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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Xia Z, Su B, Tu C, Sun S, Tan Y, Xu Y, Li Q. Single-tube protocol for culture-independent spoligotyping of Mycobacterium tuberculosis based on MeltArray. J Clin Microbiol 2024; 62:e0118323. [PMID: 38112521 PMCID: PMC10793361 DOI: 10.1128/jcm.01183-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Accepted: 11/13/2023] [Indexed: 12/21/2023] Open
Abstract
IMPORTANCE Spacer oligonucleotide typing (spoligotyping), the first-line genotyping assay for Mycobacterium tuberculosis (MTB), plays a fundamental role in the investigation of its epidemiology and evolution. In this study, we established a single-tube spoligotyping assay using MeltArray, a highly multiplex polymerase chain reaction (PCR) approach that runs on a real-time PCR thermocycler. The MeltArray protocol included an internal positive control, gyrB, to indicate the abundance of MTB via the quantification cycle and 43 spacers to identify the spoligotype via melting curve analysis. The entire protocol was completed in a single step within 2.5 hours. The lowest detectable copy number for the tested strains was 20 copies/reaction and thus sufficient for analyzing both culture and sputum samples. We conclude that MeltArray-based spoligotyping could be used immediately in low- and middle-income countries with a high tuberculosis burden, given its easy access, improved throughput, and potential applicability to clinical samples.
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Affiliation(s)
- Zihan Xia
- Engineering Research Centre of Molecular Diagnostics of the Ministry of Education, State Key Laboratory of Cellular Stress Biology, State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen, China
| | - Biyi Su
- Guangzhou Chest Hospital, Guangzhou, China
| | - Chunxia Tu
- Engineering Research Centre of Molecular Diagnostics of the Ministry of Education, State Key Laboratory of Cellular Stress Biology, State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen, China
| | - Siyang Sun
- Engineering Research Centre of Molecular Diagnostics of the Ministry of Education, State Key Laboratory of Cellular Stress Biology, State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen, China
| | - Yaoju Tan
- Guangzhou Chest Hospital, Guangzhou, China
| | - Ye Xu
- Engineering Research Centre of Molecular Diagnostics of the Ministry of Education, State Key Laboratory of Cellular Stress Biology, State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen, China
| | - Qingge Li
- Engineering Research Centre of Molecular Diagnostics of the Ministry of Education, State Key Laboratory of Cellular Stress Biology, State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen, China
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Flores-Aréchiga A, Zacarías-Hernández JL, Vázquez-Cortés CG, Tamez-Guerra RS, De la O-Cavazos M, Rivera-Morales LG, Llaca-Díaz JM, Castro-Garza J, Casillas-Vega N, Vázquez-Guillén JM, Rodríguez-Padilla C. Molecular epidemiology and drug resistance of Mycobacterium tuberculosis in a tertiary care hospital in northeastern Mexico. J Infect Dev Ctries 2023; 17:1753-1760. [PMID: 38252727 DOI: 10.3855/jidc.18026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Accepted: 05/21/2023] [Indexed: 01/24/2024] Open
Abstract
INTRODUCTION Tuberculosis (TB) is a re-emerging disease considered a public health concern. In the present study, we analyzed the epidemiology and drug resistance of Mycobacterium tuberculosis strains isolated from patients with pulmonary TB. METHODOLOGY Mycobacterium tuberculosis isolates (n = 190) were obtained from patients with pulmonary TB admitted to Dr. José Eleuterio González University Hospital (UH). Each M. tuberculosis isolate was analyzed by spoligotyping (spacer oligonucleotide typing) and MIRU-VNTR (Mycobacterial Interspersed Repetitive Units-Variable Number Tandem Repeat). Drug resistance was evaluated using the Anyplex™ II MTB/MDR/XDR assay. RESULTS The predominant spoligotypes observed were X1 (SIT 119, n = 46), T1 (SIT 53, n = 40), H3 (SIT 50, n = 13), Beijing (SIT 1, n = 11), and EAI2-Manila (SIT 19, n = 8). MIRU-VNTR analysis showed that the locus QUB-26 had the highest allelic variability. The observed drug resistance included monoresistance to rifampicin (2.6%; n = 5), isoniazid (3.2%; n = 6), and fluoroquinolones (1.6%; n = 3) as well as multidrug resistance (5.3%; n = 10). All of the Beijing strains were susceptible. Regarding comorbidities, 13.7% (26/190) of the patients were co-infected with TB and HIV (TB+HIV+), and 31.6% (55/190) had TB along with diabetes (TB + diabetes). CONCLUSIONS The most prevalent lineages were X1 (SIT 119; 24.3%) and T1 (SIT 53; 21%). An alarming proportion (12.6%) of M. tuberculosis isolates presented drug resistance. To effectively manage TB, continuous surveillance of regional strain dissemination, drug resistance profiles, and TB-associated comorbidities is crucial.
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Affiliation(s)
- Amador Flores-Aréchiga
- Universidad Autónoma de Nuevo León, Facultad de Medicina y Hospital Universitario Dr. José Eleuterio González, Departamento de Patología Clínica. Monterrey, Nuevo León, México
| | - José Luis Zacarías-Hernández
- Universidad Autónoma de Nuevo León, Facultad de Ciencias Biológicas. Laboratorio de Inmunología y Virología. Ciudad Universitaria, San Nicolás de los Garza, Nuevo León, México
| | - Cecilia Gabriela Vázquez-Cortés
- Universidad Autónoma de Nuevo León, Facultad de Medicina y Hospital Universitario Dr. José Eleuterio González, Departamento de Patología Clínica. Monterrey, Nuevo León, México
| | - Reyes S Tamez-Guerra
- Universidad Autónoma de Nuevo León, Facultad de Ciencias Biológicas. Laboratorio de Inmunología y Virología. Ciudad Universitaria, San Nicolás de los Garza, Nuevo León, México
| | - Manuel De la O-Cavazos
- Universidad Autónoma de Nuevo León, Facultad de Medicina y Hospital Universitario Dr. José Eleuterio González, Departamento de Pediatría. Monterrey, Nuevo León, México
| | - Lydia Guadalupe Rivera-Morales
- Universidad Autónoma de Nuevo León, Facultad de Ciencias Biológicas. Laboratorio de Inmunología y Virología. Ciudad Universitaria, San Nicolás de los Garza, Nuevo León, México
| | - Jorge Martín Llaca-Díaz
- Universidad Autónoma de Nuevo León, Facultad de Medicina y Hospital Universitario Dr. José Eleuterio González, Departamento de Patología Clínica. Monterrey, Nuevo León, México
| | - Jorge Castro-Garza
- Universidad Autónoma de Nuevo León, Facultad de Ciencias Biológicas. Laboratorio de Bioquímica y Genética de Microorganismos. Ciudad Universitaria, San Nicolás de los Garza, Nuevo León, México
| | - Néstor Casillas-Vega
- Universidad Autónoma de Nuevo León, Facultad de Medicina y Hospital Universitario Dr. José Eleuterio González, Departamento de Patología Clínica. Monterrey, Nuevo León, México
| | - José Manuel Vázquez-Guillén
- Universidad Autónoma de Nuevo León, Facultad de Ciencias Biológicas. Laboratorio de Inmunología y Virología. Ciudad Universitaria, San Nicolás de los Garza, Nuevo León, México
| | - Cristina Rodríguez-Padilla
- Universidad Autónoma de Nuevo León, Facultad de Ciencias Biológicas. Laboratorio de Inmunología y Virología. Ciudad Universitaria, San Nicolás de los Garza, Nuevo León, México
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Castillos de Ibrahim das Neves Y, Reis AJ, Xavier Maio N, Vianna J, Perdigão J, Bastos Ramis I, Almeida da Silva PE, Von Groll A. Genotyping methods and their contributions to the study of tuberculosis dynamic in Latin America. J Infect Dev Ctries 2023; 17:1373-1386. [PMID: 37956372 DOI: 10.3855/jidc.17840] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Accepted: 04/06/2023] [Indexed: 11/15/2023] Open
Abstract
INTRODUCTION Mycobacterium tuberculosis genotyping has impacted evolutionary studies worldwide. Nonetheless, its application and the knowledge generated depend on the genetic marker evaluated and the detection technologies that have evolved over the years. Here we describe the timeline of main genotypic methods related to M. tuberculosis in Latin America and the main findings obtained. METHODOLOGY Systematic searches through the PubMed database were performed from 1993 to May 2021. A total of 345 articles met the inclusion criteria and were selected. RESULTS Spacer oligonucleotide typing (spoligotyping) was the most widely used method in Latin America, with decreasing use in parallel with increasing use of mycobacterial interspersed repetitive unit-variable number tandem repeat (MIRU-VNTR) and whole genome sequencing (WGS). Among the countries, Brazil, Mexico, and Argentina had the most publications, and a considerable part of the articles were in collaboration with Latin American or non-Latin American institutions; a small proportion of studies needed partnerships to perform the genotypic methods. The genotypic methods allowed the identification of M. tuberculosis genotypes with greater capacity for clonal expansion and revealed the predominance of the Euro-American lineage in Latin America. There was a notable presence of the Beijing family in Peru and Colombia. CONCLUSIONS The data obtained demonstrated the importance of expanding collaborative networks of tuberculosis (TB) research groups to countries with low productivity in this area, the commitment of the few Latin American countries to advance TB research, as well as the inestimable value of building a Latin America database, considering ease of population mobility between countries.
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Affiliation(s)
| | - Ana Julia Reis
- Medical Microbiology Research Center, Faculty of Medicine, Universidade Federal do Rio Grande - FURG, Rio Grande, Rio Grande do Sul, Brazil
| | - Nathália Xavier Maio
- Medical Microbiology Research Center, Faculty of Medicine, Universidade Federal do Rio Grande - FURG, Rio Grande, Rio Grande do Sul, Brazil
| | - Júlia Vianna
- Medical Microbiology Research Center, Faculty of Medicine, Universidade Federal do Rio Grande - FURG, Rio Grande, Rio Grande do Sul, Brazil
| | - João Perdigão
- iMed.ULisboa - Instituto de Investigação do Medicamento, Faculdade de Farmácia, Universidade de Lisboa, Lisboa, Portugal
| | - Ivy Bastos Ramis
- Medical Microbiology Research Center, Faculty of Medicine, Universidade Federal do Rio Grande - FURG, Rio Grande, Rio Grande do Sul, Brazil
| | - Pedro Eduardo Almeida da Silva
- Medical Microbiology Research Center, Faculty of Medicine, Universidade Federal do Rio Grande - FURG, Rio Grande, Rio Grande do Sul, Brazil
| | - Andrea Von Groll
- Medical Microbiology Research Center, Faculty of Medicine, Universidade Federal do Rio Grande - FURG, Rio Grande, Rio Grande do Sul, Brazil
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Faye LM, Hosu MC, Oostvogels S, Dippenaar A, Warren RM, Sineke N, Vasaikar S, Apalata T. The Detection of Mutations and Genotyping of Drug-Resistant Mycobacterium tuberculosis Strains Isolated from Patients in the Rural Eastern Cape Province. Infect Dis Rep 2023; 15:403-416. [PMID: 37489395 PMCID: PMC10366782 DOI: 10.3390/idr15040041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Revised: 07/01/2023] [Accepted: 07/06/2023] [Indexed: 07/26/2023] Open
Abstract
Drug-resistant tuberculosis (DR-TB) is still a major public health concern in South Africa. Mutations in M. tuberculosis can cause varying levels of phenotypic resistance to anti-TB medications. There have been no prior studies on gene mutations and the genotyping of DR-TB in the rural Eastern Cape Province; hence, we aimed to identify DR-TB mutations, genetic diversity, and allocated lineages among patients in this area. Using Xpert® MTB/RIF, we assessed the rifampin resistance of sputum samples collected from 1157 patients suspected of having tuberculosis. GenoType MTBDR plus VER 2.0 was used for the detection of mutations causing resistance to anti-TB medications. The next step was to spoligotype 441 isolates. The most prevalent rifampin resistance-conferring mutations were in rpoB codon S531L in INH-resistant strains; the katG gene at codon S315TB and the inhA gene at codon C-15TB had the most mutations; 54.5% and 24.7%, respectively. In addition, 24.6% of strains showed mutations in both the rpoB and inhA genes, while 69.9% of strains showed mutations in both the katG and rpoB genes. Heteroresistance was seen in 17.9% of all cases in the study. According to spoligotyping analysis, Beijing families predominated. Investigation of the evolutionary lineages of M. tuberculosis isolates can be carried out using the information provided by the study's diversity of mutations. In locations wherein these mutations have been discovered, decision-making regarding the standardization of treatment regimens or individualized treatment may be aided by the detection frequency of rpoB, katG, and inhA mutations in various study areas.
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Affiliation(s)
- Lindiwe M Faye
- Department of Laboratory Medicine and Pathology, Walter Sisulu University, Mthatha 5099, South Africa
- National Health Laboratory Services (NHLS), Mthatha 5099, South Africa
| | - Mojisola C Hosu
- Department of Laboratory Medicine and Pathology, Walter Sisulu University, Mthatha 5099, South Africa
- National Health Laboratory Services (NHLS), Mthatha 5099, South Africa
| | - Selien Oostvogels
- Family Medicine and Population Health (FAMPOP), Faculty of Medicine and Health Sciences, University of Antwerp, BE-2000 Antwerp, Belgium
| | - Anzaan Dippenaar
- Family Medicine and Population Health (FAMPOP), Faculty of Medicine and Health Sciences, University of Antwerp, BE-2000 Antwerp, Belgium
| | - Robin M Warren
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council, Parowvallei, Cape Town 7505, South Africa
- Centre for Molecular and Cellular Biology, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town 7505, South Africa
| | - Ncomeka Sineke
- Department of Laboratory Medicine and Pathology, Walter Sisulu University, Mthatha 5099, South Africa
- National Health Laboratory Services (NHLS), Mthatha 5099, South Africa
| | - Sandeep Vasaikar
- Department of Laboratory Medicine and Pathology, Walter Sisulu University, Mthatha 5099, South Africa
- National Health Laboratory Services (NHLS), Mthatha 5099, South Africa
| | - Teke Apalata
- Department of Laboratory Medicine and Pathology, Walter Sisulu University, Mthatha 5099, South Africa
- National Health Laboratory Services (NHLS), Mthatha 5099, South Africa
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Gürer Giray B, Aslantürk A, Şimşek H, Özgür D, Kılıç S, Aslan G. Determination of genetic diversity of multidrug-resistant Mycobacterium tuberculosis strains in Turkey using 15 locus MIRU-VNTR and spoligotyping methods. Pathog Glob Health 2023; 117:85-91. [PMID: 35642888 PMCID: PMC9848327 DOI: 10.1080/20477724.2022.2084807] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Tuberculosis (TB) remains the leading cause of deaths from infectious disease worldwide. Nowadays, the tendency of Mycobacterium tuberculosis complex (MTBC) to spread between continents due to uncontrolled migration movements shows that TB is a global health problem. The number of studies for the detection of MTBC strains' epidemiological features in areas with TB spread risk using molecular-based methods such as spoligotyping and Mycobacterial Interspersed Repetitive Unit (MIRU) Variable Number Tandem Repeats (VNTR) at the clonal level is insufficient. In this study, it was aimed to determine the phylogenetic relationships of MTBC strains at the species level by spoligotyping and 15 locus MIRU-VNTR (MIRU-VNTR15) molecular methods of 96 multidrug-resistant (MDR) MTBC strains isolated from sputum samples of patients with a preliminary diagnosis of pulmonary TB or suspected contact history those sent to National Tuberculosis Reference Laboratory from the centers that are members of the Tuberculosis Laboratory Surveillance Network. The phylogenetic relationship between 96 MDR-TB strains was investigated with the combination of bead-based spoligotyping and MIRU-VNTR15 methods on the MAGPIX® Milliplex Map device. In this study, it was determined that the T1 family is more common in our country and LAM7-TUR family is less common than the Beijing family unlike other studies. It was determined that the strains in the same cluster had different locus profiles, and there was no transmission from the same clone in the clonal typing we performed with spoligotyping and MIRU-VNTR15.
