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Chemeda A, Mihret A, Abebe T, Worku A, Ameni G. Genotyping of mycobacterium tuberculosis isolated from pulmonary tuberculosis patients among people living with HIV in Addis Ababa: Cross-sectional study. J Clin Tuberc Other Mycobact Dis 2018; 12:34-37. [PMID: 31720396 PMCID: PMC6830125 DOI: 10.1016/j.jctube.2018.06.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2017] [Revised: 06/03/2018] [Accepted: 06/13/2018] [Indexed: 11/17/2022] Open
Abstract
Background Tuberculosis is a serious infection that is common in people living with HIV and increases the mortality and morbidity from the diseases. The study of genetic diversity among strains of M. tuberculosis has a great impact in studying pathogenicity and transmissibility, design for vaccines production, identification of nominee genes for drug targets, and improving molecular diagnostic techniques. The aim of this study was to characterize Mycobacterium tuberculosis (Mtb) isolated from suspected pulmonary tuberculosis among people living with HIV. Method A total of 143 sputum samples was collected and transported to Akililu Lemma TB laboratory. The collected samples were processed for culture using Lowenstein-Jensen medium. For 45 culture positive isolates, genotyping of mycobacterial DNA was performed by spoligotyping and isolates were assigned to families using the SpolDB4 and the model-based program 'SPOTCLUST'. Categorical data were analyzed by Chi-square test. Result A high level of diversity was found among the 45 isolates. Twenty six different Spoligo patterns were obtained. The T (46.7%), Family33 (44.4%) and Central Asian (CAS): (4.4%) families were the dominant isolates comprising 91.5% of the total strains. Of 44% of the Euro-American, 6/20(30%) and 9/20(45%), identified were lineage belonged to Spoligo-International-Type (SIT336) and SIT149. Of the total strains, 12 (22%) were unique and have not been described in SpolDB4 to date. Conclusion We found the high diversity of Mtb in pulmonary tuberculosis patients in this setting. T3_ETH family identified as the numerous M.tuberculosis strains circulating in the community.
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Affiliation(s)
- Alemu Chemeda
- Arbaminch University, College of Natural Science, Department of Biology, Arba Minch, Addis Ababa, Ethiopia
| | - Adane Mihret
- Addis Ababa University, School of Medicine, College of Health Science, Department of Medical Microbiology, Immunology and Parasitology, Addis Ababa, Ethiopia.,Armauer Hansen Research Institute, Immunology Unit, Addis Ababa, Ethiopia
| | - Tamrat Abebe
- Addis Ababa University, School of Medicine, College of Health Science, Department of Medical Microbiology, Immunology and Parasitology, Addis Ababa, Ethiopia
| | - Adane Worku
- Aklilu Lema Pathobiology Research Institution, Addis Ababa University, Addis Ababa, Ethiopia
| | - Gobena Ameni
- Aklilu Lema Pathobiology Research Institution, Addis Ababa University, Addis Ababa, Ethiopia
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Pedersen MK, Lillebaek T, Andersen AB, Soini H, Haanperä M, Groenheit R, Jonsson J, Svensson E. Trends and differences in tuberculosis incidences and clustering among natives in Denmark, Sweden and Finland: comparison of native incidences and molecular epidemiology among three low-incidence countries. Clin Microbiol Infect 2017; 24:717-723. [PMID: 29031789 DOI: 10.1016/j.cmi.2017.10.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2017] [Revised: 09/29/2017] [Accepted: 10/02/2017] [Indexed: 11/19/2022]
Abstract
OBJECTIVES To compare the epidemiology of tuberculosis (TB) in Denmark, Sweden and Finland, by focusing on the native population in order to identify epidemiologic differences and thus indirectly possible differences in TB control. METHODS TB incidence trends from 1990 through 2015 were compared among the countries. In addition, for the periods 2012-2013 and 2014-2015, genotyping data were compared. Genotyping was performed using the 24-locus mycobacterial interspersed repetitive unit-variable number of tandem repeat (MIRU-VNTR) method in Denmark and Sweden. For Finland, spoligotyping in conjunction with the 15-locus MIRU-VNTR method was used for 2012-2013 and translated into the 24-locus MIRU-VNTR when feasible, and for 2014-2015 only MIRU-VNTR was used. Both incidence trends and molecular epidemiology were assessed for native cases. RESULTS The average annual rate of change in TB incidence for native Danes was -2.4% vs. -6.1% and -6.9% for native Swedes and Finns respectively. In 2012-2013 Denmark had 52 native cases in the largest transmission chain vs. three cases in Sweden and ten in Finland, and during the same period the clustering rate for native Danes was 48.8% vs. 6.5% and 18.2% for native Swedes and Finns respectively. For 2014-2015, a similar pattern was seen. CONCLUSIONS The decline of TB among natives in Denmark is slower than for Sweden and Finland, and it seems Denmark has more active transmission among natives. The focused assessment on basic native TB epidemiology reveals striking differences in TB transmission among otherwise similar low-TB-incidence countries.
