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Valencia-Trujillo D, Avila-Trejo AM, García-Reyes RL, Narváez-Díaz L, Segura del Pilar M, Mújica-Sánchez MA, Becerril-Vargas E, León-Juárez M, Mata-Miranda MM, Rivera-Gutiérrez S, Cerna-Cortés JF. Genetic Diversity of Mycobacterium tuberculosis Strains Isolated from HIV-Infected Patients in Mexico. Pathogens 2024; 13:428. [PMID: 38787280 PMCID: PMC11124049 DOI: 10.3390/pathogens13050428] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2024] [Revised: 05/14/2024] [Accepted: 05/17/2024] [Indexed: 05/25/2024] Open
Abstract
There has been very limited investigation regarding the genetic diversity of Mycobacterium tuberculosis (MTb) strains isolated from human immunodeficiency virus (HIV)-infected patients in Mexico. In this study, we isolated 93 MTb strains from pulmonary and extrapulmonary samples of HIV-infected patients treated in a public hospital in Mexico City to evaluate the genetic diversity using spoligotyping and mycobacterial interspersed repetitive unit-variable-number tandem-repeat (MIRU-VNTR) typing (based on 24 loci). The cohort comprised 80 male and 13 female individuals. There was a positive correlation between a high HIV viral load (>100,000 copies) and extrapulmonary tuberculosis (TB) (r = 0.306, p = 0.008). Lineage 4 was the most frequent lineage (79 strains). In this lineage, we found the H clade (n = 24), including the Haarlem, H3, and H1 families; the T clade (n = 22), including T1 and T2; the X clade (n = 15), including X1 and X3; the LAM clade (n = 14), including LAM1, LAM2, LAM3, LAM6, and LAM9; the S clade (n = 2); Uganda (n = 1); and Ghana (n = 1). We also found 12 strains in the EAI clade belonging to lineage 1, including the EAI2-Manila and EAI5 families. Interestingly, we identified one strain belonging to the Beijing family, which is part of lineage 2. One strain could not be identified. This study reports high genetic diversity among MTb strains, highlighting the need for a molecular epidemiological surveillance system that can help to monitor the spread of these strains, leading to more appropriate measures for TB control in HIV-infected patients.
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Affiliation(s)
- Daniel Valencia-Trujillo
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Ciudad de México 11340, Mexico; (D.V.-T.); (R.L.G.-R.); (S.R.-G.)
- Servicio de Microbiología Clínica, Instituto Nacional de Enfermedades Respiratorias, Ciudad de México 14080, Mexico; (L.N.-D.); (M.S.d.P.); (M.A.M.-S.); (E.B.-V.)
- Escuela Militar de Medicina, Centro Militar de Ciencias de la Salud, Secretaría de la Defensa Nacional, Ciudad de México 11200, Mexico; (A.M.A.-T.); (M.M.M.-M.)
| | - Amanda Marineth Avila-Trejo
- Escuela Militar de Medicina, Centro Militar de Ciencias de la Salud, Secretaría de la Defensa Nacional, Ciudad de México 11200, Mexico; (A.M.A.-T.); (M.M.M.-M.)
| | - Rocío Liliana García-Reyes
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Ciudad de México 11340, Mexico; (D.V.-T.); (R.L.G.-R.); (S.R.-G.)
| | - Luis Narváez-Díaz
- Servicio de Microbiología Clínica, Instituto Nacional de Enfermedades Respiratorias, Ciudad de México 14080, Mexico; (L.N.-D.); (M.S.d.P.); (M.A.M.-S.); (E.B.-V.)
| | - Mariela Segura del Pilar
- Servicio de Microbiología Clínica, Instituto Nacional de Enfermedades Respiratorias, Ciudad de México 14080, Mexico; (L.N.-D.); (M.S.d.P.); (M.A.M.-S.); (E.B.-V.)
| | - Mario Alberto Mújica-Sánchez
- Servicio de Microbiología Clínica, Instituto Nacional de Enfermedades Respiratorias, Ciudad de México 14080, Mexico; (L.N.-D.); (M.S.d.P.); (M.A.M.-S.); (E.B.-V.)
| | - Eduardo Becerril-Vargas
- Servicio de Microbiología Clínica, Instituto Nacional de Enfermedades Respiratorias, Ciudad de México 14080, Mexico; (L.N.-D.); (M.S.d.P.); (M.A.M.-S.); (E.B.-V.)
| | - Moises León-Juárez
- Departamento de Inmunobioquímica, Instituto Nacional de Perinatología Isidro Espinosa de los Reyes, Ciudad de México 11000, Mexico;
| | - Mónica Maribel Mata-Miranda
- Escuela Militar de Medicina, Centro Militar de Ciencias de la Salud, Secretaría de la Defensa Nacional, Ciudad de México 11200, Mexico; (A.M.A.-T.); (M.M.M.-M.)
| | - Sandra Rivera-Gutiérrez
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Ciudad de México 11340, Mexico; (D.V.-T.); (R.L.G.-R.); (S.R.-G.)
| | - Jorge Francisco Cerna-Cortés
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Ciudad de México 11340, Mexico; (D.V.-T.); (R.L.G.-R.); (S.R.-G.)
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Madadi-Goli N, Ahmadi K, Kamakoli MK, Azizi M, Khanipour S, Dizaji SP, Nasehi M, Siadat SD, Fateh A, Vaziri F. The importance of heteroresistance and efflux pumps in bedaquiline-resistant Mycobacterium tuberculosis isolates from Iran. Ann Clin Microbiol Antimicrob 2024; 23:36. [PMID: 38664815 PMCID: PMC11046812 DOI: 10.1186/s12941-024-00694-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Accepted: 04/04/2024] [Indexed: 04/28/2024] Open
Abstract
BACKGROUND Tuberculosis (TB) continues to pose a threat to communities worldwide and remains a significant public health issue in several countries. We assessed the role of heteroresistance and efflux pumps in bedaquiline (BDQ)-resistant Mycobacterium tuberculosis isolates. METHODS Nineteen clinical isolates were included in the study, of which fifteen isolates were classified as MDR or XDR, while four isolates were fully susceptible. To evaluate BDQ heteroresistance, the Microplate Alamar Blue Assay (MABA) method was employed. For screening mixed infections, MIRU-VNTR was performed on clinical isolates. Mutations in the atpE and Rv0678 genes were determined based on next-generation sequencing data. Additionally, real-time PCR was applied to assess the expression of efflux pump genes in the absence and presence of verapamil (VP). RESULTS All 15 drug-resistant isolates displayed resistance to BDQ. Among the 19 total isolates, 21.05% (4/19) exhibited a heteroresistance pattern to BDQ. None of the isolates carried a mutation of the atpE and Rv0678 genes associated with BDQ resistance. Regarding the MIRU-VNTR analysis, most isolates (94.73%) showed the Beijing genotype. Fifteen (78.9%) isolates showed a significant reduction in BDQ MIC after VP treatment. The efflux pump genes of Rv0676c, Rv1258c, Rv1410c, Rv1634, Rv1819, Rv2459, Rv2846, and Rv3065 were overexpressed in the presence of BDQ. CONCLUSIONS Our results clearly demonstrated the crucial role of heteroresistance and efflux pumps in BDQ resistance. Additionally, we established a direct link between the Rv0676c gene and BDQ resistance. The inclusion of VP significantly reduced the MIC of BDQ in both drug-susceptible and drug-resistant clinical isolates.
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Affiliation(s)
- Nahid Madadi-Goli
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, No. 358, 12th Farvardin Ave., Jomhoori St, Tehran, 1316943551, Iran
- Microbiology Research Center (MRC), Pasteur Institute of Iran, Tehran, Iran
- Student Research Committee, Pasteur Institute of Iran, Tehran, Iran
| | - Kamal Ahmadi
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, No. 358, 12th Farvardin Ave., Jomhoori St, Tehran, 1316943551, Iran
- Microbiology Research Center (MRC), Pasteur Institute of Iran, Tehran, Iran
- Department of Microbiology, School of Medicine, Kermanshah University of Medical Sciences, Kermanshah, Iran
- Student Research Committee, Pasteur Institute of Iran, Tehran, Iran
| | - Mansour Kargarpour Kamakoli
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, No. 358, 12th Farvardin Ave., Jomhoori St, Tehran, 1316943551, Iran
- Microbiology Research Center (MRC), Pasteur Institute of Iran, Tehran, Iran
| | - Mohsen Azizi
- Department of Microbiology, School of Medicine, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Sharareh Khanipour
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, No. 358, 12th Farvardin Ave., Jomhoori St, Tehran, 1316943551, Iran
- Microbiology Research Center (MRC), Pasteur Institute of Iran, Tehran, Iran
| | - Shahin Pourazar Dizaji
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, No. 358, 12th Farvardin Ave., Jomhoori St, Tehran, 1316943551, Iran
- Microbiology Research Center (MRC), Pasteur Institute of Iran, Tehran, Iran
| | - Mahshid Nasehi
- Department of Epidemiology and Biostatistics, School of Public Health, Iran University of Medical Sciences, Tehran, Iran
- Center for Communicable Diseases Control, Ministry of Health and Medical Education, Tehran, Iran
| | - Seyed Davar Siadat
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, No. 358, 12th Farvardin Ave., Jomhoori St, Tehran, 1316943551, Iran
- Microbiology Research Center (MRC), Pasteur Institute of Iran, Tehran, Iran
| | - Abolfazl Fateh
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, No. 358, 12th Farvardin Ave., Jomhoori St, Tehran, 1316943551, Iran.
- Microbiology Research Center (MRC), Pasteur Institute of Iran, Tehran, Iran.
| | - Farzam Vaziri
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, No. 358, 12th Farvardin Ave., Jomhoori St, Tehran, 1316943551, Iran.
- Microbiology Research Center (MRC), Pasteur Institute of Iran, Tehran, Iran.
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Castro-Rodriguez B, Franco-Sotomayor G, Benitez-Medina JM, Cardenas-Franco G, Jiménez-Pizarro N, Cardenas-Franco C, Aguirre-Martinez JL, Orlando SA, Hermoso de Mendoza J, Garcia-Bereguiain MA. Prevalence, drug resistance, and genotypic diversity of the RD Rio subfamily of Mycobacterium tuberculosis in Ecuador: a retrospective analysis for years 2012-2016. Front Public Health 2024; 12:1337357. [PMID: 38689770 PMCID: PMC11060180 DOI: 10.3389/fpubh.2024.1337357] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2023] [Accepted: 03/15/2024] [Indexed: 05/02/2024] Open
Abstract
Introduction A major sublineage within the Mycobacterium tuberculosis (MTB) LAM family characterized by a new in-frame fusion gene Rv3346c/55c was discovered in Rio de Janeiro (Brazil) in 2007, called RDRio, associated to drug resistance. The few studies about prevalence of MTB RDRio strains in Latin America reported values ranging from 3% in Chile to 69.8% in Venezuela, although no information is available for countries like Ecuador. Methods A total of 814 MTB isolates from years 2012 to 2016 were screened by multiplex PCR for RDRio identification, followed by 24-loci MIRU-VNTR and spoligotyping. Results A total number of 17 MTB RDRio strains were identified, representing an overall prevalence of 2.09% among MTB strains in Ecuador. While 10.9% of the MTB isolates included in the study were multidrug resistance (MDR), 29.4% (5/17) of the RDRio strains were MDR. Discussion This is the first report of the prevalence of MTB RDRio in Ecuador, where a strong association with MDR was found, but also a very low prevalence compared to other countries in Latin America. It is important to improve molecular epidemiology tools as a part of MTB surveillance programs in Latin America to track the transmission of potentially dangerous MTB stains associated to MDR TB like MTB RDRio.
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Affiliation(s)
| | - Greta Franco-Sotomayor
- Instituto Nacional de Investigación en Salud Pública “Leopoldo Izquieta Pérez”, Guayaquil, Ecuador
- Universidad Católica Santiago de Guayaquil, Guayaquil, Ecuador
| | | | | | - Natalia Jiménez-Pizarro
- Departamento de Sanidad Animal, Facultad de Veterinaria, Universidad de Extremadura, Cáceres, Spain
| | | | | | - Solon Alberto Orlando
- Instituto Nacional de Investigación en Salud Pública “Leopoldo Izquieta Pérez”, Guayaquil, Ecuador
- Universidad Espiritu Santo, Guayaquil, Ecuador
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Castro-Rodriguez B, León-Ordóñez K, Franco-Sotomayor G, Benítez-Medina JM, Jiménez-Pizarro N, Cárdenas-Franco G, Granda JC, Aguirre-Martínez JL, Orlando SA, Hermoso de Mendoza J, García-Bereguiain MÁ. Population structure of Mycobacterium tuberculosis in El Oro: A first insight into Ecuador-Peru tuberculosis transmission. J Infect Public Health 2024; 17:527-534. [PMID: 38310744 DOI: 10.1016/j.jiph.2024.01.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Revised: 01/17/2024] [Accepted: 01/22/2024] [Indexed: 02/06/2024] Open
Abstract
BACKGROUND Tuberculosis (TB) is a major public health concern in Ecuador and Peru, both settings of high burden of drug resistance TB. Molecular epidemiology tools are important to understand the transmission dynamics of Mycobacterium tuberculosis Complex (MTBC) and to track active transmission clusters of regional importance. This study is the first to address the transmission of TB between Peru and Ecuador through the population structure of MTBC lineages circulating in the Ecuadorian border province of "El Oro". METHODS A total number of 56 MTBC strains from this province for years 2012-2015 were included in the study and analyzed by 24-loci MIRU-VNTR and spoligotyping. RESULTS Genotyping revealed a high degree of diversity for MTBC in "El Oro", without active transmission clusters. MTBC L4 was predominant, with less than 2% of strains belonging to MTBC L2-Beijing. CONCLUSIONS These results may suggest that TB dynamics in this rural and semi-urban area would not be linked to highly transmitted strains like MTBC L2-Beijing from Peru, but related to TB relapse; although further studies with larger MTBC cultures collection from recent years are needed. Nevertheless, we recommend to reinforce TB surveillance programs in remote rural settings and border regions in Ecuador.
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Affiliation(s)
| | - Kerly León-Ordóñez
- One Health Research Group. Universidad de las Américas, Quito, Ecuador; Yachay Tech University, Urcuquí, Ecuador
| | - Greta Franco-Sotomayor
- Instituto Nacional de Investigación en Salud Pública "Leopoldo Izquieta Pérez", Guayaquil, Ecuador; Universidad Católica Santiago de Guayaquil, Guayaquil, Ecuador
| | | | - Natalia Jiménez-Pizarro
- Departamento de Sanidad Animal. Facultad de Veterinaria, Universidad de Extremadura, Cáceres, Spain
| | | | - Juan Carlos Granda
- Instituto Nacional de Investigación en Salud Pública "Leopoldo Izquieta Pérez", Guayaquil, Ecuador
| | | | - Solon Alberto Orlando
- Instituto Nacional de Investigación en Salud Pública "Leopoldo Izquieta Pérez", Guayaquil, Ecuador; Universidad Espíritu Santo, Guayaquil, Ecuador
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Castro-Rodriguez B, Espinoza-Andrade S, Franco-Sotomayor G, Benítez-Medina JM, Jiménez-Pizarro N, Cárdenas-Franco C, Granda JC, Jouvin JL, Orlando SA, Hermoso de Mendoza J, García-Bereguiain MÁ. A first insight into tuberculosis transmission at the border of Ecuador and Colombia: a retrospective study of the population structure of Mycobacterium tuberculosis in Esmeraldas province. Front Public Health 2024; 12:1343350. [PMID: 38384875 PMCID: PMC10879341 DOI: 10.3389/fpubh.2024.1343350] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Accepted: 01/18/2024] [Indexed: 02/23/2024] Open
Abstract
Objective Tuberculosis (TB) is a major public health concern in Ecuador and Colombia, considering that both countries are high-burden TB settings. Molecular epidemiology is crucial to understand the transmission dynamics of Mycobacterium tuberculosis complex (MTBC) and to identify active transmission clusters of regional importance. Methods We studied the potential transmission of TB between Colombia and Ecuador through the analysis of the population structure of MTBC lineages circulating in the Ecuadorian province of Esmeraldas at the border with Colombia. A total of 105 MTBC strains were characterized by 24-loci MIRU-VNTR and spoligotyping. Results MTBC lineage 4 is only present in Esmeraldas; no MTBC strains belonging to Lineage 2-sublineage Beijing were found despite its presence in other provinces of Ecuador and, in Colombia. Genotyping results revealed a high degree of diversity for MTBC in Esmeraldas: Neither active transmission clusters within this province nor including MTBC strains from Colombia or other provinces of Ecuador were found. Conclusion Our data suggest that tuberculosis dynamics in this rural and isolated area may be not related to highly transmitted strains but could be influenced by other health determinants that favor TB relapse such as poverty and poor health system access. Further studies including a larger number of MTBC strains from Esmeraldas are necessary to test this hypothesis.