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Affiliation(s)
- Burcu Gürer Giray
- Ankara Provincial Health Directorate Public Health Molecular Diagnosis Laboratory, Ankara, Turkey,CONTACT Burcu Gürer Giray Molecular Diagnosis Laboratory, Public Health Institution of Ankara, Turkey
| | - Ahmet Aslantürk
- National Tuberculosis Reference Laboratory, Public Health Institution of Turkey (PHIT), Ankara, Turkey
| | - Hülya Şimşek
- Faculty of Medicine, Department of Medical Microbiology, Yozgat Bozok University, Yozgat, Turkey
| | - Didem Özgür
- Department of Medical Microbiology, Kafkas University, Kars, Turkey
| | - Selçuk Kılıç
- Department of Medical CBRN, University of Health Sciences, Institute of Dedenxe Health Sciences, Ankara, Turkey
| | - Gönül Aslan
- Mersin University Faculty of Medicine, Department of Medical Microbiology, Mersin, Turkey
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Lapa S, Kuzmin A, Сhernousova L, Mikhailovich V. Spoligotyping of the Mycobacterium tuberculosis complex using on-Chip PCR. J Appl Microbiol 2022; 134:lxac046. [PMID: 36626798 DOI: 10.1093/jambio/lxac046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Revised: 10/27/2022] [Accepted: 11/04/2022] [Indexed: 01/12/2023]
Abstract
AIMS The aim of this study was to develop a rapid PCR-based method for spoligotyping of Mycobacteria in the microarray format and to compare it to conventional spoligotyping by hybridization. METHODS AND RESULTS The method employs the on-Chip PCR technique with primers specific for 43 spacers that separate direct repeats (DRs) in the DR region of mycobacterial DNA. The primers were immobilized on gel-based microarrays, and PCR was performed directly on the chips. The PCR fluorescence images were acquired and processed using a portable fluorescence analyzer equipped with dedicated software. Analysis takes 1.5-2 hours and can be carried out on clinical samples without additional handling. The analytical sensitivity of the method was 103 copies of target DNA. The spoligotyping results of 51 samples produced by the proposed method and by conventional reverse hybridization approach were in full concordance. CONCLUSIONS High throughput capacity, computerized data analysis, compact equipment, and reliable results make the on-Chip PCR an attractive alternative to intra- and interspecific spoligotyping of Mycobacterium tuberculosis complex bacteria. SIGNIFICANCE AND IMPACT OF STUDY Fast microarray-based spoligotyping technique using on-Chip PCR was developed.
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Affiliation(s)
- Sergey Lapa
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia
| | - Alexey Kuzmin
- Central Tuberculosis Research Institute, Russian Academy of Sciences, Moscow 107564, Russia
| | - Larisa Сhernousova
- Central Tuberculosis Research Institute, Russian Academy of Sciences, Moscow 107564, Russia
| | - Vladimir Mikhailovich
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia
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Worku G, Gumi B, Mohammedbirhan B, Girma M, Sileshi H, Hailu M, Wondimu A, Ashagre W, Tschopp R, Carruth L, Ameni G. Molecular epidemiology of tuberculosis in the Somali region, eastern Ethiopia. Front Med (Lausanne) 2022; 9:960590. [PMID: 36313999 PMCID: PMC9614095 DOI: 10.3389/fmed.2022.960590] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Accepted: 09/21/2022] [Indexed: 12/03/2022] Open
Abstract
Background Tuberculosis (TB) is one of the leading causes of morbidity and mortality in low-income countries like Ethiopia. However, because of the limited laboratory infrastructure there is a shortage of comprehensive data on the genotypes of clinical isolates of Mycobacterium tuberculosis (M. tuberculosis) complex (MTBC) in peripheral regions of Ethiopia. The objective of this study was to characterize MTBC isolates in the Somali region of eastern Ethiopia. Methods A cross-sectional study was conducted in three health institutions between October 2018 and December 2019 in the capital of Somali region. A total of 323 MTBC isolates (249 from pulmonary TB and 74 from extrapulmonary TB) were analyzed using regions of difference 9 (RD 9)-based polymerase chain reaction (PCR) and spoligotyping. Results Of the 323 MTBC isolates, 99.7% (95% CI: 99.1–100%) were M. tuberculosis while the remaining one isolate was M. bovis based on RD 9-based PCR. Spoligotyping identified 71 spoligotype patterns; 61 shared types and 10 orphans. A majority of the isolates were grouped in shared types while the remaining grouped in orphans. The M. tuberculosis lineages identified in this study were lineage 1, 2, 3, 4, and 7 with the percentages of 7.4, 2.2, 28.2, 60.4, and 0.6%, respectively. Most (87.9%) of the isolates were classified in clustered spoligotypes while the remaining 12.1% isolates were singletons. The predominant clustered spoligotypes identified were SIT 149, SIT 21, SIT 26, SIT 53, and SIT 52, each consisting of 17.6, 13.3, 8.4, 7.4, and 5%, respectively. Lineage 3 and lineage 4, as well as the age group (15–24), were associated significantly with clustering. Conclusion The MTBC isolated from TB patients in Somali region were highly diverse, with considerable spoligotype clustering which suggests active TB transmission. In addition, the Beijing spoligotype was isolated in relatively higher frequency than the frequencies of its isolation from the other regions of Ethiopia warranting the attention of the TB Control Program of the Somali region.
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Affiliation(s)
- Getnet Worku
- Department of Medical Laboratory Science, College of Medicine and Health Sciences, Jigjiga University, Jigjiga, Ethiopia,Aklilu Lemma Institute of Pathobiology, Addis Ababa University, Addis Ababa, Ethiopia
| | - Balako Gumi
- Aklilu Lemma Institute of Pathobiology, Addis Ababa University, Addis Ababa, Ethiopia
| | - Binyam Mohammedbirhan
- Department of Pathology, College of Medicine and Health Sciences, Jigjiga University, Jigjiga, Ethiopia
| | - Musse Girma
- Aklilu Lemma Institute of Pathobiology, Addis Ababa University, Addis Ababa, Ethiopia
| | - Henok Sileshi
- Department of Medical Laboratory Science, College of Medicine and Health Sciences, Jigjiga University, Jigjiga, Ethiopia
| | - Michael Hailu
- National Tuberculosis Reference Laboratory, Ethiopian Public Health Institute, Addis Ababa, Ethiopia
| | - Amanuel Wondimu
- National Tuberculosis Reference Laboratory, Ethiopian Public Health Institute, Addis Ababa, Ethiopia
| | - Wondimu Ashagre
- One-Health Unit, Armauer Hansen Research Institute, Addis Ababa, Ethiopia
| | - Rea Tschopp
- One-Health Unit, Armauer Hansen Research Institute, Addis Ababa, Ethiopia,Department of Epidemiology and Public Health, Swiss Tropical and Public Health Institute, Basel, Switzerland
| | - Lauren Carruth
- School of International Studies, American University, Washington, DC, United States
| | - Gobena Ameni
- Aklilu Lemma Institute of Pathobiology, Addis Ababa University, Addis Ababa, Ethiopia,Department of Veterinary Medicine, College of Agriculture and Veterinary Medicine, United Arab Emirates University, Al Ain, United Arab Emirates,*Correspondence: Gobena Ameni
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Genestet C, Hodille E, Bernard A, Vallée M, Lina G, Le Meur A, Refrégier G, Dumitrescua O; Lyon TB study group. Consistency of Mycobacterium tuberculosis Complex Spoligotyping between the Membrane-Based Method and In Silico Approach. Microbiol Spectr 2022; 10:e0022322. [PMID: 35467406 DOI: 10.1128/spectrum.00223-22] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
To tackle the spread of tuberculosis (TB), epidemiological studies are undertaken worldwide to investigate TB transmission chains. Clustered regulatory interspaced short palindromic repeats (CRISPR) locus diversity, also called spoligotyping, is a widely used genotyping assay for the characterization of Mycobacterium tuberculosis complex (MTBC). We compared herein the spoligotyping of MTBC clinical isolates using a membrane-based method (following an initial PCR step) and whole-genome sequencing (WGS)-based method (i.e., in silico spoligotyping). All MTBC strains isolated at the Lyon University Hospital, France, between November 2016 and December 2020 were included (n = 597). Spoligotyping profiles were also used for species identification among the MTBC. Outputs of both methods were analyzed, and discrepant results were investigated thanks to CRISPRbuilder-TB. The overall agreement was 85.7%. Spacer discrepancies observed between the methods were due to the insertion of IS6110 within the direct repeat (DR) sequence upstream or downstream of spacers, mutated DR sequences, or truncated spacers. Discrepancies did not impact species identification. Although spoligotyping-based species identification was inconclusive for 29 isolates, SNP-based phylogeny conducted after WGS allowed the identification of 23 M. tuberculosis (Mtb), 2 M. canettii, and 4 mixed MTBC infections. WGS yielded very few discrepancies compared to membrane-based spoligotyping. Overall agreement was significantly improved (92.4%) by the CRISPR locus reconstruction using CRISPRbuilder-TB for the MTBC isolates with the shared international type 53 in silico spoligotyping. A smooth transition from the membrane-based to the in silico-based genotyping of M. tuberculosis isolates is, therefore, possible for TB diagnosis and epidemiologic survey. IMPORTANCE Whole-genome sequencing (WGS) has profoundly transformed the perspectives of tuberculosis (TB) diagnosis, providing a better discriminatory power to determine relatedness between Mycobacterium tuberculosis complex (MTBC) isolates. Previous genotyping approaches, such as spoligotyping consisting of an initial PCR step followed by reverse dot hybridization, are currently being replaced by WGS. Several pipelines have been developed to extract a spoligotype from WGS data (in silico spoligotyping) allowing for the continuity of MTBC molecular surveys before and after WGS implementation. The present study found very good overall agreement between hybridization to membrane-based spoligotyping and in silico spoligotyping, indicating the possibility of a smooth transition from the traditional to the in silico-based genotyping of MTBC isolates for TB diagnosis and epidemiological survey.
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Hussien B, Zewude A, Wondale B, Hailu A, Ameni G. Spoligotyping of Clinical Isolates of Mycobacterium tuberculosis Complex Species in the Oromia Region of Ethiopia. Front Public Health 2022; 10:808626. [PMID: 35372211 PMCID: PMC8970530 DOI: 10.3389/fpubh.2022.808626] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Accepted: 02/03/2022] [Indexed: 11/22/2022] Open
Abstract
Background Tuberculosis (TB) is a leading cause of morbidity and mortality in Ethiopia. Investigation of the Mycobacterium tuberculosis complex (MTBC) species circulating in the Ethiopian population would contribute to the efforts made to control TB in the country. Therefore, this study was conducted to investigate the MTBC species and spoligo patterns in the Oromia region (central) of Ethiopia. Methods A cross-sectional study design was used to recruit 450 smear positive pulmonary TB (PTB) cases from the Oromia region between September 2017 and August 2018. Mycobacteria were isolated from sputum samples on the Lowenstein Jensen (LJ) medium. Molecular identification of the isolates was performed by spoligotyping. The results of spoligotyping were transferred into a query box in the SITVIT2 database and Run TB-Lineage in the TB Insight website for the identification of spoligo international type (SIT) number and linages of the isolates, respectively. Statistical Product and Service Solutions (SPSS) 20 was applied for statistical analysis. Results Three hundred and fifteen isolates were grouped under 181 different spoligotype patterns. The most dominantly isolated spoligotype pattern was SIT149 and it consisted of 23 isolates. The majority of the isolates were grouped under Euro-American (EA), East-African-Indian (EAI), and Indo-Oceanic (IO) lineages. These lineages consisted of 79.4, 9.8, and 9.8% of the isolates, respectively. One hundred and sixty-five of the isolates were classified under 31 clustered spoligotypes whereas the remaining 150 were singleton types. Furthermore, 91.1% of the total isolates were classified as orphan types. Clustering of spoligotypes was associated (p < 0.001) with EAI lineage. Conclusion SIT149 and EA lineage were predominantly isolated from the Oromia region substantiating the findings of the similar studies conducted in other regions of Ethiopia. The observation of significant number of singleton and orphan spoligotypes warrants for additional genetic typing of the isolates using method(s) with a better discriminatory power than spoligotyping.
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Affiliation(s)
- Bedru Hussien
- Department of Public Health, Goba Referral Hospital, Madda Walabu University, Goba, Ethiopia
| | - Aboma Zewude
- Malaria and Neglected Tropical Diseases Research Team, Ethiopian Public Health Institute, Ministry of Health, Addis Ababa, Ethiopia
- Department of Veterinary Medicine, College of Agriculture and Veterinary Medicine, United Arab Emirates University, Al Ain, United Arab Emirates
| | - Biniam Wondale
- Department of Biology, Arba Minch University, Arba Minch, Ethiopia
| | - Awraris Hailu
- Department of Public Health, College of Health Sciences, Debre Birhan University, Debre Birhan, Ethiopia
| | - Gobena Ameni
- Department of Veterinary Medicine, College of Agriculture and Veterinary Medicine, United Arab Emirates University, Al Ain, United Arab Emirates
- Aklilu Lemma Institute of Pathobiology, Addis Ababa University, Addis Ababa, Ethiopia
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Rahman SMM, Rahman A, Nasrin R, Ather MF, Ferdous SS, Ahmed S, Uddin MKM, Khatun R, Sarker MS, Mahmud AM, Rahman MM, Banu S. Molecular Epidemiology and Genetic Diversity of Multidrug-Resistant Mycobacterium tuberculosis Isolates in Bangladesh. Microbiol Spectr 2022; 10:e0184821. [PMID: 35196788 DOI: 10.1128/spectrum.01848-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Although the number of multidrug-resistant (MDR) tuberculosis (TB) cases is high overall, a major gap exists in our understanding of the molecular characteristics and transmission dynamics of the MDR Mycobacterium tuberculosis isolates circulating in Bangladesh. The present study aims to characterize the MDR-TB isolates of Bangladesh and to investigate the mode of transmission. A total of 544 MDR-TB isolates were obtained from a nationwide drug-resistant TB surveillance study conducted between October 2011 and March 2017 covering all geographic divisions of Bangladesh. The isolates were characterized using TbD1 deletion analysis, spoligotyping, and mycobacterial interspersed repetitive-unit–variable-number tandem-repeat (MIRU-VNTR) typing. Deletion analysis showed that 440 (80.9%) isolates were the modern type, while the remainder were the ancestral type. The largest circulating lineage was the Beijing type, comprising 208 isolates (38.2%), followed by T, EAI, and LAM with 93 (17.1%), 58 (10.7%), and 52 (9.5%) isolates, respectively. Combined MIRU-VNTR and spoligotyping analysis demonstrated that the majority of the clustered isolates were of the Beijing and T1 lineages. The overall rate of recent transmission was estimated at 33.8%. In conclusion, the MDR M. tuberculosis isolates circulating in Bangladesh are mostly of the modern virulent type. The Beijing and T lineages are the predominant types and most of the transmission of MDR-TB can be attributed to them. The findings also suggest that, along with the remarkable transmission, the emergence of MDR-TB in Bangladesh is largely due to acquired resistance. Rapid and accurate diagnosis and successful treatment will be crucial for controlling MDR-TB in Bangladesh. IMPORTANCE Multidrug-resistant TB is considered to be the major threat to tuberculosis control activities worldwide, including in Bangladesh. Despite the fact that the number of MDR-TB cases is high, a major gap exists in our understanding of the molecular epidemiology of the MDR-TB isolates in Bangladesh. In our study, we characterized and classified the MDR-TB isolates circulating in Bangladesh and investigated their mode of transmission. Our results demonstrated that the MDR M. tuberculosis isolates circulating in Bangladesh are mostly of the modern virulent type. The Beijing and T lineages are the predominant types and are implicated in the majority of MDR-TB transmission. Our findings reveal that, along with the remarkable transmission, the emergence of MDR-TB in Bangladesh is largely due to acquired resistance, which may be due to nonadherence to treatment or inadequate treatment of TB patients. Rapid diagnosis and adherence to an appropriate treatment regimen are therefore crucial to controlling MDR-TB in Bangladesh.
