time PCR using MGB-probes was used for simultaneous detection of TB infection and INH resistance. Partial sequencing of the katG gene was used to confirm INH resistance results. A standard 15 Mycobacterial Interspersed Repetitive Unit Variable Number Tandem Repeat (15-MIRU-VNTR) approach was used for genotyping through the MIRU-VNTRplus online platform.
Results. Only seven specimens showed phenotypic resistance to INH.
M. tuberculosis
was detected in all samples, while a mutation in the katG gene codon 315 was detected only in five samples, which were also phenotypically INH-resistant. Sequencing of the katG gene showed codon 315 mutation genotypically and phenotypically in the five INH-resistant isolates. Molecular genotyping of
M. tuberculosis
isolates revealed that the majority of isolates (26/50, 52 %) belonged to the S family of lineage_4. A low clustering rate (2 %) was observed among our isolates. According to the Hunter-Gaston Discriminatory Index (HGDI), 11 MIRU-VNTR loci were highly or moderately discriminative, while four loci were less polymorphic.
Conclusion. MIRU-VNTR genotyping revealed a low clustering rate with a low recent transmission rate of
M. tuberculosis
strains in Alexandria, Egypt.
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Affiliation(s)
- Ahmed Gaballah
- Department of Microbiology, Medical Research Institute, Alexandria University, Egypt
| | - Abeer Ghazal
- Department of Microbiology, Medical Research Institute, Alexandria University, Egypt
| | - Reda Almiry
- Department of Clinical Pathology, Alexandria Armed Forces Hospital, Alexandria, Egypt
| | - Somaya Hussein
- Elmamoura Chest Hospital, Egyptian Ministry of Health, Alexandria, Egypt
| | - Rasha Emad
- Alexandria Main University Hospital, Alexandria University, Alexandria, Egypt
| | - Eglal El-Sherbini
- Department of Microbiology, Medical Research Institute, Alexandria University, Egypt
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Al-Mutairi NM, Ahmad S, Mokaddas E, Al-Hajoj S. First insights into the phylogenetic diversity of Mycobacterium tuberculosis in Kuwait and evaluation of REBA MTB-MDR assay for rapid detection of MDR-TB. PLoS One 2022; 17:e0276487. [PMID: 36264939 PMCID: PMC9584360 DOI: 10.1371/journal.pone.0276487] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Accepted: 10/07/2022] [Indexed: 11/06/2022] Open
Abstract
Early detection of Mycobacterium tuberculosis (Mtb) in clinical specimens, its susceptibility to anti-TB drugs and disruption of infection transmission to new hosts are essential components for global tuberculosis (TB) control efforts. This study investigated major Mtb genotypes circulating in Kuwait and evaluated the performance of REBA MTB-MDR (REBA) test in comparison to GenoType MTBDRplus (gMTBDR+) assay for rapid detection of resistance of Mtb to isoniazid and rifampicin (MDR-TB). M. tuberculosis isolates (n = 256) originating predominantly from expatriate patients during a 6-month period were tested by spoligotyping and a dendrogram was created by UPGMA using MIRU-VNTRplus software. Phenotypic drug susceptibility testing (DST) was performed by MGIT 960 system. Genotypic DST for isoniazid and rifampicin was done by REBA and gMTBDR+ assays. Spoligotyping assigned 188 (73.4%) isolates to specific spoligotype international type (SIT) while 68 isolates exhibited orphan patterns. All major M. tuberculosis lineages were detected and EAI, CAS and Beijing families were predominant. Phylogenetic tree showed 131 patterns with 105 isolates exhibiting a unique pattern while 151 isolates clustered in 26 patterns. Fifteen isolates were resistant to one/more drugs. REBA and gMTBDR+ detected isoniazid resistance in 11/12 and 10/12 and rifampicin resistance in 4/5 and 4/5 resistant isolates, respectively. The diversity of SIT patterns are highly suggestive of infection of most expatriate patients with unique Mtb strains, likely acquired in their native countries before their arrival in Kuwait. Both, REBA and gMTBDR+ assays performed similarly for detection of resistance of Mtb to isoniazid and rifampicin for rapid detection of MDR-TB.
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Affiliation(s)
- Noura M. Al-Mutairi
- Department of Microbiology, Faculty of Medicine, Kuwait University, Safat, Kuwait
| | - Suhail Ahmad
- Department of Microbiology, Faculty of Medicine, Kuwait University, Safat, Kuwait
- * E-mail: ,
| | - Eiman Mokaddas
- Department of Microbiology, Faculty of Medicine, Kuwait University, Safat, Kuwait
- Kuwait National TB Control Laboratory, Shuwaikh, Kuwait
| | - Sahal Al-Hajoj
- Department of Infection and Immunity, Mycobacteriology Research Section, King Faisal Special Hospital and Research Center (KFSH & RC), Riyadh, Saudi Arabia
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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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Compilation of 10 Years of MIRU-VNTR Data: Canadian National Tuberculosis Laboratory’s Experience. CANADIAN JOURNAL OF INFECTIOUS DISEASES AND MEDICAL MICROBIOLOGY 2022; 2022:3505142. [PMID: 36046174 PMCID: PMC9424012 DOI: 10.1155/2022/3505142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Revised: 07/06/2022] [Accepted: 08/02/2022] [Indexed: 11/17/2022]
Abstract
Tuberculosis is a significant cause of morbidity worldwide and is a priority at the provincial and federal levels in Canada. It is known that tuberculosis transmission networks are complex and span many years as well as different jurisdictions and countries. MIRU-VNTR is a universal tuberculosis genotyping method that utilizes a 24-loci pattern and it has shown promise in identifying inter and intrajurisdictional clusters within Canada. MIRU-VNTR data collected over 10 years from the National Reference Centre for Mycobacteriology (NRCM) were analyzed in this study. Some clusters were unique to a single province/territory, while others spanned multiple provinces and/or territories in Canada. The use of a universal laboratory test can enhance contact tracing, provide geographical information on circulating genotypes, and hence, aid in tuberculosis investigation by public health. The housing of all data on one platform, technical ease of the method, easy exchange of data between jurisdictions, and strong collaboration with laboratories and surveillance units at the provincial and federal levels have the potential to identify possible outbreaks in real time.
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Acquah SEK, Asare P, Danso EK, Tetteh P, Tetteh AY, Boateng D, Osei-Wusu S, Afum T, Ayamdooh YI, Akugre EA, Samad OA, Quaye L, Obiri-Danso K, Kock R, Asante-Poku A, Yeboah-Manu D. Molecular epidemiology of bovine tuberculosis in Northern Ghana identifies several uncharacterized bovine spoligotypes and suggests possible zoonotic transmission. PLoS Negl Trop Dis 2022; 16:e0010649. [PMID: 35951638 PMCID: PMC9398027 DOI: 10.1371/journal.pntd.0010649] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 08/23/2022] [Accepted: 07/09/2022] [Indexed: 11/18/2022] Open
Abstract
Objective
We conducted an abattoir-based cross-sectional study in the five administrative regions of Northern Ghana to determine the distribution of bovine tuberculosis (BTB) among slaughtered carcasses and identify the possibility of zoonotic transmission.