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Affiliation(s)
| | | | - Greta Franco-Sotomayor
- Instituto Nacional de Investigación en Salud Pública “Leopoldo Izquieta Pérez”, Guayaquil, Ecuador
- Facultad de Medicina, Universidad Católica Santiago de Guayaquil, Guayaquil, Ecuador
| | - José Manuel Benítez-Medina
- Departamento de Patología Infecciosa, Facultad de Veterinaria, Universidad de Extremadura, Cáceres, Spain
| | - Natalia Jiménez-Pizarro
- Departamento de Patología Infecciosa, Facultad de Veterinaria, Universidad de Extremadura, Cáceres, Spain
| | | | - Juan Carlos Granda
- Instituto Nacional de Investigación en Salud Pública “Leopoldo Izquieta Pérez”, Guayaquil, Ecuador
| | - Jose Luis Jouvin
- Facultad de Medicina, Universidad Católica Santiago de Guayaquil, Guayaquil, Ecuador
| | - Solon Alberto Orlando
- Instituto Nacional de Investigación en Salud Pública “Leopoldo Izquieta Pérez”, Guayaquil, Ecuador
- Universidad Espíritu Santo, Guayaquil, Ecuador
| | - Javier Hermoso de Mendoza
- Departamento de Patología Infecciosa, Facultad de Veterinaria, Universidad de Extremadura, Cáceres, Spain
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Shamebo T, Gumi B, Zewude A, Gashaw F, Mohammed T, Girma M, Zerihun B, Getu M, Mekasha S, Getahun M, Wondale B, Petros B, Ameni G. Molecular epidemiology and drug sensitivity of Mycobacterium tuberculosis in homeless individuals in the Addis Ababa city, Ethiopia. Sci Rep 2023; 13:21370. [PMID: 38049519 PMCID: PMC10695943 DOI: 10.1038/s41598-023-48407-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2023] [Accepted: 11/26/2023] [Indexed: 12/06/2023] Open
Abstract
Although homeless segment of the society could be the hotspots for tuberculosis (TB) transmission, there is little data on TB in homeless individuals in Ethiopia. The objective of this study was to investigate the molecular epidemiology and drug sensitivity of Mycobacterium tuberculosis (M. tuberculosis) isolated from homeless individuals in Addis Ababa, Ethiopia. The study was conducted on 59 M. tuberculosis isolates, which were recovered by the clinical screening of 5600 homeless individuals and bacteriological examination of 641 individuals with symptoms of pulmonary tuberculosis (PTB). Region of difference-9 (RD9) based polymerase-chain reaction (PCR), Spoligotyping and 24-loci Mycobacterial Interspersed Repetitive Unit-Variable Number Tandem Repeat (MIRU-VNTR) typing were used for genotyping of the isolates. In addition, drug sensitivity test was performed on the isolates using BD Bactec Mycobacterial Growth Inhibition Tube (MGIT) 960. Fifty-eight of the 59 isolates were positive by spoligotyping and spoligotyping International type (SIT) 53, SIT 37, and SIT 149 were the dominant spoligotypes; each consisting of 19%, 15.5%, and10.3% of the isolates, respectively. The majority of the isolates (89.7%) were members of the Euro-American (EA) major lineage. MIRU-VNTR identified Ethiopia_3, Delhi/CAS, Ethiopia_2, TUR, X-type, Ethiopia_H37Rv-like strain, Haarlem and Latin-American Mediterranean (LAM) sub lineages. The proportion of clustering was 77.6% (45/58) in spoligotyping while it was 39.7% (23/58) in 24-loci MIRU-VNTR typing. Furthermore, the proportion of clustering was significantly lowered to 10.3% (6/58) when a combination of spoligotyping and 24-loci MIRU-VNTRplus was used. The recent transmission index (RTI) recorded by spoligotyping, 24-loci MIRU-VNTR typing, and a combination of the two genotyping methods were 58.6%, 27.6% and 5.2%, respectively. Young age and living in groups were significantly associated with strain clustering (P < 0.05). The drug sensitivity test (DST) result showed 8.9% (4/58) of the isolates were resistant to one or more first line ant-TB drugs; but multidrug resistant isolate was not detected. Clustering and RTI could suggest the transmission of TB in the homeless individuals, which could suggest a similar pattern of transmission between homeless individuals and the general population. Hence, the TB control program should consider homeless individuals during the implementation of TB control program.
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Affiliation(s)
- Tsegaye Shamebo
- Department of Microbial, Cellular and Molecular Biology, College of Natural and Computational Sciences, Addis Ababa University, PO. Box 1176, Addis Ababa, Ethiopia
| | - Balako Gumi
- Aklilu Lemma Institute of Pathobiology, Addis Ababa University, Po. Box 1176, Addis Ababa, Ethiopia
| | - Aboma Zewude
- Ethiopian National Tuberculosis Reference Laboratory, Ethipian Public Health Institute, PO. Box 1242 or 5654, Addis Ababa, Ethiopia
- Arba Minch University, Araba Minch, Ethiopia
| | - Fikru Gashaw
- Kotebe University of Education, Addis Ababa, Ethiopia
| | - Temesgen Mohammed
- Department of Veterinary Medicine, College of Agriculture and Veterinary Medicine, United Arab Emirates University, PO Box 15551, Al Ain, United Arab Emirates
- Arba Minch University, Araba Minch, Ethiopia
| | - Muse Girma
- Aklilu Lemma Institute of Pathobiology, Addis Ababa University, Po. Box 1176, Addis Ababa, Ethiopia
| | - Betselot Zerihun
- Ethiopian National Tuberculosis Reference Laboratory, Ethipian Public Health Institute, PO. Box 1242 or 5654, Addis Ababa, Ethiopia
| | - Melak Getu
- Ethiopian National Tuberculosis Reference Laboratory, Ethipian Public Health Institute, PO. Box 1242 or 5654, Addis Ababa, Ethiopia
| | - Sindew Mekasha
- Ethiopian National Tuberculosis Reference Laboratory, Ethipian Public Health Institute, PO. Box 1242 or 5654, Addis Ababa, Ethiopia
| | - Muluwork Getahun
- Ethiopian National Tuberculosis Reference Laboratory, Ethipian Public Health Institute, PO. Box 1242 or 5654, Addis Ababa, Ethiopia
| | | | - Beyene Petros
- Department of Microbial, Cellular and Molecular Biology, College of Natural and Computational Sciences, Addis Ababa University, PO. Box 1176, Addis Ababa, Ethiopia
| | - Gobena Ameni
- Aklilu Lemma Institute of Pathobiology, Addis Ababa University, Po. Box 1176, Addis Ababa, Ethiopia.
- Department of Veterinary Medicine, College of Agriculture and Veterinary Medicine, United Arab Emirates University, PO Box 15551, Al Ain, United Arab Emirates.
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Bezos J, Sáez-Llorente JL, Álvarez J, Romero B, Díez-Guerrier A, Domínguez L, de Juan L. Bovine tuberculosis in Spain, is it really the final countdown? Ir Vet J 2023; 76:13. [PMID: 37491275 PMCID: PMC10369685 DOI: 10.1186/s13620-023-00241-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Accepted: 07/10/2023] [Indexed: 07/27/2023] Open
Abstract
Bovine tuberculosis (bTB) is a severe zoonotic disease that has major impacts on both health and the economy, and which has been subjected to specific eradication programmes in many countries for decades. This manuscript highlights the relevance of this disease in the context of the European Union (EU) and summarizes the epidemiological situation and the main tools (e.g. antemortem diagnostic tests, slaughterhouse surveillance, laboratories, comprehensive databases, etc.) used to control and eradicate bTB in the various EU countries with a focus on the situation in Spain. A comprehensive description of the specific bTB epidemiological situation in Spain is provided, together with an assessment of the evolution of different epidemiological indicators throughout the last decades. Moreover, the main features of the Spanish bTB eradication programme and its control tools are described, along with the studies carried out in Spain that have allowed the updating of and improvement to the programme over the years with the aim of eradication, which has been established for 2030.
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Affiliation(s)
- Javier Bezos
- Departamento de Sanidad Animal, Facultad de Veterinaria, Universidad Complutense de Madrid, Madrid, Spain
- VISAVET Health Surveillance Centre, Complutense University of Madrid, Madrid, Spain
| | | | - Julio Álvarez
- Departamento de Sanidad Animal, Facultad de Veterinaria, Universidad Complutense de Madrid, Madrid, Spain
- VISAVET Health Surveillance Centre, Complutense University of Madrid, Madrid, Spain
| | - Beatriz Romero
- Departamento de Sanidad Animal, Facultad de Veterinaria, Universidad Complutense de Madrid, Madrid, Spain
- VISAVET Health Surveillance Centre, Complutense University of Madrid, Madrid, Spain
| | - Alberto Díez-Guerrier
- Departamento de Sanidad Animal, Facultad de Veterinaria, Universidad Complutense de Madrid, Madrid, Spain
- VISAVET Health Surveillance Centre, Complutense University of Madrid, Madrid, Spain
| | - Lucas Domínguez
- Departamento de Sanidad Animal, Facultad de Veterinaria, Universidad Complutense de Madrid, Madrid, Spain
- VISAVET Health Surveillance Centre, Complutense University of Madrid, Madrid, Spain
| | - Lucía de Juan
- Departamento de Sanidad Animal, Facultad de Veterinaria, Universidad Complutense de Madrid, Madrid, Spain
- VISAVET Health Surveillance Centre, Complutense University of Madrid, Madrid, Spain
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Shibabaw A, Gelaw B, Ghanem M, Legall N, Schooley AM, Soehnlen MK, Salvador LCM, Gebreyes W, Wang SH, Tessema B. Molecular epidemiology and transmission dynamics of multi-drug resistant tuberculosis strains using whole genome sequencing in the Amhara region, Ethiopia. BMC Genomics 2023; 24:400. [PMID: 37460951 DOI: 10.1186/s12864-023-09502-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Accepted: 07/03/2023] [Indexed: 07/20/2023] Open
Abstract
BACKGROUND Drug resistant Mycobacterium tuberculosis prevention and care is a major challenge in Ethiopia. The World health organization has designated Ethiopia as one of the 30 high burden multi-drug resistant tuberculosis (MDR-TB) countries. There is limited information regarding genetic diversity and transmission dynamics of MDR-TB in Ethiopia. OBJECTIVE To investigate the molecular epidemiology and transmission dynamics of MDR-TB strains using whole genome sequence (WGS) in the Amhara region. METHODS Forty-five MDR-TB clinical isolates from Amhara region were collected between 2016 and 2018, and characterized using WGS and 24-loci Mycobacterium Interspersed Repetitive Units Variable Number of Tandem Repeats (MIRU-VNTR) typing. Clusters were defined based on the maximum distance of 12 single nucleotide polymorphisms (SNPs) or alleles as the upper threshold of genomic relatedness. Five or less SNPs or alleles distance or identical 24-loci VNTR typing is denoted as surrogate marker for recent transmission. RESULTS Forty-one of the 45 isolates were analyzed by WGS and 44% (18/41) of the isolates were distributed into 4 clusters. Of the 41 MDR-TB isolates, 58.5% were classified as lineage 4, 36.5% lineage 3 and 5% lineage 1. Overall, TUR genotype (54%) was the predominant in MDR-TB strains. 41% (17/41) of the isolates were clustered into four WGS groups and the remaining isolates were unique strains. The predominant cluster (Cluster 1) was composed of nine isolates belonging to lineage 4 and of these, four isolates were in the recent transmission links. CONCLUSIONS Majority of MDR-TB strain cluster and predominance of TUR lineage in the Amhara region give rise to concerns for possible ongoing transmission. Efforts to strengthen TB laboratory to advance diagnosis, intensified active case finding, and expanded contact tracing activities are needed in order to improve rapid diagnosis and initiate early treatment. This would lead to the interruption of the transmission chain and stop the spread of MDR-TB in the Amhara region.
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Affiliation(s)
- Agumas Shibabaw
- Department of Medical Laboratory Sciences, College of Medicine and Health Sciences, Wollo University, Dessie, Ethiopia.
- Global One Health Initiative (GOHi), The Ohio State University, Columbus, OH, USA.
- Department of Medical Microbiology, School of Medical Laboratory Sciences, College of Medicine and Health Sciences, University of Gondar, Gondar, Ethiopia.
- Michigan Department of Health and Human Services, Infectious disease, Lansing, MI, USA.
- Department of Veterinary Preventive Medicine, College of Veterinary Medicine, The Ohio State University, Columbus, OH, USA.
| | - Baye Gelaw
- Department of Medical Microbiology, School of Medical Laboratory Sciences, College of Medicine and Health Sciences, University of Gondar, Gondar, Ethiopia
| | - Mostafa Ghanem
- Department of Veterinary Medicine, Virginia-Maryland College of Veterinary Medicine, University of Maryland, College Park, MD, USA
| | - Noah Legall
- Institute of Bioinformatics, University of Georgia, Athens, GA, USA
| | - Angie M Schooley
- Michigan Department of Health and Human Services, Infectious disease, Lansing, MI, USA
| | - Marty K Soehnlen
- Michigan Department of Health and Human Services, Infectious disease, Lansing, MI, USA
| | - Liliana C M Salvador
- School of Animal and Comparative Biomedical Sciences, College of Agriculture and life sciences, University of Arizona, Tucson, AZ, USA
| | - Wondwossen Gebreyes
- Global One Health Initiative (GOHi), The Ohio State University, Columbus, OH, USA
- Department of Veterinary Preventive Medicine, College of Veterinary Medicine, The Ohio State University, Columbus, OH, USA
| | - Shu-Hua Wang
- Global One Health Initiative (GOHi), The Ohio State University, Columbus, OH, USA
- Department of Internal Medicine, Division of Infectious Diseases, College of Medicine, The Ohio State University, Columbus, OH, USA
| | - Belay Tessema
- Department of Medical Microbiology, School of Medical Laboratory Sciences, College of Medicine and Health Sciences, University of Gondar, Gondar, Ethiopia
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9
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Noorizhab MNF, Zainal Abidin N, Teh LK, Tang TH, Onyejepu N, Kunle-Ope C, Tochukwu NE, Sheshi MA, Nwafor T, Akinwale OP, Ismail AI, Nor NM, Salleh MZ. Exploration of the diversity of multi-drug resistant Mycobacterium tuberculosis complex in Lagos, Nigeria using WGS: Distribution of lineages, drug resistance patterns and genetic mutations. Tuberculosis (Edinb) 2023; 140:102343. [PMID: 37080082 DOI: 10.1016/j.tube.2023.102343] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 03/19/2023] [Accepted: 04/12/2023] [Indexed: 04/22/2023]
Abstract
Multidrug-resistant (MDR) or extensively drug-resistant (XDR) Tuberculosis (TB) is a major challenge to global TB control. Therefore, accurate tracing of in-country MDR-TB transmission are crucial for the development of optimal TB management strategies. This study aimed to investigate the diversity of MTBC in Nigeria. The lineage and drug-resistance patterns of the clinical MTBC isolates of TB patients in Southwestern region of Nigeria were determined using the WGS approach. The phenotypic DST of the isolates was determined for nine anti-TB drugs. The sequencing achieved average genome coverage of 65.99X. The most represented lineages were L4 (n = 52, 83%), L1 (n = 8, 12%), L2 (n = 2, 3%) and L5 (n = 1, 2%), suggesting a diversified MTB population. In term of detection of M/XDR-TB, while mutations in katG and rpoB genes are the strong predictors for the presence of M/XDR-TB, the current study also found the lack of good genetic markers for drug resistance amongst the MTBC in Nigeria which may pose greater problems on local tuberculosis management efforts. This high-resolution molecular epidemiological data provides valuable insights into the mechanistic for M/XDR TB in Lagos, Nigeria.
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Affiliation(s)
- Mohd Nur Fakhruzzaman Noorizhab
- Integrative Pharmacogenomics Institute, Universiti Teknologi MARA Selangor Branch, Puncak Alam Campus, Selangor, Malaysia; Faculty of Pharmacy, Universiti Teknologi MARA Selangor Branch, Puncak Alam Campus, Selangor, Malaysia
| | - Norzuliana Zainal Abidin
- Integrative Pharmacogenomics Institute, Universiti Teknologi MARA Selangor Branch, Puncak Alam Campus, Selangor, Malaysia
| | - Lay Kek Teh
- Integrative Pharmacogenomics Institute, Universiti Teknologi MARA Selangor Branch, Puncak Alam Campus, Selangor, Malaysia; Faculty of Pharmacy, Universiti Teknologi MARA Selangor Branch, Puncak Alam Campus, Selangor, Malaysia
| | - Thean Hock Tang
- Advance Medical & Dental Institute (AMDI), Universiti Sains Malaysia, Kepala Batas, Pulau Pinang, Malaysia
| | - Nneka Onyejepu
- Microbiology Department, Nigerian Institute of Medical Research (NIMR), Lagos, Nigeria
| | - Chioma Kunle-Ope
- Microbiology Department, Nigerian Institute of Medical Research (NIMR), Lagos, Nigeria
| | - Nwanneka E Tochukwu
- Microbiology Department, Nigerian Institute of Medical Research (NIMR), Lagos, Nigeria
| | | | - Timothy Nwafor
- Public Health and Epidemiology Department, Nigerian Institute of Medical Research (NIMR), Lagos, Nigeria
| | - Olaoluwa P Akinwale
- Public Health and Epidemiology Department, Nigerian Institute of Medical Research (NIMR), Lagos, Nigeria.
| | | | - Norazmi Mohd Nor
- School of Health Sciences, Health Campus, Universiti Sains Malaysia, Kubang Kerian, Kelantan, Malaysia
| | - Mohd Zaki Salleh
- Integrative Pharmacogenomics Institute, Universiti Teknologi MARA Selangor Branch, Puncak Alam Campus, Selangor, Malaysia.
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10
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Bakuła Z, Marczak M, Bluszcz A, Proboszcz M, Kościuch J, Krenke R, Stakėnas P, Mokrousov I, Jagielski T. Phylogenetic relationships of Mycobacterium tuberculosis isolates in Poland: The emergence of Beijing genotype among multidrug-resistant cases. Front Cell Infect Microbiol 2023; 13:1161905. [PMID: 37009494 PMCID: PMC10061152 DOI: 10.3389/fcimb.2023.1161905] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Accepted: 02/28/2023] [Indexed: 03/18/2023] Open
Abstract
IntroductionThe epidemiological situation of tuberculosis (TB) in Poland urges for its continuous and scrupulous monitoring. The objective of this study was to explore the genetic diversity of multidrug-resistant (MDR) and drug-susceptible (DS) Mycobacterium tuberculosis isolates from Poland with a combination of spoligotyping and high-resolution mycobacterial interspersed repetitive unit-variable number tandem repeat (MIRU-VNTR) analysis. The results were placed in the Northern and Eastern Europe context.MethodsThe study included 89 (39 MDR and 50 DS) M. tuberculosis isolates collected from as many patients between 2018 and 2021 in Poland. The analysis was done using spoligotyping, and MIRU-VNTR typing at 24 standard loci. The data were compared to those available on Poland and neighbors and global M. tuberculosis datasets.ResultsThe main identified families were Beijing (28.1%) and Haarlem (16.8%) while 34.8% of isolates were in the heterogeneous L4-unclassified group. Although the Beijing family was the most prevalent (61.5%) among MDR-TB cases, it accounted for only 2% of DS isolates. Among foreign-born patients, a higher ratio of MDR isolates were observed when compared with those who Poland-born (64.3% vs. 40%). Furthermore, all patients from the Former Soviet Union (FSU) countries were infected with MDR-TB.DiscussionWhereas DS M. tuberculosis population in Poland is dominated by L4 isolates, MDR isolates are mostly of the Beijing genotype. The rise in the prevalence of the Beijing isolates in Poland, coupled with high proportion of the Beijing genotype among foreign-born TB patients may reflect an ongoing transmission of this family, imported to Poland mainly from FSU countries.