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Singh J, Singh N, Suresh G, Srivastava R, Aggarwal U, Behera D, Munisamy M, Malhotra AG, Singh S. A comparative analysis of molecular genotypes of Mycobacterium tuberculosis isolates from HIV-positive and HIV-negative patients. Front Cell Infect Microbiol 2022; 12:953443. [PMID: 36310875 PMCID: PMC9597297 DOI: 10.3389/fcimb.2022.953443] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Accepted: 08/30/2022] [Indexed: 02/05/2023] Open
Abstract
SETTING Tuberculosis Research Laboratory, Division of Clinical Microbiology and Molecular Medicine, Department of Laboratory Medicine, All India Institute of Medical Sciences, and the National Institute of Tuberculosis and Respiratory Diseases (NITRD), both situated in New Delhi. OBJECTIVES We aimed to identify the distribution of various genotypes of M. tuberculosis among HIV-positive and HIV-negative patients suspected of having Tuberculosis, seen at the National Institute of Tuberculosis and Respiratory Diseases, New Delhi, which is a tertiary care dedicated TB hospital. PATIENTS AND METHODS Genotyping by Spoligotyping and 24 loci MIRU-VNTR was performed and analyzed using SITVITWEB and MIRU-VNTRplus. Drug susceptibility patterns were also analyzed. RESULTS A total of 503 subjects who were PTB/EPTB suspected were recruited and 287 were culture positive. Among them, 276 had growth of Mycobacterium tuberculosis (MTB) and in 11 patients non-tuberculous mycobacteria (NTM) were grown. The isolation rate of NTM was predominantly from HIV positive [10 of 130 (7.6%)] patients. Of the total isolates of MTB, 156 (56.5%) were from HIV negative patients and 120 (43.5%) were from HIV positive patients. All 276 M. tuberculosis isolates were genotyped and tested for drug susceptibility patterns. The CAS genotype was most predominant [153 (55.4%)], followed by Beijing lineage [44 (15.9%)], East African India [25 (9.1%)] and others [54 (19.6%)]. Beijing genotype was significantly more common in HIV positive patients (22.5%) than in HIV negative patients (10.9%). In MIRU-VNTR analysis, clustering was found to be more frequent in CAS strains irrespective of HIV status. In the HIV positive group, spoligotyping could differentiate various genotypes in 90% of isolates and MIRU-VNTR analysis in 84.2% of isolates. The clustering of various MTB strains was more associated with drug resistance. CONCLUSION The Beijing lineage was predominant in HIV-TB coinfected cases, even though the Central Asian Strain (CAS) was overall more predominant in the region.
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Affiliation(s)
- Jitendra Singh
- Division of Clinical Microbiology and Molecular Medicine, All India Institute of Medical Sciences, New Delhi, India
- Translational Medicine Centre, All India Institute of Medical Sciences, Bhopal, India
| | - Niti Singh
- Department of Microbiology, National Institute of Tuberculosis and Respiratory Diseases (NITRD), New Delhi, India
| | - Gayatri Suresh
- Department of Microbiology, National Institute of Tuberculosis and Respiratory Diseases (NITRD), New Delhi, India
| | - Rahul Srivastava
- Department of Microbiology, National Institute of Tuberculosis and Respiratory Diseases (NITRD), New Delhi, India
| | - Upasna Aggarwal
- Department of Microbiology, National Institute of Tuberculosis and Respiratory Diseases (NITRD), New Delhi, India
| | - Digamber Behera
- Department of Microbiology, National Institute of Tuberculosis and Respiratory Diseases (NITRD), New Delhi, India
- Department of Pulmonary Medicine, PGIMER, Chandigarh, India
| | - Murali Munisamy
- Translational Medicine Centre, All India Institute of Medical Sciences, Bhopal, India
| | | | - Sarman Singh
- Division of Clinical Microbiology and Molecular Medicine, All India Institute of Medical Sciences, New Delhi, India
- Department of Microbiology, All India Institute of Medical Sciences, Bhopal, India
- Medical Science and Engineering Research Centre, Indian Institute of Science Education and Research, Bhopal, India
- *Correspondence: Sarman Singh, ;
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Daniyarov A, Molkenov A, Rakhimova S, Akhmetova A, Yerezhepov D, Chingissova L, Bismilda V, Toksanbayeva B, Rakisheva A, Akilzhanova A, Kozhamkulov U, Kairov U. Genomic Analysis of Multidrug-Resistant Mycobacterium tuberculosis Strains From Patients in Kazakhstan. Front Genet 2021; 12:683515. [PMID: 34858467 PMCID: PMC8630622 DOI: 10.3389/fgene.2021.683515] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2021] [Accepted: 10/15/2021] [Indexed: 11/13/2022] Open
Abstract
Tuberculosis (TB) is an infectious disease that remains an essential public health problem in many countries. Despite decreasing numbers of new cases worldwide, the incidence of antibiotic-resistant forms (multidrug resistant and extensively drug-resistant) of TB is increasing. Next-generation sequencing technologies provide a high-throughput approach to identify known and novel potential genetic variants that are associated with drug resistance in Mycobacterium tuberculosis (Mtb). There are limited reports and data related to whole-genome characteristics of drug-resistant Mtb strains circulating in Kazakhstan. Here, we report whole-genome sequencing and analysis results of eight multidrug-resistant strains collected from TB patients in Kazakhstan. Genotyping and validation of all strains by MIRU-VNTR and spoligotyping methodologies revealed that these strains belong to the Beijing family. The spectrum of specific and potentially novel genomic variants (single-nucleotide polymorphisms, insertions, and deletions) related to drug resistance was identified and annotated. ResFinder, CARD, and CASTB antibiotic resistance databases were used for the characterization of genetic variants in genes associated with drug resistance. Our results provide reference data and genomic profiles of multidrug-resistant isolates for further comparative studies and investigations of genetic patterns in drug-resistant Mtb strains.
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Affiliation(s)
- Asset Daniyarov
- Laboratory of Bioinformatics and Systems Biology, Center for Life Sciences, National Laboratory Astana, Nazarbayev University, Nur-Sultan, Kazakhstan
| | - Askhat Molkenov
- Laboratory of Bioinformatics and Systems Biology, Center for Life Sciences, National Laboratory Astana, Nazarbayev University, Nur-Sultan, Kazakhstan
| | - Saule Rakhimova
- Laboratory of Genomic and Personalized Medicine, Center for Life Sciences, National Laboratory Astana, Nazarbayev University, Nur-Sultan, Kazakhstan
| | - Ainur Akhmetova
- Laboratory of Genomic and Personalized Medicine, Center for Life Sciences, National Laboratory Astana, Nazarbayev University, Nur-Sultan, Kazakhstan
| | - Dauren Yerezhepov
- Laboratory of Genomic and Personalized Medicine, Center for Life Sciences, National Laboratory Astana, Nazarbayev University, Nur-Sultan, Kazakhstan
| | - Lyailya Chingissova
- National Scientific Center of Phthisiopulmonology of the Republic of Kazakhstan, Almaty, Kazakhstan
| | - Venera Bismilda
- National Scientific Center of Phthisiopulmonology of the Republic of Kazakhstan, Almaty, Kazakhstan
| | - Bekzat Toksanbayeva
- National Scientific Center of Phthisiopulmonology of the Republic of Kazakhstan, Almaty, Kazakhstan
| | - Anar Rakisheva
- Department of Phthisiopulmonology, School of General Medicine, Asfendiyarov Kazakh National Medical University, Almaty, Kazakhstan
| | - Ainur Akilzhanova
- Laboratory of Genomic and Personalized Medicine, Center for Life Sciences, National Laboratory Astana, Nazarbayev University, Nur-Sultan, Kazakhstan
| | - Ulan Kozhamkulov
- Laboratory of Genomic and Personalized Medicine, Center for Life Sciences, National Laboratory Astana, Nazarbayev University, Nur-Sultan, Kazakhstan
| | - Ulykbek Kairov
- Laboratory of Bioinformatics and Systems Biology, Center for Life Sciences, National Laboratory Astana, Nazarbayev University, Nur-Sultan, Kazakhstan
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de Melo EH, Gomes HM, Suffys PN, Lopes MQP, de Figueiredo Teixeira RL, Dos Santos ÍR, Franco MMJ, Langoni H, Paes AC, Afonso JAB, de Mendonça CL. Genotypic Characterization of Mycobacterium bovis Isolates From Dairy Cattle Diagnosed With Clinical Tuberculosis. Front Vet Sci 2021; 8:747226. [PMID: 34708105 PMCID: PMC8542897 DOI: 10.3389/fvets.2021.747226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2021] [Accepted: 08/31/2021] [Indexed: 11/30/2022] Open
Abstract
Molecular diagnosis of bovine tuberculosis plays an essential role in the epidemiological knowledge of the disease. Bovine tuberculosis caused by Mycobacterium bovis represents a risk to human health. This study aimed to perform the genotypic characterization of M. bovis isolated from bovines diagnosed as tuberculosis from dairy herds in the state of Pernambuco, Brazil. Granulomas from 30 bovines were sent for microbiological culture, and colonies compatible with Mycobacterium spp. were obtained in at least one culture from 17/30 granulomas. All isolates were confirmed to be M. bovis by spoligotyping and 24loci MIRU-VNTR typing. While spoligotyping characterized the isolates as SB0121, SB0295, SB0852, SB0120, and an unclassified genotype, 24loci MIRU-VNTR rendered two clusters of two isolates each and 13 unique profiles. Loci ETR-A showed higher discriminatory power, and loci (ETR-B, ETR-C, MIRU16, MIRU27, and QUB26) showed moderate allelic diversity. This is the first study on the genetic variability of the infectious agent cause of bovine TB in Pernambuco and demonstrates variability of strains in the state. Thus, it corroborates the importance of this microorganism as agent of bovine tuberculosis and its zoonotic potential, this epidemiological tool being a determinant in the rigor of the sanitary practices of disease control in dairy herds.
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Affiliation(s)
| | - Harrison Magdinier Gomes
- Laboratório de Biologia Molecular Aplicada à Micobactérias, Fundação Oswaldo Cruz, Laboratório de Biologia Molecular Aplicada à Micobactérias, Rio de Janeiro, Brazil
| | - Philip Noel Suffys
- Laboratório de Biologia Molecular Aplicada à Micobactérias, Fundação Oswaldo Cruz, Laboratório de Biologia Molecular Aplicada à Micobactérias, Rio de Janeiro, Brazil
| | - Márcia Quinhones Pires Lopes
- Laboratório de Biologia Molecular Aplicada à Micobactérias, Fundação Oswaldo Cruz, Laboratório de Biologia Molecular Aplicada à Micobactérias, Rio de Janeiro, Brazil
| | - Raquel Lima de Figueiredo Teixeira
- Laboratório de Biologia Molecular Aplicada à Micobactérias, Fundação Oswaldo Cruz, Laboratório de Biologia Molecular Aplicada à Micobactérias, Rio de Janeiro, Brazil
| | - Ícaro Rodrigues Dos Santos
- Laboratório de Biologia Molecular Aplicada à Micobactérias, Fundação Oswaldo Cruz, Laboratório de Biologia Molecular Aplicada à Micobactérias, Rio de Janeiro, Brazil
| | - Marília Masello Junqueira Franco
- Departamento de Higiene Veterinária e Saúde Pública, Faculdade de Medicina Veterinária e Zootecnia, Universidade Estadual Paulista, Botucatu, Brazil
| | - Helio Langoni
- Departamento de Higiene Veterinária e Saúde Pública, Faculdade de Medicina Veterinária e Zootecnia, Universidade Estadual Paulista, Botucatu, Brazil
| | - Antonio Carlos Paes
- Departamento de Higiene Veterinária e Saúde Pública, Faculdade de Medicina Veterinária e Zootecnia, Universidade Estadual Paulista, Botucatu, Brazil
| | | | - Carla Lopes de Mendonça
- Clínica de Bovinos de Garanhuns, Universidade Federal Rural de Pernambuco, Garanhuns, Brazil
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18
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Rudeeaneksin J, Phetsuksiri B, Nakajima C, Bunchoo S, Suthum K, Tipkrua N, Fukushima Y, Suzuki Y. Drug-resistant Mycobacterium tuberculosis and its genotypes isolated from an outbreak in western Thailand. Trans R Soc Trop Med Hyg 2021; 115:886-895. [PMID: 33320938 DOI: 10.1093/trstmh/traa148] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Revised: 10/29/2020] [Accepted: 11/16/2020] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND Multidrug-resistant TB (MDR-TB) outbreaks have occurred in the Thamaka district, Kanchanaburi province in Thailand. METHODS Seventy-two isolates, which included 7% mono-, 30.6% MDR and extensively drug-resistant TB (XDR-TB), were genotyped by spoligotyping, mycobacterial interspersed repetitive unit-variable-number tandem repeat (MIRU-VNTR) and single nucleotide polymorphism genotyping, and their drug resistance was analysed. RESULTS The spoligotyping results showed that Beijing spoligo-international type (SIT)1 was predominant (n=38; 52.8%) while the remaining were non-Beijing sublineages (n=34). The MIRU-VNTR analysis showed that Beijing isolates, most of which belonged to the modern type (n=37), formed 5 clusters and 13 individual patterns. In katG, only mutation Ser315Thr was identified. In rpoB, Ser531Leu was predominant, except for His526Arg and Leu533Pro, which were found in two isolates. A cluster of 14 Beijing strains contained these common mutations and shared the MIRU-VNTR genotype with isolates in the Thamaka district that had spread previously. Two U SIT523 isolates contained the mutations A1400G in rrs and Asp94Gly in gyrA genes, indicating a spread of XDR-TB. CONCLUSIONS Most mutations were associated with drug resistance and the specific MDR Beijing and XDR-TB in U SIT523 isolates remain. This genotyping is a key tool for tracking TB transmission in the Thamaka district of Thailand.
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Affiliation(s)
- Janisara Rudeeaneksin
- National Insti tute of Health, Department of Medical Sciences, Nonthaburi Province, Thailand
| | - Benjawan Phetsuksiri
- National Insti tute of Health, Department of Medical Sciences, Nonthaburi Province, Thailand
| | - Chie Nakajima
- Division of Bioresources, Hokkaido University Research Center for Zoonosis Control, Sapporo, Japan.,International Collaboration Unit, Hokkaido University Research Center for Zoonosis Control, Sapporo, Japan
| | - Supranee Bunchoo
- National Insti tute of Health, Department of Medical Sciences, Nonthaburi Province, Thailand
| | - Krairerk Suthum
- The Office of Disease Prevention and Control 5thRatchaburi, Department of Disease Control, Thailand
| | - Nattakan Tipkrua
- The Office of Disease Prevention and Control 5thRatchaburi, Department of Disease Control, Thailand
| | - Yukari Fukushima
- Division of Bioresources, Hokkaido University Research Center for Zoonosis Control, Sapporo, Japan
| | - Yasuhiko Suzuki
- Division of Bioresources, Hokkaido University Research Center for Zoonosis Control, Sapporo, Japan.,International Collaboration Unit, Hokkaido University Research Center for Zoonosis Control, Sapporo, Japan
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19
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Barandiaran S, Marfil MJ, Capobianco G, Pérez Aguirreburualde MS, Zumárraga MJ, Eirin ME, Cuerda MX, Winter M, Martínez Vivot M, Perez AM, La Sala LF. Epidemiology of Pig Tuberculosis in Argentina. Front Vet Sci 2021; 8:693082. [PMID: 34381835 PMCID: PMC8350762 DOI: 10.3389/fvets.2021.693082] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Accepted: 07/01/2021] [Indexed: 11/23/2022] Open
Abstract
Bovine tuberculosis (bTB) is a disease caused mainly by the Mycobacterium bovis and that is endemic to livestock populations in most Latin American countries. Traditionally, bTB control programs are costly and targeted to cattle, largely disregarding other species such as swine and wildlife. According to official services, in Argentina disease prevalence in pigs is comparable to that observed in cattle, suggesting the need for efficient control programs to manage the disease in both species. Additionally, extensive farming systems, which are commonly practiced in Argentina, allow the interaction between livestock and wildlife such as wild boar (Sus scrofa), which is considered a natural host of the disease. Here, we evaluated the bTB pigs- cattle interface, studying the dynamics of M. bovis isolates in the pig population and identifying farm-level epidemiological variables associated with the disease confirmation at slaughterhouses. Additionally, to assess the potential multi-host systems in the transmission of bTB, the molecular characterization of wild boar mycobacterial strains was included in the study, as this interaction has not been previously evaluated in this region. Multivariable logistic regression models were used to assess the association between farm-level epidemiological variables (location, farm size, and co-existence with cattle and goats) and bTB confirmation in pig tuberculosis-like lesions samples. Results showed that when cattle were present, the odds of bTB in pigs decreased 0.3 or 0.6% for every additional sow when cattle were present or absent in the farm, respectively. Pigs shared 60% (18/30) of the genotypes with cattle and wild boar, suggesting transmission at the interface between pigs and cattle and highlighting the potential role of wild boar in bTB maintenance. These results provide novel information about the molecular diversity of M. bovis strains in pigs in Argentina and proposes the potential relevance of a multi-host system in the epidemiology of bTB in the region. The statistical models presented here may be used in the design of a low cost, abattoir-based surveillance program for bTB in the pig industry in Argentina, with potential extension to other settings with similar epidemiological conditions.
