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Esteves LS, Gomes LL, Brites D, Fandinho FCO, Bhering M, Pereira MADS, Conceição EC, Salvato R, da Costa BP, Medeiros RFDM, Caldas PCDS, Redner P, Dalcolmo MP, Eldholm V, Gagneux S, Rossetti ML, Kritski AL, Suffys PN. Genetic Characterization and Population Structure of Drug-Resistant Mycobacterium tuberculosis Isolated from Brazilian Patients Using Whole-Genome Sequencing. Antibiotics (Basel) 2024; 13:496. [PMID: 38927163 PMCID: PMC11200758 DOI: 10.3390/antibiotics13060496] [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: 04/12/2024] [Revised: 05/21/2024] [Accepted: 05/22/2024] [Indexed: 06/28/2024] Open
Abstract
The present study aimed to determine the genetic diversity of isolates of Mycobacterium tuberculosis (Mtb) from presumed drug-resistant tuberculosis patients from several states of Brazil. The isolates had been submitted to conventional drug susceptibility testing for first- and second-line drugs. Multidrug-resistant (MDR-TB) (54.8%) was the most frequent phenotypic resistance profile, in addition to an important high frequency of pre-extensive resistance (p-XDR-TB) (9.2%). Using whole-genome sequencing (WGS), we characterized 298 Mtb isolates from Brazil. Besides the analysis of genotype distribution and possible correlations between molecular and clinical data, we determined the performance of an in-house WGS pipeline with other online pipelines for Mtb lineages and drug resistance profile definitions. Sub-lineage 4.3 (52%) was the most frequent genotype, and the genomic approach revealed a p-XDR-TB level of 22.5%. We detected twenty novel mutations in three resistance genes, and six of these were observed in eight phenotypically resistant isolates. A cluster analysis of 170 isolates showed that 43.5% of the TB patients belonged to 24 genomic clusters, suggesting considerable ongoing transmission of DR-TB, including two interstate transmissions. The in-house WGS pipeline showed the best overall performance in drug resistance prediction, presenting the best accuracy values for five of the nine drugs tested. Significant associations were observed between suffering from fatal disease and genotypic p-XDR-TB (p = 0.03) and either phenotypic (p = 0.006) or genotypic (p = 0.0007) ethambutol resistance. The use of WGS analysis improved our understanding of the population structure of MTBC in Brazil and the genetic and clinical data correlations and demonstrated its utility for surveillance efforts regarding the spread of DR-TB, hopefully helping to avoid the emergence of even more resistant strains and to reduce TB incidence and mortality rates.
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Affiliation(s)
- Leonardo Souza Esteves
- Programa Acadêmico de Tuberculose da Faculdade de Medicina, Centro de Ciências da Saúde, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro 21941-590, RJ, Brazil;
- Centro de Desenvolvimento Científico e Tecnológico (CDCT), Secretaria Estadual de Saúde (SES-RS), Porto Alegre 90450-190, RS, Brazil;
- Laboratório de Biologia Molecular Aplicado à Micobactérias, Fundação Oswaldo Cruz (FIOCRUZ), Instituto Oswaldo Cruz (IOC), Rio de Janeiro 21040-360, RJ, Brazil; (L.L.G.); (P.N.S.)
| | - Lia Lima Gomes
- Laboratório de Biologia Molecular Aplicado à Micobactérias, Fundação Oswaldo Cruz (FIOCRUZ), Instituto Oswaldo Cruz (IOC), Rio de Janeiro 21040-360, RJ, Brazil; (L.L.G.); (P.N.S.)
| | - Daniela Brites
- Swiss Tropical and Public Health Institute (Swiss TPH), CH-4123 Allschwil, Switzerland; (D.B.); (S.G.)
- University of Basel, CH-4001 Basel, Switzerland
| | - Fátima Cristina Onofre Fandinho
- Centro de Referência Professor Hélio Fraga, Fundação Oswaldo Cruz (FIOCRUZ), Rio de Janeiro 22780-195, RJ, Brazil; (F.C.O.F.); (M.B.); (M.A.d.S.P.); (B.P.d.C.); (R.F.d.M.M.); (P.C.d.S.C.); (P.R.); (M.P.D.)
| | - Marcela Bhering
- Centro de Referência Professor Hélio Fraga, Fundação Oswaldo Cruz (FIOCRUZ), Rio de Janeiro 22780-195, RJ, Brazil; (F.C.O.F.); (M.B.); (M.A.d.S.P.); (B.P.d.C.); (R.F.d.M.M.); (P.C.d.S.C.); (P.R.); (M.P.D.)
| | - Márcia Aparecida da Silva Pereira
- Centro de Referência Professor Hélio Fraga, Fundação Oswaldo Cruz (FIOCRUZ), Rio de Janeiro 22780-195, RJ, Brazil; (F.C.O.F.); (M.B.); (M.A.d.S.P.); (B.P.d.C.); (R.F.d.M.M.); (P.C.d.S.C.); (P.R.); (M.P.D.)
| | - Emilyn Costa Conceição
- Department of Science and Innovation—National Research Foundation Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town 7505, South Africa;
| | - Richard Salvato
- Centro de Desenvolvimento Científico e Tecnológico (CDCT), Secretaria Estadual de Saúde (SES-RS), Porto Alegre 90450-190, RS, Brazil;
| | - Bianca Porphirio da Costa
- Centro de Referência Professor Hélio Fraga, Fundação Oswaldo Cruz (FIOCRUZ), Rio de Janeiro 22780-195, RJ, Brazil; (F.C.O.F.); (M.B.); (M.A.d.S.P.); (B.P.d.C.); (R.F.d.M.M.); (P.C.d.S.C.); (P.R.); (M.P.D.)
| | - Reginalda Ferreira de Melo Medeiros
- Centro de Referência Professor Hélio Fraga, Fundação Oswaldo Cruz (FIOCRUZ), Rio de Janeiro 22780-195, RJ, Brazil; (F.C.O.F.); (M.B.); (M.A.d.S.P.); (B.P.d.C.); (R.F.d.M.M.); (P.C.d.S.C.); (P.R.); (M.P.D.)
| | - Paulo Cesar de Souza Caldas
- Centro de Referência Professor Hélio Fraga, Fundação Oswaldo Cruz (FIOCRUZ), Rio de Janeiro 22780-195, RJ, Brazil; (F.C.O.F.); (M.B.); (M.A.d.S.P.); (B.P.d.C.); (R.F.d.M.M.); (P.C.d.S.C.); (P.R.); (M.P.D.)
| | - Paulo Redner
- Centro de Referência Professor Hélio Fraga, Fundação Oswaldo Cruz (FIOCRUZ), Rio de Janeiro 22780-195, RJ, Brazil; (F.C.O.F.); (M.B.); (M.A.d.S.P.); (B.P.d.C.); (R.F.d.M.M.); (P.C.d.S.C.); (P.R.); (M.P.D.)
| | - Margareth Pretti Dalcolmo
- Centro de Referência Professor Hélio Fraga, Fundação Oswaldo Cruz (FIOCRUZ), Rio de Janeiro 22780-195, RJ, Brazil; (F.C.O.F.); (M.B.); (M.A.d.S.P.); (B.P.d.C.); (R.F.d.M.M.); (P.C.d.S.C.); (P.R.); (M.P.D.)
| | - Vegard Eldholm
- Norwegian Institute of Public Health, 0213 Oslo, Norway;
| | - Sebastien Gagneux
- Swiss Tropical and Public Health Institute (Swiss TPH), CH-4123 Allschwil, Switzerland; (D.B.); (S.G.)
- University of Basel, CH-4001 Basel, Switzerland
| | - Maria Lucia Rossetti
- Laboratório de Biologia Molecular, Universidade Luterana do Brasil (ULBRA), Canoas 92425-020, RS, Brazil;
| | - Afrânio Lineu Kritski
- Programa Acadêmico de Tuberculose da Faculdade de Medicina, Centro de Ciências da Saúde, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro 21941-590, RJ, Brazil;
| | - Philip Noel Suffys
- Laboratório de Biologia Molecular Aplicado à Micobactérias, Fundação Oswaldo Cruz (FIOCRUZ), Instituto Oswaldo Cruz (IOC), Rio de Janeiro 21040-360, RJ, Brazil; (L.L.G.); (P.N.S.)
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Chen Y, Jiang Q, Liu Q, Gan M, Takiff HE, Gao Q. Whole-Genome Sequencing Exhibits Better Diagnostic Performance than Variable-Number Tandem Repeats for Identifying Mixed Infections of Mycobacterium tuberculosis. Microbiol Spectr 2023; 11:e0357022. [PMID: 37098911 PMCID: PMC10269500 DOI: 10.1128/spectrum.03570-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Accepted: 04/10/2023] [Indexed: 04/27/2023] Open
Abstract
Mixed infections of Mycobacterium tuberculosis, defined as the coexistence of multiple genetically distinct strains within a single host, have been associated with unfavorable treatment outcomes. Different methods have been used to detect mixed infections, but their performances have not been carefully evaluated. To compare the sensitivity of whole-genome sequencing (WGS) and variable-number tandem repeats (VNTR) typing to detect mixed infections, we prepared 10 artificial samples composed of DNA mixtures from two strains in different proportions and retrospectively collected 1,084 clinical isolates. The limit of detection (LOD) for the presence of a minor strain was 5% for both WGS and VNTR typing. The overall clinical detection rate of mixed infections was 3.7% (40/1,084) for the two methods combined, WGS identified 37/1,084 (3.4%), and VNTR typing identified 14/1,084 (1.3%), including 11 also identified by WGS. Multivariate analysis demonstrated that retreatment patients had a 2.7 times (95% confidence interval [CI], 1.2 to 6.0) higher risk of mixed infections than new cases. Collectively, WGS is a more reliable tool to identify mixed infections than VNTR typing, and mixed infections are more common in retreated patients. IMPORTANCE Mixed infections of M. tuberculosis have the potential to render treatment regimens ineffective and affect the transmission dynamics of the disease. VNTR typing, currently the most widely used method for the detection of mixed infections, detects mixed infections only by interrogating a small fraction of the M. tuberculosis genome, which necessarily limits sensitivity. With the introduction of WGS, it became possible to study the entire genome, but no quantitative comparison has yet been undertaken. Our systematic comparison of the ability of WGS and VNTR typing to detect mixed infections, using both artificial samples and clinical isolates, revealed the superior performance of WGS at a high sequencing depth (~100×) and found that mixed infections are more common in patients being retreated for tuberculosis (TB) in the populations studied. This provides valuable information for the application of WGS in the detection of mixed infections and the implications of mixed infections for tuberculosis control.
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Affiliation(s)
- Yiwang Chen
- National Clinical Research Center for Infectious Diseases, Shenzhen Third People’s Hospital, Shenzhen, Guangdong, China
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai, China
| | - Qi Jiang
- School of Public Health, Public Health Research Institute of Renmin Hospital, Wuhan University, Wuhan, China
| | - Qingyun Liu
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, Massachusetts, USA
| | - Mingyu Gan
- Molecular Medical Center, Children’s Hospital of Fudan University, Shanghai, China
| | - Howard E. Takiff
- Instituto Venezolano de Investigaciones Cientificas (IVIC), Caracas, Venezuela
| | - Qian Gao
- National Clinical Research Center for Infectious Diseases, Shenzhen Third People’s Hospital, Shenzhen, Guangdong, China
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai, China
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Ghazvini K, Khoshbakht R, Tadayon K, Mosavari N, BahramiTaghanaki HR, Mohammadi GR, Rashti Baf M, Nourian K, Samiei A, Ghavidel M. Genotyping of Mycobacterium tuberculosis complex isolated from humans and animals in northeastern Iran. Sci Rep 2023; 13:6746. [PMID: 37185604 PMCID: PMC10127167 DOI: 10.1038/s41598-023-33740-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Accepted: 04/18/2023] [Indexed: 05/17/2023] Open
Abstract
The objective of this study was to genotype Mycobacterium tuberculosis complex isolated from humans and cattle in northern Iran. Over the course of one year, a total of 120 human and 21 cattle isolates were tested using region of difference (RD)-based polymerase chain reaction (PCR) and mycobacterial interspersed repetitive unites-variable number tandem repeats (MIRU-VNTR). In M. tuberculosis, out of 120 isolates investigated, the most common genotype detected was NEW-1 (53.3%), followed by CAS/ Delhi (24.1%), Haarlem (5%), Beijing (4.16%), Uganda I (4.16%), S (3.3%), Ural (0.83%), TUR (0.83%), Uganda II (0.83%), Lam (0.83%) and Cameroon (0.83%). The HGDI rate was 0.9981 and the clustering rate was 10.83. Of the isolates, QUB26 had the highest allele diversity (h: 0.76), while the loci Mtub29 and MIRU24 had the lowest (h: 0). In M. Bovis, out of 123 collected tissue samples, 21 (17%) grew on culture media. The HGDI rate was 0.71 and clustering rate was 85.7%. The locus ETRC had the highest allele diversity (h: 0.45). The findings of this study suggest that there is high genetic diversity among M. tuberculosis isolates in Khorasan Razavi Province, which is consistent with similar results from other studies in other provinces in Iran and neighboring countries. This indicates that the prevalent genotypes in this study are spreading in the Middle East region. Furthermore, considering that M. Bovis isolates were identified in two clusters, it seems that all of them have a common origin and are circulating among the livestock farms in the province.
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Affiliation(s)
- Kiarash Ghazvini
- Antimicrobial Resistance Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
- Department of Microbiology and Virology, School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Reza Khoshbakht
- Department of Laboratory Sciences, School of Paramedical Sciences, Mashhad University of Medical Sciences, Mashhad, Iran
- Student Research Committee, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Keyvan Tadayon
- Department of Microbiology, Razi Vaccine and Serum Research Institute (RVSRI), Agricultural Research, Education and Extension Organization (AREEO), Karaj, Iran
| | - Nader Mosavari
- PPD Tuberculin Department, Razi Vaccine and Serum Research Institute, (RVSRI), Agricultural Research, Education and Extension Organization (AREEO), Karaj, Iran
| | | | - Gholam Reza Mohammadi
- Department of Clinical Sciences, School of Veterinary Medicine, Ferdowsi University of Mashhad, Mashhad, Iran
| | - Mohammad Rashti Baf
- Deputy of Veterinary Administration of Khorasan Razavi Province, Mashhad, Iran
| | - Kimiya Nourian
- Department of Veterinary Medicine, Ferdowsi University of Mashhad, Mashhad, Iran
| | - Amin Samiei
- Tuberculosis and Leprosy Coordinator at Health Chancellor, Health Center of Khorasan State, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Mahdis Ghavidel
- Shahid Hasheminejad Hospital, Mashhad University of Medical Sciences, Mashhad, Iran.