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Affiliation(s)
- Zofia Bakuła
- Department of Medical Microbiology, Institute of Microbiology, University of Warsaw, Faculty of Biology, Warsaw, Poland
| | - Mateusz Marczak
- Department of Medical Microbiology, Institute of Microbiology, University of Warsaw, Faculty of Biology, Warsaw, Poland
| | - Agata Bluszcz
- Department of Medical Microbiology, Institute of Microbiology, University of Warsaw, Faculty of Biology, Warsaw, Poland
| | - Małgorzata Proboszcz
- Department of Internal Medicine, Pulmonary Diseases & Allergy, Medical University of Warsaw, Warsaw, Poland
| | - Justyna Kościuch
- Department of Internal Medicine, Pulmonary Diseases & Allergy, Medical University of Warsaw, Warsaw, Poland
| | - Rafał Krenke
- Department of Internal Medicine, Pulmonary Diseases & Allergy, Medical University of Warsaw, Warsaw, Poland
| | - Petras Stakėnas
- Department of Immunology and Cell Biology, Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Igor Mokrousov
- Laboratory of Molecular Epidemiology and Evolutionary Genetics, St. Petersburg Pasteur Institute, St. Petersburg, Russia
- Henan International Joint Laboratory of Children’s Infectious Diseases, Henan Children’s Hospital, Zhengzhou Children’s Hospital, Zhengzhou, China
- *Correspondence: Tomasz Jagielski, ; Igor Mokrousov,
| | - Tomasz Jagielski
- Department of Medical Microbiology, Institute of Microbiology, University of Warsaw, Faculty of Biology, Warsaw, Poland
- *Correspondence: Tomasz Jagielski, ; Igor Mokrousov,
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11
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Perchlozone Resistance in Clinical Isolates of Mycobacterium tuberculosis. Antibiotics (Basel) 2023; 12:antibiotics12030590. [PMID: 36978456 PMCID: PMC10044601 DOI: 10.3390/antibiotics12030590] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Revised: 02/28/2023] [Accepted: 03/13/2023] [Indexed: 03/18/2023] Open
Abstract
The emergence of drug-resistant tuberculosis forced the development of new drugs and the screening of more effective or less toxic analogues. Mycolic acid biosynthesis is targeted by several antituberculosis drugs, isoniazid being one of the most important in tuberculosis therapy. Recently, perchlozone, acting on another step in the FAS-II cycle, was officially approved for tuberculosis treatment in the Russian Federation and was included in the Russian national clinical guidelines. Using the serial dilution method on 7H10 agar plates for perchlozone and a Sensititre MYCOTB microdilution plate, we analyzed the phenotypic properties of primary clinical isolates of M. tuberculosis and analyzed the molecular determinants of resistance to isoniazid, ethionamide, and perchlozone. We found a wide variation in the MIC of perchlozone from 2 to 64 mg/L, correlating with the overall resistance profile: the MIC was higher for MDR and pre-XDR isolates. The cross-resistance between ethionamide and perchlozone was driven by mutations in the ethA gene encoding monooxygenase responsible for the activation of both drugs. The presumably susceptible to perchlozone and wild-type strains had MICs ranging from 2 to 4 mg/L, and the breakpoint was estimated to be 4 or 8 mg/L. In conclusion, susceptibility to perchlozone is retained for a part of the MDR strains, as is susceptibility to ethionamide, providing the possibility of therapy for such cases based on phenotypic or molecular analysis.
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12
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Busatto C, Possuelo LG, Bierhals D, de Oliveira CL, de Souza MQ, Fanfa D, Barreto É, Schwarzbold P, Von Groll A, Portugal I, Perdigão J, Croda J, Andrews JR, da Silva PA, Ramis IB. Spread of Mycobacterium tuberculosis in Southern Brazilian persons deprived of liberty: a molecular epidemiology study. Eur J Clin Microbiol Infect Dis 2023; 42:297-304. [PMID: 36701032 DOI: 10.1007/s10096-023-04546-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Accepted: 01/10/2023] [Indexed: 01/27/2023]
Abstract
To evaluate the genetic diversity and clustering rates of M. tuberculosis strains to better understand transmission among persons deprived of liberty (PDL) in Rio Grande do Sul (RS), southern Brazil. This is a cross-sectional study, including strains of M. tuberculosis isolated from PDL, stored at the Central Laboratory of RS, in the period from 2013 to 2018. The molecular characterization was performed using the MIRU-VNTR 15 loci method. A total of 598 M. tuberculosis strains were genotyped, and 37.5% were grouped into 53 clusters. Cluster sizes ranged from 2 to 34 strains. The largest cluster of the study had strains from 34 PDL, and 58.8% of the PDL of this cluster were in P01. Among the clusters formed, in 60.3%, there was at least one strain from P01. The most common strains in RS were LAM (53.2%) and Haarlem (31.1%). The LAM strain was the most likely to form clusters, and Haarlem was associated with anti-TB drug resistance. This was translational research, and the results can collaborate with the TB control programs, leading to improved strategies that allow the reduction of the TB burden in prisons.
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Affiliation(s)
- Caroline Busatto
- Núcleo de Pesquisa Em Microbiologia Medica, Faculdade de Medicina, Universidade Federal Do Rio Grande, Rio Grande, Rio Grande Do Sul, Brazil
| | - Lia Gonçalves Possuelo
- Programa de Pós-Graduação Em Promoção da Saúde, Universidade de Santa Cruz Do Sul, Santa Cruz Do Sul, Rio Grande Do Sul, Brazil
| | - Dienefer Bierhals
- Núcleo de Pesquisa Em Microbiologia Medica, Faculdade de Medicina, Universidade Federal Do Rio Grande, Rio Grande, Rio Grande Do Sul, Brazil
| | - Carolina Larrosa de Oliveira
- Núcleo de Pesquisa Em Microbiologia Medica, Faculdade de Medicina, Universidade Federal Do Rio Grande, Rio Grande, Rio Grande Do Sul, Brazil
| | - Mariana Quaresma de Souza
- Núcleo de Pesquisa Em Microbiologia Medica, Faculdade de Medicina, Universidade Federal Do Rio Grande, Rio Grande, Rio Grande Do Sul, Brazil
| | - Dandara Fanfa
- Programa de Pós-Graduação Em Promoção da Saúde, Universidade de Santa Cruz Do Sul, Santa Cruz Do Sul, Rio Grande Do Sul, Brazil
| | - Érika Barreto
- Programa de Pós-Graduação Em Promoção da Saúde, Universidade de Santa Cruz Do Sul, Santa Cruz Do Sul, Rio Grande Do Sul, Brazil
| | - Pauline Schwarzbold
- 8ª Delegacia Penitenciária Regional, Superintendência Dos Serviços Penitenciários, Santa Cruz Do Sul, RS, Brazil
| | - Andrea Von Groll
- Núcleo de Pesquisa Em Microbiologia Medica, Faculdade de Medicina, Universidade Federal Do Rio Grande, Rio Grande, Rio Grande Do Sul, Brazil
| | - Isabel Portugal
- Research Institute for Medicines - iMed.ULisboa, Faculdade de Farmácia, Universidade de Lisboa, Lisbon, Portugal
| | - João Perdigão
- Research Institute for Medicines - iMed.ULisboa, Faculdade de Farmácia, Universidade de Lisboa, Lisbon, Portugal
| | - Julio Croda
- Faculdade de Medicina, Universidade Federal Do Mato Grosso Do Sul, Campo Grande, Mato Grosso Do Sul, Brazil
| | - Jason R Andrews
- Division of Infectious Diseases and Geographic Medicine, Stanford University School of Medicine, Stanford, Palo Alto, CA, US
| | - Pedro Almeida da Silva
- Núcleo de Pesquisa Em Microbiologia Medica, Faculdade de Medicina, Universidade Federal Do Rio Grande, Rio Grande, Rio Grande Do Sul, Brazil.
- Rua General Osório S/N, Centro, Rio Grande Do Sul, Rio Grande, 96200190, Brazil.
| | - Ivy Bastos Ramis
- Núcleo de Pesquisa Em Microbiologia Medica, Faculdade de Medicina, Universidade Federal Do Rio Grande, Rio Grande, Rio Grande Do Sul, Brazil
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13
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Tuberculosis control at a South African correctional centre: Diagnosis, treatment and strain characterisation. PLoS One 2022; 17:e0277459. [DOI: 10.1371/journal.pone.0277459] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Accepted: 10/28/2022] [Indexed: 11/13/2022] Open
Abstract
Background
Correctional centres provide ideal conditions for tuberculosis (TB) transmission and disease progression. Despite the high TB incidence and incarceration rate in South Africa, data from South African correctional centres are scarce. Thus, the study evaluated TB diagnosis, treatment initiation and completion, and identified prevalent Mycobacterium tuberculosis strains among detainees entering a South African correctional centre.
Methods
This study was a prospective observational study that enrolled participants between February and September 2017 from a correctional centre located in the Western Cape, South Africa. All adult male detainees who tested positive for TB during admission screening were eligible to participate in the study. Sputum samples from enrolled participants underwent smear microscopy and culture. Strain typing was performed on culture-positive samples. The time between specimen collection and diagnosis, the time between diagnosis and treatment initiation, and the proportion of detainees completing TB treatment at the correctional centre were calculated.
Results
During the study period, 130 TB cases were detected through routine admission screening (126 male, 2 female, 2 juvenile). Out of the 126 eligible male detainees, 102 were enrolled in the study (81%, 102/126). All TB cases were detected within 30 hrs of admission screening. The majority (78%, 80/102) of participants started treatment within 48 hrs of TB diagnosis. However, only 8% (9/102) of participants completed treatment at the correction centre. Sputa from 90 of the 102 participants were available for smear and culture. There was a high smear positivity, with 49% (44/90) of isolates being smear positive. The Beijing family was the most frequent lineage (55.2%) in the study.
Conclusion
The strengths of the current TB control efforts at the correctional centre include rapid detection of cases through admission screening and prompt treatment initiation. However, a high number of detainees exiting before treatment completion highlights the need to strengthen links between correctional TB services and community TB services to ensure detainees complete TB treatment after release and prevent TB transmission.
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14
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Gaballah A, Ghazal A, Almiry R, Hussein S, Emad R, El-Sherbini E. Fingerprinting of Mycobacterium tuberculosis isolates by MIRU-VNTR genotyping and detection of isoniazid resistance by real-time PCR. J Med Microbiol 2022; 71. [DOI: 10.1099/jmm.0.001603] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Introduction. Tuberculosis (TB) is a great public health problem in developing countries such as Egypt. Genotyping of
Mycobacterium tuberculosis
isolates has a prominent role in the field of TB prevention.
Aim. This study aimed to evaluate real-time PCR using Minor Groove Binder (MGB) probes and to identify circulating lineages/sub-lineages of
M. tuberculosis
and their transmission patterns.
Hypothesis. We hypothesize that MIRU-VNTR technique is efficient in identifying circulating
M. tuberculosis
lineages in Egypt.
Methodology. Fifty sputum specimens positive for acid-fast bacilli were included. Isoniazid (INH) resistance was detected using the 1 % proportion method. Real-time PCR using MGB-probes was used for simultaneous detection of TB infection and INH resistance. Partial sequencing of the katG gene was used to confirm INH resistance results. A standard 15 Mycobacterial Interspersed Repetitive Unit Variable Number Tandem Repeat (15-MIRU-VNTR) approach was used for genotyping through the MIRU-VNTRplus online platform.
Results. Only seven specimens showed phenotypic resistance to INH.
M. tuberculosis
was detected in all samples, while a mutation in the katG gene codon 315 was detected only in five samples, which were also phenotypically INH-resistant. Sequencing of the katG gene showed codon 315 mutation genotypically and phenotypically in the five INH-resistant isolates. Molecular genotyping of
M. tuberculosis
isolates revealed that the majority of isolates (26/50, 52 %) belonged to the S family of lineage_4. A low clustering rate (2 %) was observed among our isolates. According to the Hunter-Gaston Discriminatory Index (HGDI), 11 MIRU-VNTR loci were highly or moderately discriminative, while four loci were less polymorphic.
Conclusion. MIRU-VNTR genotyping revealed a low clustering rate with a low recent transmission rate of
M. tuberculosis
strains in Alexandria, Egypt.
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Affiliation(s)
- Ahmed Gaballah
- Department of Microbiology, Medical Research Institute, Alexandria University, Egypt
| | - Abeer Ghazal
- Department of Microbiology, Medical Research Institute, Alexandria University, Egypt
| | - Reda Almiry
- Department of Clinical Pathology, Alexandria Armed Forces Hospital, Alexandria, Egypt
| | - Somaya Hussein
- Elmamoura Chest Hospital, Egyptian Ministry of Health, Alexandria, Egypt
| | - Rasha Emad
- Alexandria Main University Hospital, Alexandria University, Alexandria, Egypt
| | - Eglal El-Sherbini
- Department of Microbiology, Medical Research Institute, Alexandria University, Egypt
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15
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Sharma MK, Janella D, McGurran A, Corbett C, Adam H, Akochy PM, Haldane D, MacKenzie H, Minion J, Needle R, Newberry C, Patterson M, Sekirov I, Tyrrell G, Soualhine H. Compilation of 10 Years of MIRU-VNTR Data: Canadian National Tuberculosis Laboratory's Experience. THE CANADIAN JOURNAL OF INFECTIOUS DISEASES & MEDICAL MICROBIOLOGY = JOURNAL CANADIEN DES MALADIES INFECTIEUSES ET DE LA MICROBIOLOGIE MEDICALE 2022; 2022:3505142. [PMID: 36046174 PMCID: PMC9424012 DOI: 10.1155/2022/3505142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Revised: 07/06/2022] [Accepted: 08/02/2022] [Indexed: 11/17/2022]
Abstract
Tuberculosis is a significant cause of morbidity worldwide and is a priority at the provincial and federal levels in Canada. It is known that tuberculosis transmission networks are complex and span many years as well as different jurisdictions and countries. MIRU-VNTR is a universal tuberculosis genotyping method that utilizes a 24-loci pattern and it has shown promise in identifying inter and intrajurisdictional clusters within Canada. MIRU-VNTR data collected over 10 years from the National Reference Centre for Mycobacteriology (NRCM) were analyzed in this study. Some clusters were unique to a single province/territory, while others spanned multiple provinces and/or territories in Canada. The use of a universal laboratory test can enhance contact tracing, provide geographical information on circulating genotypes, and hence, aid in tuberculosis investigation by public health. The housing of all data on one platform, technical ease of the method, easy exchange of data between jurisdictions, and strong collaboration with laboratories and surveillance units at the provincial and federal levels have the potential to identify possible outbreaks in real time.
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Affiliation(s)
- Meenu K. Sharma
- National Reference Centre for Mycobacteriology, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Canada
- Department of Medical Microbiology, University of Manitoba, Winnipeg, Canada
| | - Debra Janella
- National Reference Centre for Mycobacteriology, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Canada
| | - Alisa McGurran
- National Reference Centre for Mycobacteriology, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Canada
| | - Cindi Corbett
- National Reference Centre for Mycobacteriology, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Canada
- Department of Medical Microbiology, University of Manitoba, Winnipeg, Canada
| | | | | | - David Haldane
- Public Health Laboratory Network, Halifax, Nova Scotia, Canada
| | - Hope MacKenzie
- Atlantic Health Sciences Corporation, Saint John, New Brunswick, Canada
| | - Jessica Minion
- Saskatchewan Health Authority, Saskatoon, Saskatchewan, Canada
| | - Robert Needle
- Newfoundland and Labrador Public Health Laboratory, Saint John, Newfoundland, Canada
| | - Caroline Newberry
- Office of Chief Public Health Officer, Yellowknife, Northwest Territories, Canada
| | | | - Inna Sekirov
- BC Centre for Disease Control, Vancouver, British Columbia, Canada
| | | | - Hafid Soualhine
- National Reference Centre for Mycobacteriology, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Canada
- Department of Medical Microbiology, University of Manitoba, Winnipeg, Canada
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16
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Lopez J, Anna F, Authié P, Pawlik A, Ku MW, Blanc C, Souque P, Moncoq F, Noirat A, Hardy D, Sougakoff W, Brosch R, Guinet F, Charneau P, Majlessi L. A lentiviral vector encoding fusion of light invariant chain and mycobacterial antigens induces protective CD4 + T cell immunity. Cell Rep 2022; 40:111142. [PMID: 35905717 DOI: 10.1016/j.celrep.2022.111142] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Revised: 05/11/2022] [Accepted: 06/07/2022] [Indexed: 12/21/2022] Open
Abstract
Lentiviral vectors (LVs) are highly efficient at inducing CD8+ T cell responses. However, LV-encoded antigens are processed inside the cytosol of antigen-presenting cells, which does not directly communicate with the endosomal major histocompatibility complex class II (MHC-II) presentation pathway. LVs are thus poor at inducing CD4+ T cell response. To overcome this limitation, we devised a strategy whereby LV-encoded antigens are extended at their N-terminal end with the MHC-II-associated light invariant chain (li), which contains an endosome-targeting signal sequence. When evaluated with an LV-encoded polyantigen composed of CD4+ T cell targets from Mycobacterium tuberculosis, intranasal vaccination in mice triggers pulmonary polyfunctional CD4+ and CD8+ T cell responses. Adjuvantation of these LVs extends the mucosal immunity to Th17 and Tc17 responses. A systemic prime and an intranasal boost with one of these LV induces protection against M. tuberculosis. This strategy improves the protective power of LVs against infections and cancers, where CD4+ T cell immunity plays an important role.