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Affiliation(s)
- Soledad Barandiaran
- Instituto de Investigaciones en Producción Animal (INPA), Consejo Nacional de Investigaciones Científicas y Técnicas-Universidad de Buenos Aires, Buenos Aires, Argentina
| | - María Jimena Marfil
- Cátedra de Enfermedades Infecciosas, Facultad de Ciencias Veterinarias, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Guillermo Capobianco
- Departamento de Matemática, Instituto de Matemática de Bahía Blanca- Consejo Nacional de Investigaciones Científicas y Técnicas, Universidad Nacional del Sur, Buenos Aires, Argentina
| | - María Sol Pérez Aguirreburualde
- Center for Animal Health and Food Safety, College of Veterinary Medicine, University of Minnesota, Minnesota City, MN, United States
| | - Martín José Zumárraga
- Instituto Nacional de Tecnología Agropecuaria (INTA), Instituto de Agrobiotecnología y Biología Molecular (IABIMO), Instituto Nacional de Tecnología Agropecuaria: Consejo Nacional de Investigaciones Científicas y Técnicas, Buenos Aires, Argentina
| | - María Emilia Eirin
- Instituto Nacional de Tecnología Agropecuaria (INTA), Instituto de Agrobiotecnología y Biología Molecular (IABIMO), Instituto Nacional de Tecnología Agropecuaria: Consejo Nacional de Investigaciones Científicas y Técnicas, Buenos Aires, Argentina
| | - María Ximena Cuerda
- Instituto Nacional de Tecnología Agropecuaria (INTA), Instituto de Agrobiotecnología y Biología Molecular (IABIMO), Instituto Nacional de Tecnología Agropecuaria: Consejo Nacional de Investigaciones Científicas y Técnicas, Buenos Aires, Argentina
| | - Marina Winter
- Centro de Investigaciones y Transferencia de Río Negro, Universidad Nacional de Río Negro, Bariloche, Argentina
| | - Marcela Martínez Vivot
- Cátedra de Enfermedades Infecciosas, Facultad de Ciencias Veterinarias, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Andres Maximiliano Perez
- Instituto Nacional de Tecnología Agropecuaria (INTA), Instituto de Agrobiotecnología y Biología Molecular (IABIMO), Instituto Nacional de Tecnología Agropecuaria: Consejo Nacional de Investigaciones Científicas y Técnicas, Buenos Aires, Argentina
| | - Luciano Francisco La Sala
- Instituto de Ciencias Biológicas y Biomédicas del Sur, Universidad Nacional del Sur - Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
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20
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Acquah SKE, Asare P, Osei-Wusu S, Morgan P, Afum T, Asandem DA, Danso EK, Otchere ID, Ofori LA, Obiri-Danso K, Kock R, Asante-Poku A, Yeboah-Manu D. Molecular epidemiology and drug susceptibility profiles of Mycobacterium tuberculosis complex isolates from Northern Ghana. Int J Infect Dis 2021; 109:294-303. [PMID: 34273514 DOI: 10.1016/j.ijid.2021.07.020] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Revised: 06/30/2021] [Accepted: 07/03/2021] [Indexed: 01/19/2023] Open
Abstract
OBJECTIVE We conducted a cross-sectional study in the five administrative regions of Northern Ghana to determine the diversity of Mycobacterium tuberculosis complex (MTBC) sub/lineages and their susceptibility to isoniazid (INH) and rifampicin (RIF). METHODS Sputum specimens were collected and cultured from 566 pulmonary tuberculosis patients reporting to 17 health facilities from 2015 to 2019. Mycobacterial isolates obtained from solid cultures were confirmed as members of the MTBC by PCR amplification of IS6110 and rpoß and assigned lineages and sub-lineages using spoligotyping. RESULTS Of 294 mycobacterial isolates recovered, MTBC species identified were: M. tuberculosis sensu stricto (Mtbss) 241 (82.0%), M. africanum 41 (13.9%) and M. bovis four (1.4%) with eight (2.7%) unidentified. The human-adapted lineages (L) identified (N=279) were L1 (8/279, 2.9%), L2 (15/279, 5.4%), L3 (7/279, 2.5%), L4 (208/279, 74.5%), L5 (13/279, 4.7%) and L6 (28/279, 10.0%) with three unidentified lineages. Among the 208 L4, the dominant sub-lineages in the region were the Cameroon 120/208 (57.7%) and Ghana 50/208 (24.0%). We found 4.4% (13/294) and 0.7% (2/294) of the patients infected with MTBC isolates resistant to INH only and RIF only, respectively, with 2.4% (7/294) being infected with MDR strains. Whereas L6 was associated with the elderly, we identified that the Ghana sub-lineage of L4 was associated with both INH and MDR (p<0.05), making them important TB pathogens in Northern Ghana and a growing public health concern.
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21
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Ealand C, Peters J, Jacobs O, Sewcharran A, Ghoor A, Golub J, Brahmbhatt H, Martinson N, Dangor Z, Lala SG, Kana B. Detection of Mycobacterium tuberculosis Complex Bacilli and Nucleic Acids From Tongue Swabs in Young, Hospitalized Children. Front Cell Infect Microbiol 2021; 11:696379. [PMID: 34195103 PMCID: PMC8238041 DOI: 10.3389/fcimb.2021.696379] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Accepted: 05/21/2021] [Indexed: 01/24/2023] Open
Abstract
Diagnosis of tuberculosis in pediatric patients remains challenging due to inherent difficulties associated with obtaining respiratory samples for molecular and culture-based testing. To address this, recent studies have highlighted the utility of tongue swabs to detect Mycobacterium tuberculosis genomic DNA in the oral epithelia of tuberculosis infected adults. It is unknown whether tongue swabs have similar utility for diagnosis of childhood tuberculosis and if the presence of DNA in these swabs was associated with whole bacilli. We therefore sought to conduct a preliminary assessment of the utility of tongue swabs to detect tubercle bacilli and their associated genetic material in young children. For this, we recruited hospitalized children with clinically diagnosed tuberculosis (n = 26) or lower respiratory tract infection (LRTI, n = 9). These categories were blinded for downstream laboratory tests, which included PCR, spoligotyping, smear microscopy, and culture. Mtb genomic DNA was detected by PCR only in clinically diagnosed TB cases [11/26 (31.4%)] and not in cases with LRTI. Of these, 5/11 [45.5%] were associated with a spoligotype. Spoligotyping also detected an additional six specimens that were negative by PCR. Using smear microscopy, 19/26 [73.1%] and 4/9 [44.4] were Mtb positive in the tuberculosis or LRTI categories respectively. We noted positive results on all three tests in 5/26 [19.2%] in the tuberculosis category and 0/9 in the LRTI category. All specimens were culture negative. Collectively, these preliminary data present a compelling case for broader testing of tongue swabs to diagnose tuberculosis in children where obtaining standard sputum specimens is not easy.
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Affiliation(s)
- Christopher Ealand
- Department of Science and Innovation/National Research Foundation (DSI/NRF) Centre of Excellence for Biomedical TB Research, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand and the National Health Laboratory Service, Johannesburg, South Africa
| | - Julian Peters
- Department of Science and Innovation/National Research Foundation (DSI/NRF) Centre of Excellence for Biomedical TB Research, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand and the National Health Laboratory Service, Johannesburg, South Africa
| | - Olivia Jacobs
- Department of Science and Innovation/National Research Foundation (DSI/NRF) Centre of Excellence for Biomedical TB Research, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand and the National Health Laboratory Service, Johannesburg, South Africa
| | - Astika Sewcharran
- Department of Science and Innovation/National Research Foundation (DSI/NRF) Centre of Excellence for Biomedical TB Research, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand and the National Health Laboratory Service, Johannesburg, South Africa
| | - Azra Ghoor
- Department of Paediatrics and Child Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Jonathan Golub
- Center for TB Research, Johns Hopkins University, Baltimore, MD, United States
| | - Heena Brahmbhatt
- United States Agency for International Development (USAID), South Africa, Pretoria, South Africa.,Perinatal HIV Research Unit (PHRU), Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Neil Martinson
- Center for TB Research, Johns Hopkins University, Baltimore, MD, United States.,Perinatal HIV Research Unit (PHRU), Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Ziyaad Dangor
- Paediatric Education and Research Ladder, Department of Paediatrics and Child Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Sanjay G Lala
- Perinatal HIV Research Unit (PHRU), Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.,Paediatric Education and Research Ladder, Department of Paediatrics and Child Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Bavesh Kana
- Department of Science and Innovation/National Research Foundation (DSI/NRF) Centre of Excellence for Biomedical TB Research, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand and the National Health Laboratory Service, Johannesburg, South Africa
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22
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Steinum TM, Turgay E, Yardımcı RE, Småge SB, Karataş S. Tenacibaculum maritimum CRISPR loci analysis and evaluation of isolate spoligotyping. J Appl Microbiol 2021; 131:1848-1857. [PMID: 33905598 DOI: 10.1111/jam.15116] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Indexed: 11/27/2022]
Abstract
AIMS We performed in silico analysis of CRISPRcas loci from Tenacibaculum maritimum, evaluated spoligotyping as a subtyping method and genotyped uncharacterized Turkish isolates from European sea bass by multilocus sequence typing (MLST). METHODS AND RESULTS Spoligotyping was performed with primers designed to allow amplification and sequencing of whole CRISPR-arrays from 23 T. maritimum isolates. Twenty-three completed/draft genomes were also downloaded from the NCBI database and analysed. MLST of Turkish isolates was achieved with a well-established 7-gene scheme. Tenacibaculum maritimum genomes carry a structurally complete but partially defective class II CRISPRcas locus due to known amino acid substitutions in encoded Cas9 proteins. Our spacer identification suggests that the host range of bacteriophage P2559Y and Vibrio phage nt-1 include T. maritimum and that the most recurrent infection recorded by isolates has been with Tenacibaculum phage PTm5. Thirty-eight isolates with this CRISPRcas locus belonged to 25 spoligotypes and to 24 sequence types by MLST, respectively. According to MLST, T. maritimum isolates from Turkey are most related to previously defined sequence types ST3, ST40 and ST41 isolates from Spain, Malta and France. CONCLUSIONS The evaluated spoligotyping offers discriminatory power comparable to MLST. SIGNIFICANCE AND IMPACT OF THE STUDY Spoligotyping has potential as a quick, easy and cheap tool for subtyping of T. maritimum isolates.
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Affiliation(s)
- T M Steinum
- Department of Molecular Biology and Genetics, Faculty of Sciences, Istanbul University, Istanbul, Turkey
| | - E Turgay
- Department of Aquaculture and Fish Diseases, Faculty of Aquatic Sciences, Istanbul University, Istanbul, Turkey
| | - R E Yardımcı
- Department of Aquaculture and Fish Diseases, Faculty of Aquatic Sciences, Istanbul University, Istanbul, Turkey
| | | | - S Karataş
- Department of Aquaculture and Fish Diseases, Faculty of Aquatic Sciences, Istanbul University, Istanbul, Turkey
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23
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Squarre D, Chizimu J, Nakajima C, Muma JB, Hang'ombe BM, Simulundu E, Mwasinga W, Katampi J, Fandamu P, Mukonka V, Suzuki Y, Sawa H, Munang'andu HM, Shanungu G, Chambaro HM, Munyeme M. First report of Mycobacterium bovis in wild chacma baboons (Papio ursinus) at the human-wildlife interface area in Zambia. Transbound Emerg Dis 2021; 69:1659-1662. [PMID: 33900037 DOI: 10.1111/tbed.14124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Revised: 03/01/2021] [Indexed: 12/01/2022]
Abstract
Mycobacterium bovis (M. bovis) causes tuberculosis in mammals and is a major public health threat worldwide. While M. bovis has been reported in humans, domestic and wild ruminants at the human-wildlife-livestock interface area in Zambia, there is paucity of information on the role of primates as reservoir hosts. We screened seven wild chacma baboons (Papio ursinus) for tuberculosis at the human-wildlife interface area in Lochinvar National Park in the Kafue Flats, Zambia. Following necropsy, lung tissue and associated lymph nodes with tuberculous-like lesions collected from four adult male baboons were prepared for Mycobacterium culture. The isolates were initially typed using the Mycobacterium tuberculosis complex-discrimination multiplex PCR assay and further characterized by spoligotyping and 26-loci MIRU-VNTR. Mycobacteria were isolated from all four animals and identified as M. bovis by PCR. On Spoligotyping, all isolates belonged to SB 0120 spoligotype, which is similar to what was previously reported in humans, cattle and Kafue lechwe antelopes in Kafue Flats ecosystem. Furthermore, on MIRU-VNTR typing, the baboon isolates clustered with cattle and Kafue lechwe isolates from the same catchment area. This finding intimates probable cross-species transmission of M. bovis in the Kafue Flats ecosystem. Due to the close interaction of baboons and humans at interface areas in Zambia, our results have potential implications for public health. Equally, this finding raises concerns for conservation.
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Affiliation(s)
- David Squarre
- Research Centre for Zoonosis Control, Hokkaido University, Sapporo, Japan.,The Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Edinburgh, UK.,Department of National Parks and Wildlife, Wildlife Veterinary Unit, Chilanga, Zambia
| | - Joseph Chizimu
- Research Centre for Zoonosis Control, Hokkaido University, Sapporo, Japan.,Ministry of Health, Lusaka, Zambia
| | - Chie Nakajima
- Research Centre for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - John B Muma
- School of Veterinary Medicine, The University of Zambia, Lusaka, Zambia
| | | | - Edgar Simulundu
- School of Veterinary Medicine, The University of Zambia, Lusaka, Zambia
| | - Wizaso Mwasinga
- School of Veterinary Medicine, The University of Zambia, Lusaka, Zambia
| | - Jackson Katampi
- Department of National Parks and Wildlife, Wildlife Veterinary Unit, Chilanga, Zambia
| | - Paul Fandamu
- Ministry of Fisheries and Livestock, Lusaka, Zambia
| | - Victor Mukonka
- Ministry of Health, Lusaka, Zambia.,Ministry of Health, Zambia National Public Health Institute, Lusaka, Zambia
| | - Yasuhiko Suzuki
- Research Centre for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Hirofumi Sawa
- Research Centre for Zoonosis Control, Hokkaido University, Sapporo, Japan.,Global Virus Network, Baltimore, MD, USA
| | | | - Griffin Shanungu
- International Crane Foundation/Endangered Wildlife Trust Partnership, Lusaka, Zambia
| | - Herman M Chambaro
- Research Centre for Zoonosis Control, Hokkaido University, Sapporo, Japan.,Ministry of Fisheries and Livestock, Lusaka, Zambia.,Central Veterinary Research Institute, Lusaka, Zambia
| | - Musso Munyeme
- School of Veterinary Medicine, The University of Zambia, Lusaka, Zambia
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24
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Kapalamula TF, Chizimu J, Belotindos L, Akapelwa M, Shrestha D, Nyenje ME, Munyeme M, Hang'ombe BM, Mkakosya RS, Gordon SV, Nakajima C, Suzuki Y. Molecular epidemiology of Mycobacterium bovis in central parts of Malawi. Transbound Emerg Dis 2021; 69:1577-1588. [PMID: 33900039 DOI: 10.1111/tbed.14127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Revised: 03/13/2021] [Accepted: 04/21/2021] [Indexed: 11/28/2022]
Abstract
Bovine tuberculosis (bTB) is a neglected disease that affects cattle and humans. The burden of bTB is higher in developing countries as compared to industrialized countries. The reasons behind this discrepancy include the fact that bTB control measures, such as testing and slaughter of infected cattle and pasteurization of milk, are not usually practised in developing countries largely because of their high cost. To improve our understanding of bTB in developing countries, molecular typing studies are essential, in particular in terms of transmission dynamics, infection sources and knowledge of circulating strains of the principal causative agent, Mycobacterium bovis. In this study, we applied a suite of molecular typing techniques encompassing deletion analysis, spoligotyping and MIRU-VNTR to isolates recovered from samples collected during the routine post-mortem of cattle at the cold storage abattoir in Lilongwe, Malawi. Out of 63 isolates, 51 (81%) belonged to the European 1. M. bovis clonal complex. Spoligotyping identified 8 profiles, with SB0131 being the predominant type (56% of isolates). Spoligotypes SB0273 and SB0425 were identified in 14% and 13%, respectively, of the isolates. MIRU-VNTR showed a high discriminatory power of 0.959 and differentiated the 8 spoligotypes to 31 genotypes. The high diversity of M. bovis within the study area suggests the infection has been circulating in the area for a considerable period of time, likely facilitated by the lack of effective control measures. We also observed genetic similarities between isolates from Malawi (this study) to isolates described in previous studies in Zambia and Mozambique, suggesting transmission links in this region. The information provided by this study provides much needed evidence for the formulation of improved bTB control strategies.