Methods
Direct smear microscopy was done on 438 tuberculosis-like lesions from selected cattle organs and cultured on Lowenstein-Jensen media. Acid-fast bacilli (AFB) isolates were confirmed as members of the Mycobacterium tuberculosis complex (MTBC) by PCR amplification of IS6110 and rpoß. Characterization and assignment into MTBC lineage and sub-lineage were done by spoligotyping, with the aid of the SITVIT2, miruvntrplus and mbovis.org databases. Spoligotype data was compared to that of clinical M. bovis isolates from the same regions to identify similarities.
Results
A total of 319/438 (72.8%) lesion homogenates were smear positive out of which, 84.6% (270/319) had microscopic grade of at least 1+ for AFB. Two hundred and sixty-five samples (265/438; 60.5%) were culture positive, of which 212 (80.0%) were MTBC. Approximately 16.7% (34/203) of the isolates with correctly defined spoligotypes were negative for IS6110 PCR but were confirmed by rpoß. Spoligotyping characterized 203 isolates as M. bovis (198, 97.5%), M. caprae (3, 1.5%), M. tuberculosis (Mtbss) lineage (L) 4 Cameroon sub-lineage, (1, 0.5%), and M. africanum (Maf) L6 (1, 0.5%). A total of 53 unique spoligotype patterns were identified across the five administrative regions (33 and 28 were identified as orphan respectively by the SITVIT2 and mbovis.org databases), with the most dominant spoligotype being SIT1037/ SB0944 (77/203, 37.93%). Analysis of the bovine and human M. bovis isolates showed 75% (3/4) human M. bovis isolates sharing the same spoligotype pattern with the bovine isolates.
Conclusion
Our study identified that approximately 29% of M. bovis strains causing BTB in Northern Ghana are caused by uncharacterized spoligotypes. Our findings suggest possible zoonotic transmission and highlight the need for BTB disease control in Northern Ghana.
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Affiliation(s)
- Samuel Ekuban Kobina Acquah
- Noguchi Memorial Institute for Medical Research, College of Health Sciences, University of Ghana, Accra, Ghana
- Department of Clinical Microbiology, School of Medicine and Health Sciences, University for Development Studies, Tamale, Ghana
- Department of Theoretical and Applied Biology, College of Science, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Prince Asare
- Noguchi Memorial Institute for Medical Research, College of Health Sciences, University of Ghana, Accra, Ghana
- * E-mail: (PA); (DYM)
| | - Emelia Konadu Danso
- Noguchi Memorial Institute for Medical Research, College of Health Sciences, University of Ghana, Accra, Ghana
| | - Phillip Tetteh
- Noguchi Memorial Institute for Medical Research, College of Health Sciences, University of Ghana, Accra, Ghana
| | - Amanda Yaa Tetteh
- Noguchi Memorial Institute for Medical Research, College of Health Sciences, University of Ghana, Accra, Ghana
| | - Daniel Boateng
- Noguchi Memorial Institute for Medical Research, College of Health Sciences, University of Ghana, Accra, Ghana
| | - Stephen Osei-Wusu
- Noguchi Memorial Institute for Medical Research, College of Health Sciences, University of Ghana, Accra, Ghana
| | - Theophilus Afum
- Noguchi Memorial Institute for Medical Research, College of Health Sciences, University of Ghana, Accra, Ghana
| | | | - Eric Agongo Akugre
- Veterinary Services Directorate, Ministry of Food and Agriculture, Bolgatanga, Ghana
| | - Omar Abdul Samad
- Veterinary Services Directorate, Ministry of Food and Agriculture, Wa, Ghana
| | - Lawrence Quaye
- Department of Biomedical Laboratory Sciences, School of Allied Health Sciences, University for Development Studies, Tamale, Ghana
| | - Kwasi Obiri-Danso
- Department of Theoretical and Applied Biology, College of Science, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Richard Kock
- Department of Pathobiology and Population Sciences, Royal Veterinary College, London, United Kingdom
| | - Adwoa Asante-Poku
- Noguchi Memorial Institute for Medical Research, College of Health Sciences, University of Ghana, Accra, Ghana
| | - Dorothy Yeboah-Manu
- Noguchi Memorial Institute for Medical Research, College of Health Sciences, University of Ghana, Accra, Ghana
- * E-mail: (PA); (DYM)
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Mutayoba BK, Michael Hoelscher, Heinrich N, Joloba ML, Lyamuya E, Kilale AM, Range NS, Ngowi BJ, Ntinginya NE, Mfaume SM, Wilfred A, Doulla B, Lyimo J, Kisonga R, Kingalu A, Kabahita JM, Guido O, Kabugo J, Adam I, Luutu M, Namaganda MM, Namutebi J, Kasule GW, Nakato H, Byabajungu H, Lutaaya P, Musisi K, Oola D, Mboowa G, Pletschette M. Phylogenetic lineages of tuberculosis isolates and their association with patient demographics in Tanzania. BMC Genomics 2022; 23:561. [PMID: 35931954 PMCID: PMC9356438 DOI: 10.1186/s12864-022-08791-3] [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] [Received: 02/09/2022] [Accepted: 07/12/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Mycobacterium tuberculosis presents several lineages each with distinct characteristics of evolutionary status, transmissibility, drug resistance, host interaction, latency, and vaccine efficacy. Whole genome sequencing (WGS) has emerged as a new diagnostic tool to reliably inform the occurrence of phylogenetic lineages of Mycobacterium tuberculosis and examine their relationship with patient demographic characteristics and multidrug-resistance development. METHODS 191 Mycobacterium tuberculosis isolates obtained from a 2017/2018 Tanzanian drug resistance survey were sequenced on the Illumina Miseq platform at Supranational Tuberculosis Reference Laboratory in Uganda. Obtained fast-q files were imported into tools for resistance profiling and lineage inference (Kvarq v0.12.2, Mykrobe v0.8.1 and TBprofiler v3.0.5). Additionally for phylogenetic tree construction, RaxML-NG v1.0.3(25) was used to generate a maximum likelihood phylogeny with 800 bootstrap replicates. The resulting trees were plotted, annotated and visualized using ggtree v2.0.4 RESULTS: Most [172(90.0%)] of the isolates were from newly treated Pulmonary TB patients. Coinfection with HIV was observed in 33(17.3%) TB patients. Of the 191 isolates, 22(11.5%) were resistant to one or more commonly used first line anti-TB drugs (FLD), 9(4.7%) isolates were MDR-TB while 3(1.6%) were resistant to all the drugs. Of the 24 isolates with any resistance conferring mutations, 13(54.2%) and 10(41.6%) had mutations in genes associated with resistance to INH and RIF respectively. The findings also show four major lineages i.e. Lineage 3[81 (42.4%)], followed by Lineage 4 [74 (38.7%)], the Lineage 1 [23 (12.0%)] and Lineages 2 [13 (6.8%)] circulaing in Tanzania. CONCLUSION The findings in this study show that Lineage 3 is the most prevalent lineage in Tanzania whereas drug resistant mutations were more frequent among isolates that belonged to Lineage 4.