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Chengalroyen MD, Beukes GM, Otwombe K, Gordhan BG, Martinson N, Kana B. The detection of mixed tuberculosis infections using culture filtrate and resuscitation promoting factor deficient filtrate. Front Cell Infect Microbiol 2022; 12:1072073. [PMID: 36506007 PMCID: PMC9729742 DOI: 10.3389/fcimb.2022.1072073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Accepted: 11/08/2022] [Indexed: 11/25/2022] Open
Abstract
Tuberculosis (TB) infected individuals harbor a heterogenous population of differentially culturable tubercle bacilli (DCTB). Herein, we describe how DCTB assays using culture filtrate either containing or deficient in resuscitation promoting factors can uncover mixed infections. We demonstrate that Mycobacterium tuberculosis (Mtb) strain genotypes can be separated in DCTB assays based on their selective requirement for growth stimulatory factors. Beijing mixed infections appear to be associated with a higher bacterial load and reduced reliance on growth stimulatory factors. These data have important implications for identifying mixed infections and hetero-resistance, which in turn can affect selection of treatment regimen and establishment of transmission links.
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Affiliation(s)
- Melissa D. Chengalroyen
- National Health Laboratory Service, DST/NRF Centre of Excellence for Biomedical TB Research, University of the Witwatersrand, Johannesburg, South Africa
| | - Germar M. Beukes
- National Health Laboratory Service, DST/NRF Centre of Excellence for Biomedical TB Research, University of the Witwatersrand, Johannesburg, South Africa
| | - Kennedy Otwombe
- Perinatal HIV Research Unit, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Bhavna G. Gordhan
- National Health Laboratory Service, DST/NRF Centre of Excellence for Biomedical TB Research, University of the Witwatersrand, Johannesburg, South Africa
| | - Neil Martinson
- National Health Laboratory Service, DST/NRF Centre of Excellence for Biomedical TB Research, University of the Witwatersrand, Johannesburg, South Africa,Perinatal HIV Research Unit, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa,Center for TB Research, Johns Hopkins University, Baltimore, MD, United States
| | - Bavesh Kana
- National Health Laboratory Service, DST/NRF Centre of Excellence for Biomedical TB Research, University of the Witwatersrand, Johannesburg, South Africa,*Correspondence: Bavesh Kana,
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Acosta F, Martínez-Lirola M, Sola-Campoy PJ, Sicilia J, Guerra-Galán T, Maus SR, Muñoz P, Pérez-Lago L, García de Viedma D. Insights into the Complexity of a Dormant Mycobacterium tuberculosis Cluster Once Transmission Is Resumed. Microbiol Spectr 2022; 10:e0138121. [PMID: 35044196 PMCID: PMC8768656 DOI: 10.1128/spectrum.01381-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Accepted: 12/13/2021] [Indexed: 12/03/2022] Open
Abstract
Genotyping tools help identify the complexity in Mycobacterium tuberculosis transmission clusters. We carried out a thorough analysis of the epidemiological and bacteriological complexity of a cluster in Almería, Spain. The cluster, initially associated with Moroccan migrants and with no secondary cases identified in 4 years, then reappeared in Spanish-born individuals. In one case, two Mycobacterium tuberculosis clonal variants were identified. We reanalyzed the cluster, supported by the characterization of multiple cultured isolates and respiratory specimens, whole-genome sequencing, and epidemiological case interviews. Our findings showed that the cluster, which was initially thought to have restarted activity with just a single case harboring a small degree of within-host diversity, was in fact currently growing due to coincidental reactivation of past exposures, with clonal diversity transmitted throughout the cluster. In one case, within-host diversity was amplified, probably due to prolonged diagnostic delay. IMPORTANCE The precise study of the dynamics of tuberculosis transmission in socio-epidemiologically complex scenarios may require more thorough analysis than the standard molecular epidemiology strategies. Our study illustrates the epidemiological and bacteriological complexity present in a transmission cluster in a challenging epidemiological setting with a high proportion of migrant cases. The combination of whole-genome sequencing, refined and refocused epidemiological interviews, and in-depth analysis of the bacterial composition of sputa and cultured isolates was crucial in order to correctly reinterpret the true nature of this cluster. Our global approach allowed us to reinterpret correctly the unnoticed epidemiological and bacteriological complexity involved in the Mycobacterium tuberculosis transmission event under study, which had been overlooked by the usual molecular epidemiology approaches.
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Affiliation(s)
- Fermin Acosta
- Servicio de Microbiología Clínica y Enfermedades Infecciosas, Hospital General Universitario Gregorio Marañón, Madrid, Spain
- Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
| | | | - Pedro J. Sola-Campoy
- Servicio de Microbiología Clínica y Enfermedades Infecciosas, Hospital General Universitario Gregorio Marañón, Madrid, Spain
- Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
| | - Jon Sicilia
- Servicio de Microbiología Clínica y Enfermedades Infecciosas, Hospital General Universitario Gregorio Marañón, Madrid, Spain
- Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
| | - Teresa Guerra-Galán
- Servicio de Microbiología Clínica y Enfermedades Infecciosas, Hospital General Universitario Gregorio Marañón, Madrid, Spain
- Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
| | - Sandra R. Maus
- Servicio de Microbiología Clínica y Enfermedades Infecciosas, Hospital General Universitario Gregorio Marañón, Madrid, Spain
- Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
| | - Patricia Muñoz
- Servicio de Microbiología Clínica y Enfermedades Infecciosas, Hospital General Universitario Gregorio Marañón, Madrid, Spain
- Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
- CIBER Enfermedades Respiratorias (CIBERES), Madrid, Spain
- Departamento de Medicina, Universidad Complutense, Madrid, Spain
| | - Laura Pérez-Lago
- Servicio de Microbiología Clínica y Enfermedades Infecciosas, Hospital General Universitario Gregorio Marañón, Madrid, Spain
- Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
| | - Darío García de Viedma
- Servicio de Microbiología Clínica y Enfermedades Infecciosas, Hospital General Universitario Gregorio Marañón, Madrid, Spain
- Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
- CIBER Enfermedades Respiratorias (CIBERES), Madrid, Spain
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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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Whole-genome sequencing as a tool for studying the microevolution of drug-resistant serial Mycobacterium tuberculosis isolates. Tuberculosis (Edinb) 2021; 131:102137. [PMID: 34673379 DOI: 10.1016/j.tube.2021.102137] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Revised: 09/14/2021] [Accepted: 10/03/2021] [Indexed: 11/21/2022]
Abstract
Treatment of drug-resistant tuberculosis requires extended use of more toxic and less effective drugs and may result in retreatment cases due to failure, abandonment or disease recurrence. It is therefore important to understand the evolutionary process of drug resistance in Mycobacterium tuberculosis. We here in describe the microevolution of drug resistance in serial isolates from six previously treated patients. Drug resistance was initially investigated through phenotypic methods, followed by genotypic approaches. The use of whole-genome sequencing allowed the identification of mutations in the katG, rpsL and rpoB genes associated with drug resistance, including the detection of rare mutations in katG and mixed populations of strains. Molecular docking simulation studies of the impact of observed mutations on isoniazid binding were also performed. Whole-genome sequencing detected 266 single nucleotide polymorphisms between two isolates obtained from one patient, suggesting a case of exogenous reinfection. In conclusion, sequencing technologies can detect rare mutations related to drug resistance, identify subpopulations of resistant strains, and identify diverse populations of strains due to exogenous reinfection, thus improving tuberculosis control by guiding early implementation of appropriate clinical and therapeutic interventions.
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Baik Y, Modongo C, Moonan PK, Click ES, Tobias JL, Boyd R, Finlay A, Oeltmann JE, Shin SS, Zetola NM. Possible Transmission Mechanisms of Mixed Mycobacterium tuberculosis Infection in High HIV Prevalence Country, Botswana. Emerg Infect Dis 2021; 26:953-960. [PMID: 32310078 PMCID: PMC7181944 DOI: 10.3201/eid2605.191638] [Citation(s) in RCA: 7] [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] [Indexed: 11/19/2022] Open
Abstract
Tuberculosis caused by concurrent infection with multiple Mycobacteriumtuberculosis strains (i.e., mixed infection) challenges clinical and epidemiologic paradigms. We explored possible transmission mechanisms of mixed infection in a population-based, molecular epidemiology study in Botswana during 2012–2016. We defined mixed infection as multiple repeats of alleles at >2 loci within a discrete mycobacterial interspersed repetitive unit–variable-number tandem-repeat (MIRU-VNTR) result. We compared mixed infection MIRU-VNTR results with all study MIRU-VNTR results by considering all permutations at each multiple allele locus; matched MIRU-VNTR results were considered evidence of recently acquired strains and nonmatched to any other results were considered evidence of remotely acquired strains. Among 2,051 patients, 34 (1.7%) had mixed infection, of which 23 (68%) had recently and remotely acquired strains. This finding might support the mixed infection mechanism of recent transmission and simultaneous remote reactivation. Further exploration is needed to determine proportions of transmission mechanisms in settings where mixed infections are prevalent.
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Asare-Baah M, Séraphin MN, Salmon LAT, Lauzardo M. Effect of mixed strain infections on clinical and epidemiological features of tuberculosis in Florida. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2021; 87:104659. [PMID: 33276149 PMCID: PMC7855629 DOI: 10.1016/j.meegid.2020.104659] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Revised: 11/18/2020] [Accepted: 11/29/2020] [Indexed: 10/22/2022]
Abstract
Mixed infections with genetically distinct Mycobacterium tuberculosis (MTB) strains within a single host have been documented in different settings; however, this phenomenon is rarely considered in the management and care of new and relapse tuberculosis (T.B.) cases. This study aims to establish the epidemiological and clinical features of mixed infections among culture-confirmed T.B. patients enrolled in tuberculosis care at the Florida Department of Health (FDOH) and measure its association with T.B. mortality. We analyzed de-identified surveillance data of T.B. cases enrolled in T.B. care from April 2008 to January 2018. Mixed MTB infection was determined by the presence of more than one Copy Number Variant (CNV) in at least one locus, based on the genotype profile pattern of at least one isolate using 24-locus Mycobacterial Interspersed Repetitive Unit-Variable Number Tandem Repeat (MIRU-VNTR). The prevalence of mixed MTB infections among the 4944 culture-confirmed TB cases included in this analysis was 2.6% (129). Increased odds of mixed infections were observed among middle-aged patients, 45-64 years (AOR = 2.38; 95% CI: 0.99, 5.69; p = 0.0513), older adults 65 years and above (AOR = 3.95; 95% CI: 1.63, 9.58; p = 0.0023) and patients with diabetes (OR = 1.77; 95% CI: 1.12, 2.80; p = 0.0150). There was no significant association between mixed infections and death. Our study provides insight into the epidemiological and clinical characteristics of patients with mixed MTB infections, which is essential in the management of T.B. patients.
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Affiliation(s)
- Michael Asare-Baah
- Department of Epidemiology, University of Florida, College of Public Health and Health Professions, College of Medicine, 2004 Mowry Road, P.O. Box 100231, Gainesville, FL 32610, United States; Emerging Pathogens Institute, University of Florida, 2055 Mowry Road, P.O. Box 100009, Gainesville, FL 32610, United States.
| | - Marie Nancy Séraphin
- Emerging Pathogens Institute, University of Florida, 2055 Mowry Road, P.O. Box 100009, Gainesville, FL 32610, United States; Division of Infectious Diseases and Global Medicine, University of Florida, College of Medicine, 2055 Mowry Road, P.O. Box 103600, Gainesville, FL 32610, United States
| | - LaTweika A T Salmon
- Florida Department of Health, Bureau of Tuberculosis Control, 4052 Bald Cypress Way, Bin A-20, Tallahassee, FL 32399, United States
| | - Michael Lauzardo
- Emerging Pathogens Institute, University of Florida, 2055 Mowry Road, P.O. Box 100009, Gainesville, FL 32610, United States; Division of Infectious Diseases and Global Medicine, University of Florida, College of Medicine, 2055 Mowry Road, P.O. Box 103600, Gainesville, FL 32610, United States
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Byrne AS, Goudreau A, Bissonnette N, Shamputa IC, Tahlan K. Methods for Detecting Mycobacterial Mixed Strain Infections-A Systematic Review. Front Genet 2020; 11:600692. [PMID: 33408740 PMCID: PMC7779811 DOI: 10.3389/fgene.2020.600692] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2020] [Accepted: 11/19/2020] [Indexed: 12/22/2022] Open
Abstract
Mixed strain infection (MSI) refers to the concurrent infection of a susceptible host with multiple strains of a single pathogenic species. Known to occur in humans and animals, MSIs deserve special consideration when studying transmission dynamics, evolution, and treatment of mycobacterial diseases, notably tuberculosis in humans and paratuberculosis (or Johne's disease) in ruminants. Therefore, a systematic review was conducted to examine how MSIs are defined in the literature, how widespread the phenomenon is across the host species spectrum, and to document common methods used to detect such infections. Our search strategy identified 121 articles reporting MSIs in both humans and animals, the majority (78.5%) of which involved members of the Mycobacterium tuberculosis complex, while only a few (21.5%) examined non-tuberculous mycobacteria (NTM). In addition, MSIs exist across various host species, but most reports focused on humans due to the extensive amount of work done on tuberculosis. We reviewed the strain typing methods that allowed for MSI detection and found a few that were commonly employed but were associated with specific challenges. Our review notes the need for standardization, as some highly discriminatory methods are not adapted to distinguish between microevolution of one strain and concurrent infection with multiple strains. Further research is also warranted to examine the prevalence of NTM MSIs in both humans and animals. In addition, it is envisioned that the accurate identification and a better understanding of the distribution of MSIs in the future will lead to important information on the epidemiology and pathophysiology of mycobacterial diseases.