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Affiliation(s)
- Thoko Flav Kapalamula
- Division of Bioresources, Research Center for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Joseph Chizimu
- Division of Bioresources, Research Center for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Lawrence Belotindos
- Division of Bioresources, Research Center for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Mwangala Akapelwa
- Division of Bioresources, Research Center for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Dipti Shrestha
- Division of Bioresources, Research Center for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Mirriam Ethel Nyenje
- Community Health Sciences Unit, National Tuberculosis Reference Laboratory, Lilongwe, Malawi
| | - Musso Munyeme
- School of Veterinary Medicine, University of Zambia, Lusaka, Zambia.,Africa Center of Excellence for Infectious Diseases of Humans and Animals, University of Zambia, Lusaka, Zambia
| | - Bernard Mudenda Hang'ombe
- School of Veterinary Medicine, University of Zambia, Lusaka, Zambia.,Africa Center of Excellence for Infectious Diseases of Humans and Animals, University of Zambia, Lusaka, Zambia
| | | | - Stephen V Gordon
- School of Veterinary Medicine, University College Dublin, Dublin, Ireland
| | - Chie Nakajima
- Division of Bioresources, Research Center for Zoonosis Control, Hokkaido University, Sapporo, Japan.,International Collaboration Unit, Research Center for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Yasuhiko Suzuki
- Division of Bioresources, Research Center for Zoonosis Control, Hokkaido University, Sapporo, Japan.,International Collaboration Unit, Research Center for Zoonosis Control, Hokkaido University, Sapporo, Japan
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25
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Ordaz-Vázquez A, Soberanis-Ramos O, Cruz-Huerta E, Retis-Sanchez-de-la-Barquera S, Chávez-Mazari B, Gudiño-Enriquez T, Santacruz-Aguilar M, Ponce-De-León-Garduño A, Sifuentes-Osornio J, Bobadilla-Del-Valle M. Genetic diversity of Mycobacterium bovis evaluated by spoligotyping and MIRU-VNTR in an intensive dairy cattle breeding area in Mexico. Transbound Emerg Dis 2021; 69:1144-1154. [PMID: 33725428 DOI: 10.1111/tbed.14074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Revised: 01/22/2021] [Accepted: 03/12/2021] [Indexed: 11/29/2022]
Abstract
Bovine tuberculosis (bTB) is mainly caused by Mycobacterium bovis. In Mexico, dairy cattle play an important role in the persistence and spread of the bacillus. In order to describe M. bovis genetic diversity, we genotyped a total of 132 strains isolated from slaughtered cattle with bTB suggestive lesions between 2009 and 2010 in Hidalgo, Mexico, using a panel of 9-loci mycobacterial interspersed repetitive unit-variable number of tandem repeats (MIRU-VNTR) and spoligotyping. We found 21 spoligotypes, and 124 isolates were grouped in 13 clusters. The most frequent spoligotypes were SB0121 (49, 37.1%) and SB0673 (27, 20.5%); three new spoligotypes were reported SB02703, SB02704 and SB02705. We observed 37 MIRU-VNTR patterns, 107 isolates were grouped in 12 clusters and 25 isolates were unique. Spoligotypes SB0121, SB0673, SB0140, SB0145 and SB0120 showed marked subdivision applying MIRU-VNTR method; meanwhile, spoligotypes SB0971 and SB0327 showed single MIRU-VNTR profiles. The Hunter-Gaston discriminatory index (HGDI) was 0.88, 0.78 and 0.90 for 9-loci MIRU-VNTR, spoligotyping and both methods, respectively. Additionally, allelic diversity (h) analysis showed high diversity for QUB3232, QUB26 and QUB11b with h = 0.79, 0.66 and 0.63, respectively. Overall, high genetic variability was observed among M. bovis isolates. Thus, the use of 9-loci MIRU-VNTR panel is enough to describe genetic diversity, evolution and distribution of M. bovis. This study supports the use of these tools for subsequent epidemiological studies in high incidence areas.
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Affiliation(s)
- Anabel Ordaz-Vázquez
- Laboratory of Clinical Microbiology, Department of Infectious Diseases, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Mexico City, Mexico
| | - Orbelin Soberanis-Ramos
- Department of Preventive Medicine and Public Health, Facultad de Medicina Veterinaria y Zootecnia, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Edith Cruz-Huerta
- Laboratory of Clinical Microbiology, Department of Infectious Diseases, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Mexico City, Mexico
| | - Sandra Retis-Sanchez-de-la-Barquera
- Laboratory of Clinical Microbiology, Department of Infectious Diseases, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Mexico City, Mexico
| | - Bárbara Chávez-Mazari
- Laboratory of Clinical Microbiology, Department of Infectious Diseases, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Mexico City, Mexico
| | - Tomasa Gudiño-Enriquez
- Laboratory of Clinical Microbiology, Department of Infectious Diseases, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Mexico City, Mexico
| | | | - Alfredo Ponce-De-León-Garduño
- Laboratory of Clinical Microbiology, Department of Infectious Diseases, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Mexico City, Mexico
| | - José Sifuentes-Osornio
- Department of Medicine, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Mexico City, Mexico
| | - Miriam Bobadilla-Del-Valle
- Laboratory of Clinical Microbiology, Department of Infectious Diseases, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Mexico City, Mexico
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26
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Tulu B, Zewede A, Belay M, Zeleke M, Girma M, Tegegn M, Ibrahim F, Jolliffe DA, Abebe M, Balcha TT, Gumi B, Martineau HM, Martineau AR, Ameni G. Epidemiology of Bovine Tuberculosis and Its Zoonotic Implication in Addis Ababa Milkshed, Central Ethiopia. Front Vet Sci 2021; 8:595511. [PMID: 33681321 PMCID: PMC7925636 DOI: 10.3389/fvets.2021.595511] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Accepted: 01/05/2021] [Indexed: 11/13/2022] Open
Abstract
Bovine tuberculosis (bTB) continues to be one of the most widely distributed chronic infectious diseases of zoonotic importance, which causes a significant economic loss in animal production. A cross-sectional study was conducted to estimate the prevalence of bTB and its associated risk factors and type the Mycobacterium bovis isolated in central Ethiopia. A total of 65 dairy farms and 654 cattle were tested for bTB using a single intradermal comparative cervical tuberculin (SICCT) test. Data on farm management, animal-related characteristics, and the owner's knowledge of the zoonotic importance of bTB were collected using a structured questionnaire. In addition, a total of 16 animals from different farms were identified for postmortem examination. Lowenstein Jensen (LJ) culture was also conducted, and spoligotyping was used to type the M. bovis strains isolated. Chi-square test and logistic regression models were used to analyze the herd- and animal-level risk factors. Herd- and animal-level prevalence rates of bTB were 58.5% (95% CI: 46.2%-69.2%) and 39.3% (95% CI: 35.5%-43.5%), respectively. At the herd level, poor farm management was the predictor for bTB positivity (p < 0.05). Animal breed, poor BCS, farm type, and poor farm management conditions were significant predictors of bTB positivity (p < 0.05) at an individual animal level. All animals identified for postmortem examination were found to have gross TB-like lesions. A total of 14 M. bovis strains were identified from 12 animals that were positive for LJ culture. The strain with the largest number of clusters (five isolates) was SB1176, followed by SB0134 (three isolates), SB0192 (two isolates), and SB2233 (two isolates), and two new strains, each consisting of only one isolate. The majority (58.5%) of the respondents did not know the zoonotic importance of bTB. The result of this study showed a high prevalence of bTB in the Addis Ababa milkshed and a low level of consciousness of the owners on its transmission to humans. Therefore, the launching of acceptable control measures of bTB and the creation of public awareness about its zoonotic transmission and prevention measures are required.
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Affiliation(s)
- Begna Tulu
- Aklilu Lemma Institute of Pathobiology, Sefere Selam Campus, Addis Ababa University, Addis Ababa, Ethiopia.,Department of Medical Laboratory Sciences, Bahir Dar University, Bahir Dar, Ethiopia
| | - Aboma Zewede
- Ethiopian Public Health Institute, Addis Ababa, Ethiopia
| | - Mulugeta Belay
- Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, United Kingdom
| | - Miserach Zeleke
- Aklilu Lemma Institute of Pathobiology, Sefere Selam Campus, Addis Ababa University, Addis Ababa, Ethiopia
| | - Mussie Girma
- Aklilu Lemma Institute of Pathobiology, Sefere Selam Campus, Addis Ababa University, Addis Ababa, Ethiopia
| | | | - Fozia Ibrahim
- Armeur Hansen Research Institute, Addis Ababa, Ethiopia
| | - David A Jolliffe
- Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, United Kingdom
| | - Markos Abebe
- Armeur Hansen Research Institute, Addis Ababa, Ethiopia
| | | | - Balako Gumi
- Aklilu Lemma Institute of Pathobiology, Sefere Selam Campus, Addis Ababa University, Addis Ababa, Ethiopia
| | - Henny M Martineau
- Department of Pathology, The Royal Veterinary College, Hatfield, United Kingdom
| | - Adrian R Martineau
- Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, United Kingdom
| | - Gobena Ameni
- Aklilu Lemma Institute of Pathobiology, Sefere Selam Campus, Addis Ababa University, Addis Ababa, Ethiopia.,Department of Veterinary Medicine, College of Food and Agriculture, United Arab Emirates University, Al Ain, United Arab Emirates
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27
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Tuzcu N, Köksal F. Genetic evaluation of Mycobacteriumbovis isolates with MIRU-VNTR and spoligotyping. Turk J Med Sci 2020; 50:2017-2023. [PMID: 32599971 PMCID: PMC7775703 DOI: 10.3906/sag-1910-138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Accepted: 06/27/2020] [Indexed: 11/26/2022] Open
Abstract
Background/aim Determining the epidemiological characteristics of
M. bovis
strains isolated from human and animal tuberculosis cases will assist in taking more appropriate and effective control measures in controlling tuberculosis originating from animals.
Materials and methods In this study, 32
M. bovis
isolates of animal origin and 10 of human origin were isolated and identified in the Çukurova region between March 2011 and June 2012. The 12-locus MIRU-VNTR and spoligotyping methods were used.
Results Six different patterns were determined by spoligotyping and 10 by MIRU-VNTR. When both methods were used together, the number of patterns was found to be 28; MIRU4, MIRU26, MIRU31, and MIRU40 had the highest locus discrimination powers by MIRU-VNTR. The isolates concentrated in the SB0120 pattern at the rate of 42.85% in spoligotyping. By the same method, it was seen that 7 isolates were
M bovis ssp. caprae
pattern and 2 human isolates were
M. bovis BCG
pattern. Nevertheless, spoligotyping and MIRU-VNTR patterns showed that 5
M. bovis
isolates of human origin were 100% compatible with isolates originating from cattle.
Conclusion In this study, we determined that the use of spoligotyping and MIRU-VNTR methods together was found to be more sensitive in the epidemiological analysis of
M. bovis
isolates.
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Affiliation(s)
- Nevin Tuzcu
- Department of Biochemistry, Faculty of Pharmacy, Selçuk University, Konya, Turkey
| | - Fatih Köksal
- Department of Medical Microbiology, Faculty of Medicine, Çukurova University, Adana, Turkey
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28
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Moe Sann WW, Namwat W, Faksri K, Swe TL, Swe KK, Thwin T, Sangka A. Genetic diversity of Mycobacterium tuberculosis using 24-locus MIRU-VNTR typing and Spoligotyping in Upper Myanmar. J Infect Dev Ctries 2020; 14:1296-1305. [PMID: 33296343 DOI: 10.3855/jidc.12998] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2020] [Accepted: 06/30/2020] [Indexed: 10/31/2022] Open
Abstract
INTRODUCTION MIRU-VNTR typing and Spoligotyping are the useful molecular tools for TB epidemiology study. Information regarding genetic diversity and tuberculosis (TB) transmission in Upper Myanmar only is scares. METHODOLOGY We determined the genetic diversity of Mycobacterium tuberculosis (Mtb) and TB transmission from Upper Myanmar TB Reference Laboratory, Mandalay Region, including Mandalay (72), Shan (22), Magway (15), Sagaing (13), Nay Pyi Taw (8), Kachin (7), Chin (2) and Kayah (1). One hundred and forty Mtb isolates were genotyped using 24-locus MIRU-VNTR typing and spoligotyping. Lineage classification and TB transmission analysis were performed. RESULTS 24-locus MIRU-VNTR typing identified 135 unique profiles and two clusters compared to 35 spoligotyping profiles which contained 12 clusters and 23 unique isolates, Beijing (n=100, 71.4%) was found to be prominent lineage by combine two methods. The expected proportion attributable to recent transmission based on clustering rate was 2.1%. One cluster case was more likely to be in MDR patient. CONCLUSIONS Our findings showed Beijing genotypes were dominant in Upper Myanmar. The usage and analysis of 24-locus MIRU-VNTR typing might prove useful for our broader understanding of TB outbreaks and epidemiology than spoligotyping. The genotypic pattern of this combined method suggests that the lower transmission rate may be due to a higher possibility of reactivation cases in Upper Myanmar.
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Affiliation(s)
- Waing Waing Moe Sann
- Medical Technology Program, Faculty of Associated medical Sciences, Khon Kaen University, Khon Kaen,Thailand.
| | - Wises Namwat
- Department of Microbiology, Faculty of Medicine, Khon Kaen University, Thailand.
| | - Kiatichai Faksri
- Department of Microbiology, Faculty of Medicine, Khon Kaen University, Thailand.
| | | | - Kyi Kyi Swe
- National TB Control Program, Upper Myanmar TB Reference Laboratory, Mandalay Region, Myanmar.
| | - Thandar Thwin
- National TB Control Program, Upper Myanmar TB Reference Laboratory, Mandalay Region, Myanmar.
| | - Arunnee Sangka
- Centre for Research and Development of Medical Diagnostic Laboratories (CMDL), Faculty of Associated Medical Sciences, Khon Kaen University, Khon Kaen, Thailand.
