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Sousa EDO, Carneiro RTDO, Montes FCOF, Conceição EC, Bartholomay P, Marinho JM, Lima KVB, Natividade MSD, Araújo WND, Matos ED, Barbosa T. Laboratory-based study of drug resistance and genotypic profile of multidrug-resistant tuberculosis isolates in Salvador, Bahia, Brazil. Rev Soc Bras Med Trop 2022; 55:e00132022. [PMID: 35894395 PMCID: PMC9359346 DOI: 10.1590/0037-8682-0013-2022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Accepted: 05/20/2022] [Indexed: 11/29/2022] Open
Abstract
Background: Surveillance of multidrug resistant/extensively drug-resistant tuberculosis (MDR/XDR-TB) is essential to guide disease dissemination control measures. Brazil contributes to a significant fraction of tuberculosis (TB) cases worldwide, but only few reports addressed MDR/XDR-TB in the country. Methods: This cross-sectional, laboratory-based study describes the phenotypic resistance profiles of isolates obtained between January 2008 and December 2011 in Bahia, Brazil, and sociodemographic, epidemiological, and clinical characteristics (obtained from mandatory national registries) of the corresponding 204 MDR/XDR-TB patients. We analyzed the mycobacterial spoligotyping and variable number of tandem repeats of mycobacterial interspersed repetitive units in 12-loci profiles obtained from Salvador. Results: MDR/XDR-TB patients were predominantly male, had a median age of 43 years, belonged to black ethnicity, and failed treatment before MDR-TB diagnosis. Nearly one-third of the isolates had phenotypic resistance (evaluated by mycobacteria growth indicator tube assay) to second-line anti-TB drugs (64/204, 31%), of which 22% cases (14/64) were diagnosed as XDR-TB. Death was a frequent outcome among these individuals and was associated with resistance to second-line anti-TB drugs. Most isolates successfully genotyped belonged to the Latin-American Mediterranean (LAM) Family, with an unprecedented high proportion of LAM10-Cameroon subfamily bacilli. More than half of these isolates were assigned to a unique cluster by the genotyping methods performed. Large clusters of identical genotypes were also observed among LAM SIT42 and SIT376 strains. Conclusions: We highlight the need for strengthening local and national efforts to perform early detection of TB drug resistance and to prevent treatment discontinuation to limit the emergence of drug-resistant strains.
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Affiliation(s)
- Erivelton de Oliveira Sousa
- Laboratório Central de Saúde Pública Professor Gonçalo Moniz (LACEN-BA), Salvador, BA, Brasil.,Fundação Oswaldo Cruz, Instituto de Pesquisa Gonçalo Moniz, Salvador, BA, Brasil
| | | | | | - Emilyn Costa Conceição
- Universidade Federal do Rio de Janeiro, Instituto de Microbiologia Paulo de Góes, Rio de Janeiro, RJ, Brasil
| | | | - Jamocyr Moura Marinho
- Escola Baiana de Medicina e Saúde Pública, Faculdade de Medicina, Salvador, Bahia, Brasil
| | | | | | | | - Eliana Dias Matos
- Escola Baiana de Medicina e Saúde Pública, Faculdade de Medicina, Salvador, Bahia, Brasil
| | - Theolis Barbosa
- Fundação Oswaldo Cruz, Instituto de Pesquisa Gonçalo Moniz, Salvador, BA, Brasil.,Rede Brasileira de Pesquisa em Tuberculose, Rio de Janeiro, RJ, Brasil
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Long R, Lau A, Egedahl ML, Paulsen C, Heffernan C, Edwards B, Cooper R. Local Transmission Plays No Important Role in the Occurrence of Multidrug-Resistant Tuberculosis in Immigrants to Canada: An In-depth Epidemiologic Analysis. J Infect Dis 2021; 224:1029-1038. [PMID: 33502538 DOI: 10.1093/infdis/jiab045] [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: 11/04/2020] [Accepted: 01/21/2021] [Indexed: 11/12/2022] Open
Abstract
BACKGROUND Multidrug-resistant (MDR) tuberculosis has increased among migrants in Canada. The cause(s) of this increase is unknown. METHODS We performed a retrospective cohort study in a Canadian province with substantially increased immigration between 1982-2001 and 2002-2019. The proportion of MDR tuberculosis among migrants arriving from high MDR (HMDR) tuberculosis burden countries during these 2 periods was used to estimate the proportion of cases due to immigration versus change in proportion in the country of birth. Epidemiologic, spatiotemporal, and drug resistance pattern data were used to confirm local transmission. RESULTS Fifty-two of 3514 (1.48%) foreign-born culture-positive tuberculosis patients had MDR tuberculosis: 8 (0.6%) in 1982-2001 and 44 (2.0%) in 2002-2019. Between time periods, the proportion of MDR tuberculosis among migrants with tuberculosis from HMDR tuberculosis countries increased from 1.11% to 3.62%, P = .003; 31.6% attributable to recent immigration and 68.4% to a higher proportion of MDR tuberculosis in cases arrived from HMDR tuberculosis countries. No cases of MDR tuberculosis were attributable to local transmission. CONCLUSIONS In stark contrast to HMDR tuberculosis countries, local transmission plays no important role in the occurrence of MDR tuberculosis in Canada. Improved tuberculosis programming in HMDR tuberculosis countries is urgently needed.