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Affiliation(s)
| | - Alex Goudreau
- Science & Health Sciences Librarian, University of New Brunswick, Saint John, NB, Canada
| | - Nathalie Bissonnette
- Sherbrooke Research and Development Center, Agriculture and Agri-Food Canada, Sherbrooke, QC, Canada
| | - Isdore Chola Shamputa
- Department of Nursing & Health Sciences, University of New Brunswick, Saint John, NB, Canada
| | - Kapil Tahlan
- Department of Biology, Memorial University of Newfoundland, St. John's, NL, Canada
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Sivakumar S, Chandramohan Y, Kathamuthu GR, Sekar G, Kandhasamy D, Padmanaban V, Hissar S, Tripathy SP, Bethunaickan R, Dhanaraj B, Babu S, Ranganathan UD. The recent trend in mycobacterial strain diversity among extra pulmonary lymph node tuberculosis and their association with drug resistance and the host immunological response in South India. BMC Infect Dis 2020; 20:894. [PMID: 33243148 PMCID: PMC7690019 DOI: 10.1186/s12879-020-05597-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Accepted: 11/08/2020] [Indexed: 11/11/2022] Open
Abstract
Background Tuberculosis (TB) though primarily affects the lungs it may also affect the other parts of the body and referred as extra pulmonary (EPTB). This study is focused on understanding the genetic diversity and molecular epidemiology of Mycobacterium tuberculosis (M.tb) among tuberculous lymphadenitis (TBL), a form of EPTB patients identified in Chennai, Tamil Nadu. Methods The genetic diversity was identified by performing spoligotyping on the M.tb clinical isolates that were recovered from lymph node samples. A total of 71 M.tb isolates were recovered from extra pulmonary lymph node samples and subjected to Drug susceptibility testing and spoligotyping was carried out. In addition, immunological characterization from blood of same individuals from whom M.tb was isolated was carried out between the two major lineages groups East African Indian 3 (EAI3) and non-EAI3 strains by ELISA. The results of spoligotyping patterns were compared with the world Spoligotyping Database of Institute Pasteur de Guadeloupe (SpolDB4). Results We found 41 spoligotype patterns and their associated lineages. Out of 41 spoligotype pattern, only 22 patterns are available in the spoldB4 database with Spoligotype international Type (SIT) number and remaining patterns were orphan strains without SIT number. The most predominant spoligotype lineage that was found in lymph node sample in this region of India was EAI (36), followed by central Asian strain (CAS) (6), T1 (5), Beijing (3), Latin American & Mediterranean (LAM) (2), U (1), X2 (1) and orphan (22). In addition to EAI, CAS and Beijing, our study identified the presence of orphan and unique spoligotyping patterns in Chennai region. We observed six drug resistant isolates. Out of six drug resistant isolates, four were resistant to isoniazid drug and associated with EAI family. Moreover, we observed increased levels of type 2 and type 17 cytokine profiles between EAI3 and non-EAI family, infected individuals. Conclusions The study confirms that EAI lineage to be the most predominant lineages in EPTB patients with lymphadenitis and were found to have increased type 1 and type 17 proinflammatory cytokine profiles. Supplementary Information The online version contains supplementary material available at 10.1186/s12879-020-05597-0.
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Affiliation(s)
- Shanmugam Sivakumar
- Department of Bacteriology, National Institute for Research in Tuberculosis, Chetpet, Chennai, 600 031, India
| | - Yuvaraj Chandramohan
- Department of Immunology, National Institute for Research in Tuberculosis, Chetpet, Chennai, 600 031, India
| | - Gokul Raj Kathamuthu
- National Institute of Health -International Center for Excellence in Research - National Institute for Research in Tuberculosis, Chennai, India
| | - Gomathi Sekar
- Department of Bacteriology, National Institute for Research in Tuberculosis, Chetpet, Chennai, 600 031, India
| | - Devika Kandhasamy
- Department of Bacteriology, National Institute for Research in Tuberculosis, Chetpet, Chennai, 600 031, India
| | - Venkatesan Padmanaban
- Department of Immunology, National Institute for Research in Tuberculosis, Chetpet, Chennai, 600 031, India
| | - Syed Hissar
- Department of Clinical Health Research, National Institute for Research in Tuberculosis, Chetpet, Chennai, 600 031, India
| | - Srikanth P Tripathy
- National Institute for Research in Tuberculosis, Chetpet, Chennai, 600 031, India
| | - Ramalingam Bethunaickan
- Department of Immunology, National Institute for Research in Tuberculosis, Chetpet, Chennai, 600 031, India
| | - Baskaran Dhanaraj
- Department of Clinical Health Research, National Institute for Research in Tuberculosis, Chetpet, Chennai, 600 031, India
| | - Subash Babu
- National Institute of Health -International Center for Excellence in Research - National Institute for Research in Tuberculosis, Chennai, India
| | - Uma Devi Ranganathan
- Department of Immunology, National Institute for Research in Tuberculosis, Chetpet, Chennai, 600 031, India.
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Solo ES, Suzuki Y, Kaile T, Bwalya P, Lungu P, Chizimu JY, Shah Y, Nakajima C. Characterization of Mycobacterium tuberculosis genotypes and their correlation to multidrug resistance in Lusaka, Zambia. Int J Infect Dis 2020; 102:489-496. [PMID: 33059094 DOI: 10.1016/j.ijid.2020.10.014] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Revised: 10/04/2020] [Accepted: 10/06/2020] [Indexed: 11/15/2022] Open
Abstract
OBJECTIVES The burden of multidrug-resistant tuberculosis (MDR-TB) has been reported to be increasing in Zambia. The reasons for the increase are still unclear. This study determined the diversity of Mycobacterium tuberculosis genotypes among isolates in Lusaka, the capital city, and investigated their association with MDR-TB. METHODS Spoligotyping, large sequence polymorphism (LSP) analysis, and sequencing of MDR associated genes were performed on a total of 274 M. tuberculosis clinical isolates stored at the University Teaching Hospital from 2013 to 2017. Of these, 134 were MDR-TB while 126 were pan-susceptible. RESULTS Spoligotyping showed the LAM family as the most predominant genotype (149/274, 54.4%) followed by the CAS family (44/274, 16.1%), T family (39/274, 14.2%), and minor proportions of X, S, Harleem, EAI and Beijing spoligofamilies were identified. Three M. bovis isolates were also observed. Among those, CAS1-Kili (SIT 21) and LAM1 (SIT 20) subfamilies showed a propensity for MDR-TB with p = 0.0001 and p = 0.001, respectively. CONCLUSIONS This phenomenon might explain the future increase in the MDR-TB burden caused by specific lineages in Zambia. Therefore, it is recommended that the National TB control program in the country complements conventional control strategies with molecular analysis for monitoring and surveillance of MDR-TB epidemiology.
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Affiliation(s)
- Eddie Samuneti Solo
- Department of Pathology and Microbiology, University Teaching Hospital, RW 1X, Ministry of Health, Lusaka, Zambia
| | - Yasuhiko Suzuki
- Division of Bioresources, Hokkaido University Research Center for Zoonosis Control, Sapporo, Japan; International Collaboration Unit, Research Center for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Trevor Kaile
- University of Zambia, School of Medicine, Lusaka, Zambia
| | - Precious Bwalya
- Department of Pathology and Microbiology, University Teaching Hospital, RW 1X, Ministry of Health, Lusaka, Zambia; Division of Bioresources, Hokkaido University Research Center for Zoonosis Control, Sapporo, Japan
| | - Patrick Lungu
- National TB Control Program, Ministry of Health, Zambia
| | - Joseph Yamweka Chizimu
- Division of Bioresources, Hokkaido University Research Center for Zoonosis Control, Sapporo, Japan; Zambia National Public Health Institute, Ministry of Health, Zambia
| | - Yogendra Shah
- Division of Bioresources, Hokkaido University Research Center for Zoonosis Control, Sapporo, Japan
| | - Chie Nakajima
- Division of Bioresources, Hokkaido University Research Center for Zoonosis Control, Sapporo, Japan; International Collaboration Unit, Research Center for Zoonosis Control, Hokkaido University, Sapporo, Japan.
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Mycobacterium tuberculosis polyclonal infections through treatment and recurrence. PLoS One 2020; 15:e0237345. [PMID: 32813724 PMCID: PMC7437862 DOI: 10.1371/journal.pone.0237345] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Accepted: 07/23/2020] [Indexed: 12/02/2022] Open
Abstract
Background Mixed/polyclonal infections due to different genotypes are reported in Tuberculosis. The current study was designed to understand the fate of mixed infections during the course of treatment and follow-up and its role in disease pathogenesis. Methods Sputum samples were collected on 0,1,2,3,6,12 and 24 months from 157 treatment-naïve patients, cultures subjected to Drug-Susceptibility-testing (MGIT 960), spoligotyping, MIRU-VNTR and SNP genotyping. All isolated colonies on thin layer agar (7H11) were subjected to spoligotyping. Findings One thirty three baseline cultures were positive (133/157, 84.7%), 43(32.3%) had mixture of genotypes. Twenty-four of these patients (55.8%) showed change in genotype while six showed different drug-susceptibility patterns while on treatment. Twenty-three (53.5%) patients with polyclonal infections showed resistance to at least one drug compared to 10/90 (11.1%) monoclonal infections (P<0.0001). Eight patients had recurrent TB, two with a new genotype and two with altered phenotypic DST. Conclusions The coexistence of different genotypes and change of genotypes during the same disease episode, while on treatment, confirms constancy of polyclonal infections. The composition of the mixture of genotypes and the relative predominance may be missed by culture due to its limit of detection. Polyclonal infections in TB could be a rule rather than exception and challenges the age-old dogma of reactivation/reinfection.
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Shi J, Zheng D, Zhu Y, Ma X, Wang S, Li H, Xing J. Role of MIRU-VNTR and spoligotyping in assessing the genetic diversity of Mycobacterium tuberculosis in Henan Province, China. BMC Infect Dis 2018; 18:447. [PMID: 30176820 PMCID: PMC6122615 DOI: 10.1186/s12879-018-3351-y] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2017] [Accepted: 08/21/2018] [Indexed: 01/31/2023] Open
Abstract
Background Tuberculosis remains a serious threat to human health as an infectious disease in China. Henan, a most populated province in China, has a high incidence of tuberculosis (TB). Though the genetic diversity of Mycobacterium tuberculosis (MTB) has been investigated in many regions, there have been only a few studies on the molecular characteristics and drug resistance phenotypes in Henan. This is the first study on the genetic profile of MTB from Henan. Methods A total of 668 MTB isolates from various areas were genotyped with spoligotyping and 26-locus MIRU-VNTR (classical 24-locus MIRU-VNTR and 2 other loci). The association between TB spoligotype signatures and drug-resistant profiles was analysed. Results Our data revealed that MTB isolates circulating in Henan had a high degree of genetic variation. The Beijing family was the most predominant genotype (83.53%,n = 558), and the typical Beijing type(ST1) was the major sublineage (81.73%,n = 546). In total,668 isolates were divided into 567 different types, forming 38 clusters (2–15 isolates per cluster), and 529 unique types by 26-locus MIRU-VNTR analysis. There was no correlation between the Beijing family and gender, age at diagnosis or treatment history, whereas the Beijing family was significantly associated with all four first-line drug resistance and multidrug-resistant phenotypes. For these samples, 15 of 26 MIRU-VNTR loci had high or moderate discriminatory power according to the Hunter-Gaston discriminatory index. A combination of the 10 most polymorphic loci had similar discriminatory power as the 26-locus set. Conclusion The Beijing genotype is the most prevalent family. Ten-locus MIRU-VNTR in combination with spoligotyping can efficiently classify the molecular type of MTB in Henan Province. Electronic supplementary material The online version of this article (10.1186/s12879-018-3351-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jie Shi
- Henan Province Center for Disease Control and Prevention, Zheng Zhou, 450016, Henan, People's Republic of China.
| | - Danwei Zheng
- Henan Province Center for Disease Control and Prevention, Zheng Zhou, 450016, Henan, People's Republic of China
| | - Yankun Zhu
- Henan Province Center for Disease Control and Prevention, Zheng Zhou, 450016, Henan, People's Republic of China
| | - Xiaoguang Ma
- Henan Province Center for Disease Control and Prevention, Zheng Zhou, 450016, Henan, People's Republic of China
| | - Shaohua Wang
- Henan Province Center for Disease Control and Prevention, Zheng Zhou, 450016, Henan, People's Republic of China
| | - Hui Li
- Henan Province Center for Disease Control and Prevention, Zheng Zhou, 450016, Henan, People's Republic of China.
| | - Jin Xing
- Henan Province Center for Disease Control and Prevention, Zheng Zhou, 450016, Henan, People's Republic of China
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Sobkowiak B, Glynn JR, Houben RMGJ, Mallard K, Phelan JE, Guerra-Assunção JA, Banda L, Mzembe T, Viveiros M, McNerney R, Parkhill J, Crampin AC, Clark TG. Identifying mixed Mycobacterium tuberculosis infections from whole genome sequence data. BMC Genomics 2018; 19:613. [PMID: 30107785 PMCID: PMC6092779 DOI: 10.1186/s12864-018-4988-z] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2017] [Accepted: 07/31/2018] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND Mixed, polyclonal Mycobacterium tuberculosis infection occurs in natural populations. Developing an effective method for detecting such cases is important in measuring the success of treatment and reconstruction of transmission between patients. Using whole genome sequence (WGS) data, we assess two methods for detecting mixed infection: (i) a combination of the number of heterozygous sites and the proportion of heterozygous sites to total SNPs, and (ii) Bayesian model-based clustering of allele frequencies from sequencing reads at heterozygous sites. RESULTS In silico and in vitro artificially mixed and known pure M. tuberculosis samples were analysed to determine the specificity and sensitivity of each method. We found that both approaches were effective in distinguishing between pure strains and mixed infection where there was relatively high (> 10%) proportion of a minor strain in the mixture. A large dataset of clinical isolates (n = 1963) from the Karonga Prevention Study in Northern Malawi was tested to examine correlations with patient characteristics and outcomes with mixed infection. The frequency of mixed infection in the population was found to be around 10%, with an association with year of diagnosis, but no association with age, sex, HIV status or previous tuberculosis. CONCLUSIONS Mixed Mycobacterium tuberculosis infection was identified in silico using whole genome sequence data. The methods presented here can be applied to population-wide analyses of tuberculosis to estimate the frequency of mixed infection, and to identify individual cases of mixed infections. These cases are important when considering the evolution and transmission of the disease, and in patient treatment.