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29
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Kohl TA, Kranzer K, Andres S, Wirth T, Niemann S, Moser I. Population Structure of Mycobacterium bovis in Germany: a Long-Term Study Using Whole-Genome Sequencing Combined with Conventional Molecular Typing Methods. J Clin Microbiol 2020; 58:e01573-20. [PMID: 32817084 DOI: 10.1128/JCM.01573-20] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Accepted: 08/10/2020] [Indexed: 01/19/2023] Open
Abstract
Mycobacterium bovis is the primary cause of bovine tuberculosis (bTB) and infects a wide range of domestic animal and wildlife species and humans. In Germany, bTB still emerges sporadically in cattle herds, free-ranging wildlife, diverse captive animal species, and humans. In order to understand the underlying population structure and estimate the population size fluctuation through time, we analyzed 131 M. bovis strains from animals (n = 38) and humans (n = 93) in Germany from 1999 to 2017 by whole-genome sequencing (WGS), mycobacterial interspersed repetitive-unit-variable-number tandem-repeat (MIRU-VNTR) typing, and spoligotyping. Based on WGS data analysis, 122 out of the 131 M. bovis strains were classified into 13 major clades, of which 6 contained strains from both human and animal cases and 7 only strains from human cases. Bayesian analyses suggest that the M. bovis population went through two sharp anticlimaxes, one in the middle of the 18th century and another one in the 1950s. WGS-based cluster analysis grouped 46 strains into 13 clusters ranging in size from 2 to 11 members and involving strains from distinct host types, e.g., only cattle and also mixed hosts. Animal strains of four clusters were obtained over a 9-year span, pointing toward autochthonous persistent bTB infection cycles. As expected, WGS had a higher discriminatory power than spoligotyping and MIRU-VNTR typing. In conclusion, our data confirm that WGS and suitable bioinformatics constitute the method of choice to implement prospective molecular epidemiological surveillance of M. bovis The population of M. bovis in Germany is diverse, with subtle, but existing, interactions between different host groups.
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30
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Mansoori N, Vaziri F, Amini S, Khanipour S, Pourazar Dizaji S, Douraghi M. Spoligotype and Drug Susceptibility Profiles of Mycobacterium tuberculosis Complex Isolates in Golestan Province, North Iran. Infect Drug Resist 2020; 13:2073-2081. [PMID: 32669860 PMCID: PMC7335844 DOI: 10.2147/idr.s255889] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2020] [Accepted: 06/18/2020] [Indexed: 11/23/2022] Open
Abstract
Introduction Despite the moderate incidence of tuberculosis (TB) in many parts of Iran, Golestan province had a permanently higher TB incidence rate than the national average. Moreover, Golestan province receives immigrants, mainly from TB-endemic areas of Iran and neighbor countries. Here, we aimed to characterize the circulating Mycobacterium tuberculosis complex (MTBC) isolates in terms of the spoligotype and drug resistance patterns, across Golestan province. Materials and Methods A set of 166 MTBC isolates was collected during July 2014 to July 2015 and subjected to drug susceptibility testing for first- and second-line anti-TB drugs and spoligotyping. Results Of 166 MTBC isolates, 139 (83.7%) isolates were assigned to 28 spoligotype international types (SITs). The most frequent SITs were SIT127/Ural-2 (n=25, 15.1%), followed by SIT1/Beijing (n=21, 12.7%) and SIT3427/Ural-2 (n=18, 10.8%). The set of 18 isolates (10.8%) showed resistance to at least one drug, which mainly belonged to SIT1/Beijing (n=7, 38.9%), orphan patterns (n=4, 22.2%) and SIT357/CAS1-Delhi (n=3, 16.7%). In addition, four isolates (2.4%) were resistant to pyrazinamide. The analysis of mutation corresponded to resistance to rifampin and isoniazid showed that two isolates had Ser531Leu substitution in rpoB, four isolates had Ser315Thr substitution in katG and one isolate had [C(−15)T] in inhA locus. Conclusion High diversity in spoligotypes of the MTBC isolates and lack of dominant genotype might be due to residence of immigrants in this region and consequent reactivation of latent infection. In addition, due to the presence of extensively drug-resistant (XDR) isolates in Golestan province, it is important to conduct future studies to determine transmission pattern of drug-resistant isolates in this region.
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Affiliation(s)
- Noormohamad Mansoori
- Division of Microbiology, Department of Pathobiology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Farzam Vaziri
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran.,Microbiology Research Center (MRC), Pasteur Institute of Iran, Tehran, Iran
| | - Sirus Amini
- Regional Tuberculosis Reference Laboratory, Tehran University of Medical Sciences, Tehran, Iran
| | - Sharareh Khanipour
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran.,Microbiology Research Center (MRC), Pasteur Institute of Iran, Tehran, Iran
| | - Shahin Pourazar Dizaji
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran.,Microbiology Research Center (MRC), Pasteur Institute of Iran, Tehran, Iran
| | - Masoumeh Douraghi
- Division of Microbiology, Department of Pathobiology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran.,Food Microbiology Research Center, Tehran University of Medical Sciences, Tehran, Iran
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31
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Gupta A, Sinha P, Rathod S, Shanmugam SK, Uma Devi KR, Anupurba S, Nema V. Genotype analysis of ofloxacin-resistant multidrug-resistant Mycobacterium tuberculosis isolates in a multicentered study from India. Indian J Med Res 2020; 151:361-370. [PMID: 32461400 PMCID: PMC7371067 DOI: 10.4103/ijmr.ijmr_493_18] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Background & objectives: Drug resistance surveillance offers useful information on trends of drug resistance and the efficacy of control measures. Studies and reports of drug-resistant mutations and phenotypic assays thus become important. This study was conducted to investigate the molecular characteristics of ofloxacin (OFX)-resistant, multidrug-resistant tuberculosis (MDR-TB) isolates from different geographical regions of India and their association with strains of different genotypes. Further, the nitrate reductase assay (NRA) was tested against Mycobacteria Growth Indicator Tube (MGIT) for the determination of OFX resistance as an alternative and cost-effective method. Methods: A total of 116 Mycobacterium tuberculosis isolates were used to assess the mutations in the gyrA, gyrB genes and resistance levels to OFX. Mutational analysis in gyrA and gyrB genes and genotype analysis of M. tuberculosis isolates was done by gene-specific polymerase chain reaction (PCR) followed by DNA sequencing and spoligotyping, respectively. Results: Three (6.25%), 12 (44.44%) and 12 (29.27%) MDR-TB isolates from western, northern and southern India, respectively, were found to be OFX-resistant MDR-TB isolates. OFX resistance was observed to be significantly higher in MDR-TB cases for all study regions. Beijing genotypes from northern India were observed to be associated with OFX-resistant MDR-TB cases (P<0.05). Among 35 (30.15%) phenotypically OFX-resistant isolates, 22 (62.86%) had mutations in the gyrA gene and two (5.71%) isolates had mutations in the gyrB gene. Interpretation & conclusions: These results caution against the PCR-based prediction of OFX resistance patterns and highlight the need for searching other genetic loci for the detection of mutations conferring resistance to OFX in M. tuberculosis. Our study also showed the usefulness of NRA as an alternative method to detect OFX resistance.
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Affiliation(s)
- Anamika Gupta
- Division of Molecular Biology, ICMR-National AIDS Research Institute, Pune, Maharashtra, India
| | - Pallavi Sinha
- Department of Microbiology, Institute of Medical Sciences, Banaras Hindu University, Varanasi, Uttar Pradesh, India
| | - Sunita Rathod
- Division of Molecular Biology, ICMR-National AIDS Research Institute, Pune, Maharashtra, India
| | - Siva Kumar Shanmugam
- Department of Bacteriology, ICMR-National Institute for Research in Tuberculosis, Chennai, Tamil Nadu, India
| | - K R Uma Devi
- Department of Immunology, ICMR-National Institute for Research in Tuberculosis, Chennai, Tamil Nadu, India
| | - Shampa Anupurba
- Department of Microbiology, Institute of Medical Sciences, Banaras Hindu University, Varanasi, Uttar Pradesh, India
| | - Vijay Nema
- Division of Molecular Biology, ICMR-National AIDS Research Institute, Pune, Maharashtra, India
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32
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Uddin MKM, Rahman A, Ather MF, Ahmed T, Rahman SMM, Ahmed S, Banu S. Distribution and Frequency of rpoB Mutations Detected by Xpert MTB/RIF Assay Among Beijing and Non-Beijing Rifampicin Resistant Mycobacterium tuberculosis Isolates in Bangladesh. Infect Drug Resist 2020; 13:789-797. [PMID: 32210593 PMCID: PMC7073589 DOI: 10.2147/idr.s240408] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2019] [Accepted: 02/07/2020] [Indexed: 12/19/2022] Open
Abstract
Background Rifampicin resistance (RR) is a key indicator of multidrug-resistant tuberculosis (MDR-TB) and 95% of the RR is associated with the mutation in the 81-bp rifampicin resistance determining region (RRDR) of the rpoB gene of Mycobacterium tuberculosis complex (MTBC). The Xpert MTB/RIF (Xpert) assay uses five overlapping molecular beacon probes (A-E) complementary to RRDR region that detect MTBC and mutations associated with RR. The objective of the study was to investigate the distribution and frequency of mutations detected by Xpert assay among Beijing and non-Beijing RR-TB isolates. Methods A total of 205 randomly selected RR-TB specimens detected by Xpert assay were included in this study. A portion of specimens was further subjected to culture, MTBDRplus test and the positive culture isolates were genotyped by spoligotyping. Results We found that the most frequent mutation occurred at probe E (S531L) binding region in both Beijing and non-Beijing isolates (61.9% and 66.9%, respectively). The Beijing family had higher mutation rates than non-Beijing (19.0% vs 12.4%) at probe B (D516V) while the non-Beijing family had higher mutations at probe D (H526D or H526Y) than the Beijing (13.2% vs 10.7%) family. Mutations at probes Aand C were less common in both Beijing and non-Beijing isolates. There was no significant difference (P=0.36) in the occurrence of mutations at different probes between Beijing and non-Beijing isolates. Conclusions The study results revealed that the most frequent mutation occurs in the region of probe E and the least common mutations at probe A and C among both Beijing and non-Beijing RR-TB cases. This first insight into the probe mutation variation and frequencies among the RR-TB cases in Bangladesh forms the baseline information for further investigation.
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Affiliation(s)
| | - Arfatur Rahman
- Infectious Diseases Division, icddr,b, Dhaka, Bangladesh.,Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University (Parkville Campus), Parkville VIC 3052, Australia
| | - Md Fahim Ather
- Infectious Diseases Division, icddr,b, Dhaka, Bangladesh
| | - Tanvir Ahmed
- Infectious Diseases Division, icddr,b, Dhaka, Bangladesh
| | | | - Shahriar Ahmed
- Infectious Diseases Division, icddr,b, Dhaka, Bangladesh
| | - Sayera Banu
- Infectious Diseases Division, icddr,b, Dhaka, Bangladesh
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Escárcega DAV, Razo CAP, Ruíz SG, Gallegos SLS, Suazo FM, Alarcón GJC. Analysis of Bovine Tuberculosis Transmission in Jalisco, Mexico through Whole-genome Sequencing. J Vet Res 2020; 64:51-61. [PMID: 32258800 DOI: 10.2478/jvetres-2020-0010] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Accepted: 02/03/2020] [Indexed: 02/08/2023] Open
Abstract
Introduction Bovine tuberculosis, caused by M. bovis, is endemic in Mexico and has had a big impact on public health. Jalisco is considered to be an important dairy region in the country, accounting for approximately 19% of the total milk production. Within Jalisco, the region of Altos Sur holds the largest proportion of the cattle inventory of the state. Material and Methods To determine the frequency of bovine tuberculosis in Altos Sur, Jalisco, as well as M. bovis genetic diversity, sampling of tissue (lymph nodes, lungs, and liver) from Holstein cattle was performed in four abattoirs belonging to three municipalities of this region (Tepatitlán de Morelos, San Miguel el Alto, and Arandas). Spoligotyping and whole-genome sequencing were carried out to assess the genetic relationships of M. bovis strains circulating in this area, as well as a comparison to isolates from other places in Mexico. Results Prevalence was 15.06%, and distribution similar among the three municipalities. The most frequent spoligotypes were SB0673, SB121, and SB0145. Whole-genome sequencing revealed three main clades (I, II, III), but isolates did not show clustering by region. Conclusion Phylogenetic analysis suggested ongoing transmission between herds of the different regions, and no unique source of infection was determined. This hinders efforts under the national program for the control and eradication of the disease, so serious attention must be paid to rural regions such as Altos Sur in order to improve its success.
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34
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Ismail S, Al Amry K, Aggor G, El Naggar H, Selim S. Spoligotyping with pncA sequencing strategy conferring the transmission of multidrug-resistant tuberculosis in Egypt. Int J Mycobacteriol 2020; 8:211-217. [PMID: 31512595 DOI: 10.4103/ijmy.ijmy_111_19] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
Abstract
Background This study explored the genetic diversity of Mycobacterium tuberculosis isolates in Egypt by spoligotyping in combination with pncA gene sequencing, spoNC. Methods First, isolates were selected from 400 isolates positive for M. tuberculosis that referred to Central Labs Ministry of Health and then were subjected to the study analyses. Results Twenty one isolates were found to be multidrug resistant (MDR) and 29 isolates were sensitive for isonizide (INH) and rifampicine (RIF) after testing by phenotypic drug susceptibility testing (DST) and Mycobacteria Growth Indicator Tube (MGIT). Spoligotyping yielded 45 patterns belonging to seven families that previously reported in neighboring countries such as Iraq, Syria, Iran, and Turkey. While four isolates were orphans. Conclusion Application of spoNC on obtained spoligotype patterns enhances to reduce the clustering rate. Bejing family the predominant (34%) were subdivided by pncA sequence into three sensitive DST pncA wild type, three MDR-DST isolates showing cys14Arg mutation in pncA, two sensitive DST isolates with pncA Gly97Asp mutation, and three sensitive DST pncAVal128Gly mutation. The next most common CASI_DELHI family (16%) were subdivided by pncA sequencing into CASI_DELHI (st 381, MDR) including two pncA silent mutation ser65ser (tcc > tct) and CASI_DELHI (st26, sensitive) which included six pncA (wild-type) results, and Latin-American-Mediterranean 6 family (6%) all had PncA Gly97Asp mutation. We concluded that spoNC provides good snap shot for MDR surveillance and its country origin and performs early identification of outbreaks in Egypt.
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Affiliation(s)
- Suzan Ismail
- Department of Biotechnology, Animal Health Research Institute, Giza, Egypt
| | - Khaled Al Amry
- Department of Microbiology, Faculty of Veterinary Medicine, Cairo University, Giza, Egypt
| | - Galal Aggor
- Department of Biotechnology, Animal Health Research Institute, Giza, Egypt
| | - Hoida El Naggar
- Mycobacteriology Unit, Central Labs of Ministry of Health and Population, Cairo, Egypt
| | - Salah Selim
- Department of Microbiology, Faculty of Veterinary Medicine, Cairo University, Giza, Egypt
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Cerezo-Cortés MI, Rodríguez-Castillo JG, Hernández-Pando R, Murcia MI. Circulation of M. tuberculosis Beijing genotype in Latin America and the Caribbean. Pathog Glob Health 2020; 113:336-351. [PMID: 31903874 DOI: 10.1080/20477724.2019.1710066] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Lineage 2 (East Asian), which includes the Beijing genotype, is one of the most prevalent lineages of Mycobacterium tuberculosis (Mtb) throughout the world. The Beijing family is associated to hypervirulence and drug-resistant tuberculosis. The study of this genotype's circulation in Latin America is crucial for achieving total control of TB, the goal established by the World Health Organization, for the American sub-continent, before 2035. In this sense, the present work presents an overview of the status of the Beijing genotype for this region, with a bibliographical review, and data analysis of MIRU-VNTRs for available Beijing isolates. Certain countries present a prevalent trend of <5%, suggesting low transmissibility for the region, with the exception of Cuba (17.2%), Perú (16%) and Colombia (5%). Minimum Spanning Tree analysis, obtained from MIRU-VNTR data, shows distribution of specific clonal complex strains in each country. From this data, in most countries, we found that molecular epidemiology has not been a tool used for the control of TB, suggesting that the Beijing genotype may be underestimated in Latin America. It is recommended that countries with the highest incidence of the Beijing genotype use effective control strategies and increased care, as a requirement for public health systems.