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Affiliation(s)
- Richard Long
- Department of Medicine, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, Canada
| | - Angela Lau
- Department of Medicine, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, Canada
| | - Mary Lou Egedahl
- Department of Medicine, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, Canada
| | - Catherine Paulsen
- Department of Medicine, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, Canada
| | - Courtney Heffernan
- Department of Medicine, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, Canada
| | - Brett Edwards
- Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Ryan Cooper
- Department of Medicine, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, Canada
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Li Y, Pang Y, Zhang T, Xian X, Yang J, Wang R, Wang P, Zhang M, Chen W. Genotypes of Mycobacterium tuberculosis isolates circulating in Shaanxi Province, China. PLoS One 2020; 15:e0242971. [PMID: 33270700 PMCID: PMC7714122 DOI: 10.1371/journal.pone.0242971] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Accepted: 11/12/2020] [Indexed: 11/19/2022] Open
Abstract
Objectives The prevalence of drug-resistant TB in Shaanxi Province is higher than other areas. This study was aimed to investigate the genetic diversity and epidemiology of Mycobacterium tuberculosis clinical strains in Shaanxi Province, China. Methods From January to December 2016, a total of 298 Mycobacterium tuberculosis clinical isolates from smear-positive pulmonary tuberculosis patients were genotyped by Mcspoligotyping and 15-locus VNTR. Results We found that the Beijing family strains was the most prominent family(81.54%, 243/298). Other family strains included T family(9.06%, 27/298), U family(0.67%, 2/298), LAM9 family(0.34%, 1/298) and Manu family(0.34%, 1/298). The rates of multidrug-resistant (MDR) M.Tuberculosis, age, type of case and education between Beijing and non-Beijing family strains were not statistically different, while the distribution in the three different regions among these was statistically significant. VNTR results showed that strains were classified into 280 genotypes, and 33 (11.07%) strains could be grouped into 14 clusters. 11 of the 15-VNTR loci were highly or moderately discriminative according to the Hunter-Gaston discriminatory index. Conclusions We concluded that the Beijing family genotype was the most prevalent genotype and 15-locus VNTR typing might be suitable for genotyping of M. tuberculosis in Shaanxi Province. There was less association between Beijing family genotypes and drug resistance in our study area.