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Affiliation(s)
- M K Pedersen
- International Reference Laboratory of Mycobacteriology, Statens Serum Institut, Copenhagen, Denmark.
| | - T Lillebaek
- International Reference Laboratory of Mycobacteriology, Statens Serum Institut, Copenhagen, Denmark
| | - A B Andersen
- Department of Infectious Diseases, Copenhagen University Hospital, Copenhagen, Denmark
| | - H Soini
- National Institute for Health and Welfare (THL), Department of Health Security, Helsinki, Finland
| | - M Haanperä
- National Institute for Health and Welfare (THL), Department of Health Security, Helsinki, Finland
| | - R Groenheit
- Department of Microbiology, Public Health Agency of Sweden, Stockholm, Sweden
| | - J Jonsson
- Department of Monitoring and Evaluation, Public Health Agency of Sweden, Stockholm, Sweden
| | - E Svensson
- International Reference Laboratory of Mycobacteriology, Statens Serum Institut, Copenhagen, Denmark
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In Vivo IS6110 Profile Changes in a Mycobacterium tuberculosis Strain as Determined by Tracking over 14 Years. J Clin Microbiol 2015; 53:2359-61. [PMID: 25948604 DOI: 10.1128/jcm.00607-15] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2015] [Accepted: 04/28/2015] [Indexed: 11/20/2022] Open
Abstract
Transposition and homologous recombination of IS6110 appear in Mycobacterium tuberculosis along in vivo sequential infections. These events were checked in different clones of a successful strain, M. tuberculosis Zaragoza, with the focus on a variant in which integration of a copy of IS6110 in the origin of replication (oriC) region occurred.
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Prodinger WM, Indra A, Koksalan OK, Kilicaslan Z, Richter E. Mycobacterium caprae infection in humans. Expert Rev Anti Infect Ther 2014; 12:1501-13. [PMID: 25345680 DOI: 10.1586/14787210.2014.974560] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Mycobacterium caprae, a member of the Mycobacterium tuberculosis complex, causes tuberculosis (TB) in man and animals. Some features distinguish M. caprae from its epidemiological twin, Mycobacterium bovis: M. caprae is evolutionarily older, accounts for a smaller burden of zoonotic TB and is not globally distributed, but primarily restricted to European countries. M. caprae occurs only in a low proportion of human TB cases and this proportion may even decrease, if progress toward eradication of animal TB in Europe continues. So why bother, if M. caprae is not an enigma for diagnostic TB tests and if resistance against first-line drugs is a rarity with M. caprae? This 'European' pathogen of zoonotic TB asks interesting questions regarding the definition of a species. The latter, seemingly only an academic question, particularly requires and challenges the collaboration between human and veterinary medicine.