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Affiliation(s)
- M I Cerezo-Cortés
- Grupo MICOBAC-UN, Departamento de Microbiología, Facultad de Medicina, Universidad Nacional de Colombia, Bogotá, Colombia
| | - J G Rodríguez-Castillo
- Grupo MICOBAC-UN, Departamento de Microbiología, Facultad de Medicina, Universidad Nacional de Colombia, Bogotá, Colombia
| | - R Hernández-Pando
- Experimental Pathology Section, Department of Pathology, National Institute of Medical Sciences and Nutrition, México D.F., Mexico
| | - M I Murcia
- Grupo MICOBAC-UN, Departamento de Microbiología, Facultad de Medicina, Universidad Nacional de Colombia, Bogotá, Colombia
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Carneiro PAM, Pasquatti TN, Takatani H, Zumárraga MJ, Marfil MJ, Barnard C, Fitzgerald SD, Abramovitch RB, Araujo FR, Kaneene JB. Molecular characterization of Mycobacterium bovis infection in cattle and buffalo in Amazon Region, Brazil. Vet Med Sci 2019; 6:133-141. [PMID: 31571406 PMCID: PMC7036311 DOI: 10.1002/vms3.203] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2019] [Revised: 05/24/2019] [Accepted: 08/30/2019] [Indexed: 11/05/2022] Open
Abstract
The aim of this study was to characterize Mycobacterium bovis from cattle and buffalo tissue samples, from two Brazilian states, and to analyse their genetic diversity by spoligotyping. Tissue samples from tuberculosis suspect animals, 57 in Amazonas State (12 cattle and 45 buffaloes) and six from Pará State (5 cattle and one buffalo) from slaughterhouses under State Veterinary Inspection, were isolated in culture medium Stonebrink. The positive cultures were confirmed by PCR and analysed by the spoligotyping technique and the patterns (spoligotypes) were identified and compared at the Mycobacterium bovis Spoligotype Database (http://www.mbovis.org/). There was bacterial growth in 44 (69.8%) of the tissues of the 63 animals, of which PCR for region of differentiation 4 identified 35/44 (79.5%) as Mycobacterium bovis. Six different spoligotypes were identified among the 35 Mycobacterium bovis isolates, of which SB0295, SB1869, SB0121 and SB1800 had already been described in Brazil, and SB0822 and SB1608 had not been described. The most frequent spoligotype in this study (SB0822) had already been described in buffaloes in Colombia, a neighbouring country of Amazonas state. The other identified spoligotypes were also described in other South American countries, such as Argentina and Venezuela, and described in the Brazilian states of Rio Grande do Sul, Santa Catarina, São Paulo, Minas Gerais, Mato Grosso do Sul, Mato Grosso and Goiás, indicating an active movement of Mycobacterium bovis strains within Brazil.
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Affiliation(s)
- Paulo A M Carneiro
- Center for Comparative Epidemiology, College of Veterinary Medicine, Michigan State University, East Lansing, MI, USA.,Amazonas State Federal Institute, Manaus, AM, Brazil
| | | | - Haruo Takatani
- Agencia de Defesa Agropecuaria do Amazonas, Manaus, AM, Brazil
| | - Martin J Zumárraga
- Instituto Nacional de Tecnología Agropecuaria (INTA), Instituto de Biotecnología, Buenos Aires, Argentina
| | - Maria J Marfil
- Instituto Nacional de Tecnología Agropecuaria (INTA), Instituto de Biotecnología, Buenos Aires, Argentina
| | | | - Scott D Fitzgerald
- Veterinary Diagnostic Laboratory, Michigan State University, Lansing, MI, USA
| | - Robert B Abramovitch
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, USA
| | - Flábio R Araujo
- Centro Nacional de Pesquisa de Gado de Corte, Campo Grande, MS, Brazil
| | - John B Kaneene
- Center for Comparative Epidemiology, College of Veterinary Medicine, Michigan State University, East Lansing, MI, USA
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Baffoe-Bonnie A, Houpt ER, Turner L, Dodge D, Heysell SK. Drug-Susceptible and Multidrug-Resistant Mycobacterium tuberculosis in a Single Patient. Emerg Infect Dis 2019; 25:2120-2121. [PMID: 31454310 PMCID: PMC6810186 DOI: 10.3201/eid2511.180638] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
A patient who had initial infection with mixed strains of drug-susceptible and multidrug-resistant tuberculosis was presumed to have acquired drug resistance before confirmation that sequential strains were genotypically distinct. Transmitted infection with mixed strains is likely underappreciated; identifying these infections requires spoligotyping and whole-genome sequencing.
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Kruczak K, Augustynowicz-Kopeć E, Kozińska M, Passak-Stańda G, Niżankowska-Mogilnicka E, Sładek K. Tuberculosis transmission in the population of patients from the Krakow Region (Poland) based on the epidemiological and molecular methods. Int J Mycobacteriol 2019; 8:60-69. [PMID: 30860181 DOI: 10.4103/ijmy.ijmy_11_19] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
Abstract
Background The transmission of tuberculosis may affect the incidence rate of the disease in Poland. Genetic methods are of assistance in tracing the infection transmission, identifying its sources, determining the risk groups, and focusing on the preventive actions. Objectives The objectives of this study lie in an assessment of tuberculosis transmission by genetic methods with the assistance of the standard epidemiologic interview. Methods The genome DNA of 275 Mycobacterium tuberculosis (Mtb) strains from tuberculosis patients, inhabitants of the city of Krakow, was subjected to a genetic analysis via the spoligotyping method and the IS6110-Mtb1-Mtb2 polymerase chain reaction (PCR) method. If the DNA profiles were identical in both of the PCRs, they were considered identical and classified within one molecular family. Results Among 275 strains, 104 genetic patterns (spoligotypes) were identified. Two hundred and three strains were divided into 66 molecular families (clusters) and analyzed with the IS6110- Mtb1-Mtb2 PCR method. Eighteen clusters were separated. In the Mtb1-Mtb2 clusters, 21 patients were in the risk groups (the homeless, prisoners, and nursing home residents). We did not confirm any direct or temporary contacts between the patients constituting the Mtb1-Mtb2 clusters (apart from the risk groups). However, the patients in these clusters often lived in the same parts of Krakow. Conclusions The standard epidemiologic interview in tuberculosis patients should be combined with genetic methods. Active transmission of tuberculosis occurs largely among the individuals maintaining probably periodic contacts. The patients who are in the risk groups may play an important role in the transmission of tuberculosis.
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Affiliation(s)
- Katarzyna Kruczak
- Department of Pulmonology, Jagiellonian University Medical College, Krakow, Poland
| | - Ewa Augustynowicz-Kopeć
- Department of Microbiology, National Tuberculosis and Lung Diseases Research Institute, Warsaw, Poland
| | - Monika Kozińska
- Department of Microbiology, National Tuberculosis and Lung Diseases Research Institute, Warsaw, Poland
| | - Grażyna Passak-Stańda
- John Poul II Hospital, Mycobacterium Tuberculosis Reference Laboratory, Krakow, Poland
| | | | - Krzysztof Sładek
- Department of Pulmonology, Jagiellonian University Medical College, Krakow, Poland
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Bai R, Chi S, Li X, Dai X, Ji Z, Jian M, Bi Y, Wang F, Ding Z, Luo L, Chen T, Liu A, Bao F. Genetic diversity and drug susceptibility patterns of the Mycobacterium tuberculosis complex in Yunnan, China. Biosci Rep 2019; 39:BSR20181746. [PMID: 30988070 DOI: 10.1042/BSR20181746] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2019] [Revised: 04/12/2019] [Accepted: 04/14/2019] [Indexed: 11/20/2022] Open
Abstract
Tuberculosis (TB) is an infectious disease caused by Mycobacterium tuberculosis (Mtb) which has been threatening global public health for many years. High genetic diversity is dominant feature of Mtb. Increasing cases of multidrug-resistant (MDR) tuberculosis (MDR-TB) is a serious public health problem to TB control in China. Spontaneous mutations in the Mtb genome can alter proteins which are the target of drugs, making the bacteria drug resistant. The purpose of the present study was to analyze the genotype of Mtb isolates from some areas in Yunnan, China and explore the association between genotypes and MDR-TB. Using spoligotyping, we identified Beijing genotypes, six non-Beijing genotypes and a number of orphan genotypes from 270 Mtb isolates from patients in Yunnan Province during 2014–2016. Of 270 Mtb isolates, 102 clinical Mtb strains were identified as drug-resistant (DR) by drug susceptibility testing (DST), among them, 52 MDR strains. Beijing genotypes occupied the highest MDR proportion (78.85%) followed by the orphan genotypes (15.38%). The characteristics of MDR strains showed high genetic diversity. The results will help to efficiently improve diagnosis and treatment and provide valuable information for Mtb molecular epidemiology.
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Elegail A, Ibrahim Mohamed NY, Mohamed Nour EO, Hoffner S, Haile M. Molecular characterization of Mycobacterium tuberculosis isolates from pulmonary tuberculosis patients in Khartoum, Sudan. Int J Mycobacteriol 2019; 7:236-241. [PMID: 30198502 DOI: 10.4103/ijmy.ijmy_82_18] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
Abstract
Background The aim of this study was to characterize the drug resistance profile, and the specific lineages of Mycobacterium tuberculosis (MTB) strains isolated from patients with pulmonary TB in the state of Khartoum in Sudan. Methods Consecutive sputum samples and clinical data were collected from 406 smear-positive TB patients with pulmonary TB in 2007-2009. The samples were cultured, and drug susceptibility testing (DST) was performed using the proportion method (PM) on solid Löwenstein-Jensen medium, and species were identified using biochemical methods at the National Reference Laboratory (NRL) in Khartoum. Extracted deoxyribonucleic acid from a total of 120, 60 suspected multidrug-resistant isolates (MDR), and 60 non-MDR isolates were subsequently sent to the WHO supranational reference laboratory (SRL) in Stockholm at the Public Health Agency of Sweden, for confirmation of the drug resistance profile, examinations by line probe assay (LPA), and molecular epidemiology analysis with Spoligotyping. Results LPA results correlated 100% for non-MDR and 62% for the suspected MDR strains when compared to the DST results obtained by PM at the NRL. Two strains were initially using the PM identified as MDR-TB but later shown by Hain GenoType Mycobacterium CM/AS to belong Mycobacterium avium complex (Mycobacterium intracelluare). These two strains were excluded from the study material for further analysis. The remaining 58 MDR strains were analyzed using LPA, and 36 strains were confirmed as MDR, 10 as rifampicin monoresistant, and eight as isoniazid-monoresistant. Spoligotyping for all the 118 MTB isolates revealed a total of 115 patterns in which four patterns represented major clusters with a total of 108 (91%) of the strains. The CAS1_Delhi/family was the predominant type and detected in 62 isolates (52%), of which 26 were MDR and 36 were susceptible. It was followed by H3/family with 19 (16%) strains, and 11 Latin American Mediterranean3/family, 16 T2/T1, and two strains each of the Beijing and S lineage. Conclusion Comparison of DST results obtained using PM and LPA showed 100% agreement for the non-MDR strains but only 62% for the MDR strains. Taking in consideration the time, risk of contamination and the cost of labour to identify MDR TB, the LPA have clear advantages in early detection of MDRTB than the PM. Additionally in this study material Spoligotyping revealed the CAS1 Delhi as the most predominant family. We could not see no major difference in lineages between MDR and non-MDR strains.
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Affiliation(s)
- Asrar Elegail
- National Tuberculosis Reference Laboratory, Khartoum, Sudan
| | | | | | - Sven Hoffner
- Department of Public Health Sciences, Karolinska Institutet, Stockholm, Sweden
| | - Melles Haile
- Department of Microbiology, Public Health Agency of Sweden, Solna, Sweden
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Ali S, Khan MT, Anwar Sheed K, Khan MM, Hasan F. Spoligotyping analysis of Mycobacterium tuberculosis in Khyber Pakhtunkhwa area, Pakistan. Infect Drug Resist 2019; 12:1363-1369. [PMID: 31190924 PMCID: PMC6535427 DOI: 10.2147/idr.s198314] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Accepted: 04/05/2019] [Indexed: 11/23/2022] Open
Abstract
Background: Spoligotyping is a reproducible, reverse hybridization approach for genotyping of Mycobacterium tuberculosis complex (MTBC). Molecular typing of MTBC is helpful for understanding and controlling tuberculosis epidemics. Methods: Spoligotyping was performed on 166 clinical isolates of Mycobacterium tuberculosis (MTB) collected from 25 districts of Khyber Pakhtunkhwa, Pakistan. Results were compared to SITVIT2, an online database developed by the Institut Pasteur de la Guadeloupe, France. Results: Spoligotyping results showed that 145 strains (88%) displayed known patterns while 21 (12%) were new. Lineage 3/Central Asian strain (L3/CAS) was the predominant family (73%, χ2=19.9, P=0.001), followed by L2/Beijing (5.4%) and L4 (4.2%). L3/CAS1-Delhi was the major sublineage (82%) among the L3/CAS family (χ2=664, P=0.0001). Analysis showed that the majority of the clinical isolates with an unknown pattern had an evolutionary link with the L3/CAS strain, and nine (5.4%) of the unknown strains were epidemiologically linked and were tentatively named L3/CAS-KP (Khyber Pakhtunkhwa). Conclusion: The present study demonstrated that L3/CAS is the predominant lineage of MTB, widely distributed in different areas of the Khyber Pakhtunkhwa province of Pakistan. Spoligotyping patterns of some clinical isolates could not be matched to other reported patterns in an international database. Other tools, such as mycobacterial interspersed repetitive unit–variable number tandem repeat (MIRU-VNTR), will be helpful in future investigations into the epidemiological characteristics of clinical isolates in the Khyber Pakhtunkhwa province.
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Affiliation(s)
- Sajid Ali
- Department of Microbiology, Quaid-i-Azam University, Islamabad, Pakistan
| | - Muhammad Tahir Khan
- Department of Bioinformatics and Biosciences, Capital University of Science and Technology, Islamabad, Pakistan
| | - Khan Anwar Sheed
- Provincial TB Reference Laboratory, Provincial TB Control Program, Khyber Pakhtunkhwa, Pakistan
| | | | - Fariha Hasan
- Department of Microbiology, Quaid-i-Azam University, Islamabad, Pakistan
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Weerasekera D, Pathirane H, Madegedara D, Dissanayake N, Thevanesam V, Magana-Arachchi DN. Evaluation of the 15 and 24-loci MIRU-VNTR genotyping tools with spoligotyping in the identification of Mycobacterium tuberculosis strains and their genetic diversity in molecular epidemiology studies. Infect Dis (Lond) 2019; 51:206-215. [PMID: 30689510 DOI: 10.1080/23744235.2018.1551619] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
Abstract
BACKGROUND The transmission dynamics of Mycobacterium tuberculosis (Mtb) using various genotyping tools has been studied globally and a particular tool for genotyping Mtb is the mycobacterial interspersed repetitive units-variable number tandem repeats (MIRU-VNTR). Tuberculosis (TB) remains an important public health problem worldwide and Sri Lanka being a country of tourist destination; because of major development projects undergoing, it has a high proportion of tourists and immigrants from Asia and Europe that are characterized with highest TB incidences and drug-resistant clinical isolates. Hence, in order to address the question of Mtb genetic diversity, we investigated the discriminatory power of both MIRU-VNTR typing of 15 and 24 loci with spoligotyping to differentiate Mtb isolates. METHOD Acid-fast bacilli positive sputum samples (n = 150) from first visit patients were collected. Decontamination of sputum and extraction of genomic DNA were carried out using standard techniques. The isolates were characterized by MIRU-VNTR for both the 15 and 24 loci and spoligotyping. RESULTS In our study population, MIRU-VNTR 15 and 24 loci did not show a significant difference among the identified M. tuberculosis strains. However, MIRU 24 loci yielded an additional strain LAM, which is of T1 origin. 15 loci strain grouping had more clusters of strains grouped together while 24 loci differentiated the same cluster of strains into distinct strain types. CONCLUSION We conclude that the use of 15-locus MIRU-VNTR typing is sufficient for a first-line epidemiological study to genotype M. tuberculosis, but the additional discriminatory power of 24 loci MIRU-VNTR has been able to differentiate samples within highly homologous groups.