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Affiliation(s)
- Beatrice Kemilembe Mutayoba
- Department of Preventive Services, Ministry of Health, Dodoma, Tanzania.
- Department of Infectious Diseases and Tropical Medicine, Medical Center of the, University of Munich, Munich, Germany.
| | - Michael Hoelscher
- Department of Infectious Diseases and Tropical Medicine, Medical Center of the, University of Munich, Munich, Germany
| | - Norbert Heinrich
- Department of Infectious Diseases and Tropical Medicine, Medical Center of the, University of Munich, Munich, Germany
| | - Moses L Joloba
- National Tuberculosis Reference Laboratory/Supranational Reference Laboratory, Luzira, Uganda
- Department of Immunology and Molecular Biology, College of Health Sciences, Makerere University, Kampala, Uganda
| | - Eligius Lyamuya
- Department of Microbiology and Immunology, Muhimbili University of Health and Allied Sciences (MUHAS), Dar es Salaam, Tanzania
| | - Andrew Martin Kilale
- Muhimbili Research Centre, National Institute for Medical Research (NIMR), Dar es Salaam, Tanzania
| | - Nyagosya Segere Range
- Muhimbili Research Centre, National Institute for Medical Research (NIMR), Dar es Salaam, Tanzania
| | - Bernard James Ngowi
- Muhimbili Research Centre, National Institute for Medical Research (NIMR), Dar es Salaam, Tanzania
- University of Dar Es Salaam, Mbeya College of Health and Allied Sciences, Mbeya, Tanzania
| | | | - Saidi Mwinjuma Mfaume
- Muhimbili Research Centre, National Institute for Medical Research (NIMR), Dar es Salaam, Tanzania
| | - Amani Wilfred
- Muhimbili Research Centre, National Institute for Medical Research (NIMR), Dar es Salaam, Tanzania
| | - Basra Doulla
- Central Tuberculosis Reference Laboratory, Ministry of Health, National TB and Leprosy Programme, Dar es Salaam, Tanzania
| | - Johnson Lyimo
- Department of Preventive Services, Ministry of Health, National Tuberculosis and Leprosy Programme, Dodoma, Tanzania
| | - Riziki Kisonga
- Department of Preventive Services, Ministry of Health, National Tuberculosis and Leprosy Programme, Dodoma, Tanzania
| | - Amri Kingalu
- Central Tuberculosis Reference Laboratory, Ministry of Health, National TB and Leprosy Programme, Dar es Salaam, Tanzania
| | - Jupiter Marina Kabahita
- National Tuberculosis Reference Laboratory/Supranational Reference Laboratory, Luzira, Uganda
| | - Ocung Guido
- National Tuberculosis Reference Laboratory/Supranational Reference Laboratory, Luzira, Uganda
| | - Joel Kabugo
- National Tuberculosis Reference Laboratory/Supranational Reference Laboratory, Luzira, Uganda
| | - Isa Adam
- National Tuberculosis Reference Laboratory/Supranational Reference Laboratory, Luzira, Uganda
| | - Moses Luutu
- Department of Immunology and Molecular Biology, College of Health Sciences, Makerere University, Kampala, Uganda
| | - Maria Magdalene Namaganda
- Department of Immunology and Molecular Biology, College of Health Sciences, Makerere University, Kampala, Uganda
| | - Joanitah Namutebi
- National Tuberculosis Reference Laboratory/Supranational Reference Laboratory, Luzira, Uganda
| | - George William Kasule
- National Tuberculosis Reference Laboratory/Supranational Reference Laboratory, Luzira, Uganda
| | - Hasfah Nakato
- National Tuberculosis Reference Laboratory/Supranational Reference Laboratory, Luzira, Uganda
| | - Henry Byabajungu
- National Tuberculosis Reference Laboratory/Supranational Reference Laboratory, Luzira, Uganda
| | - Pius Lutaaya
- National Tuberculosis Reference Laboratory/Supranational Reference Laboratory, Luzira, Uganda
| | - Kenneth Musisi
- National Tuberculosis Reference Laboratory/Supranational Reference Laboratory, Luzira, Uganda
| | - Denis Oola
- National Tuberculosis Reference Laboratory/Supranational Reference Laboratory, Luzira, Uganda
| | - Gerald Mboowa
- Africa Centres for Disease Control and Prevention, African Union Commission, Addis Ababa, Ethiopia
| | - Michel Pletschette
- Department of Infectious Diseases and Tropical Medicine, Medical Center of the, University of Munich, Munich, Germany
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Monir BB, Sultana SS, Tarafder S. 24 loci MIRU-VNTR analysis and pattern of drug resistance in pre-extensively drug resistant pulmonary tuberculosis in Bangladesh. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2022; 102:105304. [PMID: 35595025 DOI: 10.1016/j.meegid.2022.105304] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Revised: 05/11/2022] [Accepted: 05/13/2022] [Indexed: 06/15/2023]
Abstract
Phylogenetic diversity and distinct phylogeographic distribution of Mycobacterium tuberculosis (MTB) contribute to regional differences in drug resistance. The emergence of pre-extensively drug resistant tuberculosis (Pre-XDR-TB) becomes obstacles to achieve End TB strategy in Bangladesh. This cross-sectional study was conducted to identify the strains of different lineages of MTB, their variations of distribution among Pre-XDR-TB cases and to observe the linkage of particular strains of MTB with drug resistance. A total of 33 Pre-XDR-TB isolates were enrolled in this study. All isolates were confirmed as MTB by MPT 64 antigen detection and genotyped by 24 loci Mycobacterial Interspersed Repetitive Unit-Variable Number of Tandem Repeats (MIRU-VNTR) analysis. Drug resistance was detected by second line Line probe assay (LPA). Beijing was the predominant strain 16 (48.48%), followed by Delhi/CAS 5(15.15%), LAM 4 (12.12%) and Harlem 3(9.10%), EAI 2(6.06%), Cameroon 2(6.06%) and NEW-1 1(3.03%). There were 31 different genotypes consisting of 2 clusters and 29 singletons. All the clustered strains were belonged to Beijing lineage. Recent transmission occurred manly by Beijing strains, showed low transmission rate (12.1%). Of 33 isolates 30(90.90%) were Fluoroquinolones resistant, the mutations involved was Asp94Gly in gyr A MUT 3C gene 13(39.39%) in quinolone resistance determining region (QRDR) followed by 11 (33.33%) in gyr A MUT 1. Three (9.10%) isolates showed resistant to injectable 2nd line drugs and all mutation occurs in G1484T of rrs MUT 2. Beijing lineage was predominant in treatment failure and relapse cases. Levofloxacin was resistant to all Pre-XDR-TB cases, but moxifloxacin showed low level resistance. QUB 26 was the most discriminatory locus (0.85) among 24 loci whereas MIRU 2 was the least (0.03). 24 loci MIRU-VNTR analysis shows high discriminatory index (0.71), found to be powerful tool for genotyping of Pre-XDR-TB, which is the first study in Bangladesh that enhanced the current TB control policy.