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Affiliation(s)
- Benjamin Sobkowiak
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, UK
| | - Judith R. Glynn
- Faculty of Epidemiology and Population Health, London School of Hygiene & Tropical Medicine, London, UK
| | - Rein M. G. J. Houben
- Faculty of Epidemiology and Population Health, London School of Hygiene & Tropical Medicine, London, UK
- TB Modelling Group, TB Centre, London School of Hygiene and Tropical Medicine, London, UK
| | - Kim Mallard
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, UK
| | - Jody E. Phelan
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, UK
| | - José Afonso Guerra-Assunção
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, UK
- Bill Lyons Informatics Centre, University College London, London, UK
| | | | | | - Miguel Viveiros
- Global Health and Tropical Medicine, Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa, Lisbon, Portugal
| | - Ruth McNerney
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, UK
| | | | - Amelia C. Crampin
- Faculty of Epidemiology and Population Health, London School of Hygiene & Tropical Medicine, London, UK
- Karonga Prevention Study, Chilumba, Malawi
| | - Taane G. Clark
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, UK
- Faculty of Epidemiology and Population Health, London School of Hygiene & Tropical Medicine, London, UK
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Genetic diversity of Mycobacterium tuberculosis complex isolates circulating in an area with high tuberculosis incidence: Using 24-locus MIRU-VNTR method. Tuberculosis (Edinb) 2018; 112:89-97. [PMID: 30205974 DOI: 10.1016/j.tube.2018.08.003] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2018] [Revised: 07/15/2018] [Accepted: 08/02/2018] [Indexed: 01/24/2023]
Abstract
We aimed to determine the genetic diversity, phylogenetic relationship and transmission dynamics of Mycobacterium tuberculosis complex (MTBC) genotypes in an area with high tuberculosis (TB) incidence. A set of 164 MTBC isolates from new TB patients of Golestan province, Iran, were subjected to genotyping using the standard 24-locus MIRU-VNTR method. Recent TB transmission was evaluated and phylogenetic relationships were analysed by minimum spanning tree and cluster-graph methods. Among the 164 isolates, 132 distinct patterns were detected. The 48 clustered isolates (29.3%) were distributed into 16 clusters ranging in size from 2 to 12 isolates. The most frequent genotype was Central Asian Strain/Delhi (CAS/Delhi) (n = 67, 40.8%), followed by NEW-1 (n = 53, 32.3%) and Beijing (n = 19, 11.6%) genotypes. Thirty five (72.9%) of NEW-1 isolates were recovered from immigrant patients and 84.2% (n = 16) of Beijing genotypes recovered from native cases. Statistically significant association was found between clustering and smoking (p = 0.047), drug addiction (p = 0.01) and prison history (p = 0.003). The estimated proportion of recent transmission was 19.5%. Presence of highly diverse MTBC isolates circulating in this province without a dominant genotype might be a consequence of importation of various genotypes in this area.
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Tarashi S, Fateh A, Mirsaeidi M, Siadat SD, Vaziri F. Mixed infections in tuberculosis: The missing part in a puzzle. Tuberculosis (Edinb) 2017; 107:168-174. [PMID: 29050766 DOI: 10.1016/j.tube.2017.09.004] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2017] [Revised: 09/05/2017] [Accepted: 09/13/2017] [Indexed: 11/26/2022]
Abstract
The mixed strains infection phenomenon is a major problem posing serious challenges in control of tuberculosis (TB). In patients with mixed infection, several different strains of Mycobacterium tuberculosis can be isolated simultaneously. Although different genotyping methods and various molecular approaches can be employed for detection of mixed infection in clinical samples, the MIRU-VNTR technique is more sensitive with higher discriminative power than many widely used techniques. Furthermore, the recent introduction of whole genome sequencing (WGS) promises to reveal more details about mixed infection with high resolution. WGS has been used for detection of mixed infection with high sensitivity and discriminatory, but the technology is currently limited to developed countries. Mixed infection may involve strains with different susceptibility patterns, which may alter the treatment outcome. In this report, we review the current concepts of mixed strains infection and also infection involving strains with a different susceptibility pattern in TB. We evaluate the importance of identifying mixed infection for diagnosis as well as treatment and highlight the accuracy and clinical utility of direct genotyping of clinical specimens.
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Affiliation(s)
- Samira Tarashi
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran; Microbiology Research Center (MRC), Pasteur Institute of Iran, Tehran, Iran
| | - Abolfazl Fateh
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran; Microbiology Research Center (MRC), Pasteur Institute of Iran, Tehran, Iran
| | - Mehdi Mirsaeidi
- Division of Pulmonary and Critical Care, University of Miami, Miami, FL, USA
| | - Seyed Davar Siadat
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran; Microbiology Research Center (MRC), Pasteur Institute of Iran, Tehran, Iran
| | - Farzam Vaziri
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran; Microbiology Research Center (MRC), Pasteur Institute of Iran, Tehran, Iran.
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McIvor A, Koornhof H, Kana BD. Relapse, re-infection and mixed infections in tuberculosis disease. Pathog Dis 2017; 75:3003284. [PMID: 28334088 DOI: 10.1093/femspd/ftx020] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2016] [Accepted: 02/16/2017] [Indexed: 01/19/2023] Open
Abstract
Tuberculosis (TB) disease can be characterized by genotypic and phenotypic complexity in Mycobacterium tuberculosis bacilli within a single patient. This microbiological heterogeneity has become an area of intense study due its perceived importance in drug tolerance, drug resistance and as a surrogate measure of transmission rates. This review presents a descriptive analysis of research describing the prevalence of mixed-strain TB infections in geographically distinct locations. Despite significant variation in disease burden and a rampant human immunodeficiency virus (HIV)-TB co-epidemic, there was no difference in the prevalence range of mixed infections reported in African countries when compared to the rest of the world. The occurrence of recurrent TB was associated with a higher prevalence of mixed-strain infections, but this difference was not reported as statistically significant. These interpretations were limited by differences in the design and overall size of the studies assessed. Factors such as sputum quality, culture media, number of repeated culture steps, molecular typing methods and HIV-infection status can affect the detection of mixed-strain infection. It is recommended that future clinical studies should focus on settings with varying TB burdens, with a common sample processing protocol to gain further insight into these phenomena and develop novel transmission blocking strategies.
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Affiliation(s)
- Amanda McIvor
- DST/NRF Centre of Excellence for Biomedical TB Research, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand and the National Health Laboratory Service, Johannesburg 2000, South Africa
| | - Hendrik Koornhof
- Centre for Tuberculosis, National Institute for Communicable Diseases and National Health Laboratory Service, Johannesburg, 2000, South Africa
| | - Bavesh Davandra Kana
- DST/NRF Centre of Excellence for Biomedical TB Research, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand and the National Health Laboratory Service, Johannesburg 2000, South Africa.,CAPRISA, Centre for the AIDS Programme of Research in South Africa, Durban, 4001, South Africa
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Use of whole-genome sequencing to distinguish relapse from reinfection in a completed tuberculosis clinical trial. BMC Med 2017; 15:71. [PMID: 28351427 PMCID: PMC5371199 DOI: 10.1186/s12916-017-0834-4] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/13/2016] [Accepted: 03/09/2017] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND RIFAQUIN was a tuberculosis chemotherapy trial in southern Africa including regimens with high-dose rifapentine with moxifloxacin. Here, the application of whole-genome sequencing (WGS) is evaluated within RIFAQUIN for identifying new infections in treated patients as either relapses or reinfections. WGS is further compared with mycobacterial interspersed repetitive units-variable number tandem repeats (MIRU-VNTR) typing. This is the first report of WGS being used to evaluate new infections in a completed clinical trial for which all treatment and epidemiological data are available for analysis. METHODS DNA from 36 paired samples of Mycobacterium tuberculosis cultured from patients before and after treatment was typed using 24-loci MIRU-VNTR, in silico spoligotyping and WGS. Following WGS, the sequences were mapped against the reference strain H37Rv, the single-nucleotide polymorphism (SNP) differences between pairs were identified, and a phylogenetic reconstruction was performed. RESULTS WGS indicated that 32 of the paired samples had a very low number of SNP differences (0-5; likely relapses). One pair had an intermediate number of SNP differences, and was likely the result of a mixed infection with a pre-treatment minor genotype that was highly related to the post-treatment genotype; this was reclassified as a relapse, in contrast to the MIRU-VNTR result. The remaining three pairs had very high SNP differences (>750; likely reinfections). CONCLUSIONS WGS and MIRU-VNTR both similarly differentiated relapses and reinfections, but WGS provided significant extra information. The low proportion of reinfections seen suggests that in standard chemotherapy trials with up to 24 months of follow-up, typing the strains brings little benefit to an analysis of the trial outcome in terms of differentiating relapse and reinfection. However, there is a benefit to using WGS as compared to MIRU-VNTR in terms of the additional genotype information obtained, in particular for defining the presence of mixed infections and the potential to identify known and novel drug-resistance markers.
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Farmanfarmaei G, Kargarpour Kamakoli M, Sadegh HR, Masoumi M, Abdolrahimi F, Fateh A, Ebrahimzadeh N, Javadi G, Rahimi Jamnani F, Vaziri F, Siadat SD. Bias in detection of Mycobacterium tuberculosis polyclonal infection: Use clinical samples or cultures? Mol Cell Probes 2017; 33:1-3. [PMID: 28130122 DOI: 10.1016/j.mcp.2017.01.002] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2016] [Revised: 12/23/2016] [Accepted: 01/23/2017] [Indexed: 01/03/2023]
Abstract
The application of MIRU-VNTR has unveiled that infection by Mycobacterium tuberculosis can be polyclonal. Our comparative study demonstrated that based on the studied samples (clinical specimen or culture) detection of polyclonal M. tuberculosis infection can be significantly different.
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Affiliation(s)
- Ghazaleh Farmanfarmaei
- Department of Biology, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | | | - Hamid Reza Sadegh
- Department of Biology, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | - Morteza Masoumi
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran
| | - Farid Abdolrahimi
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran
| | - Abolfazl Fateh
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran; Microbiology Research Center (MRC), Pasteur Institute of Iran, Tehran, Iran
| | - Nayereh Ebrahimzadeh
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran
| | - Gholamreza Javadi
- Department of Biology, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | - Fatemeh Rahimi Jamnani
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran; Microbiology Research Center (MRC), Pasteur Institute of Iran, Tehran, Iran
| | - Farzam Vaziri
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran; Microbiology Research Center (MRC), Pasteur Institute of Iran, Tehran, Iran.
| | - Seyed Davar Siadat
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran; Microbiology Research Center (MRC), Pasteur Institute of Iran, Tehran, Iran
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Sadegh H, Kargarpour Kamakoli M, Farmanfarmaei G, Masoumi M, Abdolrahimi F, Fateh A, Ebrahimzadeh N, Rahimi Jamnani F, Vaziri F, Siadat SD. Pros and cons of direct genotyping on tuberculosis clinical samples. Microb Pathog 2016; 103:135-138. [PMID: 28034830 DOI: 10.1016/j.micpath.2016.12.025] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2016] [Revised: 12/16/2016] [Accepted: 12/16/2016] [Indexed: 11/28/2022]
Abstract
OBJECTIVE Prompt genotyping of Mycobacterium tuberculosis (M. tuberculosis) is crucial for improving molecular epidemiological investigation of tuberculosis (TB). METHODS We performed a retrospective study to evaluate the use of 24 loci MIRU-VNTR (mycobacterial interspersed repetitive unit-variable number of tandem-repeat) directly on 135 clinical samples from 84 TB patients. RESULTS There was a direct correlation between genotyping on clinical samples by MIRU-VNTR and bacterial load (P = 0.001). VNTR loci were amplified successfully for 41.5% of the clinical samples (19-24 loci), 32.6% (13-18 loci), 23.7% (7-12 loci) and 2.2% (1-6 loci). Loci of 2401, 577, 2996 and 154 had the highest power to show the mixed strains infection in clinical samples. CONCLUSIONS Direct MIRU-VNTR is partially successful in complete genotyping of M. tuberculosis strains. On the other hand, detection of polyclonal infection is undoubtedly reliable based on the direct MIRU-VNTR.
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Affiliation(s)
- Hamidreza Sadegh
- Department of Biology, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | | | - Ghazaleh Farmanfarmaei
- Department of Biology, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | - Morteza Masoumi
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran
| | - Farid Abdolrahimi
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran
| | - Abolfazl Fateh
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran; Microbiology Research Center (MRC), Pasteur Institute of Iran, Tehran, Iran
| | - Nayereh Ebrahimzadeh
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran
| | - Fatemeh Rahimi Jamnani
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran; Microbiology Research Center (MRC), Pasteur Institute of Iran, Tehran, Iran
| | - Farzam Vaziri
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran; Microbiology Research Center (MRC), Pasteur Institute of Iran, Tehran, Iran.
| | - Seyed Davar Siadat
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran; Microbiology Research Center (MRC), Pasteur Institute of Iran, Tehran, Iran
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Mohajeri P, Moradi S, Atashi S, Farahani A. Mycobacterium tuberculosis Beijing Genotype in Western Iran: Distribution and Drug Resistance. J Clin Diagn Res 2016; 10:DC05-DC07. [PMID: 27891336 DOI: 10.7860/jcdr/2016/20893.8689] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2016] [Accepted: 08/24/2016] [Indexed: 11/24/2022]
Abstract
INTRODUCTION Mycobacterium tuberculosis Beijing genotype is gaining importance all over the world because this genotype is highly prevalent in several areas and is also frequently associated with drug resistance. AIM To identify and determine the frequency of Beijing genotype and mix infection with Beijing and non-Beijing in west of Iran and analyse the association between Beijing genotype and drug resistance. MATERIALS AND METHODS This cross-sectional study was conducted on 146 Tuberculosis (TB) samples collected at the TB reference laboratory in Kermanshah west of Iran from January 2014 to February 2015, Mycobacterium tuberculosis isolates from sputum samples, detected by microcopy, biochemical tests and solid culture were included and then the confirmed samples with Cepheid Xpert MTB/RIF assay were subjected to drug susceptibility tests for rifampicin, isoniazid, ethambutol using proportional method. The prevalence rate of Beijing and non-Beijing genotype was determined by Multiplex- Polymerase Chain Reaction (PCR). RESULT A total of 15/146 (10%) isolates were diagnosed as Beijing genotypes and the remaining 131/146(90%) isolates were non-Beijing genotypes by Multiplex PCR method. Among the 15 Beijing cases, 14 samples have shown mix infection indicating the presence of both Beijing and non-Beijing strains in samples. Three isolates from all cases were drug resistant. Interestingly all drug resistance isolates were from Beijing genotype which shows strong association between drug resistance and Beijing genotype. Also this genotype was more prevalent in younger age-group people (p=0.035). CONCLUSION Frequency of Beijing genotype in west of Iran is more than other sites of Iran but less than Asia. According to our result, mix infections with Beijing and non-Beijing, had the most prevalence therefore we should be concerned more about mix infections. Multiplex-PCR method is feasible, trustworthy and can distinguish mix infections. It is suggested to perform spoligotyping in addition to multiplex PCR method to discriminate mix infections.