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Affiliation(s)
| | | | | | - Neranjan Dissanayake
- c Consultant Respiratory Unit , District General Hospital , Nuwara-Eliya , Sri Lanka
| | - Vasanthi Thevanesam
- d Department of Microbiology, Faculty of Medicine , University of Peradeniya , Peradeniya , Sri Lanka
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Chawla K, Kumar A, Shenoy VP, Chauhan DS, Sharma P. Genetic diversity of Mycobacterium tuberculosis in south coastal Karnataka, India, using spoligotyping. Indian J Med Res 2018; 147:278-286. [PMID: 29923517 PMCID: PMC6022373 DOI: 10.4103/ijmr.ijmr_2026_16] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
Background & objectives: Despite high occurrence of tuberculosis in India very little information is available about the genetic diversity of Mycobacterium tuberculosis isolates prevailing in coastal Karnataka, India. Thus, the present study was undertaken to explore the genetic biodiversity of M. tuberculosis isolates prevailing in south coastal region of Karnataka (Udupi District), India. Methods: A total of 111 Mycobacterial isolates were cultured in Lowenstein Jensen (LJ) medium and after obtaining growth, DNA was extracted and spoligotyping was performed. SITVIT WEB database was used to locate families of spoligotypes. Results: On analyzing the hybridization results of all 111 isolates on SITVIT WEB database 57 (51.35%) isolates were clustered into 11 Spoligotype International Types (SIT). The largest cluster of 14 (12.61%) isolates was SIT-48 (EAI1-SOM), followed by SIT-1942 (CAS1-Delhi) with 11 isolates (9.9%) and SIT-11 with seven (6.30%). Moreover, 23 isolates (20.72%) had unique spoligotypes and 31 (27.92%) were orphans. Spotclust analysis revealed that majority (67%) of orphan isolates were variants of CAS (37%) and EAI-5 (34%). Interpretation & conclusions: The present study revealed high biodiversity among the circulating isolates of M. tuberculosis in this region with the presence of mixed genotypes earlier reported from north and south India along with certain new genotypes with unique SITs. The study highlights the need for further longitudinal studies to explore the genetic diversity and to understand the transmission dynamics of prevailing isolates.
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Affiliation(s)
- Kiran Chawla
- Department of Microbiology, Kasturba Medical College, MAHE, Manipal, India
| | - Ajay Kumar
- Department of Microbiology, Kasturba Medical College, MAHE, Manipal, India
| | | | - Devendra Singh Chauhan
- Department of Microbiology & Molecular Biology, ICMR-National JALMA Institute for Leprosy & other Mycobacterial Diseases, Agra, India
| | - Pragya Sharma
- Department of Microbiology & Molecular Biology, ICMR-National JALMA Institute for Leprosy & other Mycobacterial Diseases, Agra, India
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Molina-Moya B, Abdurrahman ST, Madukaji LI, Gomgnimbou MK, Spinasse L, Gomes-Fernandes M, Gomes HM, Kacimi S, Dacombe R, Bimba JS, Lawson L, Sola C, Cuevas LE, Dominguez J. Genetic characterization of Mycobacterium tuberculosis complex isolates circulating in Abuja, Nigeria. Infect Drug Resist 2018; 11:1617-1625. [PMID: 30319278 PMCID: PMC6171509 DOI: 10.2147/idr.s166986] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Objective Nigeria ranks fourth among the high tuberculosis (TB) burden countries. This study describes the prevalence of drug resistance and the genetic diversity of Mycobacterium tuberculosis in Abuja’s Federal Capital Territory. Materials and methods Two hundred and seventy-eight consecutive sputum samples were collected from adults with presumptive TB during 2013–2014. DNA was extracted from Löwenstein–Jensen cultures and analyzed for the identification of nontuberculous mycobacteria species, detection of drug resistance with line probe assays, and high-throughput spacer oligonucleotide typing (spoligotyping) using microbead-based hybridization. Results Two hundred and two cultures were positive for M. tuberculosis complex, 24 negative, 38 contaminated, and 15 positive for nontuberculous mycobacteria. Five (2.5%) M. tuberculosis complex isolates were resistant to rifampicin (RIF) and isoniazid (multidrug resistant), nine (4.5%) to RIF alone, and 15 (7.4%) to isoniazid alone; two RIF-resistant isolates were also resistant to fluoroquinolones and ethambutol, and one multidrug resistant isolate was also resistant to ethambutol. Among the 180 isolates with spoligotyping results, 164 (91.1%) were classified as lineage 4 (Euro-American), 13 (7.2%) as lineage 5 (West African 1), two (1.1%) as lineage 2 (East Asia), and one (0.6%) as lineage 6 (West African 2). One hundred and fifty-six (86.7%) isolates were grouped in 17 clusters (2–108 isolates/cluster), of which 108 (60.0%) were grouped as L4.6.2/Cameroon (spoligotype international type 61). Conclusion The description of drug resistance prevalence and genetic diversity of M. tuberculosis in this study may be useful for improving TB control in Nigeria.
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Affiliation(s)
- Barbara Molina-Moya
- Hospital Universitari Germans Trias i Pujol, Institut d'Investigació Germans Trias i Pujol, Universitat Autònoma de Barcelona, Badalona, Barcelona, Spain, .,CIBER Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, Madrid, Spain,
| | | | | | - Michel Kiréopori Gomgnimbou
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette cedex, France.,Centre Muraz, Bobo-Dioulasso, Burkina Faso
| | - Lizania Spinasse
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette cedex, France
| | - Meissiner Gomes-Fernandes
- Hospital Universitari Germans Trias i Pujol, Institut d'Investigació Germans Trias i Pujol, Universitat Autònoma de Barcelona, Badalona, Barcelona, Spain, .,CIBER Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, Madrid, Spain, .,CAPES Foundation, Ministry of Education of Brazil, Brasília, Brazil
| | - Harrison Magdinier Gomes
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette cedex, France
| | - Sarah Kacimi
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette cedex, France
| | | | | | | | - Christophe Sola
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette cedex, France
| | - Luis E Cuevas
- Liverpool School of Tropical Medicine, Liverpool, UK
| | - Jose Dominguez
- Hospital Universitari Germans Trias i Pujol, Institut d'Investigació Germans Trias i Pujol, Universitat Autònoma de Barcelona, Badalona, Barcelona, Spain, .,CIBER Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, Madrid, Spain,
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Kohl TA, Utpatel C, Niemann S, Moser I. Mycobacterium bovis Persistence in Two Different Captive Wild Animal Populations in Germany: a Longitudinal Molecular Epidemiological Study Revealing Pathogen Transmission by Whole-Genome Sequencing. J Clin Microbiol 2018; 56:e00302-18. [PMID: 29950330 PMCID: PMC6113487 DOI: 10.1128/jcm.00302-18] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2018] [Accepted: 06/15/2018] [Indexed: 11/20/2022] Open
Abstract
Bovine tuberculosis (bTB) caused by Mycobacterium bovis is a transmissible disease notifiable to the World Organization for Animal Health and to the European Union, with ongoing efforts of surveillance and eradication in every EU member state. In Germany, a country which has been declared officially free from bovine tuberculosis since 1997 by the EU, M. bovis infections still occur sporadically in cattle and other mammals, including humans. Here, the transmission routes of a bTB outbreak in a wildlife park in Germany affecting different cervid species, bison, lynx, and pot-bellied pigs were followed by employing whole-genome sequencing (WGS) combined with spoligotyping and mycobacterial interspersed repetitive-unit-variable-number tandem-repeat (MIRU-VNTR) typing. One single M. bovis strain persisted from 2002 to 2015, and transmission between the park and a distantly located captive cervid farm was verified. The spoligotyping patterns remained identical, while MIRU-VNTR typing of 24 loci of the standardized panel and locus 2163a as an additional locus revealed one change at locus 2165 in a strain from a fallow deer and one at locus 2461 in isolates from red deer over the whole time period. WGS analysis confirmed the close relatedness of the isolates, with a maximum of 12 single nucleotide polymorphisms (SNPs) detected between any two sequenced isolates. In conclusion, our data confirm a longitudinal outbreak of M. bovis in a German wildlife park and provide the first insights into the dynamics of different genotyping markers in M. bovis.
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Affiliation(s)
- Thomas A Kohl
- Molecular and Experimental Mycobacteriology, Priority Area Infections, Research Center Borstel, Borstel, Germany
- German Center for Infection Research, TTU-TB, Borstel, Germany
| | - Christian Utpatel
- Molecular and Experimental Mycobacteriology, Priority Area Infections, Research Center Borstel, Borstel, Germany
- German Center for Infection Research, TTU-TB, Borstel, Germany
| | - Stefan Niemann
- Molecular and Experimental Mycobacteriology, Priority Area Infections, Research Center Borstel, Borstel, Germany
- German Center for Infection Research, TTU-TB, Borstel, Germany
| | - Irmgard Moser
- Friedrich-Loeffler-Institut, Federal Institute for Animal Health, Institute of Molecular Pathogenesis, Jena, Germany
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Zeng X, Xu Y, Zhou Y, Li H, Zheng R, Tan Y, Sun B, Zhao Y, Li Q. Mc Spoligotyping, a One-Step Melting Curve Analysis-Based Protocol for Spoligotyping of Mycobacterium tuberculosis. J Clin Microbiol 2018; 56:e00539-18. [PMID: 29875194 DOI: 10.1128/JCM.00539-18] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2018] [Accepted: 05/31/2018] [Indexed: 11/20/2022] Open
Abstract
The direct repeat (DR) region in the Mycobacterium tuberculosis (MTB) genome is composed of highly polymorphic direct variant repeats, which are the basis of spacer oligonucleotide typing (spoligotyping) to study the population structure and epidemiology of M. tuberculosis However, the membrane hybridization-based detection format requires various post-PCR manipulations and is prone to carryover contamination, restricting its wide use in high-TB-burden and resource-limited countries. We developed a one-step spoligotyping protocol, termed McSpoligotyping, based on real-time PCR. The typing results can be generated within 3 h by a single step of DNA addition. When evaluated with a collection of 1,968 isolates of MTB, McSpoligotyping agreed 97.71% (1,923/1,968) by sample and 99.93% (84,568/84,624) by spacer with traditional spoligotyping. Sequencing results showed that McSpoligotyping was even more accurate than spoligotyping (99.34% versus 98.37%). Further exploration of the false results of McSpoligotyping revealed the presence of single-nucleotide polymorphisms in the DR region. We concluded that McSpoligotyping could be used in epidemiology studies of tuberculosis by taking advantage of the shortened procedure, ease of use, and compatibility of results with standard spoligotyping.
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Lombardi G, Botti I, Pacciarini ML, Boniotti MB, Roncarati G, Dal Monte P. Five-year surveillance of human tuberculosis caused by Mycobacterium bovis in Bologna, Italy: an underestimated problem. Epidemiol Infect 2017; 145:3035-9. [PMID: 28879829 DOI: 10.1017/S0950268817001996] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Human tuberculosis (TB) caused by Mycobacterium bovis surveillance is affected by a lack of data. The aims of the present study were: (i) to estimate the proportion of human TB caused by M. bovis over a period of 5 years in Bologna, Northern Italy, which, like most Western European countries, has been declared bovine TB-free; (ii) to compare the genetic profiles of M. bovis strains identified in humans with those circulating in cattle in the last 15 years in Italy. Among 511 TB patients, the proportion of human TB caused by M. bovis was 1·76%, significantly associated to extra-pulmonary localization (P = 0·004) and to being elderly (P < 0·001) and Italy-born (P = 0·036). The molecular epidemiology analysis by spoligotyping and Multilocus Variable Tandem Repeat Analysis confirmed that most M. bovis strains from Italy-born patients matched those circulating in cattle herds in Italy between 2001 and 2016. Two cases of Mycobacterium bovis BCG infection were also characterized. In conclusion, the rate of human TB caused by M. bovis was not negligible, highlighting the relevance of molecular typing in evaluating the effectiveness of programmes designed to eradicate TB in cattle in Italy.
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Zhang H, Huang H, Liu C, Jia T, Zhang L, Zhou D, Wei S, Wang C. Genotyping and drug-resistance epidemiology of mycobacterium tuberculosis in Xuzhou, China. Int J Clin Exp Pathol 2017; 10:9675-9682. [PMID: 31966848 PMCID: PMC6965968] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 06/08/2017] [Accepted: 08/09/2017] [Indexed: 06/10/2023]
Abstract
BACKGROUND To explore the genetic diversity and drug resistance status of MTB in Xuzhou, China. METHODS A total of 325 clinical MTB strains were genotyped by spacer-oligonucleotide typing (spoligotyping) and mycobacterial interspersed repetitive unit variable number of tandem repeats (MIRU-VNTR). Phenotypic resistance was assessed by drug susceptibility testing (DST). RESULT Based on the spoligotyping method, 325 MTB isolates were classified into 5 known genotypes and 12 unknown genotypes, and the largest branch comprised 268 strains belonging to the Beijing family. Based on the 15-loci VNTR typing method, 325 MTB isolates were divided into 35 clusters and 220 unique patterns. Compared to the low discriminatory power of spoligotyping genotyping (HGDI = 0.3444), 15-loci VNTR genotyping had a significantly higher discriminatory power for all strains (HGDI = 0.9980), particularly for the Beijing family strains (HGDI = 0.9892). When spoligotyping and 15-loci VNTR methods were used together, the discriminatory power increased to 0.9991. The Beijing family strain presented increased risks for developing multi-drug resistance TB (P < 0.05). CONCLUSION The Beijing family isolates is the most prevalent strains in Xuzhou. Spoligotyping, in combination with 15-loci MIRU-VNTR, is useful for epidemiological analysis of MTB transmission in Xuzhou.
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Affiliation(s)
- Haiqing Zhang
- Department of Tuberculosis, Xuzhou Infectious Disease HospitalXuzhou, China
| | - Haibin Huang
- Department of Tuberculosis, Xuzhou Infectious Disease HospitalXuzhou, China
| | - Chengyong Liu
- Department of Tuberculosis, Xuzhou Infectious Disease HospitalXuzhou, China
| | - Tong Jia
- Department of Tuberculosis, Xuzhou Infectious Disease HospitalXuzhou, China
| | - Limao Zhang
- Department of Tuberculosis, Xuzhou Infectious Disease HospitalXuzhou, China
| | - Dongqing Zhou
- Department of Tuberculosis, Xuzhou Infectious Disease HospitalXuzhou, China
| | - Sumei Wei
- Department of Tuberculosis, Xuzhou Infectious Disease HospitalXuzhou, China
| | - Chunying Wang
- Department of Infectious Diseases, Xuzhou Infectious Disease HospitalXuzhou, China
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Suzana S, Shanmugam S, Uma Devi KR, Swarna Latha PN, Michael JS. Spoligotyping of Mycobacterium tuberculosis isolates at a tertiary care hospital in India. Trop Med Int Health 2017; 22:703-707. [PMID: 28374900 DOI: 10.1111/tmi.12875] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
OBJECTIVE Spoligotyping is a valuable genotyping tool to study the genetic diversity and molecular epidemiology of Mycobacterium tuberculosis (M. tb). The aim of this study was to analyse different spoligotype patterns of M. tb strains isolated from patients with tuberculosis from different parts of India. MATERIALS AND METHODS A total of 163 M. tb isolates were spoligotyped between January 2014 and January 2015. About 47% (n = 77) were from patients with extrapulmonary tuberculosis; of these, 10 were MDR, and seven were Pre-XDR. Of the 86 M. tb isolates from patients with pulmonary tuberculosis, 25 were MDR, and 25 were Pre-XDR. RESULTS We found 61 spoligo patterns, 128 clusters in the spoligotype data base (spoldb4 data base) with spoligo international type (SIT) number and 35 true unique isolates. The most pre-dominant spoligotype was EAI lineage (56), followed by Beijing (28), CAS (20), T(9), U(7), X(3), H(3), BOVIS_1 BCG(1) and LAM(1). CONCLUSION Although our study identified EAI, CAS and Beijing strain lineages as pre-dominant, we also found a large number of orphan strains (20%) in our study. Beijing strains were more significantly associated with MDR TB than CAS and EAI lineages. Further studies on large sample sizes would help to clearly describe the epidemiology of M. tb in India.
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Affiliation(s)
- Shirly Suzana
- Department of Clinical Microbiology, Christian Medical College, Vellore, India
| | - Sivakumar Shanmugam
- Department of Bacteriology, National Institute for Research in Tuberculosis, Chennai, India
| | - K R Uma Devi
- Department of Bacteriology, National Institute for Research in Tuberculosis, Chennai, India
| | - P N Swarna Latha
- Department of Bacteriology, National Institute for Research in Tuberculosis, Chennai, India
| | - Joy S Michael
- Department of Clinical Microbiology, Christian Medical College, Vellore, India
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