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Affiliation(s)
- Wolfgang M Prodinger
- Division of Hygiene and Medical Microbiology, Innsbruck Medical University, Innsbruck, Schoepfstrasse 41, 6020 Austria
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Diversity and evolution of Mycobacterium tuberculosis: moving to whole-genome-based approaches. Cold Spring Harb Perspect Med 2014; 4:a021188. [PMID: 25190252 DOI: 10.1101/cshperspect.a021188] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Genotyping of clinical Mycobacterium tuberculosis complex (MTBC) strains has become a standard tool for epidemiological tracing and for the investigation of the local and global strain population structure. Of special importance is the analysis of the expansion of multidrug (MDR) and extensively drug-resistant (XDR) strains. Classical genotyping and, more recently, whole-genome sequencing have revealed that the strains of the MTBC are more diverse than previously anticipated. Globally, several phylogenetic lineages can be distinguished whose geographical distribution is markedly variable. Strains of particular (sub)lineages, such as Beijing, seem to be more virulent and associated with enhanced resistance levels and fitness, likely fueling their spread in certain world regions. The upcoming generalization of whole-genome sequencing approaches will expectedly provide more comprehensive insights into the molecular and epidemiological mechanisms involved and lead to better diagnostic and therapeutic tools.
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Comparative study of IS6110 restriction fragment length polymorphism and variable-number tandem-repeat typing of Mycobacterium tuberculosis isolates in the Netherlands, based on a 5-year nationwide survey. J Clin Microbiol 2013; 51:1193-8. [PMID: 23363841 DOI: 10.1128/jcm.03061-12] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
In order to switch from IS6110 and polymorphic GC-rich repetitive sequence (PGRS) restriction fragment length polymorphism (RFLP) to 24-locus variable-number tandem-repeat (VNTR) typing of Mycobacterium tuberculosis complex isolates in the national tuberculosis control program in The Netherlands, a detailed evaluation on discriminatory power and agreement with findings in a cluster investigation was performed on 3,975 tuberculosis cases during the period of 2004 to 2008. The level of discrimination of the two typing methods did not differ substantially: RFLP typing yielded 2,733 distinct patterns compared to 2,607 in VNTR typing. The global concordance, defined as isolates labeled unique or identically distributed in clusters by both methods, amounted to 78.5% (n = 3,123). Of the remaining 855 cases, 12% (n = 479) of the cases were clustered only by VNTR, 7.7% (n = 305) only by RFLP typing, and 1.8% (n = 71) revealed different cluster compositions in the two approaches. A cluster investigation was performed for 87% (n = 1,462) of the cases clustered by RFLP. For the 740 cases with confirmed or presumed epidemiological links, 92% were concordant with VNTR typing. In contrast, only 64% of the 722 cases without an epidemiological link but clustered by RFLP typing were also clustered by VNTR typing. We conclude that VNTR typing has a discriminatory power equal to IS6110 RFLP typing but is in better agreement with findings in a cluster investigation performed on an RFLP-clustering-based cluster investigation. Both aspects make VNTR typing a suitable method for tuberculosis surveillance systems.
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Bidovec-Stojkovic U, Zolnir-Dovc M, Supply P. One year nationwide evaluation of 24-locus MIRU-VNTR genotyping on Slovenian Mycobacterium tuberculosis isolates. Respir Med 2012; 105 Suppl 1:S67-73. [PMID: 22015090 DOI: 10.1016/s0954-6111(11)70014-2] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/16/2022]
Abstract
BACKGROUND Slovenia is one of the few countries where IS6110 RFLP is applied for genotyping M. tuberculosis at a nationwide level, which has been in effect since 2000. Based on S6110 RFLP clustering, typical risk factors and routes of M. tuberculosis transmission were identified, such as alcohol abuse, homelessness, and bars. However, IS6110 RFLP typing suffers from important limitations including a long wait for results, which reduces the potential benefit of molecular-guided tuberculosis (TB) control. PCR-based 24-locus MIRU-VNTR typing combined with spoligotyping has recently emerged as a potential alternative for faster, large-scale genotyping of M. tuberculosis. METHODS We compared these genotyping methods for analyzing 196 Slovenian Mycobacterium tuberculosis isolates representing 97.5% of all culture-positive cases included in the Slovenian TB Registry in 2008. RESULTS IS6110 RFLP and 24-locus MIRU-VNTR typing combined with spoligotyping identified 157 and 155 distinct profiles, 135 and 125 unique isolates, and 61 and 71 clustered isolates grouped into 22 and 29 clusters, respectively. The discriminatory indexes were very close, at 0.9963 and 0.9965, respectively. The majority of the molecular clusters defined by either of the two methods were identical, including in the few cases for which epidemiological links were available. The differences frequently consisted of single-band changes in IS6170-RFLP profiles subdividing a MIRU-VNTR/spoligotype-based cluster. CONCLUSIONS Our one-year nationwide study showed that the results of 24-locus MIRU-VNTR typing combined with spoligotyping reached a high level of concordance with those obtained from IS6110 RFLP typing.