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Affiliation(s)
- Bayzid Bin Monir
- National Institute of Laboratory Medicine and Referral Centre, Dhaka, Bangladesh
| | - Sabia Shahin Sultana
- Department of Microbiology, Shaheed Suhrawardy Medical College, Dhaka, Bangladesh
| | - Shirin Tarafder
- Bangabandhu Sheikh Mujib Medical University (BSMMU), Dhaka 1000, Bangladesh.
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Lau A, Lin C, Barrie J, Winter C, Armstrong G, Egedahl ML, Doroshenko A, Heffernan C, Asadi L, Fisher D, Paulsen C, Moolji J, Long R. The Radiographic and Mycobacteriologic Correlates of Subclinical Pulmonary TB in Canada: A Retrospective Cohort Study. Chest 2022; 162:309-320. [PMID: 35122750 DOI: 10.1016/j.chest.2022.01.047] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2021] [Revised: 01/13/2022] [Accepted: 01/22/2022] [Indexed: 10/19/2022] Open
Abstract
BACKGROUND Very little is known about subclinical pulmonary TB (PTB), a recently described intermediate state, in high-income countries. RESEARCH QUESTION What is the prevalence of subclinical PTB in Canada? What are its diagnostic chest radiography features? What is the relationship between those features and time to culture positivity, and what is the association between DNA fingerprint clustering, a measure of local transmission, and radiographic or other features in the foreign-born? STUDY DESIGN AND METHODS We used primary source data to identify a 16-year retrospective cohort of patients with PTB. Demographic and mycobacteriologic features in patients with subclinical and clinical disease were compared, and the reason for assessment of patients with subclinical disease was described. Diagnostic chest radiographs in patients with subclinical disease were read by two independent readers and were arbitrated by a third reader. Linear regression was used to compute time to culture positivity (in days) in relationship to the change in chest radiograph findings from normal or minimally abnormal to moderately or far advanced, adjusted for age and sex and stratified by reason for assessment. Multivariate logistic regression was used in foreign-born patients with subclinical disease to determine associations between DNA fingerprint clustering of Mycobacterium TB isolates and age, sex, chest radiograph features, and time since arrival. RESULTS We identified 1,656 patients with PTB, 347 of whom (21%) were subclinical. Compared with patients with clinical disease, patients with subclinical disease were more likely to be foreign-born (90.2% vs 79.6%) and to demonstrate negative smear results (88.2% vs 43.5%). The median time to culture-positivity was 18 days (interquartile range [IQR], 14-25 days) vs 12 days (IQR, 7-17 days). Most patients with PTB (75.2%) were identified during active case finding. Parenchymal disease was absent or minimal on chest radiography in 86.4% of patients. More advanced disease on chest radiography was associated with shorter times to culture positivity in nonstratified (by 3.3 days) and stratified (by 4.5-5.8 days) analysis (active case-finding groups). DNA fingerprint clustering was associated with male sex and a longer time between arrival and diagnosis. INTERPRETATION Subclinical patients with PTB constitute a substantial and heterogeneous minority of patients with PTB in high-income countries. DNA fingerprint clustering is consistent with some, albeit limited, local transmission.
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Affiliation(s)
- Angela Lau
- Department of Medicine, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB, Canada
| | - Christopher Lin
- Department of Family Medicine, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB, Canada
| | - James Barrie
- Department of Radiology and Diagnostic Imaging, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB, Canada
| | - Christopher Winter
- Department of Radiology and Diagnostic Imaging, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB, Canada
| | - Gavin Armstrong
- Department of Radiology and Diagnostic Imaging, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB, Canada
| | - Mary Lou Egedahl
- Department of Medicine, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB, Canada
| | - Alexander Doroshenko
- Department of Medicine, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB, Canada
| | - Courtney Heffernan
- Department of Medicine, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB, Canada
| | - Leyla Asadi
- Department of Medicine, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB, Canada
| | - Dina Fisher
- Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Catherine Paulsen
- Department of Medicine, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB, Canada
| | - Jalal Moolji
- Department of Medicine, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB, Canada
| | - Richard Long
- Department of Medicine, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB, Canada.
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Kanyala E, Shuaib YA, Schwarz NG, Andres S, Richter E, Sawadogo B, Sawadogo M, Germaine M, Lassina O, Poppert S, Frickmann H. Prevalence and Molecular Characterization of Mycobacterium bovis in Slaughtered Cattle Carcasses in Burkina Faso; West Africa. Microorganisms 2022; 10:microorganisms10071378. [PMID: 35889097 PMCID: PMC9316762 DOI: 10.3390/microorganisms10071378] [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: 05/31/2022] [Revised: 07/01/2022] [Accepted: 07/06/2022] [Indexed: 11/22/2022] Open
Abstract
This cross-sectional study was conducted at the slaughterhouses/slabs of Oudalan and Ouagadougou in Burkina Faso, between August and September 2013. It aimed at determining the prevalence of bovine tuberculosis (bTB) suggestive lesions in slaughtered cattle carcasses and to identify and characterize the mycobacteria isolated from these lesions. A thorough postmortem examination was conducted on carcasses of a total of 2165 randomly selected cattle. The overall prevalence of bTB suggestive lesions was 2.7% (58/2165; 95% CI 2.1–3.5%). Due to the low number of positive samples, data were descriptively presented. The lesions were either observed localized in one or a few organs or generalized (i.e., miliary bTB) in 96.6% (n = 57) and 3.4% (n = 2), respectively. The identified mycobacteria were M. bovis (44.4%, n = 20), M. fortuitum (8.9%, n = 4), M. elephantis (6.7%, n = 3), M. brumae (4.4%, n = 2), M. avium (2.2%, n = 1), M. asiaticum (2.2%, n = 1), M. terrae (2.2%, n = 1), and unknown non-tuberculous mycobacteria (NTM) (11.1%, n = 5). Moreover, eight mixed cultures with more than one Mycobacterium species growing were also observed, of which three were M. bovis and M. fortuitum and three were M. bovis and M. elephantis. In conclusion, M. bovis is the predominant causative agent of mycobacterial infections in the study area. Our study has identified a base to broaden the epidemiological knowledge on zoonotic transmission of mycobacteria in Burkina Faso by future studies investigating further samples from humans and animals, including wild animals employing molecular techniques.