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Affiliation(s)
- Jodie Lopez
- Institut Pasteur-TheraVectys Joint Lab, Université Paris Cité, 28 rue du Dr. Roux, 75015 Paris, France
| | - François Anna
- Institut Pasteur-TheraVectys Joint Lab, Université Paris Cité, 28 rue du Dr. Roux, 75015 Paris, France
| | - Pierre Authié
- Institut Pasteur-TheraVectys Joint Lab, Université Paris Cité, 28 rue du Dr. Roux, 75015 Paris, France
| | - Alexandre Pawlik
- Institut Pasteur, Integrated Mycobacterial Pathogenomics Unit, CNRS UMR 3525, Université Paris Cité, 25 rue du Dr. Roux, 75015 Paris, France
| | - Min-Wen Ku
- Institut Pasteur-TheraVectys Joint Lab, Université Paris Cité, 28 rue du Dr. Roux, 75015 Paris, France
| | - Catherine Blanc
- Institut Pasteur-TheraVectys Joint Lab, Université Paris Cité, 28 rue du Dr. Roux, 75015 Paris, France
| | - Philippe Souque
- Institut Pasteur-TheraVectys Joint Lab, Université Paris Cité, 28 rue du Dr. Roux, 75015 Paris, France
| | - Fanny Moncoq
- Institut Pasteur-TheraVectys Joint Lab, Université Paris Cité, 28 rue du Dr. Roux, 75015 Paris, France
| | - Amandine Noirat
- Institut Pasteur-TheraVectys Joint Lab, Université Paris Cité, 28 rue du Dr. Roux, 75015 Paris, France
| | - David Hardy
- Institut Pasteur, Histopathology Platform, Université Paris Cité, 28 rue du Dr. Roux, 75015 Paris, France
| | - Wladimir Sougakoff
- Sorbonne Universités, UPMC Université Paris 06, CIMI-Paris, AP-HP, Hôpital Pitié-Salpêtrière, CNR-MyRMA, 75013 Paris, France
| | - Roland Brosch
- Institut Pasteur, Integrated Mycobacterial Pathogenomics Unit, CNRS UMR 3525, Université Paris Cité, 25 rue du Dr. Roux, 75015 Paris, France
| | - Françoise Guinet
- Institut Pasteur, Lymphocytes and Immunity Unit, Université Paris Cité, 25 rue du Dr. Roux, 75015 Paris, France
| | - Pierre Charneau
- Institut Pasteur-TheraVectys Joint Lab, Université Paris Cité, 28 rue du Dr. Roux, 75015 Paris, France
| | - Laleh Majlessi
- Institut Pasteur-TheraVectys Joint Lab, Université Paris Cité, 28 rue du Dr. Roux, 75015 Paris, France.
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17
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Bakhtiyariniya P, Khosravi AD, Hashemzadeh M, Savari M. Genetic diversity of drug-resistant Mycobacterium tuberculosis clinical isolates from Khuzestan province, Iran. AMB Express 2022; 12:85. [PMID: 35789443 PMCID: PMC9253214 DOI: 10.1186/s13568-022-01425-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2022] [Accepted: 06/21/2022] [Indexed: 11/10/2022] Open
Abstract
The emergence of drug-resistant strains of the Mycobacterium tuberculosis (MTB) has challenged tuberculosis control programs. So far, few studies using the 24-locus mycobacterial interspersed repetitive unit variable number tandem repeats (MIRU-VNTR) have investigated the genetic diversity of MTB in Iran. This study aimed to determine the genetic diversity of MTB isolates resistant to first-line anti-tuberculosis drugs using 24-locus MIRU-VNTR in southwestern Iran. Out of 6620 MTB clinical isolates, 29 resistant isolates to one or more isoniazid, rifampin, and ethambutol were detected using drug susceptibility testing by the proportional method. The manual 24-locus MIRU-VNTR was used to determine the MTB resistant isolates’ phylogenetic relationship. MIRU-VNTRplus web application tools were applied to analyze the associated data. Using 24-locus MIRU-VNTR, 13.8% of isolates (n = 4) were distributed in two clusters, and the remaining 86.2% (n = 25) showed a unique pattern. Four clonal complexes were observed in the minimum spanning tree based on the double-locus variant. Most isolates belonged to Delhi/CAS (34.5%, 10/29) and NEW-1 (24.1%, 7/29) sub-lineages, followed by EAI and LAM with a frequency of 6.9% (2/29) and 3.5% (1/29), respectively. Eight isolates (27.6%) did not match any genotype in the database. The 24-locus MIRU-VNTR showed a high discriminatory power; however, the 15-locus and 12-locus set analyses were more discriminative. Our study revealed a high degree of genetic diversity among drug-resistant MTB isolates, which could be interpreted as the low rate of person-to-person transmission in this region. The 15-locus MIRU-VNTR would be recommended for preliminary genotyping of drug-resistant MTB.
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Affiliation(s)
- Pejman Bakhtiyariniya
- Infectious and Tropical Diseases Research Center, Health Research Institute, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran.,Department of Microbiology, Faculty of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Azar Dokht Khosravi
- Infectious and Tropical Diseases Research Center, Health Research Institute, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran. .,Department of Microbiology, Faculty of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran. .,Iranian Study Group on Microbial Drug Resistance, Tehran, Iran.
| | - Mohammad Hashemzadeh
- Infectious and Tropical Diseases Research Center, Health Research Institute, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran.,Department of Microbiology, Faculty of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Mohammad Savari
- Infectious and Tropical Diseases Research Center, Health Research Institute, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran.,Department of Microbiology, Faculty of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
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18
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Mosadegh M, Habibi Ghahfarokhi S, Ahmadi A, Pourmand MR, Erfani Y, Mashhadi R. Identification and molecular characterization of penicillin-nonsusceptible Streptococcus pneumoniae isolates recovered from invasive infections in a pre-pneumococcal vaccine era. J Clin Lab Anal 2022; 36:e24566. [PMID: 35748026 PMCID: PMC9396163 DOI: 10.1002/jcla.24566] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Revised: 05/27/2022] [Accepted: 06/09/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Given the significant role of penicillin-nonsusceptible Streptococcus pneumoniae in inducing severe infectious diseases, identifying serotypes and genotypes that can mediate antimicrobial resistance has become a pillar of treatment strategies. This study aims to determine the correlation between the minimum inhibitory concentration of antimicrobial agents and amino acid mutations in penicillin-binding proteins. Moreover, molecular serotyping and multiple-locus variable number tandem repeat analysis typing were first-ever performed to characterize the invasive penicillin-nonsusceptible S. pneumoniae isolates in Iran. METHODS Of 149 isolates, antimicrobial susceptibility tests were performed against penicillin, ceftriaxone, and cefotaxime by the MIC Test Strip, and sequence analysis of the pbp genes was performed through PCR-sequencing method. All penicillin-nonsusceptible S. pneumoniae isolates were serotyped and genotyped by sequential multiplex PCR and multiple-locus variable-number tandem repeat analysis, respectively. RESULTS Among pneumococcal isolates, 53 isolates were classified as penicillin-nonsusceptible S. pneumoniae, of which 38 (71.7%) and 15 (28.3%) were resistant and intermediate to penicillin, respectively. Furthermore, ceftriaxone- and cefotaxime-nonsusceptible pneumococci constituted 33 (62.2%) and 29 cases (54.7%), respectively. Of note, there were 8 and 41 different serotypes and multiple-locus variable-number tandem repeat analysis types, respectively. CONCLUSIONS Due to the increasing resistance to antimicrobial agents, the most efficient approach to preventing pneumococcal infection mortality as vaccine-preventable diseases is focusing on wide-spectrum vaccination. Based on our findings, the 13-valent pneumococcal conjugate vaccine could considerably reduce the incidence of invasive pneumococcal diseases due to the high rate of serotype coverage.
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Affiliation(s)
- Mehrdad Mosadegh
- Department of Pathobiology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Soheila Habibi Ghahfarokhi
- Department of Pathobiology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Ali Ahmadi
- Applied Microbiology Research Center, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - Mohammad Reza Pourmand
- Department of Pathobiology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Yousef Erfani
- Department of Medical Laboratory Sciences, School of Allied Medical Sciences, Tehran University of Medical Sciences, Tehran, Iran
| | - Rahil Mashhadi
- Urology Research Center, Tehran University of Medical Sciences, Tehran, Iran
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19
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Bakhtiyariniya P, Khosravi AD, Hashemzadeh M, Savari M. Identification of mutations in rpoB, pncA, embB, and ubiA genes among drug-resistant Mycobacterium tuberculosis clinical isolates from Iran. Acta Microbiol Immunol Hung 2022. [PMID: 35452411 DOI: 10.1556/030.2022.01730] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Accepted: 04/12/2022] [Indexed: 11/19/2022]
Abstract
Mycobacterium tuberculosis resistant to effective first-line drugs (FLDs) has challenged national and global tuberculosis control programs. This study aimed to identify mutations in 4 genes related to rifampin, pyrazinamide, and ethambutol resistance among clinical isolates of M. tuberculosis from southwestern Iran. After drug susceptibility testing of 6620 M. tuberculosis clinical isolates by proportional method, a total of 24 FLD-resistant strains were included in the study. Fragments of rpoB, pncA, embB, and ubiA genes were amplified and sequenced to mine the mutations by pairwise alignment with the corresponding M. tuberculosis H37Rv genes. Phenotypic resistance to rifampin, isoniazid, and ethambutol was detected in 67, 54, and 33% (n = 16, 13, and 8) of the isolates, respectively. Of rifampin-resistant isolates, 31% (5/16) were mono-resistant, and 56% (9/16) were multidrug-resistant (MDR). In 100% of rifampin-resistant isolates, mutations were found in the rifampin resistance-determining region (RRDR) of the rpoB, with S450L substitution being the most common, especially in MDRs (77.8%, 7/9). Resistance-conferring mutations in pncA were present in 12.5% (3/24) of FLD-resistant isolates. The embB and ubiA mutations were found in 62.5 and 12.5% (5/8 and 1/8) of ethambutol-resistant isolates, respectively, of which the embB D354A was the most common substitution (37.5%, 3/8). Sixteen distinct mutations were identified, one of which was novel. The sequence analysis of the RRDR segment was the best way to detect rifampin resistance. The rpoB S450L substitution could be a helpful molecular marker to predict MDR. In other genes, no mutation was identified as a reliable marker.
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Affiliation(s)
- Pejman Bakhtiyariniya
- 1 Infectious and Tropical Diseases Research Center, Health Research Institute, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
- 2 Department of Microbiology, Faculty of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Azar Dokht Khosravi
- 1 Infectious and Tropical Diseases Research Center, Health Research Institute, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
- 2 Department of Microbiology, Faculty of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
- 3 Iranian Study Group on Microbial Drug Resistance, Iran
| | - Mohammad Hashemzadeh
- 1 Infectious and Tropical Diseases Research Center, Health Research Institute, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
- 2 Department of Microbiology, Faculty of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Mohammad Savari
- 1 Infectious and Tropical Diseases Research Center, Health Research Institute, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
- 2 Department of Microbiology, Faculty of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
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20
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Country-wide genotyping of Mycobacterium tuberculosis complex in Singapore, 2011–2017. Tuberculosis (Edinb) 2022; 134:102204. [DOI: 10.1016/j.tube.2022.102204] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2021] [Revised: 03/23/2022] [Accepted: 03/29/2022] [Indexed: 11/18/2022]
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21
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Kone B, Somboro AM, Kone M, Holl JL, Baya B, Dabitao D, Diallo D, Diarra B, Kone A, Sarro YDS, Sanogo M, Togo AC, Murphy RL, Diallo S, Coulibaly N, Camara F, Samake S, Diakite M, Doumbia S, Maiga M. Molecular epidemiology and genetic diversity of Mycobacterium tuberculosis complex in referral health centers of Bamako, Mali: What is new? Int J Infect Dis 2022; 117:204-211. [PMID: 35134562 PMCID: PMC9055845 DOI: 10.1016/j.ijid.2022.01.061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Revised: 01/22/2022] [Accepted: 01/27/2022] [Indexed: 11/29/2022] Open
Abstract
Background and Aims: Tuberculosis (TB) remains an important global health issue worldwide. Despite this scourge threatening many human lives, especially in developing countries, thus far, no advanced molecular epidemiology study using recent and more accurate tools has been conducted in Mali. Therefore, this study aimed to use variable-number tandem repeats of mycobacterial interspersed repetitive units (MIRU-VNTR) technology coupled with the spoligotyping method to accurately determine the hot spots and establish the epidemiological transmission links of TB in Bamako, Mali. Methods: In a cross-sectional study, 245 isolates of Mycobacterium tuberculosis complex (MTBC) were characterized using spoligotyping and MIRU-VNTR, and an epidemiological investigation was conducted. Results: Of the 245 isolates, 184 (75.1%) were formally identified. The most widespread strain was the Cameroon strain (83; 45.1%). Eight major clusters were identified: Ghana (27; 14.7%), West African 2 (22; 12%), Haarlem (13; 7.1%), H37Rv (t) (8; 4.3%), Latin American Mediterranean (8; 4.3%), and Uganda I and II (6; 3.3%). Statistical analysis showed a significant difference between lineages from the respective referral health centers of Bamako, Mali (P = 0.01). Conclusion: This study establishes, for the first time, an accurate spatial distribution of circulating MTB strains in Bamako, Mali. The data was used to identify strains and “hot spots” causing TB infection and can also be used for more targeted public health responses, particularly for hot spots of drug-resistant strains.
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Affiliation(s)
- Bourahima Kone
- University Clinical Research Center (UCRC) Laboratory, University of Sciences, Techniques and Technologies of Bamako (USTTB), Bamako, Mali.
| | - Anou M Somboro
- University Clinical Research Center (UCRC) Laboratory, University of Sciences, Techniques and Technologies of Bamako (USTTB), Bamako, Mali; School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Mahamadou Kone
- University Clinical Research Center (UCRC) Laboratory, University of Sciences, Techniques and Technologies of Bamako (USTTB), Bamako, Mali
| | - Jane L Holl
- Center for Healthcare Delivery Science and Innovation, University of Chicago, Chicago, Illinois, USA
| | - Bocar Baya
- University Clinical Research Center (UCRC) Laboratory, University of Sciences, Techniques and Technologies of Bamako (USTTB), Bamako, Mali
| | - Djeneba Dabitao
- University Clinical Research Center (UCRC) Laboratory, University of Sciences, Techniques and Technologies of Bamako (USTTB), Bamako, Mali
| | - Dramane Diallo
- University Clinical Research Center (UCRC) Laboratory, University of Sciences, Techniques and Technologies of Bamako (USTTB), Bamako, Mali
| | - Bassirou Diarra
- University Clinical Research Center (UCRC) Laboratory, University of Sciences, Techniques and Technologies of Bamako (USTTB), Bamako, Mali
| | - Amadou Kone
- University Clinical Research Center (UCRC) Laboratory, University of Sciences, Techniques and Technologies of Bamako (USTTB), Bamako, Mali
| | - Yeya Dit Sadio Sarro
- University Clinical Research Center (UCRC) Laboratory, University of Sciences, Techniques and Technologies of Bamako (USTTB), Bamako, Mali
| | - Moumine Sanogo
- University Clinical Research Center (UCRC) Laboratory, University of Sciences, Techniques and Technologies of Bamako (USTTB), Bamako, Mali
| | - Antieme Cg Togo
- University Clinical Research Center (UCRC) Laboratory, University of Sciences, Techniques and Technologies of Bamako (USTTB), Bamako, Mali
| | - Robert L Murphy
- Biomedical Engineering Department, Northwestern University, Evanston, Illinois, USA
| | - Souleymane Diallo
- University Clinical Research Center (UCRC) Laboratory, University of Sciences, Techniques and Technologies of Bamako (USTTB), Bamako, Mali
| | - Nadie Coulibaly
- University Clinical Research Center (UCRC) Laboratory, University of Sciences, Techniques and Technologies of Bamako (USTTB), Bamako, Mali
| | - Fatoumata Camara
- University Clinical Research Center (UCRC) Laboratory, University of Sciences, Techniques and Technologies of Bamako (USTTB), Bamako, Mali
| | - Seydou Samake
- University Clinical Research Center (UCRC) Laboratory, University of Sciences, Techniques and Technologies of Bamako (USTTB), Bamako, Mali
| | - Mahamadou Diakite
- University Clinical Research Center (UCRC) Laboratory, University of Sciences, Techniques and Technologies of Bamako (USTTB), Bamako, Mali
| | - Seydou Doumbia
- University Clinical Research Center (UCRC) Laboratory, University of Sciences, Techniques and Technologies of Bamako (USTTB), Bamako, Mali
| | - Mamoudou Maiga
- University Clinical Research Center (UCRC) Laboratory, University of Sciences, Techniques and Technologies of Bamako (USTTB), Bamako, Mali; Biomedical Engineering Department, Northwestern University, Evanston, Illinois, USA.