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Affiliation(s)
- Urska Bidovec-Stojkovic
- Laboratory for Mycobacteria, University Clinic of Respiratory and Allergic Diseases Colnik, Colnik, Slovenia.
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Noguti EN, Leite CQF, Malaspina AC, Santos ACB, Hirata RDC, Hirata MH, Mamizuka EM, Cardoso RF. Genotyping of Mycobacterium tuberculosis isolates from a low-endemic setting in northwestern state of Paraná in Southern Brazil. Mem Inst Oswaldo Cruz 2011; 105:779-85. [PMID: 20944992 DOI: 10.1590/s0074-02762010000600008] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2010] [Accepted: 05/13/2010] [Indexed: 11/22/2022] Open
Abstract
The purpose of this study was to provide information about the genetic diversity and prevalent genotype of Mycobacterium tuberculosis in a low-endemic setting in northwestern state of Paraná in Southern Brazil. We employed spoligotyping and mycobacterial interspersed repetitive units-variable number tandem repeat (MIRU-VNTR) techniques to genotype M. tuberculos isisolates from patients with pulmonary tuberculosis (TB). The 93 isolates analyzed by spoligotyping were divided into 36 different patterns, 30 of which were described in the SITVIT database. Latin American and Mediterranean, Haarlem and T families were responsible for 26.9%, 17.2% and 11.8% of TB cases, respectively. From the 84 isolates analyzed by MIRU-VNTR, 58 shared a unique pattern and the remaining 26 belonged to nine clusters. The MIRU loci 40, 23, 10 and 16 were the most discriminatory. A combination of MIRU-VNTR and spoligotyping resulted in 85.7% discriminatory power (Hunter-Gaston index = 0.995). Thus, combining spoligotyping and MIRU-VNTR typing proved to be most useful for epidemiological study in this low-endemic setting in Southern Brazil. The current study demonstrated that there is significant diversity in circulating strains in the city of Maringá and the surrounding regions, with no single genotype of M. tuberculosis predominating.
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Affiliation(s)
- Erika Noda Noguti
- Departamento de Análises Clínicas, Universidade Estadual de Maringá, Maringá, PR, Brazil
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Marcun R, Sustic A. Sonographic evaluation of unexplained pleural exudate: a prospective case series. Wien Klin Wochenschr 2009; 121:334-8. [PMID: 19562297 DOI: 10.1007/s00508-009-1188-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
BACKGROUND Thoracic ultrasound may be helpful in differentiating between malignant and tuberculosis-associated pleural exudate. This study aimed to evaluate its utility in patients with unexplained pleural exudate. METHODS Consecutive patients were screened and pleural effusion was found in 278 patients. Pleural exudate was present in 106 patients and remained undiagnosed after biochemical and cytological evaluation in 40 patients (median age 58 years, 67% men) who then underwent detailed thoracic ultrasound for the presence of complex (septated or fibrous) or anechoic patterns. Pleural needle biopsy or thoracoscopy with histological evaluation were used for definitive diagnosis. RESULTS History, clinical characteristics and routine procedures including cytology were not helpful in differential diagnosis. Pleural specimens for histological evaluation were obtained from all 40 patients and confirmed tuberculosis in 12 patients, cancer in nine and nonspecific pleuritis in 19. Sonographic finding of a complex septal pattern was present only in patients with tuberculosis (positive predictive value 100%); anechoic appearance was suggestive of nonspecific pleuritis (positive predictive value 65%). CONCLUSIONS Thoracic ultrasound is a useful bedside method for differentiation of the etiology of pleural exudate. When a complex septal pattern is found, pleural needle biopsy should be the next diagnostic procedure, whereas with less complex pleural sonography findings other methods should be pursued.