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Affiliation(s)
- Parviz Mohajeri
- Associate Professor of Medical Bacteriology, Department of Microbiology, School of Medicine, Kermanshah University of Medical Sciences , Kermanshah, Iran
| | - Sakineh Moradi
- Research Assistant of Medical Bacteriology, Department of Microbiology, School of Medicine, Kermanshah University of Medical Sciences , Kermanshah, Iran
| | - Sara Atashi
- Research Assistant of Medical Bacteriology, West Tuberculosis Center, Kermanshah University of Medical Sciences , Kermanshah, Iran
| | - Abbas Farahani
- Ph.D student of Medical Bacteriology, Department of Microbiology, School of Medicine, Ahvaz Jundishapur University of Medical Sciences , Ahvaz, IR Iran. Student Research Committee, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, IR Iran
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Standard Genotyping Overestimates Transmission of Mycobacterium tuberculosis among Immigrants in a Low-Incidence Country. J Clin Microbiol 2016; 54:1862-1870. [PMID: 27194683 DOI: 10.1128/jcm.00126-16] [Citation(s) in RCA: 76] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2016] [Accepted: 04/29/2016] [Indexed: 11/20/2022] Open
Abstract
Immigrants from regions with a high incidence of tuberculosis (TB) are a risk group for TB in low-incidence countries such as Switzerland. In a previous analysis of a nationwide collection of 520 Mycobacterium tuberculosis isolates from 2000 to 2008, we identified 35 clusters comprising 90 patients based on standard genotyping (24-locus mycobacterial interspersed repetitive-unit-variable-number tandem-repeat [MIRU-VNTR] typing and spoligotyping). Here, we used whole-genome sequencing (WGS) to revisit these transmission clusters. Genome-based transmission clusters were defined as isolate pairs separated by ≤12 single nucleotide polymorphisms (SNPs). WGS confirmed 17/35 (49%) MIRU-VNTR typing clusters; the other 18 clusters contained pairs separated by >12 SNPs. Most transmission clusters (3/4) of Swiss-born patients were confirmed by WGS, as opposed to 25% (4/16) of the clusters involving only foreign-born patients. The overall clustering proportion was 17% (90 patients; 95% confidence interval [CI], 14 to 21%) by standard genotyping but only 8% (43 patients; 95% CI, 6 to 11%) by WGS. The clustering proportion was 17% (67/401; 95% CI, 13 to 21%) by standard genotyping and 7% (26/401; 95% CI, 4 to 9%) by WGS among foreign-born patients and 19% (23/119; 95% CI, 13 to 28%) and 14% (17/119; 95% CI, 9 to 22%), respectively, among Swiss-born patients. Using weighted logistic regression, we found weak evidence of an association between birth origin and transmission (adjusted odds ratio of 2.2 and 95% CI of 0.9 to 5.5 comparing Swiss-born patients to others). In conclusion, standard genotyping overestimated recent TB transmission in Switzerland compared to WGS, particularly among immigrants from regions with a high TB incidence, where genetically closely related strains often predominate. We recommend the use of WGS to identify transmission clusters in settings with a low incidence of TB.
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Mbugi EV, Katale BZ, Streicher EM, Keyyu JD, Kendall SL, Dockrell HM, Michel AL, Rweyemamu MM, Warren RM, Matee MI, van Helden PD, Couvin D, Rastogi N. Mapping of Mycobacterium tuberculosis Complex Genetic Diversity Profiles in Tanzania and Other African Countries. PLoS One 2016; 11:e0154571. [PMID: 27149626 PMCID: PMC4858144 DOI: 10.1371/journal.pone.0154571] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2016] [Accepted: 04/15/2016] [Indexed: 11/23/2022] Open
Abstract
The aim of this study was to assess and characterize Mycobacterium tuberculosis complex (MTBC) genotypic diversity in Tanzania, as well as in neighbouring East and other several African countries. We used spoligotyping to identify a total of 293 M. tuberculosis clinical isolates (one isolate per patient) collected in the Bunda, Dar es Salaam, Ngorongoro and Serengeti areas in Tanzania. The results were compared with results in the SITVIT2 international database of the Pasteur Institute of Guadeloupe. Genotyping and phylogeographical analyses highlighted the predominance of the CAS, T, EAI, and LAM MTBC lineages in Tanzania. The three most frequent Spoligotype International Types (SITs) were: SIT21/CAS1-Kili (n = 76; 25.94%), SIT59/LAM11-ZWE (n = 22; 7.51%), and SIT126/EAI5 tentatively reclassified as EAI3-TZA (n = 18; 6.14%). Furthermore, three SITs were newly created in this study (SIT4056/EAI5 n = 2, SIT4057/T1 n = 1, and SIT4058/EAI5 n = 1). We noted that the East-African-Indian (EAI) lineage was more predominant in Bunda, the Manu lineage was more common among strains isolated in Ngorongoro, and the Central-Asian (CAS) lineage was more predominant in Dar es Salaam (p-value<0.0001). No statistically significant differences were noted when comparing HIV status of patients vs. major lineages (p-value = 0.103). However, when grouping lineages as Principal Genetic Groups (PGG), we noticed that PGG2/3 group (Haarlem, LAM, S, T, and X) was more associated with HIV-positive patients as compared to PGG1 group (Beijing, CAS, EAI, and Manu) (p-value = 0.03). This study provided mapping of MTBC genetic diversity in Tanzania (containing information on isolates from different cities) and neighbouring East African and other several African countries highlighting differences as regards to MTBC genotypic distribution between Tanzania and other African countries. This work also allowed underlining of spoligotyping patterns tentatively grouped within the newly designated EAI3-TZA lineage (remarkable by absence of spacers 2 and 3, and represented by SIT126) which seems to be specific to Tanzania. However, further genotyping information would be needed to confirm this specificity.
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Affiliation(s)
- Erasto V. Mbugi
- Department of Biochemistry, Muhimbili University of Health and Allied Sciences, P. O. Box 65001, Dar es Salaam, Tanzania
- Department of Microbiology and Immunology, Muhimbili University of Health and Allied Sciences, P.O. Box 65001, Dar es Salaam, Tanzania
| | - Bugwesa Z. Katale
- Department of Microbiology and Immunology, Muhimbili University of Health and Allied Sciences, P.O. Box 65001, Dar es Salaam, Tanzania
- Tanzania Wildlife Research Institute (TAWIRI), P.O. Box 661, Arusha, Tanzania
| | - Elizabeth M. Streicher
- DST/NRF Centre of Excellence for Biomedical Tuberculosis Research/ South African Medical Research Council (MRC) Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Health Sciences, Stellenbosch University, P.O. Box 241, Cape Town, 8000, South Africa
| | - Julius D. Keyyu
- Tanzania Wildlife Research Institute (TAWIRI), P.O. Box 661, Arusha, Tanzania
| | - Sharon L. Kendall
- Department of Immunology and Infection, London School of Hygiene and Tropical Medicine, Keppel Street, London, WC1E 7HT, United Kingdom
| | - Hazel M. Dockrell
- The Royal Veterinary College, Royal College Street, London, NW1 0TU, United Kingdom
| | - Anita L. Michel
- Department of Veterinary Tropical Diseases, Faculty of Veterinary Science, University of Pretoria, Pretoria, South Africa
| | - Mark M. Rweyemamu
- Southern African Centre for Infectious Disease Surveillance, Sokoine University of Agriculture, Morogoro, Tanzania
| | - Robin M. Warren
- DST/NRF Centre of Excellence for Biomedical Tuberculosis Research/ South African Medical Research Council (MRC) Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Health Sciences, Stellenbosch University, P.O. Box 241, Cape Town, 8000, South Africa
| | - Mecky I. Matee
- Department of Microbiology and Immunology, Muhimbili University of Health and Allied Sciences, P.O. Box 65001, Dar es Salaam, Tanzania
| | - Paul D. van Helden
- DST/NRF Centre of Excellence for Biomedical Tuberculosis Research/ South African Medical Research Council (MRC) Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Health Sciences, Stellenbosch University, P.O. Box 241, Cape Town, 8000, South Africa
| | - David Couvin
- WHO Supranational TB Reference Laboratory, Tuberculosis & Mycobacteria Unit, Institut Pasteur de la Guadeloupe, Morne Joliviere, BP 484, 97183, Abymes, Guadeloupe
| | - Nalin Rastogi
- WHO Supranational TB Reference Laboratory, Tuberculosis & Mycobacteria Unit, Institut Pasteur de la Guadeloupe, Morne Joliviere, BP 484, 97183, Abymes, Guadeloupe
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Hajimiri ES, Masoomi M, Ebrahimzadeh N, Fateh A, Hadizadeh Tasbiti A, Rahimi Jamnani F, Bahrmand AR, Mirsaeidi M, Vaziri F, Siadat SD. High prevalence of Mycobacterium tuberculosis mixed infection in the capital of moderate tuberculosis incidence country. Microb Pathog 2016; 93:213-8. [PMID: 26944666 DOI: 10.1016/j.micpath.2016.02.015] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2016] [Revised: 02/24/2016] [Accepted: 02/26/2016] [Indexed: 11/27/2022]
Abstract
OBJECTIVE Recent studies using molecular epidemiological techniques have demonstrated mixed infection with multiple strains of Mycobacterium tuberculosis especially in countries with high tuberculosis (TB) burden. We aimed to determine the prevalence of mixed infection among patients with TB in the capital of Iran as a country with moderate incidence rate. METHODS Samples were collected randomly from January 2011 to December 2013 in Tehran, capital of Iran. A total of 75 M. tuberculosis isolates were genotyped by 24 loci mycobacterial interspersed repetitive unit-variable number tandem repeat typing (MIRU-VNTR) for screening the mixed infection. RESULTS Twenty patients (20/75) were identified with mixed infection, and the estimated rate of mixed infection was 26.6%. Thirteen out of the 24 loci were able to detect the mixed infection in our study. CONCLUSIONS Mixed infections occur at high prevalence among studied Iranian TB patients. Further research is inevitable to evaluate the association of mixed infection and disease progression and treatment.
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Affiliation(s)
- Elahe Sadat Hajimiri
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran; Department of Microbiology, Zanjan Branch, Islamic Azad University, Zanjan, Iran
| | - Morteza Masoomi
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran; Department of Microbiology, Qom Branch, Islamic Azad University, Qom, Iran
| | - Nayereh Ebrahimzadeh
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran
| | - Abolfazl Fateh
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran; Microbiology Research Center (MRC), Pasteur Institute of Iran, Tehran, Iran
| | | | - Fatemeh Rahimi Jamnani
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran; Microbiology Research Center (MRC), Pasteur Institute of Iran, Tehran, Iran
| | - Ahmad Reza Bahrmand
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran
| | - Mehdi Mirsaeidi
- Division of Pulmonary and Critical Care, University of Miami, Miami, FL, USA
| | - Farzam Vaziri
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran; Microbiology Research Center (MRC), Pasteur Institute of Iran, Tehran, Iran.
| | - Seyed Davar Siadat
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran; Microbiology Research Center (MRC), Pasteur Institute of Iran, Tehran, Iran
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N'guessan Kouassi K, Riccardo A, Dutoziet Christian C, André G, Férilaha C, Hortense SA, Jean-Marc A, Daniela Maria C, Mireille D. Genotyping of mutations detected with GeneXpert. Int J Mycobacteriol 2016; 5:142-7. [PMID: 27242224 DOI: 10.1016/j.ijmyco.2016.01.001] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2015] [Revised: 01/25/2016] [Accepted: 01/30/2016] [Indexed: 11/26/2022] Open
Abstract
OBJECTIVE/BACKGROUND Tuberculosis remains an important cause of mortality worldwide. Previous tuberculosis treatment is a strong determinant of multi-drug resistant tuberculosis. The study objective was to describe the mutations detected of Mycobacterium tuberculosis (MTB) complex clinical strains screened with GeneXpert isolated from previously treated patients in Côte d'Ivoire. METHODS Sputum collected and decontaminated by the n-acetyl-l-cysteine method was used to perform Ziehl-Neelsen staining, GeneXpert MTB/rifampicin, and culture on Lowenstein-Jensen medium. Drug susceptibility testing (DST) for first-line drugs was performed in a Bactec 960 Automated System. After strain identification by antigen MPT64 detection, DNA extraction, and genotyping with MTBDRplus assay was performed and interpreted. The strains muted in rpoB without a specific protein identified and were sequenced. RESULTS Mutant sequences were detected in 60 sputum samples with GeneXpert MTB/rifampicin of which 55 were confirmed multi-drug resistant MTB strains after DST. The most frequent mutations responsible for rifampin resistance were detected with MTBDRplus assay for 49 (81.7%) clinical strains, while sequencing was required for 11 (18.3%). H526Q mutation, L533P, and D516V associated respectively with L533P, A532A, and S522L, and were observed for three relapse cases. For these cases, GeneXpert and sequencing results were concordant. Discrepancies between GeneXpert and mycobacteria growth indicator tube-DST for rifampin were observed for three strains, on which D516Y, H526C, and L533P were identified. CONCLUSION In the setting of a high prevalence of drug resistance, characterization of the genetic basis of MTB strains resistant to rifampin could be screened first with MTBDRplus.
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Affiliation(s)
- K N'guessan Kouassi
- Laboratoire National de Référence de la Tuberculose, Institut Pasteur de Côte d'Ivoire, 01 BP 490 Abidjan 01, Cote d'Ivoire.
| | | | - C Dutoziet Christian
- Laboratoire National de Référence de la Tuberculose, Institut Pasteur de Côte d'Ivoire, 01 BP 490 Abidjan 01, Cote d'Ivoire
| | - Guei André
- Laboratoire National de Référence de la Tuberculose, Institut Pasteur de Côte d'Ivoire, 01 BP 490 Abidjan 01, Cote d'Ivoire
| | - Coulibaly Férilaha
- Laboratoire National de Référence de la Tuberculose, Institut Pasteur de Côte d'Ivoire, 01 BP 490 Abidjan 01, Cote d'Ivoire
| | - Seck-Angu Hortense
- Laboratoire National de Référence de la Tuberculose, Institut Pasteur de Côte d'Ivoire, 01 BP 490 Abidjan 01, Cote d'Ivoire
| | - Assandé Jean-Marc
- Laboratoire National de Référence de la Tuberculose, Institut Pasteur de Côte d'Ivoire, 01 BP 490 Abidjan 01, Cote d'Ivoire
| | | | - Dosso Mireille
- Laboratoire National de Référence de la Tuberculose, Institut Pasteur de Côte d'Ivoire, 01 BP 490 Abidjan 01, Cote d'Ivoire
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An investigation on the population structure of mixed infections of Mycobacterium tuberculosis in Inner Mongolia, China. Tuberculosis (Edinb) 2015; 95:695-700. [PMID: 26542224 DOI: 10.1016/j.tube.2015.08.006] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2015] [Revised: 08/04/2015] [Accepted: 08/10/2015] [Indexed: 11/24/2022]
Abstract
OBJECTIVES Mixed infections of Mycobacterium tuberculosis strains have attracted more attention due to their increasing frequencies worldwide, especially in the areas of high tuberculosis (TB) prevalence. In this study, we accessed the rates of mixed infections in a setting with high TB prevalence in Inner Mongolia Autonomous Region of China. METHODS A total of 384 M. tuberculosis isolates from the local TB hospital were subjected to mycobacterial interspersed repetitive unit-variable number tandem repeat (MIRU-VNTR) typing method. The single clones of the strains with mixed infections were separated by subculturing them on the Löwenstein-Jensen medium. RESULTS Of these 384 isolates, twelve strains (3.13%) were identified as mixed infections by MIRU-VNTR. Statistical analysis indicated that demographic characteristics and drug susceptibility profiles showed no statistically significant association with the mixed infections. We further subcultured the mixed infection strains and selected 30 clones from the subculture for each mixed infection. Genotyping data revealed that eight (8/12, 66.7%) strains with mixed infections had converted into single infection through subculture. The higher growth rate was associated with the increasing proportion of variant subpopulation through subculture. CONCLUSIONS In conclusion, by using the MIRU-VNTR method, we demonstrate that the prevalence of mixed infections in Inner Mongolia is low. Additionally, our findings reveal that the subculture changes the population structures of mixed infections, and the subpopulation with higher growth rate show better fitness, which is associated with high proportion among the population structure after subculture. This study highlights that the use of clinical specimens, rather than subcultured isolates, is preferred to estimate the prevalence of mixed infections in the specific regions.