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22
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Micheni LN, Kassaza K, Kinyi H, Ntulume I, Bazira J. Detection of Mycobacterium tuberculosis multiple strains in sputum samples from patients with pulmonary tuberculosis in south western Uganda using MIRU-VNTR. Sci Rep 2022; 12:1656. [PMID: 35102181 PMCID: PMC8803872 DOI: 10.1038/s41598-022-05591-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2021] [Accepted: 01/11/2022] [Indexed: 11/25/2022] Open
Abstract
Infections with multiple strains of Mycobacterium tuberculosis are now widely recognized as a common occurrence. Identification of patients infected with multiple strains provides both insight into the disease dynamics and the epidemiology of tuberculosis. Analysis of Mycobacterial Interspersed Repetitive Unit-Variable-Number Tandem Repeats (MIRU-VNTR) has been shown to be highly sensitive in detecting multiple M. tuberculosis strains even in sputum. The goal of this study was to identify cases of multiple M. tuberculosis strain infections among patients diagnosed with pulmonary tuberculosis in Southwestern Uganda and assessment of factors associated with multiple strain infections. DNA extracted directly from 78 sputum samples, each from an individual patient, was analyzed using the standard 24 loci MIRU-VNTR typing. Five (6.4%) of the 78 patients were infected with multiple strains of M. tuberculosis with all of them being the newly diagnosed cases while two-thirds of them were co-infected with HIV. Exact regression analysis projected that the natives were more likely to harbor multiple strains (OR; 0.981, 95% CI 0–7.926) as well as those with a high microbial load (OR; 0.390, 95% CI 0–3.8167). Despite these findings being not statistically significant due to the small sample size, this points to a critical component of disease dynamics that has clinical implications and emphasizes a need for a study using a larger cohort. It is also essential to study the potential factors associated with higher risk of exposure to newly diagnosed and HIV positive patients at the community level. In addition, our ability to detect multiple M. tuberculosis strains using the standard 24 loci MIRU-VNTR typing especially with allelic diversity in loci 2059 and 3171, which are excluded from the 15-locus MIRU-VNTR, lead us to recommend the use of this genotyping technique, especially in areas with tuberculosis endemicity similar to this study.
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Affiliation(s)
- Lisa Nkatha Micheni
- Department of Microbiology, Mbarara University of Science and Technology, Box 1410, Mbarara, Uganda. .,Department of Microbiology and Immunology, Kampala International University Western Campus, Box 71, Bushenyi, Uganda.
| | - Kennedy Kassaza
- Department of Microbiology, Mbarara University of Science and Technology, Box 1410, Mbarara, Uganda
| | - Hellen Kinyi
- Department of Biochemistry, School of Medicine, Kabale University, Box 317, Kabale, Uganda
| | - Ibrahim Ntulume
- Department of Microbiology and Immunology, Kampala International University Western Campus, Box 71, Bushenyi, Uganda
| | - Joel Bazira
- Department of Microbiology, Mbarara University of Science and Technology, Box 1410, Mbarara, Uganda.
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23
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Guyeux C, Senelle G, Refrégier G, Bretelle-Establet F, Cambau E, Sola C. Connection between two historical tuberculosis outbreak sites in Japan, Honshu, by a new ancestral Mycobacterium tuberculosis L2 sublineage. Epidemiol Infect 2022; 150:1-25. [PMID: 35042579 PMCID: PMC8931808 DOI: 10.1017/s0950268822000048] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Revised: 12/24/2021] [Accepted: 01/03/2022] [Indexed: 11/07/2022] Open
Abstract
By gathering 680 publicly available Sequence Read Archives from isolates of Mycobacterium tuberculosis complex (MTBC) including 190 belonging to the lineage 2 Beijing , and using an in-house bioinformatical pipeline, the TB-Annotator , that analyses more than 50 000 characters, we describe herein a new L2 sublineage from 20 isolates found in the Tochigi province, (Japan), that we designate as asia ancestral 5 (AAnc5). These isolates harbour a number of specific criteria (42 SNPs) and their intra-cluster pairwise distance suggests historical and not epidemiological transmission. These isolates harbour a mutation in rpoC , and do not fulfil, any of the modern Beijing lineage criteria, nor any of the other ancestral Beijing lineages described so far. Asia ancestral 5 isolates do not possess mutT2 58 and ogt 12 characteristics of modern Beijing , but possess ancestral Beijing SNPs characteristics. By looking into the literature, we found a reference isolate ID381, described in Kobe and Osaka belonging to the ‘G3’ group, sharing 36 out of the 42 specific SNPs found in AAnc5. We also assessed the intermediate position of the asia ancestral 4 (AAnc4) sublineage recently described in Thailand and propose an improved classification of the L2 that now includes AAnc4 and AAnc5. By increasing the recruitment into TB-Annotator to around 3000 genomes (including 642 belonging to L2), we confirmed our results and discovered additional historical ancestral L2 branches that remain to be investigated in more detail. We also present, in addition, some anthropological and historical data from Chinese and Japan history of tuberculosis, as well as from Korea, that could support our results on L2 evolution. This study shows that the reconstruction of the early history of tuberculosis in Asia is likely to reveal complex patterns since its emergence.
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Affiliation(s)
- Christophe Guyeux
- DISC Computer Science Department, FEMTO-ST Institute, UMR 6174 CNRS, Univ. Bourgogne Franche-Comté (UBFC), 16 Route de Gray, 25000Besançon, France
| | - Gaetan Senelle
- DISC Computer Science Department, FEMTO-ST Institute, UMR 6174 CNRS, Univ. Bourgogne Franche-Comté (UBFC), 16 Route de Gray, 25000Besançon, France
| | - Guislaine Refrégier
- Université Paris-Saclay, Saint-Aubin, France
- Université Paris-Saclay, CNRS, AgroParisTech, UMR ESE, 91405, Orsay, France
| | | | - Emmanuelle Cambau
- Université de Paris, IAME, UMR1137, INSERM, Paris, France
- AP-HP, GHU Nord, service de mycobactériologie spécialisée et de référence, Laboratoire associé du Centre National de Référence des mycobactéries et résistance des mycobactéries aux antituberculeux (CNR-MyRMA), Paris, France
| | - Christophe Sola
- Université Paris-Saclay, Saint-Aubin, France
- Université de Paris, IAME, UMR1137, INSERM, Paris, France
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24
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Panaiotov S, Madzharov D, Hodzhev Y. Biodiversity of Mycobacterium tuberculosis in Bulgaria Related to Human Migrations or Ecological Adaptation. Microorganisms 2022; 10:microorganisms10010146. [PMID: 35056596 PMCID: PMC8778017 DOI: 10.3390/microorganisms10010146] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Revised: 01/04/2022] [Accepted: 01/06/2022] [Indexed: 01/27/2023] Open
Abstract
Bulgaria is among the 18 high-priority countries of the WHO European Region with high rates of tuberculosis. The causative agent of tuberculosis is thought to have emerged in Africa 70,000 years ago, or during the Neolithic age, and colonized the world through human migrations. The established main lineages of tuberculosis correlate highly with geography. The goal of our study was to investigate the biodiversity of Mycobacteriumtuberculosis in Bulgaria in association with human migration history during the last 10 centuries. We analyzed spoligotypes and MIRU-VNTR genotyping data of 655 drug-sensitive and 385 multidrug-resistant M. tuberculosis strains collected in Bulgaria from 2008 to 2018. We assigned the genotype of all isolates using SITVITWEB and MIRU-VNTRplus databases and software. We investigated the major well-documented historical events of immigration to Bulgaria that occurred during the last millennium. Genetic profiles demonstrated that, with the exceptions of 3 strains of Mycobacterium bovis and 18 strains of Lineage 2 (W/Beijing spoligotype), only Lineage 4 (Euro-American) was widely diffused in Bulgaria. Analysis of well-documented immigrations of Roma from the Indian subcontinent during the 10th to the 12th centuries, Turkic peoples from Central Asia in the medieval centuries, and more recently Armenians, Russians, and Africans in the 20th century influenced the biodiversity of M. tuberculosis in Bulgaria but only with genotypes of sublineages within the L4. We hypothesize that these sublineages were more virulent, or that ecological adaptation of imported M. tuberculosis genotypes was the main driver contributing to the current genetic biodiversity of M. tuberculosis in Bulgaria. We also hypothesize that some yet unknown local environmental factors may have been decisive in the success of imported genotypes. The ecological factors leading to local genetic biodiversity in M. tuberculosis are multifactorial and have not yet been fully clarified. The coevolution of long-lasting pathogen hosts should be studied, taking into account environmental and ecological changes.
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Affiliation(s)
- Stefan Panaiotov
- National Center of Infectious and Parasitic Diseases, 1504 Sofia, Bulgaria;
- Correspondence: ; Tel.: +359-887-720-061
| | | | - Yordan Hodzhev
- National Center of Infectious and Parasitic Diseases, 1504 Sofia, Bulgaria;
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25
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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] [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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María Irene CC, Juan Germán RC, Gamaliel LL, Dulce Adriana ME, Estela Isabel B, Brenda Nohemí M, Payan Jorge B, Zyanya Lucía ZB, Myriam BDV, Fernanda CG, Adrian OL, Martha Isabel M, Rogelio HP. Profiling the immune response to Mycobacterium tuberculosis Beijing family infection: a perspective from the transcriptome. Virulence 2021; 12:1689-1704. [PMID: 34228582 PMCID: PMC8265813 DOI: 10.1080/21505594.2021.1936432] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Revised: 03/24/2021] [Accepted: 05/14/2021] [Indexed: 01/15/2023] Open
Abstract
Tuberculosis continues to be an important public health problem. Particularly considering Beijing-family strains of Mycobacterium tuberculosis, which have been associated with drug-resistance and hypervirulence. The Beijing-like SIT190 (BL) is the most prevalent Beijing strain in Colombia. The pathogenic mechanism and immune response against this pathogen is unknown. Thus, we compared the course of pulmonary TB in BALB/c mice infected with Classical-Beijing strain 391 and BL strain 323. The disease course was different among infected animals with Classical-Beijing and BL strain. Mice infected with BL had a 100% mortality at 45 days post-infection (dpi), with high bacillary loads and massive pneumonia, whereas infected animals with Classical-Beijing survived until 60 dpi and showed extensive pneumonia and necrosis. Lung RNA extraction was carried out at early (day 3 dpi), intermediate (day 14 dpi), and late (days 28 and 60 dpi) time points of infection. Transcriptional analysis of infected mice with Classical-Beijing showed several over-expressed genes, associated with a pro-inflammatory profile, including those for coding for CCL3 and CCL4 chemokines, both biomarkers of disease severity. Conversely, mice infected with BL displayed a profile which included the over-expression of several genes associated with immune-suppression, including Nkiras, Dleu2, and Sphk2, highlighting an anti-inflammatory milieu which would allow high bacterial replication followed by an intense inflammatory response. In summary, both Beijing strains induced a non-protective immune response which induced extensive tissue damage, BL strain induced rapidly extensive pneumonia and death, whereas Classical-Beijing strain produced slower extensive pneumonia later associated with extensive necrosis.
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Affiliation(s)
- Cerezo-Cortés María Irene
- Universidad Nacional De Colombia, Facultad De Medicina, Departamento De Microbiología, Laboratorio De Micobacterias
| | | | - López-Leal Gamaliel
- Departamento De Microbiología Molecular, Instituto De Biotecnología, Universidad Nacional Autónoma De México, Avenida Universidad 2001, Colonia Chamilpa, Cuernavaca, Morelos, México
| | - Mata-Espinosa Dulce Adriana
- Sección De Patología Experimental, Departamento De Patología, Instituto Nacional De Ciencias Médicas Y Nutrición Salvador Zubirán, Ciudad De México, México
| | - Bini Estela Isabel
- Sección De Patología Experimental, Departamento De Patología, Instituto Nacional De Ciencias Médicas Y Nutrición Salvador Zubirán, Ciudad De México, México
| | - Marquina–Casitllo Brenda Nohemí
- Sección De Patología Experimental, Departamento De Patología, Instituto Nacional De Ciencias Médicas Y Nutrición Salvador Zubirán, Ciudad De México, México
| | - Barrios Payan Jorge
- Sección De Patología Experimental, Departamento De Patología, Instituto Nacional De Ciencias Médicas Y Nutrición Salvador Zubirán, Ciudad De México, México
| | - Zatarain-Barrón Zyanya Lucía
- Sección De Patología Experimental, Departamento De Patología, Instituto Nacional De Ciencias Médicas Y Nutrición Salvador Zubirán, Ciudad De México, México
| | - Bobadilla del Valle Myriam
- Departamento De Microbiología Clínica, Instituto Nacional De Ciencias Médicas Y Nutrición Salvador Zubirán Ciudad De México, México
| | - Cornejo-Granados Fernanda
- Departamento De Microbiología Molecular, Instituto De Biotecnología, Universidad Nacional Autónoma De México, Avenida Universidad 2001, Colonia Chamilpa, Cuernavaca, Morelos, México
| | - Ochoa-Leyva Adrian
- Departamento De Microbiología Molecular, Instituto De Biotecnología, Universidad Nacional Autónoma De México, Avenida Universidad 2001, Colonia Chamilpa, Cuernavaca, Morelos, México
| | - Murcia Martha Isabel
- Universidad Nacional De Colombia, Facultad De Medicina, Departamento De Microbiología, Laboratorio De Micobacterias
| | - Hernández-Pando Rogelio
- Sección De Patología Experimental, Departamento De Patología, Instituto Nacional De Ciencias Médicas Y Nutrición Salvador Zubirán, Ciudad De México, México
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Zenteno-Cuevas R, Munro-Rojas D, Pérez-Martínez D, Fernandez-Morales E, Jimenez-Ruano AC, Montero H, Escobar L, de Igartua E, Trigos Á, Fuentes-Dominguez J. Genetic diversity and drug susceptibility of Mycobacterium tuberculosis in a city with a high prevalence of drug resistant tuberculosis from Southeast of Mexico. BMC Infect Dis 2021; 21:1202. [PMID: 34847856 PMCID: PMC8630842 DOI: 10.1186/s12879-021-06904-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2021] [Accepted: 11/17/2021] [Indexed: 12/15/2022] Open
Abstract
Background Mexico is on the top five countries with the highest number of TB cases in America continent, nevertheless, information about genotypes circulating is practically unknown. Considering the above this study aims to characterize the genetic diversity of TB in the city of Veracruz, México. Methods A cross-sectional study was conducted among positive smear samples from patients living in Veracruz City, samples were cultured, and first-line drug profiles determined. Genotyping was made by spoligotyping and MIRU-VNTR 24 loci. Associations of lineages, clusters, and variables were also analyzed. Results Among the 202 isolates analyzed resistance to at least one drug was observed in 60 (30%) isolates and 41(20%) were multidrug-resistant. Three major lineages were identified: L4/Euro-American (88%), L1/Indo-Oceanic (9%), and L2/East Asian (3%). The Euro-American lineage included more than six sublineages, the most abundant were: H (32%), T (23%), LAM (18%), and X (12%). 140 isolates (70%) were placed in 42 SITs patterns. Conclusions These results provide the first baseline data on the genetic structure of TB in the city of Veracruz. Sublineages H, X and LAM were predominant; however, it was founded an important diversity of genotypes that could contribute to the dispersion of TB and explain the high prevalence. This information might be useful for the development of further interventions to reduce impact of TB. Supplementary Information The online version contains supplementary material available at 10.1186/s12879-021-06904-z.
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Affiliation(s)
- Roberto Zenteno-Cuevas
- Public Health Institute, University of Veracruz, Av. Luis Castelazo Ayala S/N, A.P. 57, Col. Industrial Ánimas, Xalapa, 91190, Veracruz, México. .,Multidisciplinary Research Network on Tuberculosis, Veracruz, Mexico.
| | | | - Damián Pérez-Martínez
- Public Health Institute, University of Veracruz, Av. Luis Castelazo Ayala S/N, A.P. 57, Col. Industrial Ánimas, Xalapa, 91190, Veracruz, México.,Doctorate in Health Sciences Program, Health Sciences Institute, University of Veracruz, Veracruz, Mexico
| | - Esdras Fernandez-Morales
- Public Health Institute, University of Veracruz, Av. Luis Castelazo Ayala S/N, A.P. 57, Col. Industrial Ánimas, Xalapa, 91190, Veracruz, México.,Master of Health Science Program, Health Sciences Institute, University of Veracruz, Xalapa, Veracruz, Mexico
| | - Ana C Jimenez-Ruano
- Master of Health Science Program, Health Sciences Institute, University of Veracruz, Xalapa, Veracruz, Mexico
| | - Hilda Montero
- Public Health Institute, University of Veracruz, Av. Luis Castelazo Ayala S/N, A.P. 57, Col. Industrial Ánimas, Xalapa, 91190, Veracruz, México
| | | | | | - Ángel Trigos
- Research Center in Applied Mycology, University of Veracruz, Xalapa, Veracruz, Mexico
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Genetic Diversity and Transmission of Multidrug Resistant Mycobacterium tuberculosis strains in Lusaka, Zambia. Int J Infect Dis 2021; 114:142-150. [PMID: 34718155 DOI: 10.1016/j.ijid.2021.10.044] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2021] [Revised: 10/15/2021] [Accepted: 10/19/2021] [Indexed: 11/20/2022] Open
Abstract
OBJECTIVE Zambia is among the 30 high tuberculosis burden countries in the world. Despite increasing reports of multidrug resistant tuberculosis (MDR-TB) in routine surveillance, information on the transmission of MDR Mycobacterium tuberculosis strains is largely unknown. This study elucidated genetic diversity and transmission of MDR M. tuberculosis strains in Lusaka, Zambia. METHODS Eighty-five MDR M. tuberculosis samples collected from the year 2013 to 2017 at the University Teaching Hospital were used. Drug-resistance associated gene sequencing, spoligotyping, 24-loci mycobacterial interspersed repetitive units-variable number of tandem repeats, and multiplex PCR for RD-Rio sub-lineage identification were applied. RESULTS Clades identified were LAM (48%), CAS (29%), T (14%), X (6%) and Harlem (2%). Strains belonging to SITs 21/CAS1-Kili and 20/LAM1 formed the largest clonal complexes. Combined spoligotyping and 24 loci-MIRU-VNTR revealed 47 genotypic patterns with clustering rate of 63%. Ninety five percent of LAM strains belonged to RD-Rio sub-lineage. CONCLUSION The high clustering rate suggested that a large proportion of MDR-TB was due to recent transmission rather than independent acquisition of MDR. This spread was attributed to clonal expansion of SIT21/CAS1-Kili and SIT20/LAM1 strains. Therefore, TB control programs recommending genotyping coupled with conventional epidemiological methods can guide measures for stopping the spread of MDR-TB.