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Affiliation(s)
- Estelle Kanyala
- Institut de Recherche en Sciences de la Santé, Bobo-Dioulasso BP 390, Burkina Faso;
| | - Yassir Adam Shuaib
- College of Veterinary Medicine, Sudan University of Science and Technology, P.O. Box 204, Khartoum North 13321, Sudan;
- Molecular and Experimental Mycobacteriology, Research Center Borstel, 23845 Borstel, Germany
| | | | - Sönke Andres
- National Reference Laboratory for Mycobacteria, Research Center Borstel, 23845 Borstel, Germany;
| | - Elvira Richter
- Tuberculosis Laboratory, Laboratory Limbach, 69126 Heidelberg, Germany;
| | - Bernard Sawadogo
- West Africa Francophone, African Field Epidemiology Network (AFENET), Ouagadougou 01 BP 364, Burkina Faso;
| | - Mamadou Sawadogo
- Laboratory of Biochemistry, Health Sciences Training and Research Unit, University of Ouagadougou, Ouagadougou BP 7021, Burkina Faso;
| | | | - Ouattara Lassina
- Direction Générale des Services Vétérinaires (DGSv), Ouagadougou 01 BP 364, Burkina Faso;
| | - Sven Poppert
- Bernhard Nocht Institute for Tropical Medicine Hamburg, 20359 Hamburg, Germany
- Correspondence: (S.P.); or (H.F.)
| | - Hagen Frickmann
- Department of Microbiology and Hospital Hygiene, Bundeswehr Hospital Hamburg, 20359 Hamburg, Germany
- Institute for Medical Microbiology, Virology and Hygiene, University Medicine Rostock, 18057 Rostock, Germany
- Correspondence: (S.P.); or (H.F.)
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Li Y, Shi J, Song W, Shao Y, Zhu L, Chen C. A retrospective Cohort Study on the Treatment Outcomes and Genotyping of Isoniazid-Resistant Tuberculosis Patients in Eastern China. J Glob Antimicrob Resist 2022; 30:335-339. [PMID: 35817264 DOI: 10.1016/j.jgar.2022.07.003] [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: 03/28/2022] [Revised: 05/31/2022] [Accepted: 07/01/2022] [Indexed: 10/17/2022] Open
Abstract
OBJECTIVES Isoniazid resistance might be overlooked due to the priority of detection of rifampicin-resistant tuberculosis. It was urgent to reveal the current situation of isoniazid-resistant tuberculosis (HR-TB), including unfavorable outcomes and bacterial factors. METHODS A retrospective cohort study was undertaken by enrolling 120 HR-TB and 193 drug-sensitive tuberculosis (DS-TB). 24 loci MIRU-VNTR and Spoligotyping were adopted for genotyping. RESULTS We found 106 (88.3%) HR-TB and 165(85.5%) DS-TB were treated with the first-line drugs. Meanwhile, 12 (10.0%) patients of the HR-TB and 7 (3.63%) patients of the DS-TB involved adverse treatment outcomes, respectively. (χ2 =5.271, P=0.028). A total of 78 DNAs from HR Mycobacterium tuberculosis and 114 DNAs from DS Mycobacterium tuberculosis were available for MIRU-VNTR and Spoligotyping. The clustering rate was 17.9% (14/78) for HR-TB and 16.7% (19/114) for DS-TB, and reached no significant difference (χ2 =0.05, P=0.8171). The Beijing family strains accounted for 83.7% (65/78) among HR-TB, 80.0% (91/114) among DS-TB (χ2=0.37, P=0.5407). The adverse treatment outcomes for HR-TB all occurred in patients infected with Beijing family strains (13.8%), but no difference was found between Beijing and non-Beijing genotypes (P=0.342). CONCLUSION the adverse outcome of HR-TB was significantly higher than that of DS-TB, and most of the HR-TB patients were receiving a standard first-line regimen. Although the clustering rate and Beijing genotype distribution among HR-TB and DS-TB showed no significant difference, Beijing genotype was the dominant genotype and the proportion of Beijing genotype was only slightly high among HR-TB than DS-TB.
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Affiliation(s)
- Yishu Li
- Center for Disease Control and Prevention of Wuzhong District, Suzhou, Jiangsu Province, PR China; Department of Epidemiology and Statistics, School of Public Health, Southeast University, Nanjing, Jiangsu Province, PR China
| | - Jinyan Shi
- The Fourth Hospital of Lianyungang City, Lianyungang, Jiangsu Province, PR China
| | - Wenlei Song
- Center for Disease Control and Prevention of Kunshan, Suzhou, Jiangsu Province, PR China
| | - Yan Shao
- Department of Chronic Communicable Disease, Center for Disease Control and Prevention of Jiangsu Province, Nanjing, Jiangsu Province, PR China
| | - Limei Zhu
- Department of Chronic Communicable Disease, Center for Disease Control and Prevention of Jiangsu Province, Nanjing, Jiangsu Province, PR China
| | - Cheng Chen
- Department of Chronic Communicable Disease, Center for Disease Control and Prevention of Jiangsu Province, Nanjing, Jiangsu Province, PR China.
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Bakhtiyariniya P, Khosravi AD, Hashemzadeh M, Savari M. Genetic diversity of drug-resistant Mycobacterium tuberculosis clinical isolates from Khuzestan province, Iran. AMB Express 2022; 12:85. [PMID: 35789443 PMCID: PMC9253214 DOI: 10.1186/s13568-022-01425-7] [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: 04/10/2022] [Accepted: 06/21/2022] [Indexed: 11/10/2022] Open
Abstract
The emergence of drug-resistant strains of the Mycobacterium tuberculosis (MTB) has challenged tuberculosis control programs. So far, few studies using the 24-locus mycobacterial interspersed repetitive unit variable number tandem repeats (MIRU-VNTR) have investigated the genetic diversity of MTB in Iran. This study aimed to determine the genetic diversity of MTB isolates resistant to first-line anti-tuberculosis drugs using 24-locus MIRU-VNTR in southwestern Iran. Out of 6620 MTB clinical isolates, 29 resistant isolates to one or more isoniazid, rifampin, and ethambutol were detected using drug susceptibility testing by the proportional method. The manual 24-locus MIRU-VNTR was used to determine the MTB resistant isolates’ phylogenetic relationship. MIRU-VNTRplus web application tools were applied to analyze the associated data. Using 24-locus MIRU-VNTR, 13.8% of isolates (n = 4) were distributed in two clusters, and the remaining 86.2% (n = 25) showed a unique pattern. Four clonal complexes were observed in the minimum spanning tree based on the double-locus variant. Most isolates belonged to Delhi/CAS (34.5%, 10/29) and NEW-1 (24.1%, 7/29) sub-lineages, followed by EAI and LAM with a frequency of 6.9% (2/29) and 3.5% (1/29), respectively. Eight isolates (27.6%) did not match any genotype in the database. The 24-locus MIRU-VNTR showed a high discriminatory power; however, the 15-locus and 12-locus set analyses were more discriminative. Our study revealed a high degree of genetic diversity among drug-resistant MTB isolates, which could be interpreted as the low rate of person-to-person transmission in this region. The 15-locus MIRU-VNTR would be recommended for preliminary genotyping of drug-resistant MTB.