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Wampande EM, Hatzios SK, Achan B, Mupere E, Nsereko M, Mayanja HK, Eisenach K, Boom WH, Gagneux S, Joloba ML. A single-nucleotide-polymorphism real-time PCR assay for genotyping of Mycobacterium tuberculosis complex in peri-urban Kampala. BMC Infect Dis 2015; 15:396. [PMID: 26423522 PMCID: PMC4590274 DOI: 10.1186/s12879-015-1121-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2015] [Accepted: 09/11/2015] [Indexed: 01/25/2023] Open
Abstract
Background Accurate and high-throughput genotyping of Mycobacterium tuberculosis complex (MTBC) may be important for understanding the epidemiology and pathogenesis of tuberculosis (TB). In this study, we report the development of a LightCycler® real-time PCR single-nucleotide-polymorphism (LRPS) assay for the rapid determination of MTBC lineages/sublineages in minimally processed sputum samples from TB patients. Method Genotyping analysis of 70 MTBC strains was performed using the Long Sequence Polymorphism-PCR (LSP-PCR) technique and the LRPS assay in parallel. For targeted sequencing, 9 MTBC isolates (three isolates per MTBC lineage) were analyzed for lineage-specific single nucleotide polymorphisms (SNPs) in the following three genes to verify LRPS results: Rv004c for MTB Uganda family, Rv2962 for MTB lineage 4, and Rv0129c for MTB lineage 3. The MTBC lineages present in 300 smear-positive sputum samples were then determined by the validated LRPS method without prior culturing. Results The LSP-PCR and LRPS assays produced consistent genotyping data for all 70 MTBC strains; however, the LSP-PCR assay was 10-fold less sensitive than the LRPS method and required higher DNA concentrations to successfully characterize the MTBC lineage of certain samples. Targeted sequencing of genes containing lineage-specific SNPs was 100 % concordant with the genotyping results and provided further validation of the LRPS assay. Of the 300 sputum samples analyzed, 58 % contained MTBC from the MTBC-Uganda family, 27 % from the MTBC lineage 4 (excluding MTBC Uganda family), 13 % from the MTBC lineage 3, and the remaining 2 % were of indeterminate lineage. Conclusion The LRPS assay is a sensitive, high-throughput technique with potential application to routine genotyping of MTBC in sputum samples from TB patients. Electronic supplementary material The online version of this article (doi:10.1186/s12879-015-1121-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Eddie M Wampande
- Department of Medical Microbiology, College of Health Sciences, School of Biomedical Sciences, Makerere University, P.O BOX 7072, Kampala, Uganda. .,Department of Bio-molecular Resources and Biolab Sciences, College of Veterinary Medicine, Animal Resources and Bio Security, Makerere University, Kampala, Uganda.
| | - Stavroula K Hatzios
- Department of Medical Microbiology, College of Health Sciences, School of Biomedical Sciences, Makerere University, P.O BOX 7072, Kampala, Uganda. .,Division of Infectious Diseases, Brigham and Women's Hospital, Boston, Massachusetts, USA Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA, USA.
| | - Beatrice Achan
- Department of Medical Microbiology, College of Health Sciences, School of Biomedical Sciences, Makerere University, P.O BOX 7072, Kampala, Uganda.
| | - Ezekiel Mupere
- Department of Pediatrics and Child Health College of Health Sciences, Makerere University, Kampala, Uganda.
| | - Mary Nsereko
- Uganda-Case Western Reserve University Research Collaboration, Kampala, Uganda.
| | - Harriet K Mayanja
- Uganda-Case Western Reserve University Research Collaboration, Kampala, Uganda.
| | - Kathleen Eisenach
- Department of Pathology, University of Arkansas for Medical Sciences, Little Rock, AR, USA.
| | - W Henry Boom
- Tuberculosis Research Unit, School of Medicine, Case Western Reserve University and University Hospitals of Cleveland, Cleveland, Ohio, USA.
| | - Sebastien Gagneux
- Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, Basel, Switzerland. .,University of Basel, Basel, Switzerland.
| | - Moses L Joloba
- Department of Medical Microbiology, College of Health Sciences, School of Biomedical Sciences, Makerere University, P.O BOX 7072, Kampala, Uganda. .,Uganda-Case Western Reserve University Research Collaboration, Kampala, Uganda.
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Glynn JR, Guerra-Assunção JA, Houben RMGJ, Sichali L, Mzembe T, Mwaungulu LK, Mwaungulu JN, McNerney R, Khan P, Parkhill J, Crampin AC, Clark TG. Whole Genome Sequencing Shows a Low Proportion of Tuberculosis Disease Is Attributable to Known Close Contacts in Rural Malawi. PLoS One 2015; 10:e0132840. [PMID: 26181760 PMCID: PMC4504505 DOI: 10.1371/journal.pone.0132840] [Citation(s) in RCA: 74] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2015] [Accepted: 06/18/2015] [Indexed: 12/12/2022] Open
Abstract
Background The proportion of tuberculosis attributable to transmission from close contacts is not well known. Comparison of the genome of strains from index patients and prior contacts allows transmission to be confirmed or excluded. Methods In Karonga District, Malawi, all tuberculosis patients are asked about prior contact with others with tuberculosis. All available strains from culture-positive patients were sequenced. Up to 10 single nucleotide polymorphisms between index patients and their prior contacts were allowed for confirmation, and ≥ 100 for exclusion. The population attributable fraction was estimated from the proportion of confirmed transmissions and the proportion of patients with contacts. Results From 1997–2010 there were 1907 new culture-confirmed tuberculosis patients, of whom 32% reported at least one family contact and an additional 11% had at least one other contact; 60% of contacts had smear-positive disease. Among case-contact pairs with sequences available, transmission was confirmed from 38% (62/163) smear-positive prior contacts and 0/17 smear-negative prior contacts. Confirmed transmission was more common in those related to the prior contact (42.4%, 56/132) than in non-relatives (19.4%, 6/31, p = 0.02), and in those with more intense contact, to younger index cases, and in more recent years. The proportion of tuberculosis attributable to known contacts was estimated to be 9.4% overall. Conclusions In this population known contacts only explained a small proportion of tuberculosis cases. Even those with a prior family contact with smear positive tuberculosis were more likely to have acquired their infection elsewhere.
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Affiliation(s)
- Judith R. Glynn
- Faculty of Epidemiology and Population Health, London School of Hygiene & Tropical Medicine, London, United Kingdom
- * E-mail:
| | - José Afonso Guerra-Assunção
- Faculty of Epidemiology and Population Health, London School of Hygiene & Tropical Medicine, London, United Kingdom
| | - Rein M. G. J. Houben
- Faculty of Epidemiology and Population Health, London School of Hygiene & Tropical Medicine, London, United Kingdom
| | | | | | | | | | - Ruth McNerney
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, United Kingdom
| | - Palwasha Khan
- Faculty of Epidemiology and Population Health, London School of Hygiene & Tropical Medicine, London, United Kingdom
| | | | - Amelia C. Crampin
- Faculty of Epidemiology and Population Health, London School of Hygiene & Tropical Medicine, London, United Kingdom
- Karonga Prevention Study, Chilumba, Malawi
| | - Taane G. Clark
- Faculty of Epidemiology and Population Health, London School of Hygiene & Tropical Medicine, London, United Kingdom
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, United Kingdom
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Prevalence and risk factors of mixed Mycobacterium tuberculosis complex infections in China. J Infect 2015; 71:231-7. [PMID: 25936744 DOI: 10.1016/j.jinf.2015.03.012] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2014] [Revised: 03/01/2015] [Accepted: 03/16/2015] [Indexed: 11/21/2022]
Abstract
OBJECTIVES Mixed infections have been considered as a potential obstacle for tuberculosis treatment and control. To date, few studies have been done to determine the rate of mixed infections of Mycobacterium tuberculosis in China. METHODS In this study, we used the standard 24-loci MIRU-VNTR method to genotype the representative M. tuberculosis isolates from the national drug-resistant survey conducted in China. A total of 3248 M. tuberculosis complex (MTBC) strains had complete 24-loci MIRU-VNTR results and available for the analyses. RESULTS Overall, MIRU-VNTR typing identified 115 (3.5%) isolates as being mixed MTBC infections in China. Statistical analysis revealed that mixed infections were significantly more likely to occur in men than women. Compared with the percentage of mixed infection from patients aged 45-56 years, the percentages of mixed infections were higher among patients aged 25-44 years [OR (95% CI): 1.844(1.129-3.014)] and old patients [older than 65 years OR (95% CI): 1.908(1.097-3.319)]. In addition, significantly higher frequencies of hemoptysis (P = 0.022) and chest pain (P = 0.012) were observed among mixed infections, using patients infected with a single strain as a reference. CONCLUSIONS In conclusion, this study has provided the first comprehensive understanding of mixed MTBC infections in China, which will be essential to generate the effective TB control strategies.
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Mixed Infections and Rifampin Heteroresistance among Mycobacterium tuberculosis Clinical Isolates. J Clin Microbiol 2015; 53:2138-47. [PMID: 25903578 DOI: 10.1128/jcm.03507-14] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2014] [Accepted: 04/16/2015] [Indexed: 11/20/2022] Open
Abstract
Mixed infections and heteroresistance of Mycobacterium tuberculosis contribute to the difficulty of diagnosis, treatment, and control of tuberculosis. However, there is still no proper solution for these issues. This study aimed to investigate the potential relationship between mixed infections and heteroresistance and to determine the high-risk groups related to these factors. A total of 499 resistant and susceptible isolates were subjected to spoligotyping and 24-locus variable-number tandem repeat methods to analyze their genotypic lineages and the occurrence of mixed infections. Two hundred ninety-two randomly selected isolates were sequenced on their rpoB gene to examine mutations and heteroresistance. The results showed that 12 patients had mixed infections, and the corresponding isolates belonged to Manu2 (n = 8), Beijing (n = 2), T (n = 1), and unknown (n = 1) lineages. Manu2 was found to be significantly associated with mixed infections (odds ratio, 47.72; confidence interval, 9.68 to 235.23; P < 0.01). Four isolates (1.37%) were confirmed to be heteroresistant, which was caused by mixed infections in three (75%) isolates; these belonged to Manu2. Additionally, 3.8% of the rifampin-resistant isolates showing no mutation in the rpoB gene were significantly associated with mixed infections (χ(2), 56.78; P < 0.01). This study revealed for the first time that Manu2 was the predominant group in the cases of mixed infections, and this might be the main reason for heteroresistance and a possible mechanism for isolates without any mutation in the rpoB gene to become rifampin resistant. Further studies should focus on this lineage to clarify its relevance to mixed infections.
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Guerra-Assunção JA, Houben RMGJ, Crampin AC, Mzembe T, Mallard K, Coll F, Khan P, Banda L, Chiwaya A, Pereira RPA, McNerney R, Harris D, Parkhill J, Clark TG, Glynn JR. Recurrence due to relapse or reinfection with Mycobacterium tuberculosis: a whole-genome sequencing approach in a large, population-based cohort with a high HIV infection prevalence and active follow-up. J Infect Dis 2015; 211:1154-63. [PMID: 25336729 PMCID: PMC4354982 DOI: 10.1093/infdis/jiu574] [Citation(s) in RCA: 118] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2014] [Accepted: 10/04/2014] [Indexed: 11/12/2022] Open
Abstract
BACKGROUND Recurrent tuberculosis is a major health burden and may be due to relapse with the original strain or reinfection with a new strain. METHODS In a population-based study in northern Malawi, patients with tuberculosis diagnosed from 1996 to 2010 were actively followed after the end of treatment. Whole-genome sequencing with approximately 100-fold coverage was performed on all available cultures. Results of IS6110 restriction fragment-length polymorphism analyses were available for cultures performed up to 2008. RESULTS Based on our data, a difference of ≤10 single-nucleotide polymorphisms (SNPs) was used to define relapse, and a difference of >100 SNPs was used to define reinfection. There was no evidence of mixed infections among those classified as reinfections. Of 1471 patients, 139 had laboratory-confirmed recurrences: 55 had relapse, and 20 had reinfection; for 64 type of recurrence was unclassified. Almost all relapses occurred in the first 2 years. Human immunodeficiency virus infection was associated with reinfection but not relapse. Relapses were associated with isoniazid resistance, treatment before 2007, and lineage-3 strains. We identified several gene variants associated with relapse. Lineage-2 (Beijing) was overrepresented and lineage-1 underrepresented among the reinfecting strains (P = .004). CONCLUSIONS While some of the factors determining recurrence depend on the patient and their treatment, differences in the Mycobacterium tuberculosis genome appear to have a role in both relapse and reinfection.
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Affiliation(s)
| | - Rein M. G. J. Houben
- Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine
| | - Amelia C. Crampin
- Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine
- Karonga Prevention Study, Malawi
| | | | - Kim Mallard
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine
| | - Francesc Coll
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine
| | - Palwasha Khan
- Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine
| | | | | | - Rui P. A. Pereira
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine
| | - Ruth McNerney
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine
| | - David Harris
- Wellcome Trust Sanger Institute, Hinxton, United Kingdom
| | | | - Taane G. Clark
- Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine
| | - Judith R. Glynn
- Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine
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Guerra-Assunção JA, Crampin AC, Houben RMGJ, Mzembe T, Mallard K, Coll F, Khan P, Banda L, Chiwaya A, Pereira RPA, McNerney R, Fine PEM, Parkhill J, Clark TG, Glynn JR. Large-scale whole genome sequencing of M. tuberculosis provides insights into transmission in a high prevalence area. eLife 2015; 4. [PMID: 25732036 PMCID: PMC4384740 DOI: 10.7554/elife.05166] [Citation(s) in RCA: 168] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2014] [Accepted: 01/22/2015] [Indexed: 11/13/2022] Open
Abstract
To improve understanding of the factors influencing tuberculosis transmission and the
role of pathogen variation, we sequenced all available specimens from patients
diagnosed over 15 years in a whole district in Malawi. Mycobacterium
tuberculosis lineages were assigned and transmission networks
constructed, allowing ≤10 single nucleotide polymorphisms (SNPs) difference.