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Ushtanit A, Mikhailova Y, Lyubimova A, Makarova M, Safonova S, Filippov A, Borisov S, Zimenkov D. Genetic Profile of Linezolid-Resistant M. tuberculosis Clinical Strains from Moscow. Antibiotics (Basel) 2021; 10:antibiotics10101243. [PMID: 34680823 PMCID: PMC8532644 DOI: 10.3390/antibiotics10101243] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Revised: 10/06/2021] [Accepted: 10/11/2021] [Indexed: 01/04/2023] Open
Abstract
Background: Linezolid, bedaquiline, and newer fluoroquinolones are currently placed as priority Group A drugs for the treatment of drug-resistant tuberculosis. The number of reported linezolid-resistant clinical strains is still low, and the correlation of molecular determinants with phenotype is not perfect. Methods: We determined the linezolid MICs for clinical isolates from the Moscow region and identified mutations in rplC and rrl genes. Results: All 16 linezolid-resistant isolates had previously reported mutations in the rplC or rrl loci, and 13 of them bore a RplC C154R substitution. Detection of this substitution in a heteroresistant state was not successful, probably, due to the more stable DNA secondary structure of the mutated fragment, which precludes its amplification in mixes with the wild-type DNA. Strains with an rplC mutation had higher linezolid MIC compared to isolates with rrl mutations. Conclusions: Linezolid resistance mostly emerged during treatment with the latest regimen. Three primary cases with linezolid resistance question the possible transmission of totally drug-resistant tuberculosis in the Moscow region, which demands further investigation.
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Affiliation(s)
- Anastasia Ushtanit
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia; (A.U.); (A.L.)
| | - Yulia Mikhailova
- The Moscow Research and Clinical Center for Tuberculosis Control, Moscow Government Health Department, 107014 Moscow, Russia; (Y.M.); (M.M.); (S.S.); (A.F.); (S.B.)
| | - Alexandra Lyubimova
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia; (A.U.); (A.L.)
| | - Marina Makarova
- The Moscow Research and Clinical Center for Tuberculosis Control, Moscow Government Health Department, 107014 Moscow, Russia; (Y.M.); (M.M.); (S.S.); (A.F.); (S.B.)
| | - Svetlana Safonova
- The Moscow Research and Clinical Center for Tuberculosis Control, Moscow Government Health Department, 107014 Moscow, Russia; (Y.M.); (M.M.); (S.S.); (A.F.); (S.B.)
| | - Alexey Filippov
- The Moscow Research and Clinical Center for Tuberculosis Control, Moscow Government Health Department, 107014 Moscow, Russia; (Y.M.); (M.M.); (S.S.); (A.F.); (S.B.)
| | - Sergey Borisov
- The Moscow Research and Clinical Center for Tuberculosis Control, Moscow Government Health Department, 107014 Moscow, Russia; (Y.M.); (M.M.); (S.S.); (A.F.); (S.B.)
| | - Danila Zimenkov
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia; (A.U.); (A.L.)
- Correspondence:
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Diriba G, Kebede A, Tola HH, Alemu A, Yenew B, Moga S, Addise D, Mohammed Z, Getahun M, Fantahun M, Tadesse M, Dagne B, Amare M, Assefa G, Abera D, Desta K. Mycobacterial Lineages Associated with Drug Resistance in Patients with Extrapulmonary Tuberculosis in Addis Ababa, Ethiopia. Tuberc Res Treat 2021; 2021:5239529. [PMID: 34589236 PMCID: PMC8476284 DOI: 10.1155/2021/5239529] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2021] [Accepted: 08/31/2021] [Indexed: 11/21/2022] Open
Abstract
BACKGROUND In Ethiopia, tuberculosis (TB) is one of the most common causes of illness and death. However, there is limited information available on lineages associated with drug resistance among extrapulmonary tuberculosis patients in Ethiopia. In this study, researchers looked into Mycobacterium tuberculosis lineages linked to drug resistance in patients with extrapulmonary tuberculosis in Addis Ababa, Ethiopia. METHODS On 151 Mycobacterium tuberculosis isolates, a cross-sectional analysis was performed. Spoligotyping was used to characterize mycobacterial lineages, while a phenotypic drug susceptibility test was performed to determine the drug resistance pattern. Data were analyzed using SPSS version 23. RESULTS Among 151 Mycobacterium tuberculosis complex (MTBC) genotyped isolates, four lineages (L1-L4), and Mycobacterium bovis were identified. The predominantly identified lineage was Euro-American (73.5%) followed by East-African-Indian (19.2%). Any drug resistance (RR) and multidrug-resistant (MDR) tuberculosis was identified among 16.2% and 7.2% of the Euro-American lineage, respectively, while it was 30.8% and 15.4% among the East-African-Indian lineages. Among all three preextensively drug-resistance (pre-XDR) cases identified, two isolates belong to T3-ETH, and the other one strain was not defined by the database. There was no statistically significant association between any type of drug resistance and either lineage or sublineages of Mycobacterium tuberculosis. CONCLUSION A higher proportion of any type of drug resistance and MDR was detected among the East-African-Indian lineage compared to others. However, there was no statistically significant association between any type of drug resistance and either lineages or sublineages. Thus, the authors recommend a large-scale study.
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Affiliation(s)
- Getu Diriba
- Ethiopian Public Health Institute, Addis Ababa, Ethiopia
- Department of Medical Laboratory Sciences, College of Health Sciences, Addis Ababa University, Addis Ababa, Ethiopia
| | - Abebaw Kebede
- Ethiopian Public Health Institute, Addis Ababa, Ethiopia
- Department of Microbial, Cellular and Molecular Biology, College of Natural and Computational Sciences, Addis Ababa University, Addis Ababa, Ethiopia
| | | | - Ayinalem Alemu
- Ethiopian Public Health Institute, Addis Ababa, Ethiopia
| | - Bazezew Yenew
- Ethiopian Public Health Institute, Addis Ababa, Ethiopia
| | - Shewki Moga
- Ethiopian Public Health Institute, Addis Ababa, Ethiopia
| | | | | | | | - Mengistu Fantahun
- St. Paul's Hospital Millennium Medical College, Addis Ababa, Ethiopia
| | | | - Biniyam Dagne
- Ethiopian Public Health Institute, Addis Ababa, Ethiopia
| | - Misikir Amare
- Ethiopian Public Health Institute, Addis Ababa, Ethiopia
| | | | - Dessie Abera
- Department of Medical Laboratory Sciences, College of Health Sciences, Addis Ababa University, Addis Ababa, Ethiopia
| | - Kassu Desta
- Department of Medical Laboratory Sciences, College of Health Sciences, Addis Ababa University, Addis Ababa, Ethiopia
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Fitzgibbon MM, Roycroft E, Sheehan G, Mc Laughlin AM, Quintyne KI, Brabazon E, O'Meara M, Flanagan PR, Seagar AL, Laurenson IF, Keane J, Rogers TR. False detection of rifampicin resistance using Xpert ® MTB/RIF Ultra assay due to an A451V mutation in Mycobacterium tuberculosis. JAC Antimicrob Resist 2021; 3:dlab101. [PMID: 34386770 PMCID: PMC8355037 DOI: 10.1093/jacamr/dlab101] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Accepted: 06/22/2021] [Indexed: 11/16/2022] Open
Abstract
Background In a 12 month period, three Irish-born adult cases with pulmonary TB were initially diagnosed by Xpert® MTB/RIF Ultra assay, which detected a rifampicin resistance-conferring mutation prompting treatment as potential MDR cases. Methods Further laboratory investigations on the cultured isolates included GenoType MTBDRplus assay, phenotypic drug susceptibility tests using the BD BACTEC MGIT culture system and MIC broth microdilution tests. Sequencing of the rpoB gene was performed using Sanger sequencing and WGS. Results Phenotypic drug susceptibility tests determined the isolates to be rifampicin susceptible. Molecular investigations identified an A451V (codon 532) mutation in the Mycobacterium tuberculosis rpoB gene that has not previously been found to cause rifampicin resistance. Genome sequencing revealed that the three isolates’ genomes differed by ≤5 SNPs, indicating a high likelihood of recent transmission events. Furthermore, a cluster of six related M. tuberculosis isolates from our in-house typing database showed four were highly related; all were rifampicin susceptible and lacked this mutation. Conclusions False detection of rifampicin resistance, albeit rare, should be considered possible with Xpert® MTB/RIF Ultra assay, particularly in low TB incidence settings. Confirmatory sequencing methods should be performed to prevent the unnecessary use of second-line anti-tuberculous drugs.
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Affiliation(s)
| | - Emma Roycroft
- Irish Mycobacteria Reference Laboratory, St James's Hospital, Dublin, Ireland
| | - Gerard Sheehan
- Mater Misericordiae University Hospital, Dublin, Ireland
| | | | | | | | - Mary O'Meara
- Department of Public Health East, Health Service Executive, Dublin, Ireland
| | - Peter R Flanagan
- Irish Mycobacteria Reference Laboratory, St James's Hospital, Dublin, Ireland
| | - A-Louise Seagar
- Scottish Mycobacteria Reference Laboratory, Edinburgh, Scotland
| | - Ian F Laurenson
- Scottish Mycobacteria Reference Laboratory, Edinburgh, Scotland
| | - Joseph Keane
- Department of Respiratory Medicine, St James's Hospital, Dublin, Ireland
| | - Thomas R Rogers
- Irish Mycobacteria Reference Laboratory, St James's Hospital, Dublin, Ireland
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Ghielmetti G, Kupca AM, Hanczaruk M, Friedel U, Weinberger H, Revilla-Fernández S, Hofer E, Riehm JM, Stephan R, Glawischnig W. Mycobacterium microti Infections in Free-Ranging Red Deer ( Cervus elaphus). Emerg Infect Dis 2021. [DOI: 10.3201/eid27.210634] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
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Ghielmetti G, Kupca AM, Hanczaruk M, Friedel U, Weinberger H, Revilla-Fernández S, Hofer E, Riehm JM, Stephan R, Glawischnig W. Mycobacterium microti Infections in Free-Ranging Red Deer (Cervus elaphus). Emerg Infect Dis 2021; 27:2025-2032. [PMID: 34286688 PMCID: PMC8314804 DOI: 10.3201/eid2708.210634] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Infections with Mycobacterium microti, a member of the M. tuberculosis complex, have been increasingly reported in humans and in domestic and free-ranging wild animals. At postmortem examination, infected animals may display histopathologic lesions indistinguishable from those caused by M. bovis or M. caprae, potentially leading to misidentification of bovine tuberculosis. We report 3 cases of M. microti infections in free-ranging red deer (Cervus elaphus) from western Austria and southern Germany. One diseased animal displayed severe pyogranulomatous pleuropneumonia and multifocal granulomas on the surface of the pericardium. Two other animals showed alterations of the lungs and associated lymph nodes compatible with parasitic infestation. Results of the phylogenetic analysis including multiple animal strains from the study area showed independent infection events, but no host-adapted genotype. Personnel involved in bovine tuberculosis–monitoring programs should be aware of the fastidious nature of M. microti, its pathogenicity in wildlife, and zoonotic potential.
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Papaventsis D, Dougas G, Kalkouni O, Karabela S, Manika K. Occupational Exposure to Zoonotic Tuberculosis Caused by Mycobacterium caprae, Northern Greece, 2019. Emerg Infect Dis 2021; 27:1997-1999. [PMID: 34152976 PMCID: PMC8237881 DOI: 10.3201/eid2707.204399] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Pulmonary tuberculosis caused by Mycobacterium caprae was diagnosed in a 65-year-old goat breeder from northern Greece. This case represents a documented occupational transmission of M. caprae and highlights the importance of enhanced laboratory screening and increased surveillance for zoonotic tuberculosis control.
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Tafess K, Beyen TK, Girma S, Girma A, Siu G. Spatial clustering and genetic diversity of Mycobacterium tuberculosis isolate among pulmonary tuberculosis suspected patients, Arsi Zone, Ethiopia. BMC Pulm Med 2021; 21:206. [PMID: 34193091 PMCID: PMC8244181 DOI: 10.1186/s12890-021-01567-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2020] [Accepted: 06/10/2021] [Indexed: 11/20/2022] Open
Abstract
BACKGROUND Tuberculosis remains a serious public health concern globally. The enormous social, economic, and health impacts of the diseases are attributed to the lack of updated data on the prevalence, geospatial distribution, population structures, and genotypic variants of the circulating M. tuberculosis. METHODS Structured questionnaire, mycobacterial culture, and standard 24-Mycobacterial Interspersed Repeated Units-Variable Number Tandem Repeats (MIRU-VNTR) were employed to collect sociodemographic characters, residence linked information, and genotype the isolates. The retrospective discrete Bernoulli model was used to identify the hot spot districts of sputum smear positivity, and Web-based Miru-VNTRPlus were used for the identification of lineages and sublineages. RESULTS Out of 832 presumptive pulmonary tuberculosis (PTB) suspects, 119 (14.3%) were smear-positive. In the multivariate binary logistic model, PTB suspected patients in the age groups of 7-25 and 25-34 and those from rural residents were 4.53 (AOR = 4.53; 95% CI 2.25-9.13), 3.00 (AOR = 3.00; 95% CI 1.41-6.35) and 1.65 (AOR = 1.65; 95% CI 1.01-2.70) times at higher risk of turning smear-positive. Eleven (47.8%) districts of Arsi Zone were shown to have a high rate of clustering (RR = 2.27; 95% CI 1.62-3.2) of smear-positive PTB. Of 72 isolates queried for the lineage assignment, 59 (81.9%) were classified into the previously known lineages and 13 (18.1%) were not assigned to any known lineages. Overall, 42 (58.3%) belong to M. tuberculosis lineage 4 (Euro-American), 16 (22.2%) M. tuberculosis lineage 3 (Delhi/CAS), and 1 (1.4%) M. tuberculosis Lineage 1 (Indo-Oceanic/ East Africa Indian). Further classification to the sublineage indicates that the predominant lineage was Delhi/CAS comprising 16 (22.2%) isolates followed by 15 (20.8%) isolates belonging to Haarlem. The remaining isolates were distributed as 13 (18.1%) TUR, 6 (8.3%) LAM, 4 (5.5%) URAL, 4 (4.5%) NEW-1 and 1 (1.4%) EAI. CONCLUSION Our study showed higher smear-positive results among PTB suspected patients and remarkable spatial variation across districts of Arsi Zone in smear-positive PTB. This information together with the genotypic features could be used as input for the efforts of designing control strategies.
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Affiliation(s)
- Ketema Tafess
- Institute of Pharmaceutical Science, School of Applied Natural Science, Adama Science and Technology University, Adama, Ethiopia
| | - Teresa Kisi Beyen
- Department of Public Health, College of Health Sciences, Arsi University, Asella, Ethiopia
| | - Sisay Girma
- Department of Clinical Study, College of Veterinary Medicine and Agriculture, Addis Ababa University, P. O. Box 34, Bishoftu, Ethiopia
| | - Asnakech Girma
- Disease Prevention, Training and Research Division, Federal Prison General Hospital, Addis Ababa, Ethiopia
| | - Gilman Siu
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hung Hom, Hong Kong
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A Novel Presentation of Tuberculosis with Intestinal Perforation in a Free-Ranging Australian Sea Lion (Neophoca cinerea). J Wildl Dis 2021; 57:220-224. [PMID: 33635989 DOI: 10.7589/jwd-d-20-00104] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Accepted: 07/30/2020] [Indexed: 11/20/2022]
Abstract
We detail a novel presentation of tuberculosis associated with intestinal perforation in an endangered Australian sea lion (Neophoca cinerea) from South Australian waters and confirm the presence of this disease in the region of highest pup production. In February 2017, a 3-yr-old juvenile male died shortly after hauling out at the Kingscote beach on Kangaroo Island. On postmortem examination, we found a mid-jejunal intestinal perforation and partial obstruction (from a strangulating fibrous and granulomatous mesenteric mass), a marked multicentric abdominal fibrosing granulomatous lymphadenitis, and a large volume serosanguinous peritoneal effusion. Acid-fast bacteria were detected postmortem in cytologic preparations of the mesenteric lymph node and in histologic sections of jejunum and the encircling mass. Mycobacterial infection was confirmed by positive culture after 3 wk. Molecular typing using mycobacterial interspersed repetitive-unit-variable-number tandem-repeat typing with 12-locus analysis identified Mycobacterium pinnipedii. This case highlights the need for vigilance of zoonotic disease risk when handling pinnipeds, including in the absence of specific respiratory signs or grossly apparent pulmonary pathology. Increased serologic population surveillance is recommended to assess the species' risk from this and other endemic diseases, especially given its endangered status.
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Koshi K, Noda M, Kadokura Y, Kameyama Y. Typing of Mycobacterium tuberculosis Strains in Gifu Prefecture, Japan, Using Variable Number Tandem Repeat Analysis. Jpn J Infect Dis 2021; 74:587-591. [PMID: 33952767 DOI: 10.7883/yoken.jjid.2020.1060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
To investigate the molecular epidemiological characteristics of Mycobacterium tuberculosis strains collected in Gifu Prefecture, Japan, 483 M. tuberculosis clinical isolates were used for Japan Anti-Tuberculosis Association (JATA) 18-variable number tandem repeats (VNTR) analysis during 2015-2019. To estimate the lineages of M. tuberculosis strains, JATA18-VNTR profiles were applied to a maximum a posteriori method. The results revealed that the ancient Beijing subfamily, accounting for 57.3% (277/483) was the most prevalent M. tuberculosis strain. Furthermore, 18 clusters (GC-1-GC-18) were found by minimum spanning tree analysis. The proportion of clustering strains was 9.9% (48/483), and epidemiological links to these clusters were unclear without GC-6 and GC-18. Meanwhile, interestingly, VNTR profiles of GC-7-GC-9 and GC-14 were indistinguishable from the regional epidemic strains of Nagoya City, which has a strong socioeconomic relationship with Gifu Prefecture, but did not match the nationwide epidemic strains. This study suggests that coordinated analyses within prefectures with strong socioeconomic relationships are important.