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Affiliation(s)
- Pejman Bakhtiyariniya
- Infectious and Tropical Diseases Research Center, Health Research Institute, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran.,Department of Microbiology, Faculty of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Azar Dokht Khosravi
- Infectious and Tropical Diseases Research Center, Health Research Institute, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran. .,Department of Microbiology, Faculty of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran. .,Iranian Study Group on Microbial Drug Resistance, Tehran, Iran.
| | - Mohammad Hashemzadeh
- Infectious and Tropical Diseases Research Center, Health Research Institute, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran.,Department of Microbiology, Faculty of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Mohammad Savari
- Infectious and Tropical Diseases Research Center, Health Research Institute, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran.,Department of Microbiology, Faculty of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
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Charles C, Conde C, Biet F, Boschiroli ML, Michelet L. IS6110 Copy Number in Multi-Host Mycobacterium bovis Strains Circulating in Bovine Tuberculosis Endemic French Regions. Front Microbiol 2022; 13:891902. [PMID: 35814675 PMCID: PMC9260277 DOI: 10.3389/fmicb.2022.891902] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Accepted: 05/03/2022] [Indexed: 11/13/2022] Open
Abstract
IS6110 is an insertion sequence found in the Mycobacterium tuberculosis complex, to which Mycobacterium bovis belongs, which can play a role in genome plasticity and in bacterial evolution. In this study, the abundance and location of IS6110 on M. bovis genomic data of French animal field strains were studied. A first analysis was performed on a panel of 81 strains that reflect the national M. bovis population’s genetic diversity. The results show that more than one-third of them are IS6110 multicopy and that 10% have IS6110 in a high copy number (more than 6 copies). Multicopy strains are those circulating in the regions where prevalence was above the national average. Further study of 93 such strains, with an IS6110 copy number of 10-12, showed stability of IS6110 copy number and genome location over time and between host species. The correlation between M. bovis multicopy strains and high bovine tuberculosis (bTB) prevalence leads us to consider whether their epidemiological success could be partly due to genetic changes originated by IS6110 transposition.
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Affiliation(s)
- Ciriac Charles
- ANSES, Animal Health Laboratory, National Reference Laboratory for Tuberculosis, Paris-Est University, Paris, France
- INRAE, ISP, Université de Tours, Nouzilly, France
| | - Cyril Conde
- INRAE, ISP, Université de Tours, Nouzilly, France
| | - Franck Biet
- INRAE, ISP, Université de Tours, Nouzilly, France
| | - Maria Laura Boschiroli
- ANSES, Animal Health Laboratory, National Reference Laboratory for Tuberculosis, Paris-Est University, Paris, France
| | - Lorraine Michelet
- ANSES, Animal Health Laboratory, National Reference Laboratory for Tuberculosis, Paris-Est University, Paris, France
- *Correspondence: Lorraine Michelet,
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Origin and Global Expansion of Mycobacterium tuberculosis Complex Lineage 3. Genes (Basel) 2022; 13:genes13060990. [PMID: 35741753 PMCID: PMC9222951 DOI: 10.3390/genes13060990] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2022] [Revised: 05/14/2022] [Accepted: 05/19/2022] [Indexed: 11/25/2022] Open
Abstract
Simple Summary Tuberculosis still causes 1.5 million deaths annually and is mainly caused by Mycobacterium tuberculosis complex strains belonging to three evolutionary modern lineages (Lineages 2–4). While Lineage 2 and Lineage 4 virtually conquered the world, Lineage 3 is particularly successful in Northern and Eastern Africa, as well as in Southern Asia, the suspected evolutionary origin of these strains. Here, we sought to understand how Lineage 3 strains came to the African continent. To this end, we performed routine genotyping to characterize over 2500 clinical isolates from 38 countries. We then selected a representative collection of 373 isolates for a whole-genome analysis and a modeling approach to infer the geographic origin of different sublineages. In fact, the origin of Lineage 3 could be located in India, and we found evidence for independent introductions of four distinct sublineages into North/East Africa, in line with known ancient exchanges and migrations between both world regions. Our study illustrates that the evolutionary history of humans and their pathogens are closely connected and further provides a systematic understanding of the genomic diversity of Lineage 3, which could be important for the development of new tuberculosis vaccines or new therapeutics. Abstract Mycobacterium tuberculosis complex (MTBC) Lineage 3 (L3) strains are abundant in world regions with the highest tuberculosis burden. To investigate the population structure and the global diversity of this major lineage, we analyzed a dataset comprising 2682 L3 strains from 38 countries over 5 continents, by employing 24-loci mycobacterial interspersed repetitive unit-variable number of tandem repeats genotyping (MIRU-VNTR) and drug susceptibility testing. We further combined whole-genome sequencing (WGS) and phylogeographic analysis for 373 strains representing the global L3 genetic diversity. Ancestral state reconstruction confirmed that the origin of L3 strains is located in Southern Asia and further revealed multiple independent introduction events into North-East and East Africa. This study provides a systematic understanding of the global diversity of L3 strains and reports phylogenetic variations that could inform clinical trials which evaluate the effectivity of new drugs/regimens or vaccine candidates.
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Bakuła Z, Wuyep VB, Bartocha Ł, Vyazovaya A, Ikeh EI, Bielecki J, Mokrousov I, Jagielski T. Molecular snapshot of drug-resistant Mycobacterium tuberculosis strains from the Plateau State, Nigeria. PLoS One 2022; 17:e0266837. [PMID: 35609028 PMCID: PMC9129033 DOI: 10.1371/journal.pone.0266837] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2021] [Accepted: 03/29/2022] [Indexed: 11/18/2022] Open
Abstract
Nigeria ranks 1st in Africa and 6th globally with the highest burden of tuberculosis (TB). However, only a relatively few studies have addressed the molecular epidemiology of Mycobacterium tuberculosis in this country. The aim of this work was to analyze the genetic structure of drug-resistant (DR) M. tuberculosis population in the Plateau State (central Nigeria), with the results placed in the broader context of West Africa. The study sample included 67 DR M. tuberculosis isolates, recovered from as many TB patients between November 2015 and January 2016, in the Plateau State. The isolates were subjected to spoligotyping and MIRU-VNTR typing. A total of 20 distinct spoligotypes were obtained, split into 3 clusters (n = 50, 74.6%, 2–33 isolates per cluster) and 17 (25.4%) unique patterns. The Cameroon clade was the largest lineage (62.7%) followed by T (28.3%), LAM (3%), and Haarlem (3%) clades. Upon MIRU-VNTR typing, the isolates produced 31 profiles, i.e. 7 clusters (n = 43, 64.2%, 2–17 isolates per cluster) and 24 singletons. A combined spoligotyping and MIRU-VNTR typing analysis showed 20.9% of the cases clustered and estimated the recent transmission rate at 11.9%. In conclusion, two lineages, namely Cameroon, and T accounted for the majority (91%) of cases. No association was observed between the most prevalent Cameroon lineage and drug resistance, including multidrug resistant (MDR) phenotype, or any of the patient demographic characteristics.