We defined disease as due to recent infection if the network-determined source was
within 5 years, and assessed transmissibility from forward transmissions resulting in
disease. High-quality sequences were available for 1687 disease episodes (72% of all
culture-positive episodes): 66% of patients linked to at least one other patient. The
between-patient mutation rate was 0.26 SNPs/year (95% CI 0.21–0.31). We showed
striking differences by lineage in the proportion of disease due to recent
transmission and in transmissibility (highest for lineage-2 and lowest for lineage-1)
that were not confounded by immigration, HIV status or drug resistance. Transmissions
resulting in disease decreased markedly over time. DOI:http://dx.doi.org/10.7554/eLife.05166.001 Tuberculosis is an important public health threat around the globe and is
particularly common in developing countries. It is difficult to control the spread of
the disease because the bacteria that cause it can spread when an infected individual
coughs or sneezes. It may take years for an infected individual to develop symptoms
of tuberculosis so it can be hard to trace the source of an outbreak, and people
infected with HIV are particularly susceptible to the disease. The bacterium that causes the majority of cases of tuberculosis is called
Mycobacterium tuberculosis. There are several different varieties
or ‘lineages’ of M. tuberculosis, and it is thought
that they may vary in their ability to spread and cause disease. However, the results
of previous studies have been inconsistent and there also seems to be a lot of
variation between strains within the same lineage. In this study, Guerra-Assunção et al. used an approach called whole
genome sequencing alongside more traditional methods to study the spread of
tuberculosis in Malawi. They sequenced the genomes of every available sample of
M. tuberculosis collected from patients in the Karonga district
of Malawi over a 15-year period. This produced high-quality DNA sequence data about
the bacteria responsible for almost 1700 cases of disease. Using this massive amount of data, Guerra-Assunção et al. constructed
networks that showed how the bacteria had spread in the community. This revealed that
there were differences between the ability of the various M.
tuberculosis lineages to cause disease and to spread in communities. For
example, lineage 1 was less likely than the other lineages to cause disease soon
after infecting an individual and was less able to spread. The data also show that the proportion of cases of disease due to recent infection
declined substantially during the 15-year period. This indicates that the
tuberculosis and HIV control programmes in the area have been successful. Guerra-Assunção et al.'s findings show that it is possible to
understand how tuberculosis is transmitted on a large scale. The next challenge is to
understand why the lineages differ in their ability to cause disease and spread
between individuals. DOI:http://dx.doi.org/10.7554/eLife.05166.002
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Affiliation(s)
- J A Guerra-Assunção
- Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - A C Crampin
- Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - R M G J Houben
- Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - T Mzembe
- Karonga Prevention Study, Malawi, Malawi
| | - K Mallard
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - F Coll
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - P Khan
- Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - L Banda
- Karonga Prevention Study, Malawi, Malawi
| | - A Chiwaya
- Karonga Prevention Study, Malawi, Malawi
| | - R P A Pereira
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - R McNerney
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - P E M Fine
- Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - J Parkhill
- Wellcome Trust Sanger Institute, Hinxton, United Kingdom
| | - T G Clark
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - J R Glynn
- Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, London, United Kingdom
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Malama S, Muma J, Munyeme M, Mbulo G, Muwonge A, Shamputa IC, Djønne B, Godfroid J, Johansen TB. Isolation and molecular characterization of Mycobacterium tuberculosis from humans and cattle in Namwala District, Zambia. ECOHEALTH 2014; 11:564-570. [PMID: 24845573 DOI: 10.1007/s10393-014-0940-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2013] [Revised: 03/25/2014] [Accepted: 03/27/2014] [Indexed: 05/28/2023]
Abstract
Mycobacterium tuberculosis, the causative agent of tuberculosis in humans, is considered primarily a human pathogen. It has, however, been reported in a wide range of domestic and wild animals, often living in close prolonged contact with humans. Sputum samples in which acid fast bacteria were detected in smears were collected from patients at three health facilities in Namwala district, Zambia. Samples from cattle presenting gross lesions compatible with bovine tuberculosis were collected at a local abattoir in the same district. Isolated mycobacteria were identified and genotyped using classical molecular methods. From a total of 33 isolates of M. tuberculosis detected (30 from humans and 3 from cattle), two cattle isolates shared the same spoligotype and MIRU-VNTR pattern with a human patient. This study has for the first time documented the isolation of M. tuberculosis from cattle in Zambia and provides molecular evidence of an epidemiological link between M. tuberculosis isolates from humans and cattle in Namwala district. A possible spill back of M. tuberculosis to humans cannot be excluded and therefore further studies documenting to what extent M. tuberculosis is shed in cattle milk are needed. This finding further suggests that veterinary public health measures to control human TB, should also take into account the bovine reservoir.
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Affiliation(s)
- Sydney Malama
- Institute of Economic and Social Research, University of Zambia, P.O. Box 30900, Munali Road, Lusaka, Zambia,
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Ahmad Khan F, Behr M. Resistant plus susceptible tuberculosis: the undiscovered country. J Infect Dis 2014; 209:1682-4. [PMID: 24523512 DOI: 10.1093/infdis/jiu078] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- Faiz Ahmad Khan
- Respiratory Epidemiology and Clinical Research Unit, Montreal Chest Institute, McGill University Health Centre
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Hingley-Wilson SM, Casey R, Connell D, Bremang S, Evans JT, Hawkey PM, Smith GE, Jepson A, Philip S, Kon OM, Lalvani A. Undetected multidrug-resistant tuberculosis amplified by first-line therapy in mixed infection. Emerg Infect Dis 2014; 19:1138-41. [PMID: 23764343 DOI: 10.3201/1907.130313] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Infections with >1 Mycobacterium tuberculosis strain(s) are underrecognized. We show, in vitro and in vivo, how first-line treatment conferred a competitive growth advantage to amplify a multidrug-resistant M. tuberculosis strain in a patient with mixed infection. Diagnostic techniques that identify mixed tubercle bacilli populations are needed to curb the spread of multidrug resistance.
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Hingley-Wilson SM, Casey R, Connell D, Bremang S, Evans JT, Hawkey PM, Smith GE, Jepson A, Philip S, Kon OM, Lalvani A. Undetected multidrug-resistant tuberculosis amplified by first-line therapy in mixed infection. Emerg Infect Dis 2014. [PMID: 23764343 PMCID: PMC3713993 DOI: 10.3201/eid1907.130313] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
Infections with >1 Mycobacterium tuberculosis strain(s) are underrecognized. We show, in vitro and in vivo, how first-line treatment conferred a competitive growth advantage to amplify a multidrug-resistant M. tuberculosis strain in a patient with mixed infection. Diagnostic techniques that identify mixed tubercle bacilli populations are needed to curb the spread of multidrug resistance.
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Current methods in the molecular typing of Mycobacterium tuberculosis and other mycobacteria. BIOMED RESEARCH INTERNATIONAL 2014; 2014:645802. [PMID: 24527454 PMCID: PMC3914561 DOI: 10.1155/2014/645802] [Citation(s) in RCA: 88] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/11/2013] [Accepted: 11/18/2013] [Indexed: 11/18/2022]
Abstract
In the epidemiology of tuberculosis (TB) and nontuberculous mycobacterial (NTM) diseases, as in all infectious diseases, the key issue is to define the source of infection and to disclose its routes of transmission and dissemination in the environment. For this to be accomplished, the ability of discerning and tracking individual Mycobacterium strains is of critical importance. Molecular typing methods have greatly improved our understanding of the biology of mycobacteria and provide powerful tools to combat the diseases caused by these pathogens. The utility of various typing methods depends on the Mycobacterium species under investigation as well as on the research question. For tuberculosis, different methods have different roles in phylogenetic analyses and person-to-person transmission studies. In NTM diseases, most investigations involve the search for environmental sources or phylogenetic relationships. Here, too, the type of setting determines which methodology is most suitable. Within this review, we summarize currently available molecular methods for strain typing of M. tuberculosis and some NTM species, most commonly associated with human disease. For the various methods, technical practicalities as well as discriminatory power and accomplishments are reviewed.
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N′guessan K, Ahui Brou JM, Assi JS, Adagra GD, Adade O, Assande JM, Guei A, Kouakou J, Dosso M. Use of rapid molecular test for multidrug-resistant tuberculosis detection among relapse cases in Cote d'Ivoire. Int J Mycobacteriol 2014; 3:71-5. [DOI: 10.1016/j.ijmyco.2013.11.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2013] [Revised: 11/27/2013] [Accepted: 11/28/2013] [Indexed: 11/25/2022] Open
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Clark TG, Mallard K, Coll F, Preston M, Assefa S, Harris D, Ogwang S, Mumbowa F, Kirenga B, O’Sullivan DM, Okwera A, Eisenach KD, Joloba M, Bentley SD, Ellner JJ, Parkhill J, Jones-López EC, McNerney R. Elucidating emergence and transmission of multidrug-resistant tuberculosis in treatment experienced patients by whole genome sequencing. PLoS One 2013; 8:e83012. [PMID: 24349420 PMCID: PMC3859632 DOI: 10.1371/journal.pone.0083012] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2013] [Accepted: 11/07/2013] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Understanding the emergence and spread of multidrug-resistant tuberculosis (MDR-TB) is crucial for its control. MDR-TB in previously treated patients is generally attributed to the selection of drug resistant mutants during inadequate therapy rather than transmission of a resistant strain. Traditional genotyping methods are not sufficient to distinguish strains in populations with a high burden of tuberculosis and it has previously been difficult to assess the degree of transmission in these settings. We have used whole genome analysis to investigate M. tuberculosis strains isolated from treatment experienced patients with MDR-TB in Uganda over a period of four years. METHODS AND FINDINGS We used high throughput genome sequencing technology to investigate small polymorphisms and large deletions in 51 Mycobacterium tuberculosis samples from 41 treatment-experienced TB patients attending a TB referral and treatment clinic in Kampala. This was a convenience sample representing 69% of MDR-TB cases identified over the four year period. Low polymorphism was observed in longitudinal samples from individual patients (2-15 SNPs). Clusters of samples with less than 50 SNPs variation were examined. Three clusters comprising a total of 8 patients were found with almost identical genetic profiles, including mutations predictive for resistance to rifampicin and isoniazid, suggesting transmission of MDR-TB. Two patients with previous drug susceptible disease were found to have acquired MDR strains, one of which shared its genotype with an isolate from another patient in the cohort. CONCLUSIONS Whole genome sequence analysis identified MDR-TB strains that were shared by more than one patient. The transmission of multidrug-resistant disease in this cohort of retreatment patients emphasises the importance of early detection and need for infection control. Consideration should be given to rapid testing for drug resistance in patients undergoing treatment to monitor the emergence of resistance and permit early intervention to avoid onward transmission.
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Affiliation(s)
- Taane G. Clark
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, United Kingdom
- Faculty of Epidemiology and Population Health, London School of Hygiene & Tropical Medicine, London, United Kingdom
| | - Kim Mallard
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, United Kingdom
| | - Francesc Coll
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, United Kingdom
| | - Mark Preston
- Faculty of Epidemiology and Population Health, London School of Hygiene & Tropical Medicine, London, United Kingdom
| | - Samuel Assefa
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, United Kingdom
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, United Kingdom
| | - David Harris
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, United Kingdom
| | - Sam Ogwang
- Joint Clinical Research Centre, Kampala, Uganda
| | - Francis Mumbowa
- Joint Clinical Research Centre, Kampala, Uganda
- Department of Medical Microbiology, Makerere University College of Health Sciences, Kampala, Uganda
| | - Bruce Kirenga
- Mulago Hospital Tuberculosis Clinic, Mulago Hospital, Kampala, Uganda
| | - Denise M. O’Sullivan
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, United Kingdom
| | - Alphonse Okwera
- Mulago Hospital Tuberculosis Clinic, Mulago Hospital, Kampala, Uganda
| | - Kathleen D. Eisenach
- Department of Pathology, University of Arkansas for Medical Sciences, Little Rock, Arkansas, United States of America
- Uganda-Case Western Reserve University Research Collaboration, Kampala, Uganda
| | - Moses Joloba
- Department of Medical Microbiology, Makerere University College of Health Sciences, Kampala, Uganda
| | | | - Jerrold J. Ellner
- Section of Infectious Diseases, Department of Medicine, Boston Medical Center and Boston University School of Medicine, Boston, Massachusetts, United States of America
| | - Julian Parkhill
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, United Kingdom
| | - Edward C. Jones-López
- Section of Infectious Diseases, Department of Medicine, Boston Medical Center and Boston University School of Medicine, Boston, Massachusetts, United States of America
| | - Ruth McNerney
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, United Kingdom
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Population structure of mixed Mycobacterium tuberculosis infection is strain genotype and culture medium dependent. PLoS One 2013; 8:e70178. [PMID: 23936157 PMCID: PMC3728311 DOI: 10.1371/journal.pone.0070178] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2013] [Accepted: 06/17/2013] [Indexed: 11/19/2022] Open
Abstract
Background Molecular genotyping methods have shown infection with more than one Mycobacterium tuberculosis strain genotype in a single sputum culture, indicating mixed infection. Aim This study aimed to develop a PCR-based genotyping tool to determine the population structure of M. tuberculosis strain genotypes in primary Mycobacterial Growth Indicator Tubes (MGIT) and Löwenstein–Jensen (LJ) cultures to identify mixed infections and to establish whether the growth media influenced the recovery of certain strain genotypes. Method A convenience sample of 206 paired MGIT and LJ M. tuberculosis cultures from pulmonary tuberculosis patients resident in Khayelitsha, South Africa were genotyped using an in-house PCR-based method to detect defined M. tuberculosis strain genotypes. Results The sensitivity and specificity of the PCR-based method for detecting Beijing, Haarlem, S-family, and LAM genotypes was 100%, and 75% and 50% for detecting the Low Copy Clade, respectively. Thirty-one (15%) of the 206 cases showed the presence of more than one M. tuberculosis strain genotype. Strains of the Beijing and Haarlem genotypes were significantly more associated with a mixed infection (on both media) when compared to infections with a single strain (Beijing MGIT p = 0.02; LJ, p<0.01) and (Haarlem: MGIT p<0.01; LJ, p = 0.01). Strains with the Beijing genotype were less likely to be with “other genotype” strains (p<0.01) while LAM, Haarlem, S-family and LCC occurred independently with the Beijing genotype. Conclusion The PCR-based method was able to identify mixed infection in at least 15% of the cases. LJ media was more sensitive in detecting mixed infections than MGIT media, implying that the growth characteristics of M. tuberculosis on different media may influence our ability to detect mixed infections. The Beijing and Haarlem genotypes were more likely to occur in a mixed infection than any of the other genotypes tested suggesting pathogen-pathogen compatibility.