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Affiliation(s)
- Katsuo Koshi
- Department of Infectious Disease, Gifu Prefectural Research Institute for Health and Environmental Sciences, Japan
| | - Makiko Noda
- Department of Infectious Disease, Gifu Prefectural Research Institute for Health and Environmental Sciences, Japan
| | - Yukiko Kadokura
- Department of Infectious Disease, Gifu Prefectural Research Institute for Health and Environmental Sciences, Japan
| | - Yoshihiko Kameyama
- Department of Infectious Disease, Gifu Prefectural Research Institute for Health and Environmental Sciences, Japan
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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] [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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Devi KR, Pradhan J, Bhutia R, Dadul P, Sarkar A, Gohain N, Narain K. Molecular diversity of Mycobacterium tuberculosis complex in Sikkim, India and prediction of dominant spoligotypes using artificial intelligence. Sci Rep 2021; 11:7365. [PMID: 33795751 PMCID: PMC8016865 DOI: 10.1038/s41598-021-86626-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2020] [Accepted: 03/12/2021] [Indexed: 02/06/2023] Open
Abstract
In India, tuberculosis is an enormous public health problem. This study provides the first description of molecular diversity of the Mycobacterium tuberculosis complex (MTBC) from Sikkim, India. A total of 399 Acid Fast Bacilli sputum positive samples were cultured on Lőwenstein-Jensen media and genetic characterisation was done by spoligotyping and 24-loci MIRU-VNTR typing. Spoligotyping revealed the occurrence of 58 different spoligotypes. Beijing spoligotype was the most dominant type constituting 62.41% of the total isolates and was associated with Multiple Drug Resistance. Minimum Spanning tree analysis of 249 Beijing strains based on 24-loci MIRU-VNTR analysis identified 12 clonal complexes (Single Locus Variants). The principal component analysis was used to visualise possible grouping of MTBC isolates from Sikkim belonging to major spoligotypes using 24-MIRU VNTR profiles. Artificial intelligence-based machine learning (ML) methods such as Random Forests (RF), Support Vector Machines (SVM) and Artificial Neural Networks (ANN) were used to predict dominant spoligotypes of MTBC using MIRU-VNTR data. K-fold cross-validation and validation using unseen testing data set revealed high accuracy of ANN, RF, and SVM for predicting Beijing, CAS1_Delhi, and T1 Spoligotypes (93-99%). However, prediction using the external new validation data set revealed that the RF model was more accurate than SVM and ANN.
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Affiliation(s)
- Kangjam Rekha Devi
- grid.420069.90000 0004 1803 0080N.E. Region, Indian Council of Medical Research (ICMR)-Regional Medical Research Centre, Post Box #105, Dibrugarh, Assam 786 001 India
| | - Jagat Pradhan
- National Tuberculosis Elimination Programme (NTEP), Gangtok, Sikkim India
| | - Rinchenla Bhutia
- National Tuberculosis Elimination Programme (NTEP), Gangtok, Sikkim India
| | - Peggy Dadul
- Department of Health Care, Human Services and Family Welfare, State Tuberculosis Control Society, Gangtok, Sikkim India
| | - Atanu Sarkar
- grid.420069.90000 0004 1803 0080N.E. Region, Indian Council of Medical Research (ICMR)-Regional Medical Research Centre, Post Box #105, Dibrugarh, Assam 786 001 India
| | - Nitumoni Gohain
- grid.420069.90000 0004 1803 0080N.E. Region, Indian Council of Medical Research (ICMR)-Regional Medical Research Centre, Post Box #105, Dibrugarh, Assam 786 001 India
| | - Kanwar Narain
- grid.420069.90000 0004 1803 0080N.E. Region, Indian Council of Medical Research (ICMR)-Regional Medical Research Centre, Post Box #105, Dibrugarh, Assam 786 001 India
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Cheng S, Hide M, Pheng SH, Kerléguer A, Delvallez G, Sam S, Mao TE, Nguyen TVA, Bañuls AL. Resistance to Second-Line Anti-TB Drugs in Cambodia: A Phenotypic and Genetic Study. Infect Drug Resist 2021; 14:1089-1104. [PMID: 33762833 PMCID: PMC7982564 DOI: 10.2147/idr.s289907] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Accepted: 01/06/2021] [Indexed: 12/25/2022] Open
Abstract
Background Due to the emergence of Mycobacterium tuberculosis (M.tb) clinical isolates resistant to most potent first-line drugs (FLD), second-line drugs (SLD) are being prescribed more frequently. We explore the genetic characteristics and molecular mechanisms of M.tb isolates phenotypically resistant to SLD, including pre-extensively drug-resistant (pre-XDR) and extensively drug-resistant (XDR) isolates. Methods Drug-resistant (DR) M.tb isolates collected from 2012 to 2017 were tested using sequencing and phenotypic drug susceptibility testing. Genotypes were determined to explore their links with SLD resistance patterns. Results Of the 272 DR M.tb isolates, 6 non-multidrug resistant (non-MDR) isolates were fluoroquinolones (FQ)-resistant, 3 were XDR and 16 were pre-XDR (14 resistant to FQ and 2 to second-line injectable drugs). The most frequent mutations in FQ-resistant and second-line injectable drugs resistant isolates were gyrA D94G (15/23) and rrs a1401g (3/5), respectively. Seventy-five percent of pre-XDR isolates and 100% of XDR isolates harbored mutations conferring resistance to pyrazinamide. All XDR isolates belonged to the Beijing genotype, of which one, named XDR+, was resistant to all drugs tested. One cluster including pre-XDR and XDR isolates was observed. Conclusion This is the first description of SLD resistance in Cambodia. The data suggest that the proportion of XDR and pre-XDR isolates remains low but is on the rise compared to previous reports. The characterization of the XDR+ isolate in a patient who refused treatment underlines the risk of transmission in the population. In addition, genotypic results show, as expected, that the Beijing family is the main involved in pre-XDR and XDR isolates and that the spread of the Beijing pre-XDR strain is capable of evolving into XDR strain. This study strongly indicates the need for rapid interventions in terms of diagnostic and treatment to prevent the spread of the pre-XDR and XDR strains and the emergence of more resistant ones.
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Affiliation(s)
- Sokleaph Cheng
- Institut Pasteur du Cambodge and Ministry of Health, Phnom Penh, Cambodia.,Medical Biology Laboratory, Institut Pasteur du Cambodge, Phnom Penh, Cambodia.,LMI Drug Resistance in South East Asia, Institut Pasteur du Cambodge, Phnom Penh, Cambodia
| | - Mallorie Hide
- LMI Drug Resistance in South East Asia, Institut Pasteur du Cambodge, Phnom Penh, Cambodia.,MIVEGEC, University of Montpellier, Institute of Research for Development, Centre National de la Recherche Scientifique, Montpellier, France.,CREES (Centre de Recherche En Écologie Et Évolution de la Santé), Montpellier, France
| | - Sok Heng Pheng
- National Center for Tuberculosis and Leprosy Control, Phnom Penh, Cambodia
| | - Alexandra Kerléguer
- Medical Biology Laboratory, Institut Pasteur du Cambodge, Phnom Penh, Cambodia
| | - Gauthier Delvallez
- Medical Biology Laboratory, Institut Pasteur du Cambodge, Phnom Penh, Cambodia
| | - Sophan Sam
- Cambodian Health Committee, Phnom Penh, Cambodia
| | - Tan Eang Mao
- National Center for Tuberculosis and Leprosy Control, Phnom Penh, Cambodia
| | - Thi Van Anh Nguyen
- LMI Drug Resistance in South East Asia, Institut Pasteur du Cambodge, Phnom Penh, Cambodia.,Department of Bacteriology, National Institute of Hygiene and Epidemiology, Hanoi, Martinique, Vietnam
| | - Anne-Laure Bañuls
- LMI Drug Resistance in South East Asia, Institut Pasteur du Cambodge, Phnom Penh, Cambodia.,MIVEGEC, University of Montpellier, Institute of Research for Development, Centre National de la Recherche Scientifique, Montpellier, France.,CREES (Centre de Recherche En Écologie Et Évolution de la Santé), Montpellier, France
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41
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Huang CC, Chu AL, Becerra MC, Galea JT, Calderón R, Contreras C, Yataco R, Zhang Z, Lecca L, Murray MB. Mycobacterium tuberculosis Beijing Lineage and Risk for Tuberculosis in Child Household Contacts, Peru. Emerg Infect Dis 2021; 26:568-578. [PMID: 32091363 PMCID: PMC7045848 DOI: 10.3201/eid2603.191314] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Few studies have prospectively compared the relative transmissibility and propensity to cause disease of Mycobacterium tuberculosis Beijing strains with other human-adapted strains of the M. tuberculosis complex. We assessed the effect of Beijing strains on the risk for M. tuberculosis infection and disease progression in 9,151 household contacts of 2,223 culture-positive pulmonary tuberculosis (TB) patients in Lima, Peru. Child contacts exposed to Beijing strains were more likely than child contacts exposed to non-Beijing strains to be infected at baseline, by 12 months of follow-up, and during follow-up. We noted an increased but nonsignificant tendency for child contacts to develop TB. Beijing strains were not associated with TB in adult contacts. These findings suggest that Beijing strains are more transmissible in children than are non-Beijing strains.
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Conceição EC, Salvato RS, Gomes KM, Guimarães AEDS, da Conceição ML, Souza e Guimarães RJDP, Sharma A, Furlaneto IP, Barcellos RB, Bollela VR, Anselmo LMP, Sisco MC, Niero CV, Ferrazoli L, Refrégier G, Lourenço MCDS, Gomes HM, de Brito AC, Catanho M, Duarte RS, Suffys PN, Lima KVB. Molecular epidemiology of Mycobacterium tuberculosis in Brazil before the whole genome sequencing era: a literature review. Mem Inst Oswaldo Cruz 2021; 116:e200517. [PMID: 33729319 PMCID: PMC7976556 DOI: 10.1590/0074-02760200517] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Accepted: 02/11/2021] [Indexed: 11/22/2022] Open
Abstract
Molecular-typing can help in unraveling epidemiological scenarios and improvement for disease control strategies. A literature review of Mycobacterium tuberculosis transmission in Brazil through genotyping on 56 studies published from 1996-2019 was performed. The clustering rate for mycobacterial interspersed repetitive units - variable tandem repeats (MIRU-VNTR) of 1,613 isolates were: 73%, 33% and 28% based on 12, 15 and 24-loci, respectively; while for RFLP-IS6110 were: 84% among prison population in Rio de Janeiro, 69% among multidrug-resistant isolates in Rio Grande do Sul, and 56.2% in general population in São Paulo. These findings could improve tuberculosis (TB) surveillance and set up a solid basis to build a database of Mycobacterium genomes.
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Affiliation(s)
- Emilyn Costa Conceição
- Fundação Oswaldo Cruz-Fiocruz, Instituto Nacional de Infectologia
Evandro Chagas, Programa de Pós-Graduação em Pesquisa Clínica e Doenças Infecciosas,
Rio de Janeiro, RJ, Brasil
- Fundação Oswaldo Cruz-Fiocruz, Instituto Nacional de Infectologia
Evandro Chagas, Laboratório de Bacteriologia e Bioensaios em Micobactérias, Rio de
Janeiro, RJ, Brasil
- Fundação Oswaldo Cruz-Fiocruz, Instituto Oswaldo Cruz, Laboratório
de Biologia Molecular Aplicada a Micobactérias, Rio de Janeiro, RJ, Brasil
| | - Richard Steiner Salvato
- Universidade Federal do Rio Grande do Sul, Programa de Pós-Graduação
em Biologia Celular e Molecular, Porto Alegre, RS, Brasil
- Secretaria Estadual de Saúde do Rio Grande do Sul, Centro Estadual
de Vigilância em Saúde, Centro de Desenvolvimento Científico e Tecnológico, Porto
Alegre, RS, Brasil
| | - Karen Machado Gomes
- Fundação Oswaldo Cruz-Fiocruz, Escola Nacional de Saúde Pública
Sergio Arouca, Centro de Referência Professor Hélio Fraga, Laboratório de Referência
Nacional para Tuberculose e outras Micobacterioses, Rio de Janeiro, RJ, Brasil
| | - Arthur Emil dos Santos Guimarães
- Universidade do Estado do Pará, Instituto de Ciências Biológicas e
da Saúde, Pós-Graduação Biologia Parasitária na Amazônia, Belém, PA, Brasil
- Instituto Evandro Chagas, Seção de Bacteriologia e Micologia,
Ananindeua, PA, Brasil
| | - Marília Lima da Conceição
- Universidade do Estado do Pará, Instituto de Ciências Biológicas e
da Saúde, Pós-Graduação Biologia Parasitária na Amazônia, Belém, PA, Brasil
- Instituto Evandro Chagas, Seção de Bacteriologia e Micologia,
Ananindeua, PA, Brasil
| | | | - Abhinav Sharma
- International Institute of Information Technology, Department of
Data Science, Bangalore, India
| | | | - Regina Bones Barcellos
- Secretaria Estadual de Saúde do Rio Grande do Sul, Centro Estadual
de Vigilância em Saúde, Centro de Desenvolvimento Científico e Tecnológico, Porto
Alegre, RS, Brasil
| | - Valdes Roberto Bollela
- Universidade de São Paulo, Departamento de Clínica Médica da
Faculdade de Medicina de Ribeirão Preto, Ribeirão Preto, SP, Brasil
| | - Lívia Maria Pala Anselmo
- Universidade de São Paulo, Departamento de Clínica Médica da
Faculdade de Medicina de Ribeirão Preto, Ribeirão Preto, SP, Brasil
| | - Maria Carolina Sisco
- Fundação Oswaldo Cruz-Fiocruz, Instituto Oswaldo Cruz, Laboratório
de Biologia Molecular Aplicada a Micobactérias, Rio de Janeiro, RJ, Brasil
- Universidade Federal do Rio de Janeiro, Instituto de Microbiologia
Paulo de Góes, Laboratório de Micobactérias, Rio de Janeiro, RJ, Brasil
| | - Cristina Viana Niero
- Universidade Federal de São Paulo, Departamento de Microbiologia,
Imunologia e Parasitologia, São Paulo, SP, Brasil
| | - Lucilaine Ferrazoli
- Instituto Adolfo Lutz, Centro de Bacteriologia, Núcleo de
Tuberculose e Micobacterioses, São Paulo, SP, Brasil
| | - Guislaine Refrégier
- Universit e Paris-Saclay, Ecologie Systematique Evolution, Centre
National de la Recherche Scientifique, AgroParisTech, Orsay, France
| | - Maria Cristina da Silva Lourenço
- Fundação Oswaldo Cruz-Fiocruz, Instituto Nacional de Infectologia
Evandro Chagas, Laboratório de Bacteriologia e Bioensaios em Micobactérias, Rio de
Janeiro, RJ, Brasil
| | - Harrison Magdinier Gomes
- Fundação Oswaldo Cruz-Fiocruz, Instituto Oswaldo Cruz, Laboratório
de Biologia Molecular Aplicada a Micobactérias, Rio de Janeiro, RJ, Brasil
| | - Artemir Coelho de Brito
- Coordenação Geral de Vigilância das Doenças de Transmissão
Respiratória de Condições Crônicas, Brasília, DF, Brasil
| | - Marcos Catanho
- Fundação Oswaldo Cruz-Fiocruz, Instituto Oswaldo Cruz, Laboratório
de Genética Molecular de Microrganismos, Rio de Janeiro, RJ, Brasil
| | - Rafael Silva Duarte
- Universidade Federal do Rio de Janeiro, Instituto de Microbiologia
Paulo de Góes, Laboratório de Micobactérias, Rio de Janeiro, RJ, Brasil
| | - Philip Noel Suffys
- Fundação Oswaldo Cruz-Fiocruz, Instituto Oswaldo Cruz, Laboratório
de Biologia Molecular Aplicada a Micobactérias, Rio de Janeiro, RJ, Brasil
| | - Karla Valéria Batista Lima
- Universidade do Estado do Pará, Instituto de Ciências Biológicas e
da Saúde, Pós-Graduação Biologia Parasitária na Amazônia, Belém, PA, Brasil
- Instituto Evandro Chagas, Seção de Bacteriologia e Micologia,
Ananindeua, PA, Brasil
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Fang Y, Ma Y, Lu Q, Sun J, Pei Y. An outbreak of pulmonary tuberculosis and a follow-up investigation of latent tuberculosis in a high school in an eastern city in China, 2016-2019. PLoS One 2021; 16:e0247564. [PMID: 33626108 PMCID: PMC7904191 DOI: 10.1371/journal.pone.0247564] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Accepted: 02/09/2021] [Indexed: 11/29/2022] Open
Abstract
Background In October 2016, a senior high school student was diagnosed with sputum-smear positive [SS(+)] pulmonary tuberculosis (TB). We conducted an investigation of an outbreak in the school, including among students and teachers diagnosed with latent TB, who we followed until July 2019. Methods We defined latent TB infection (LTBI) as a tuberculin skin test (TST) induration of 15mm or larger; probable TB as a chest radiograph indicative of TB plus productive cough/hemoptysis for at least 2 weeks, or TST induration of 15mm or larger; and confirmed TB as two or more positive sputum smears or one positive sputum smear plus a chest radiograph indicative of TB or culture positive with M. tuberculosis. We conducted mycobacterial interspersed repetitive unit–variable number tandem repeat (MIRU-VNTR) typing based on 24 loci in the isolates. Results Between October 2016 and July 2019, we identified 52 cases, including nine probable, six confirmed, and 37 LTBI cases. The index case-student had attended school continuously despite having TB symptoms for almost three months before being diagnosed with TB. We obtained three isolates from classmates of the index case in 2016; all had identical MIRU-VNTR alleles with the index case. The LTBI rate was lower among students (7.41%, 30/405) than among teachers (26.92%, 7/26) (rate ratio [RR] = 0.28, 95% confidential interval [CI]: 0.13–0.57). Among the 17 students who had latent TB and refused prophylaxis in October 2016, 23.53% (4/17) became probable/confirmed cases by July 2019. None of the six teachers who also refused prophylaxis became probable or confirmed cases. Of the 176 students who were TST(-) in October 2016, 1.70% (3/176) became probable/confirmed cases, and among the 20 teachers who were TST(-), 1 became a probable case. Conclusions Delayed diagnosis of TB in the index patient may have contributed to the start of this outbreak; lack of post-exposure chemoprophylaxis facilitated spread of the outbreak. Post-exposure prophylaxis is strongly recommended for all TST-positive students; TST-negative students exposed to an SS(+) case should be followed up regularly so that prophylaxis can be started if LTBI is detected.