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Affiliation(s)
- Zofia Bakuła
- Department of Medical Microbiology, Institute of Microbiology, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | | | - Łukasz Bartocha
- Department of Medical Microbiology, Institute of Microbiology, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Anna Vyazovaya
- Laboratory of Molecular Epidemiology and Evolutionary Genetics, St. Petersburg Pasteur Institute, St. Petersburg, Russia
| | - Eugene I. Ikeh
- Department of Medical Microbiology, School of Medical and Health Sciences, College of Medical Sciences, University of Jos, Jos, Nigeria
| | - Jacek Bielecki
- Department of Medical Microbiology, Institute of Microbiology, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Igor Mokrousov
- Laboratory of Molecular Epidemiology and Evolutionary Genetics, St. Petersburg Pasteur Institute, St. Petersburg, Russia
- * E-mail: (IM); (TJ)
| | - Tomasz Jagielski
- Department of Medical Microbiology, Institute of Microbiology, Faculty of Biology, University of Warsaw, Warsaw, Poland
- * E-mail: (IM); (TJ)
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Dynamics of Mycobacterium tuberculosis Lineages in Oman, 2009 to 2018. Pathogens 2022; 11:pathogens11050541. [PMID: 35631062 PMCID: PMC9148118 DOI: 10.3390/pathogens11050541] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Revised: 04/28/2022] [Accepted: 04/29/2022] [Indexed: 01/27/2023] Open
Abstract
Study aim. Effective Tuberculosis (TB) control measures in Oman have reduced the annual incidence of tuberculosis cases by 92% between 1981 and 2016. However, the current incidence remains above the program control target of <1 TB case per 100,000 population. This has been partly attributed to a high influx of migrants from countries with high TB burdens. The present study aimed to elucidate Mycobacterium tuberculosis infection dynamics among nationals and foreigners over a period of 10 years. Methods. The study examined TB cases reported between 2009 and 2018 and examined the spatial heterogeneity of TB cases and the distribution of M. tuberculosis genotypes defined by spoligotypes and MIRU-VNTR among Omanis and foreigners. Results. A total of 484 spoligoprofiles were detected among the examined isolates (n = 1295). These include 943 (72.8%) clustered and 352 (27.2%) unique isolates. Diverse M. tuberculosis lineages exist in all provinces in Oman, with most lineages shared between Omanis and foreigners. The most frequent spoligotypes were found to belong to EAI (318, 30.9%), CAS (310, 30.1%), T (154, 14.9%), and Beijing (88, 8.5%) lineages. However, the frequencies of these lineages differed between Omanis and foreigners. Of the clustered strains, 192 MTB isolates were further analysed via MIRU-VNTR. Each isolate exhibited a unique MIRU-VNTR profile, indicative of absence of ongoing transmission. Conclusions. TB incidence exhibits spatial heterogeneity across Oman, with high levels of diversity of M. tuberculosis lineages among Omanis and foreigners and sub-lineages shared between the two groups. However, MIRU-VNTR analysis ruled out ongoing transmission.
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Wedlich N, Figl J, Liebler-Tenorio EM, Köhler H, von Pückler K, Rissmann M, Petow S, Barth SA, Reinhold P, Ulrich R, Grode L, Kaufmann SHE, Menge C. Video Endoscopy-Guided Intrabronchial Spray Inoculation of Mycobacterium bovis in Goats and Comparative Assessment of Lung Lesions With Various Imaging Methods. Front Vet Sci 2022; 9:877322. [PMID: 35591868 PMCID: PMC9113525 DOI: 10.3389/fvets.2022.877322] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Accepted: 04/01/2022] [Indexed: 11/13/2022] Open
Abstract
Bovine tuberculosis (bTB) not only poses a zoonotic threat to humans but also has a significant economic impact on livestock production in many areas of the world. Effective vaccines for humans, livestock, and wildlife are highly desirable to control tuberculosis. Suitable large animal models are indispensable for meaningful assessment of vaccine candidates. Here, we describe the refinement of an animal model for bTB in goats. Intrabronchial inoculation procedure via video-guided endoscopy in anesthetized animals, collection of lungs after intratracheal fixation in situ, and imaging of lungs by computed tomography (CT) were established in three goats using barium sulfate as surrogate inoculum. For subsequent infection experiments, four goats were infected with 4.7 × 102 colony-forming units of M. bovis by intrabronchial inoculation using video-guided endoscopy with spray catheters. Defined amounts of inoculum were deposited at five sites per lung. Four age-matched goats were mock-inoculated. None of the goats developed clinical signs until they were euthanized 5 months post infection, but simultaneous skin testing confirmed bTB infection in all goats inoculated with M. bovis. In tissues collected at necropsy, M. bovis was consistently re-isolated from granulomas in lymph nodes, draining the lungs of all the goats infected with M. bovis. Further dissemination was observed in one goat only. Pulmonary lesions were quantified by CT and digital 2D radiography (DR). CT revealed mineralized lesions in all the infected goats ranging from <5 mm to >10 mm in diameter. Small lesions <5 mm predominated. The DR failed to detect small lesions and to determine the exact location of lesions because of overlapping of pulmonary lobes. Relative volume of pulmonary lesions was low in three but high in one goat that also had extensive cavitation. CT lesions could be correlated to gross pathologic findings and histologic granuloma types in representative pulmonary lobes. In conclusion, video-guided intrabronchial inoculation with spray catheters, mimicking the natural way of infection, resulted in pulmonary infection of goats with M. bovis. CT, but not DR, presented as a highly sensitive method to quantify the extent of pulmonary lesions. This goat model of TB may serve as a model for testing TB vaccine efficacy.