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Borgdorff MW, van Soolingen D. The re-emergence of tuberculosis: what have we learnt from molecular epidemiology? Clin Microbiol Infect 2013; 19:889-901. [PMID: 23731470 DOI: 10.1111/1469-0691.12253] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Tuberculosis (TB) has re-emerged over the past two decades: in industrialized countries in association with immigration, and in Africa owing to the human immunodeficiency virus epidemic. Drug-resistant TB is a major threat worldwide. The variable and uncertain impact of TB control necessitates not only better tools (diagnostics, drugs, and vaccines), but also better insights into the natural history and epidemiology of TB. Molecular epidemiological studies over the last two decades have contributed to such insights by answering long-standing questions, such as the proportion of cases attributable to recent transmission, risk factors for recent transmission, the occurrence of multiple Mycobacterium tuberculosis infection, and the proportion of recurrent TB cases attributable to re-infection. M. tuberculosis lineages have been identified and shown to be associated with geographical origin. The Beijing genotype is strongly associated with multidrug resistance, and may have escaped from bacille Calmette-Guérin-induced immunity. DNA fingerprinting has quantified the importance of institutional transmission and laboratory cross-contamination, and has helped to focus contact investigations. Questions to be answered in the near future with whole genome sequencing include identification of chains of transmission within clusters of patients, more precise quantification of mixed infection, and transmission probabilities and rates of progression from infection to disease of various M. tuberculosis lineages, as well as possible variations in vaccine efficacy by lineage. Perhaps most importantly, dynamics in the population structure of M. tuberculosis in response to control measures in high-prevalence areas should be better understood.
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Affiliation(s)
- M W Borgdorff
- Department of Infectious Diseases, Public Health Service Amsterdam, Amsterdam, The Netherlands; Department of Clinical Epidemiology, Biostatistics and Bioinformatics, Academic Medical Centre, University of Amsterdam and Centre for Infection and Immunity Amsterdam (CINIMA), Amsterdam, The Netherlands
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43
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Mixed-strain mycobacterium tuberculosis infections and the implications for tuberculosis treatment and control. Clin Microbiol Rev 2013; 25:708-19. [PMID: 23034327 DOI: 10.1128/cmr.00021-12] [Citation(s) in RCA: 142] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Numerous studies have reported that individuals can simultaneously harbor multiple distinct strains of Mycobacterium tuberculosis. To date, there has been limited discussion of the consequences for the individual or the epidemiological importance of mixed infections. Here, we review studies that documented mixed infections, highlight challenges associated with the detection of mixed infections, and discuss possible implications of mixed infections for the diagnosis and treatment of patients and for the community impact of tuberculosis control strategies. We conclude by highlighting questions that should be resolved in order to improve our understanding of the importance of mixed-strain M. tuberculosis infections.
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44
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Yimer SA, Hailu E, Derese Y, Bjune GA, Holm-Hansen C. Spoligotyping of Mycobacterium tuberculosis isolates among pulmonary tuberculosis patients in Amhara Region, Ethiopia. APMIS 2013; 121:878-85. [PMID: 23336257 DOI: 10.1111/apm.12046] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2012] [Accepted: 12/07/2012] [Indexed: 11/28/2022]
Abstract
The aim of this study was to characterize Mycobacterium tuberculosis isolates circulating in the Amhara Region of Ethiopia. Sputum samples were collected from new pulmonary tuberculosis (TB) patients in the Region. Genotyping of mycobacterial DNA was performed by spoligotyping and isolates were assigned to families using the SpolDB4 and the model-based program 'Spotclust'. A high level of diversity was found among the 237 isolates. Sixty-five different spoligopatterns were obtained. The T (30.8%), Central Asian (CAS; 21.1%) and U (17.7%) families were the predominant isolates comprising 69.6% of the total strains. Eighty-five per cent of the U lineage belonged to Spoligo-International-Type (SIT) 910 and SIT 1729. Only a few of these strains are included in SpolDB4 to date. Of the total strains, 41 (17.3%) were unique and have not been described in SpolDB4 to date. This study indicated that the TB epidemic in Amhara Region, Ethiopia, is characterized by the circulation of numerous M. tuberculosis strain families. The high proportion of SIT 910 and SIT 1729 strains may indicate an increase in the importance of these lineages in the transmission of TB in the study region.
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45
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Sankar MM, Singh J, Diana SCA, Singh S. Molecular characterization of Mycobacterium tuberculosis isolates from North Indian patients with extrapulmonary tuberculosis. Tuberculosis (Edinb) 2013; 93:75-83. [PMID: 23140853 DOI: 10.1016/j.tube.2012.10.005] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2012] [Revised: 10/11/2012] [Accepted: 10/12/2012] [Indexed: 02/07/2023]
Abstract
Genotypic studies are important to understand the molecular epidemiology and transmission routes of Mycobacterium tuberculosis. In the first and largest study from India, spoligotyping and 24 loci mycobacterial interspersed repetitive units (MIRU) were performed to find genetic profiles of 125 M. tuberculosis strains isolated from patients with extrapulmonary tuberculosis (EPTB) and their drug susceptibility test was performed using BACTEC-MGIT 960. Spoligotyping results were compared with the world Spoligotyping Database of Institute Pasteur de Guadeloupe (SpolDB4). The spoligotyping results showed that 110 (88%) displayed known patterns while 15 (12%) isolates had no matching database. Predominant spoligotypes belonged to CAS family (57.27%). The largest clade comprised of 38 isolates belonging to the CAS1_DEL lineage. Though there was no significant association between specific mycobacterial lineage and extrapulmonary site, a significantly high (p < 0.001) number of Beijing type isolates (28.6%) were isolated from bone and joint samples as compared to cerebrospinal fluid (5%). There was a significant association between Beijing family isolates and multi-drug-resistance, while all MANU genotypes were pan-drug sensitive. The CAS family lineage was most prevalent genotype in the EPTB cases in our population.
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Affiliation(s)
- Manimuthu Mani Sankar
- Clinical Microbiology Division, Department of Laboratory Medicine, All India Institute of Medical Sciences, New Delhi 110029, India
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Walter ND, Strong M, Belknap R, Ordway DJ, Daley CL, Chan ED. Translating basic science insight into public health action for multidrug- and extensively drug-resistant tuberculosis. Respirology 2012; 17:772-91. [PMID: 22458269 PMCID: PMC4540333 DOI: 10.1111/j.1440-1843.2012.02176.x] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Multidrug (MDR)- and extensively drug-resistant (XDR) tuberculosis (TB) impose a heavy toll of human suffering and social costs. Controlling drug-resistant TB is a complex global public health challenge. Basic science advances including elucidation of the genetic basis of resistance have enabled development of new assays that are transforming the diagnosis of MDR-TB. Molecular epidemiological approaches have provided new insights into the natural history of TB with important implications for drug resistance. In the future, progress in understanding Mycobacterium tuberculosis strain-specific human immune responses, integration of systems biology approaches with traditional epidemiology and insight into the biology of mycobacterial persistence have potential to be translated into new tools for diagnosis and treatment of MDR- and XDR-TB. We review recent basic sciences developments that have contributed or may contribute to improved public health response.
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Affiliation(s)
- Nicholas D Walter
- Division of Pulmonary Sciences and Critical Care Medicine, University of Colorado Denver, Aurora, Colorado, USA.
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Barrios-Payán J, Saqui-Salces M, Jeyanathan M, Alcántara-Vazquez A, Castañon-Arreola M, Rook G, Hernandez-Pando R. Extrapulmonary Locations of Mycobacterium tuberculosis DNA During Latent Infection. J Infect Dis 2012; 206:1194-205. [DOI: 10.1093/infdis/jis381] [Citation(s) in RCA: 82] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Vorkas C, Kayira D, van der Horst C, Hoffman I, Hosseinipour M, Kanyemba C, Nguluwe N, Chikaonda T, Kalikhoka M, Kalaundi D, Namarika D, Gilligan P, Krysiak R. Tuberculosis drug resistance and outcomes among tuberculosis inpatients in Lilongwe, Malawi. Malawi Med J 2012; 24:21-24. [PMID: 23638265 PMCID: PMC3588213] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/02/2023] Open
Abstract
UNLABELLED SETTING/OBJECTIVE: We evaluated clinical characteristics, yield of solid vs. liquid culture, polymerase chain reaction (PCR)-based drug-resistance profiles, and clinical outcomes of tuberculosis (TB) inpatients in Lilongwe, Malawi. DESIGN We enrolled adult patients admitted to the Bwaila TB Ward from Jan-Aug/2010. Evaluations included questionnaires, clinical exam, chest radiograph, HIV status, CD4 lymphocyte count, plasma HIVRNA and sputum analysis including Auramine-O stain, Lowenstein-Jensen (LJ) and Mycobacterial Growth Indicator Tube (MGIT) culture, and susceptibility testing using the HAIN GenoType® MTBDRplus. RESULTS Eighty-eight patients were enrolled (88% re-treatment, 42% smear positive, 93% pulmonary TB, 74% HIV co-infected). At baseline, 44/88 (50%) MGIT and 28 (32%) LJ cultures were positive with a mean time to positivity of 12.1 (Range 1-42) and 21.5 (Range 7-58) days, respectively. Four percent (3/77) of retreatment patients or 8% of the 38 MGIT+ PCR-confirmed retreatment cases had multi-drug resistant tuberculosis (MDR TB). One MDR TB patient was smear negative and only one MDR patient was identified with LJ. Lower mean hemoglobin at admission was associated with mortality (10.5 vs. 7.5; p<0.01; CI 101 9.8-11.0). CONCLUSIONS The MDR TB burden among the retreatment population in Lilongwe, Malawi is similar to regional estimates by the WHO (7.7% 95% CI 0-18.1). MDR TB patients are not routinely identified with sputum smear or LJ, suggesting more efficient technology should be adopted.
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Affiliation(s)
- Charles Vorkas
- University of North Carolina Hospitals Department of Medicine
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Namouchi A, Didelot X, Schöck U, Gicquel B, Rocha EPC. After the bottleneck: Genome-wide diversification of the Mycobacterium tuberculosis complex by mutation, recombination, and natural selection. Genome Res 2012; 22:721-34. [PMID: 22377718 DOI: 10.1101/gr.129544.111] [Citation(s) in RCA: 130] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Many of the most virulent bacterial pathogens show low genetic diversity and sexual isolation. Accordingly, Mycobacterium tuberculosis, the deadliest human pathogen, is thought to be clonal and evolve by genetic drift. Yet, its genome shows few of the concomitant signs of genome degradation. We analyzed 24 genomes and found an excess of genetic diversity in regions encoding key adaptive functions including the type VII secretion system and the ancient horizontally transferred virulence-related regions. Four different approaches showed evident signs of recombination in M. tuberculosis. Recombination tracts add a high density of polymorphisms, and many are thus predicted to arise from outside the clade. Some of these tracts match Mycobacterium canettii sequences. Recombination introduced an excess of non-synonymous diversity in general and even more in genes expected to be under positive or diversifying selection, e.g., cell wall component genes. Mutations leading to non-synonymous SNPs are effectively purged in MTBC, which shows dominance of purifying selection. MTBC mutation bias toward AT nucleotides is not compensated by biased gene conversion, suggesting the action of natural selection also on synonymous changes. Together, all of these observations point to a strong imprint of recombination and selection in the genome affecting both non-synonymous and synonymous positions. Hence, contrary to some other pathogens and previous proposals concerning M. tuberculosis, this lineage may have come out of its ancestral bottleneck as a very successful pathogen that is rapidly diversifying by the action of mutation, recombination, and natural selection.
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Affiliation(s)
- Amine Namouchi
- Unité de Génétique Mycobactérienne, Institut Pasteur, 75015 Paris, France.
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Visser ME, Stead MC, Walzl G, Warren R, Schomaker M, Grewal HMS, Swart EC, Maartens G. Baseline predictors of sputum culture conversion in pulmonary tuberculosis: importance of cavities, smoking, time to detection and W-Beijing genotype. PLoS One 2012; 7:e29588. [PMID: 22238625 PMCID: PMC3251579 DOI: 10.1371/journal.pone.0029588] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2011] [Accepted: 11/30/2011] [Indexed: 01/13/2023] Open
Abstract
BACKGROUND Time to detection (TTD) on automated liquid mycobacterial cultures is an emerging biomarker of tuberculosis outcomes. The M. tuberculosis W-Beijing genotype is spreading globally, indicating a selective advantage. There is a paucity of data on the association between baseline TTD and W-Beijing genotype and tuberculosis outcomes. AIM To assess baseline predictors of failure of sputum culture conversion, within the first 2 months of antitubercular therapy, in participants with pulmonary tuberculosis. DESIGN Between May 2005 and August 2008 we conducted a prospective cohort study of time to sputum culture conversion in ambulatory participants with first episodes of smear and culture positive pulmonary tuberculosis attending two primary care clinics in Cape Town, South Africa. Rifampicin resistance (diagnosed on phenotypic susceptibility testing) was an exclusion criterion. Sputum was collected weekly for 8 weeks for mycobacterial culture on liquid media (BACTEC MGIT 960). Due to missing data, multiple imputation was performed. Time to sputum culture conversion was analysed using a Cox-proportional hazards model. Bayesian model averaging determined the posterior effect probability for each variable. RESULTS 113 participants were enrolled (30.1% female, 10.5% HIV-infected, 44.2% W-Beijing genotype, and 89% cavities). On Kaplan Meier analysis 50.4% of participants underwent sputum culture conversion by 8 weeks. The following baseline factors were associated with slower sputum culture conversion: TTD (adjusted hazard ratio (aHR) = 1.11, 95% CI 1.02; 1.2), lung cavities (aHR = 0.13, 95% CI 0.02; 0.95), ever smoking (aHR = 0.32, 95% CI 0.1; 1.02) and the W-Beijing genotype (aHR = 0.51, 95% CI 0.25; 1.07). On Bayesian model averaging, posterior probability effects were strong for TTD, lung cavitation and smoking and moderate for W-Beijing genotype. CONCLUSION We found that baseline TTD, smoking, cavities and W-Beijing genotype were associated with delayed 2 month sputum culture. Larger studies are needed to confirm the relationship between the W-Beijing genotype and sputum culture conversion.
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Affiliation(s)
- Marianne E Visser
- School of Public Health, University of the Western Cape, Cape Town, South Africa.
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