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Affiliation(s)
- Yirong Fang
- Department of Infectious Disease, Shaoxing Center for Disease Control and Prevention, Shaoxing City, Zhejiang Province, China
| | - Yan Ma
- Department of Infectious Disease, Shaoxing Center for Disease Control and Prevention, Shaoxing City, Zhejiang Province, China
| | - Qiaoling Lu
- Department of Infectious Disease, Shaoxing Center for Disease Control and Prevention, Shaoxing City, Zhejiang Province, China
| | - Jiamei Sun
- Department of Infectious Disease, Shaoxing Center for Disease Control and Prevention, Shaoxing City, Zhejiang Province, China
| | - Yingxin Pei
- Chinese Field Epidemiology Training Program, Office of Education and Training, Chinese Center for Disease Control and Prevention, Beijing, China
- * E-mail:
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Ilic M, Ilic I. Importance of MIRU-VNTRplus tool for identification and tracking of the spread of tuberculosis. Travel Med Infect Dis 2021; 40:101998. [PMID: 33639264 DOI: 10.1016/j.tmaid.2021.101998] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Accepted: 02/18/2021] [Indexed: 10/22/2022]
Affiliation(s)
- Milena Ilic
- Department of Epidemiology, Faculty of Medical Sciences, University of Kragujevac, Serbia.
| | - Irena Ilic
- Faculty of Medicine, University of Belgrade, Belgrade, Serbia
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Venske Bierhals D, Busatto C, Silveira MDPDR, da Matta Talaier E, Silva ABS, Reis AJ, von Groll A, da Silva PEA, Ramis IB. Tuberculosis cases in a prison in the extreme south of Brazil. J Med Microbiol 2021; 70. [PMID: 33555247 DOI: 10.1099/jmm.0.001319] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Introduction. Tuberculosis (TB) control is a challenge, especially in vulnerable populations, such as prisoners.Hypothesis. In prison houses, the transmission of micro-organisms that cause infectious diseases can occur due to the susceptibility and immune compromise of prisoners, and due to the precarious physical conditions of the prison houses. However, strategies such as monitoring by health professionals, can mitigate the transmission of these micro-organisms, as well as, reduce the number of coinfections and antimicrobials resistance.Aim. This study attempted to analyse the dynamics of transmission and the antimicrobial resistance profile of Mycobacterium tuberculosis strains obtained from prisoners and to characterize the epidemiological, clinical and laboratory profiles of prisoners diagnosed with TB.Methodology. A cross-sectional and retrospective study was conducted with sputum samples collected from 228 distinct prisoners who were treated at the Health Unit located in the Regional Penitentiary of Rio Grande, Rio Grande do Sul, Brazil. The antimicrobial resistance profile of the strains was evaluated using the Resazurin Microtiter Assay and the transmission dynamics was investigated using 15-loci MIRU-VNTR.Results. Thirty-five patients (15.4 %) were diagnosed with TB, and when a TB/HIV coinfection was assessed, 8.6 % (3/35) of the patients were positive. In addition, all patients with results available for HBV, HCV, syphilis and diabetes mellitus were negative. Based on the genotypic profile, 55.9 % of the clinical isolates were grouped into five groups. One isolate with mono-resistance to isoniazid and two with mono-resistance to streptomycin were found.Conclusion. The presence of a Health Unit may have influenced the low numbers of TB/HIV, TB/HBV, TB/HCV, TB/syphilis coinfections and TB cases resistant to antimicrobials. Recent M. tuberculosis transmission can be inferred based on the high percentage of formatting of clusters. This situation stresses the need to improve active and passive detection, the screening of individuals for TB upon entrance into prison for early detection, and the implementation of prophylactic measures to reduce M. tuberculosis transmission.
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Affiliation(s)
- Dienefer Venske Bierhals
- Medical Microbiology Research Center, Faculty of Medicine, Federal University of Rio Grande (FURG), Rio Grande, Rio Grande do Sul, Brazil
| | - Caroline Busatto
- Medical Microbiology Research Center, Faculty of Medicine, Federal University of Rio Grande (FURG), Rio Grande, Rio Grande do Sul, Brazil
| | | | - Edilon da Matta Talaier
- Rio Grande City Hall, Basic Prison Health Unit - SMS/PERG, Rio Grande, Rio Grande do Sul, Brazil
| | - Ana Bárbara Scholante Silva
- Medical Microbiology Research Center, Faculty of Medicine, Federal University of Rio Grande (FURG), Rio Grande, Rio Grande do Sul, Brazil
| | - Ana Julia Reis
- Medical Microbiology Research Center, Faculty of Medicine, Federal University of Rio Grande (FURG), Rio Grande, Rio Grande do Sul, Brazil
| | - Andrea von Groll
- Medical Microbiology Research Center, Faculty of Medicine, Federal University of Rio Grande (FURG), Rio Grande, Rio Grande do Sul, Brazil
| | - Pedro Eduardo Almeida da Silva
- Medical Microbiology Research Center, Faculty of Medicine, Federal University of Rio Grande (FURG), Rio Grande, Rio Grande do Sul, Brazil
| | - Ivy Bastos Ramis
- Medical Microbiology Research Center, Faculty of Medicine, Federal University of Rio Grande (FURG), Rio Grande, Rio Grande do Sul, Brazil
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Lopez K, Arriaga MB, Aliaga JG, Barreda NN, Sanabria OM, Huang CC, Zhang Z, García-de-la-Guarda R, Lecca L, Calçada Carvalho AC, Kritski AL, Calderon RI. Dysglycemia is associated with Mycobacterium tuberculosis lineages in tuberculosis patients of North Lima-Peru. PLoS One 2021; 16:e0243184. [PMID: 33507930 PMCID: PMC7843012 DOI: 10.1371/journal.pone.0243184] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Accepted: 01/08/2021] [Indexed: 12/13/2022] Open
Abstract
This study was performed to investigate the role of dysglycemia on the genetic diversity of Mycobacterium tuberculosis (MTB) among pulmonary tuberculosis (TB) patients to build scientific evidence about the possible mechanisms of TB transmission. MTB isolates obtained of patients affected by pulmonary tuberculosis from health care facilities of North Lima-Peru, were analyzed using whole genome sequencing and 24-locus mycobacterial interspersed repetitive-unit -variable-number tandem repeats (MIRU-VNTR). Subsequently, clinical and epidemiological characteristics were associated with clustering, lineages and comorbid conditions. The analysis carried out 112 pulmonary TB patients from various health centers in North Lima, 17 (15%) had diabetes mellitus (DM) and 33 (29%) had pre-diabetes (PDM). Latin American-Mediterranean, Haarlem and Beijing were the most frequent MTB lineages found in those patients. Previous TB (adjusted odds ratio [aOR] = 3.65; 95%CI: 1.32-17.81), age (aOR = 1.12; 95%CI: 1.03-1.45) and Beijing lineage (aOR = 3.53; 95%CI: 1.08-13.2) were associated with TB-DM comorbidity. Alcoholism (aOR = 2.92; 95%CI: 1.10-8.28), age (aOR = 1.05; 95%CI: 1.03-1.12) and Haarlem lineage (aOR = 2.54; 95%CI: 1.04-6.51) were associated with TB-PDM comorbidity. Beijing and Haarlem lineages were independently associated with TB-DM and TB-PDM comorbidities, respectively. Although these findings may be surprising, we must be cautious to suggest that dysglycemia could be associated with a highly clustering and predisposition of MTB lineages related to a serious impact on the severity of TB disease, which requires further research.
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Affiliation(s)
- Kattya Lopez
- Socios En Salud Sucursal Peru, Lima, Peru
- Facultad de Ciencias Biológicas, Universidad Nacional Mayor de San Marcos, Lima, Peru
- Division of Rheumatology, Immunity and Inflammation, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
| | - María B. Arriaga
- Instituto Gonçalo Moniz, Fundação Oswaldo Cruz, Salvador, Bahia, Brazil
- Faculdade de Medicina, Universidade Federal da Bahia, Salvador, Bahia, Brazil
- Instituto Brasileiro para Investigação da Tuberculose, Fundação José Silveira, Salvador, Bahia, Brazil
| | | | | | | | - Chuan-Chin Huang
- Division of Global Health Equity, Brigham and Women’s Hospital, Boston, Massachusetts, United States of America
| | - Zibiao Zhang
- Department of Global Health and Social Medicine, Harvard Medical School, Boston, Massachusetts, United States of America
| | | | | | - Anna Cristina Calçada Carvalho
- Laboratório de Inovações em Terapias, Ensino e Bioprodutos, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| | - Afrânio L. Kritski
- Faculdade de Medicina, Programa Acadêmico de Tuberculose, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Roger I. Calderon
- Socios En Salud Sucursal Peru, Lima, Peru
- Faculdade de Medicina, Programa Acadêmico de Tuberculose, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
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Marín AV, Rastogi N, Couvin D, Mape V, Murcia MI. First approach to the population structure of Mycobacterium tuberculosis complex in the indigenous population in Puerto Nariño-Amazonas, Colombia. PLoS One 2021; 16:e0245084. [PMID: 33411781 PMCID: PMC7790298 DOI: 10.1371/journal.pone.0245084] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2020] [Accepted: 12/21/2020] [Indexed: 11/18/2022] Open
Abstract
Introduction Tuberculosis affects vulnerable groups to a greater degree, indigenous population among them. Objective To determine molecular epidemiology of clinical isolates of Mycobacterium tuberculosis circulating in an indigenous population through Spoligotyping and 24-loci MIRU-VNTR. Methodology A descriptive cross-sectional study was conducted in 23 indigenous communities of Puerto Nariño-Amazonas, Colombia. Recovered clinical isolates were genotyped. For genotyping analyzes global SITVIT2 database and the MIRU-VNTRplus web portal were used. Results 74 clinical isolates were recovered. Genotyping of clinical isolates by spoligotyping determined 5 different genotypes, all of them belonged to Euro-American lineage. By MIRU-VNTR typing, a total of 14 different genotypes were recorded. Furthermore, polyclonal infection was found in two patients from the same community. The combination of the two methodologies determined the presence of 19 genotypes, 8 formed clusters with 63 clinical isolates in total. Based on epidemiological information, it was possible to establish a potential chain of active transmission in 10/63 (15.9%) patients. Conclusions High genomic homogeneity was determined in the indigenous population suggesting possible chains of active transmission. The results obtained showed that specific genotypes circulating among the indigenous population of Colombia are significantly different from those found in the general population.
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Affiliation(s)
- Alejandro Vega Marín
- MICOBAC-UN, Departamento de Microbiología, Facultad de Medicina, Universidad Nacional de Colombia, Bogotá, Colombia
| | - Nalin Rastogi
- WHO Supranational TB Reference Laboratory, Unité de la Tuberculose et des Mycobactéries, Institut Pasteur de la Guadeloupe, Abymes, Guadeloupe, France
| | - David Couvin
- WHO Supranational TB Reference Laboratory, Unité de la Tuberculose et des Mycobactéries, Institut Pasteur de la Guadeloupe, Abymes, Guadeloupe, France
| | - Viviana Mape
- MICOBAC-UN, Departamento de Microbiología, Facultad de Medicina, Universidad Nacional de Colombia, Bogotá, Colombia
| | - Martha Isabel Murcia
- MICOBAC-UN, Departamento de Microbiología, Facultad de Medicina, Universidad Nacional de Colombia, Bogotá, Colombia
- * E-mail:
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Perdigão J, Silva C, Maltez F, Machado D, Miranda A, Couto I, Rabna P, Florez de Sessions P, Phelan J, Pain A, McNerney R, Hibberd ML, Mokrousov I, Clark TG, Viveiros M, Portugal I. Emergence of multidrug-resistant Mycobacterium tuberculosis of the Beijing lineage in Portugal and Guinea-Bissau: a snapshot of moving clones by whole-genome sequencing. Emerg Microbes Infect 2020; 9:1342-1353. [PMID: 32538300 PMCID: PMC7473242 DOI: 10.1080/22221751.2020.1774425] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Revised: 04/17/2020] [Accepted: 05/14/2020] [Indexed: 11/22/2022]
Abstract
The Beijing genotype comprises a highly disseminated strain type that is frequently associated with multidrug resistant (MDR) tuberculosis (TB) and increased transmissibility but, countries such as Portugal and Guinea-Bissau fall outside the regions phylogeographically associated with this specific genotype. Nevertheless, recent data shows that this genotype might be gradually emerging in these two countries as an underlying cause of primary MDR-TB. Here, we describe the emergence of Mycobacterium tuberculosis Beijing strains associated with MDR-TB in Portugal and Guinea-Bissau demonstrating the presence of the well described superclusters 100-32 and 94-32 in Portugal and Guinea-Bissau, respectively. Genome-wide analysis and comparison with a global genomic dataset of M. tuberculosis Beijing strains, revealed the presence of two genomic clusters encompassing isolates from Portugal and Guinea-Bissau, GC1 (n = 121) and GC2 (n = 39), both of which bore SNP signatures compatible with the 100-32/B0/W148 and 94-32/Central Asia Outbreak clades, respectively. Moreover, GC2 encompasses a cross-border cluster between Portugal, Guinea-Bissau and Brazil thus supporting migration-associated introduction of MDR-TB and subsequent clonal expansion at the community-level. The comparison with global Beijing datasets demonstrates the global reach of the disease and its complex dissemination across multiple countries while in parallel there are clear microevolutionary trajectories towards extensively drug resistant TB.
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Affiliation(s)
- João Perdigão
- iMed.ULisboa – Instituto de Investigação do Medicamento, Faculdade de Farmácia, Universidade de Lisboa, Lisboa, Portugal
| | - Carla Silva
- iMed.ULisboa – Instituto de Investigação do Medicamento, Faculdade de Farmácia, Universidade de Lisboa, Lisboa, Portugal
| | - Fernando Maltez
- Serviço de Doenças Infecciosas, Hospital de Curry Cabral-CHLC, Lisboa, Portugal
| | - Diana Machado
- Global Health and Tropical Medicine, GHTM, Instituto de Higiene e Medicina Tropical, IHMT, Universidade Nova de Lisboa, UNL, Lisboa, Portugal
| | - Anabela Miranda
- National Mycobacterium Reference Laboratory, Instituto Nacional de Saúde Dr. Ricardo Jorge, Porto, Portugal
| | - Isabel Couto
- Global Health and Tropical Medicine, GHTM, Instituto de Higiene e Medicina Tropical, IHMT, Universidade Nova de Lisboa, UNL, Lisboa, Portugal
| | - Paulo Rabna
- Instituto Nacional de Saúde Pública/Projecto de Saúde de Bandim (INASA/PSB), Bissau,Guiné-Bissau
| | | | - Jody Phelan
- London School of Hygiene & Tropical Medicine, London, UK
| | - Arnab Pain
- Pathogen Genomics Laboratory, BESE Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Kingdom of Saudi Arabia
| | - Ruth McNerney
- Department of Medicine, University of Cape Town, Cape Town, South Africa
| | | | - Igor Mokrousov
- Laboratory of Molecular Epidemiology and Evolutionary Genetics, St Petersburg Pasteur Institute, St Petersburg, Russia
| | - Taane G. Clark
- London School of Hygiene & Tropical Medicine, London, UK
| | - Miguel Viveiros
- Global Health and Tropical Medicine, GHTM, Instituto de Higiene e Medicina Tropical, IHMT, Universidade Nova de Lisboa, UNL, Lisboa, Portugal
| | - Isabel Portugal
- iMed.ULisboa – Instituto de Investigação do Medicamento, Faculdade de Farmácia, Universidade de Lisboa, Lisboa, Portugal
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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:JCM.01573-20. [PMID: 32817084 DOI: 10.1128/jcm.01573-20] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 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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Molecular epidemiology of clinical Mycobacterium tuberculosis complex isolates in South Omo, Southern Ethiopia. BMC Infect Dis 2020; 20:750. [PMID: 33050903 PMCID: PMC7557052 DOI: 10.1186/s12879-020-05394-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2020] [Accepted: 09/02/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Tuberculosis (TB) is caused by Mycobacterium tuberculosis complex (MTBC). Mapping the genetic diversity of MTBC in high TB burden country like Ethiopia is important to understand principles of the disease transmission and to strengthen the regional TB control program. The aim of this study was to investigate the genetic diversity of Mycobacterium tuberculosis complex (MTBC) isolates circulating in the South Omo, southern Ethiopia. METHODS MTBC isolates (N = 156) were genetically analyzed using spacer oligotyping (spoligotyping) and mycobacterial interspersed repetitive unit-variable number of tandem repeat (MIRU-VNTR) typing. Major lineages and lineages were identified using MTBC databases. Logistic regression was used to correlate patient characteristics with strain clustering. RESULTS The study identified Euro-American (EA), East-African-Indian (EAI), Indo-Oceanic (IO), Lineage_7/Aethiops vertus, Mycobacterium bovis and Mycobacterium africanum major lineages in proportions of 67.3% (105/156), 22.4% (35/156), 6.4% (10/156), 1.9% (3/156), 1.3% (2/156) and 0.6% (1/156), respectively. Lineages identified were Delhi/CAS 23.9% (37/155), Ethiopia_2 20.6% (32/155), Haarlem 14.2% (22/155), URAL 14.2%(22/155), Ethiopia_3 8.4% (13/155), TUR 6.5% (10/155), Lineage_7/Aethiops vertus 1.9% (3/155), Bovis 1.3% (2/155), LAM 1.3% (2/155), EAI 0.6% (1/155), X 0.6% (1/155) and Ethiopia H37Rv-like strain 0.6% (1/155). Of the genotyped isolates 5.8% (9/155) remained unassigned. The recent transmission index (RTI) was 3.9%. Orphan strains compared to shared types (AOR: 0.09, 95% CI: 0.04-0.25) were associated with reduced odds of clustering. The dominant TB lineage in pastoral areas was EAI and in non-pastoral areas was EA. CONCLUSION The epidemiological data, highly diverse MTBC strains and a low RTI in South Omo, provide information contributing to the TB Control Program of the country.
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