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Affiliation(s)
- Nadine Wedlich
- Institute of Molecular Pathogenesis, Friedrich-Loeffler-Institute (FLI), Jena, Germany
| | - Julia Figl
- Institute of Molecular Pathogenesis, Friedrich-Loeffler-Institute (FLI), Jena, Germany
| | - Elisabeth M. Liebler-Tenorio
- Institute of Molecular Pathogenesis, Friedrich-Loeffler-Institute (FLI), Jena, Germany
- *Correspondence: Elisabeth M. Liebler-Tenorio
| | - Heike Köhler
- Institute of Molecular Pathogenesis, Friedrich-Loeffler-Institute (FLI), Jena, Germany
| | - Kerstin von Pückler
- Clinic for Small Animals – Radiology, Justus-Liebig-University Giessen, Giessen, Germany
| | - Melanie Rissmann
- Department of Experimental Animal Facilities and Biorisk Management, Friedrich-Loeffler-Institute, Greifswald-Insel Riems, Germany
| | - Stefanie Petow
- Institute for Animal Welfare and Animal Husbandry, Friedrich-Loeffler-Institute, Celle, Germany
| | - Stefanie A. Barth
- Institute of Molecular Pathogenesis, Friedrich-Loeffler-Institute (FLI), Jena, Germany
| | - Petra Reinhold
- Institute of Molecular Pathogenesis, Friedrich-Loeffler-Institute (FLI), Jena, Germany
| | - Reiner Ulrich
- Department of Experimental Animal Facilities and Biorisk Management, Friedrich-Loeffler-Institute, Greifswald-Insel Riems, Germany
| | | | - Stefan H. E. Kaufmann
- Director Emeritus, Max Planck Institute for Infection Biology, Berlin, Germany
- Emeritus Group for Systems Immunology, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
- Hagler Institute for Advanced Study, Texas A&M University, College Station, TX, United States
| | - Christian Menge
- Institute of Molecular Pathogenesis, Friedrich-Loeffler-Institute (FLI), Jena, Germany
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Nelson KN, Talarico S, Poonja S, McDaniel CJ, Cilnis M, Chang AH, Raz K, Noboa WS, Cowan L, Shaw T, Posey J, Silk BJ. Mutation of Mycobacterium tuberculosis and Implications for Using Whole-Genome Sequencing for Investigating Recent Tuberculosis Transmission. Front Public Health 2022; 9:790544. [PMID: 35096744 PMCID: PMC8793027 DOI: 10.3389/fpubh.2021.790544] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Accepted: 12/09/2021] [Indexed: 11/26/2022] Open
Abstract
Tuberculosis (TB) control programs use whole-genome sequencing (WGS) of Mycobacterium tuberculosis (Mtb) for detecting and investigating TB case clusters. Existence of few genomic differences between Mtb isolates might indicate TB cases are the result of recent transmission. However, the variable and sometimes long duration of latent infection, combined with uncertainty in the Mtb mutation rate during latency, can complicate interpretation of WGS results. To estimate the association between infection duration and single nucleotide polymorphism (SNP) accumulation in the Mtb genome, we first analyzed pairwise SNP differences among TB cases from Los Angeles County, California, with strong epidemiologic links. We found that SNP distance alone was insufficient for concluding that cases are linked through recent transmission. Second, we describe a well-characterized cluster of TB cases in California to illustrate the role of genomic data in conclusions regarding recent transmission. Longer presumed latent periods were inconsistently associated with larger SNP differences. Our analyses suggest that WGS alone cannot be used to definitively determine that a case is attributable to recent transmission. Methods for integrating clinical, epidemiologic, and genomic data can guide conclusions regarding the likelihood of recent transmission, providing local public health practitioners with better tools for monitoring and investigating TB transmission.
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Affiliation(s)
- Kristin N Nelson
- Rollins School of Public Health, Emory University, Atlanta, GA, United States
| | - Sarah Talarico
- Division of Tuberculosis Elimination, National Center for HIV/AIDS (Human Immunodeficiency Virus/Acquired Immunodeficiency Syndrome), Viral Hepatitis, STD (Sexually Transmitted Diseases), and Tuberculosis (TB) Prevention, Centers for Disease Control and Prevention, Atlanta, GA, United States
| | - Shameer Poonja
- Los Angeles County Department of Public Health, Los Angeles, CA, United States
| | - Clinton J McDaniel
- Division of Tuberculosis Elimination, National Center for HIV/AIDS (Human Immunodeficiency Virus/Acquired Immunodeficiency Syndrome), Viral Hepatitis, STD (Sexually Transmitted Diseases), and Tuberculosis (TB) Prevention, Centers for Disease Control and Prevention, Atlanta, GA, United States
| | - Martin Cilnis
- TB Control Branch, California Department of Public Health, Richmond, CA, United States
| | - Alicia H Chang
- Los Angeles County Department of Public Health, Los Angeles, CA, United States
| | - Kala Raz
- Division of Tuberculosis Elimination, National Center for HIV/AIDS (Human Immunodeficiency Virus/Acquired Immunodeficiency Syndrome), Viral Hepatitis, STD (Sexually Transmitted Diseases), and Tuberculosis (TB) Prevention, Centers for Disease Control and Prevention, Atlanta, GA, United States
| | - Wendy S Noboa
- Los Angeles County Department of Public Health, Los Angeles, CA, United States
| | - Lauren Cowan
- Division of Tuberculosis Elimination, National Center for HIV/AIDS (Human Immunodeficiency Virus/Acquired Immunodeficiency Syndrome), Viral Hepatitis, STD (Sexually Transmitted Diseases), and Tuberculosis (TB) Prevention, Centers for Disease Control and Prevention, Atlanta, GA, United States
| | - Tambi Shaw
- TB Control Branch, California Department of Public Health, Richmond, CA, United States
| | - James Posey
- Division of Tuberculosis Elimination, National Center for HIV/AIDS (Human Immunodeficiency Virus/Acquired Immunodeficiency Syndrome), Viral Hepatitis, STD (Sexually Transmitted Diseases), and Tuberculosis (TB) Prevention, Centers for Disease Control and Prevention, Atlanta, GA, United States
| | - Benjamin J Silk
- Division of Tuberculosis Elimination, National Center for HIV/AIDS (Human Immunodeficiency Virus/Acquired Immunodeficiency Syndrome), Viral Hepatitis, STD (Sexually Transmitted Diseases), and Tuberculosis (TB) Prevention, Centers for Disease Control and Prevention, Atlanta, GA, United States
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Characterizing tuberculosis transmission dynamics in high-burden urban and rural settings. Sci Rep 2022; 12:6780. [PMID: 35474076 PMCID: PMC9042872 DOI: 10.1038/s41598-022-10488-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Accepted: 04/06/2022] [Indexed: 12/23/2022] Open
Abstract
Mycobacterium tuberculosis transmission dynamics in high-burden settings are poorly understood. Growing evidence suggests transmission may be characterized by extensive individual heterogeneity in secondary cases (i.e., superspreading), yet the degree and influence of such heterogeneity is largely unknown and unmeasured in high burden-settings. We conducted a prospective, population-based molecular epidemiology study of TB transmission in both an urban and rural setting of Botswana, one of the highest TB burden countries in the world. We used these empirical data to fit two mathematical models (urban and rural) that jointly quantified both the effective reproductive number, \documentclass[12pt]{minimal}
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\begin{document}$$R$$\end{document}R, and the propensity for superspreading in each population. We found both urban and rural populations were characterized by a high degree of individual heterogeneity, however such heterogeneity disproportionately impacted the rural population: 99% of secondary transmission was attributed to only 19% of infectious cases in the rural population compared to 60% in the urban population and the median number of incident cases until the first outbreak of 30 cases was only 32 for the rural model compared to 791 in the urban model. These findings suggest individual heterogeneity plays a critical role shaping local TB epidemiology within subpopulations.
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