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Affiliation(s)
- Robert Marcun
- University Clinic of Respiratory and Allergic Diseases Golnik, Golnik, Slovenia.
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Mendes JM, Machado SMA, Lourenço MC, Ferreira RMC, Fonseca LDS, Saad MHF. Molecular diversity of Mycobacterium tuberculosis strains in a slum area of Rio de Janeiro, Brazil. J Bras Pneumol 2009; 34:1063-8. [PMID: 19180342 DOI: 10.1590/s1806-37132008001200012] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2008] [Accepted: 04/24/2008] [Indexed: 11/21/2022] Open
Abstract
This retrospective molecular study involving restriction fragment length polymorphism, using insertion sequence 6110 as a marker, was conducted in order to provide an initial insight into the genetic diversity of Mycobacterium tuberculosis strains isolated in the slums of the Complexo de Manguinhos, located in the city of Rio de Janeiro, Brazil. Of the 67 strains evaluated, 23 (34.3%) were found to belong to clusters (total clusters, 10). Household and social chains of transmission were associated with clustering, in 20% and 60%, respectively. Living in the Conjunto Habitacional Programado 2 slum was associated with clustering. Although not significant, it is relevant that 26% of the clustered strains presented primary resistance. These findings, although possibly underestimating the prevalence due to the failure to analyze all strains, could help improve the local tuberculosis control program.
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Affiliation(s)
- Joycenea Matsuda Mendes
- Centro de Pesquisa Leônidas & Maria Deane, Fundação Instituto Oswaldo Cruz, Manaus, AM, Brazil
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Factors associated with differences between conventional contact tracing and molecular epidemiology in study of tuberculosis transmission and analysis in the city of Barcelona, Spain. J Clin Microbiol 2008; 47:198-204. [PMID: 19020067 DOI: 10.1128/jcm.00507-08] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The aim of this study was to analyze the factors associated with conventional contact tracing (CCT) and molecular epidemiology (ME) methods in assessing tuberculosis (TB) transmission, comparing the populations studied and the epidemiological links established by both methods. Data were obtained from TB case and CCT registries, and ME was performed using IS6110-based restriction fragment length polymorphism (RFLP) analysis and mycobacterial interspersed repetitive unit 12 (MIRU12) typing as a secondary typing method. During two years (2003 and 2004), 892 cases of TB were reported, of which 687 (77%) were confirmed by culture. RFLP analysis was performed with 463 (67.4%) of the 687 isolated strains, and MIRU12 types in 75 strains were evaluated; 280 strains (60.5%) had a unique RFLP pattern, and 183 (39.5%) shared patterns, grouping into 65 clusters. CCT of 613 (68.7%) of 892 cases detected 44 clusters involving 101 patients. The results of both CCT and ME methods yielded 96 clusters involving 255 patients. The household link was the one most frequently identified by CCT (corresponding to 80.7% of the cases clustered by this method), whereas nonhousehold and unknown links were associated with 94.1% of the strains clustered by ME. When both methods were used in 351 cases (39.3%), they showed the same results in 214 cases (61%). Of the remainder, 106 (30.2%) were clustered only by ME, 19 (5.5%) were clustered only by CCT, and 12 (3.4%) were clustered by both methods but into different clusters. Patients with factors potentially associated with social problems were less frequently studied by CCT (P = 0.002), whereas patients of <15 years of age, most with negative cultures, were less frequently studied by ME (P = 0.005). Significant differences in the populations studied by ME versus CCT were observed, possibly explaining the scarce correlation found between the results of these methods. Moreover, ME allowed the detection of nonhousehold contact relationships, whereas CCT was more useful for tracing transmission chains involving patients of <15 years of age. In conclusion, the two methods are complementary, suggesting the need to improve the methodology of contact study protocols.
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