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Affiliation(s)
- Yan Li
- Clinical Laboratory, The First Affiliated Hospital, School of Medicine, Xi’an Jiaotong University, Xi’an, China
- Clinical Laboratory, Shaanxi Provincial Institute for Tuberculosis Control and Prevention, Xi’an, China
| | - Yu Pang
- National Clinical Laboratory on Tuberculosis, Beijing Chest Hospital, Capital Medical University, Beijing Tuberculosis and Thoracic Tumor Institute, Beijing, China
| | - Tianhua Zhang
- Clinical Laboratory, Shaanxi Provincial Institute for Tuberculosis Control and Prevention, Xi’an, China
| | - Xiaoping Xian
- Clinical Laboratory, Shaanxi Provincial Institute for Tuberculosis Control and Prevention, Xi’an, China
| | - Jian Yang
- Clinical Laboratory, Shaanxi Provincial Institute for Tuberculosis Control and Prevention, Xi’an, China
| | - Rui Wang
- Clinical Laboratory, Shaanxi Provincial Institute for Tuberculosis Control and Prevention, Xi’an, China
| | - Panting Wang
- Clinical Laboratory, Shaanxi Provincial Institute for Tuberculosis Control and Prevention, Xi’an, China
| | - Meng Zhang
- Clinical Laboratory, Shaanxi Provincial Institute for Tuberculosis Control and Prevention, Xi’an, China
| | - Wei Chen
- Clinical Laboratory, The First Affiliated Hospital, School of Medicine, Xi’an Jiaotong University, Xi’an, China
- * E-mail:
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24-locus MIRU-VNTR and Spoligotyping analysis of drug-resistant Mycobacterium tuberculosis strains isolated from Northeastern Thailand. INFECTION GENETICS AND EVOLUTION 2020; 85:104449. [PMID: 32622079 DOI: 10.1016/j.meegid.2020.104449] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Revised: 06/19/2020] [Accepted: 06/25/2020] [Indexed: 01/19/2023]
Abstract
Tuberculosis, caused by Mycobacterium tuberculosis (MTB) infection, remains a global health problem with increased concerns due to drug-resistant tuberculosis. However, molecular genotyping profiles may give insight of the transmission of TB in a particular region. The present study aimed to characterize the genetic diversity of drug-resistant MTB and evaluate primer sets applied for the epidemiological study of circulating MTB in Northeastern Thailand. A total of 92 MTB isolates, resistant to rifampicin and/or isoniazid, were collected from the Office of Disease Prevention and Control between 2013 and 2016. All isolates were genotyped by 24-locus MIRU-VNTR typing combined with spoligotyping. We also analyzed the distributions of drug susceptibility pattern and demographic data among different genotypes. In comparison with different loci sets, discriminatory power based on 12, 15, 24 standard primers were investigated. Eighty-six particular profiles were found; among the patterns, two clusters were produced in 8 strains. East African Indians (EAI) were the most prevalent strains (33 isolates, 35.87%) followed by Beijing (30 isolates, 32.61%), with 23 unknown isolates strains also found. The HGDI based on combination of 24 loci analysis and spoligotyping was 0.9962. The number of tandem repeat generated was highly discriminant (HGDI>0.6) at locus 580 (0.66), 960 (0.67), 2163b (0.73), 2165 (0.62), 2461 (0.68) 3690 (0.73) and 4052 (0.79), respectively. In contrast, the diversity at locus 154 and 2059 was not revealed. The results emphasized that 24-locus MIRU-VNTR and spoligotyping could be useful for epidemiological surveillance of drug-resistant MTB in this region. At a given allelic diversity, 7 primer sets containing MIRU04, MIRU10, QUB2163b, ETRA, ETRB, Mtub39 and QUB26 may be considered for screening the VNTR patterns. In addition, this study gathered both demographics and genotypic data within the same investigation for further tuberculosis prevention and control.
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Arora J, Suresh N, Porwal C, Pandey P, Pande JN, Singh UB. Genotyping Mycobacterium tuberculosis isolates with few copies of IS6110: Value of additional genetic markers. INFECTION GENETICS AND EVOLUTION 2020; 81:104230. [PMID: 32035976 DOI: 10.1016/j.meegid.2020.104230] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Revised: 01/22/2020] [Accepted: 01/28/2020] [Indexed: 10/25/2022]
Abstract
PURPOSE IS6110 restriction fragment length polymorphism (RFLP) analysis is widely used for molecular epidemiological studies of tuberculosis. Role of spoligotyping and Fluorescent Amplified Fragment Length Polymorphism (FAFLP) was studied in low-copy number IS6110 strains of Mycobacterium tuberculosis complex (Mtbc). METHODS The study isolates included 70 strains of Mtbc collected from different regions of India. IS6110 restriction fragment, spoligotyping and FAFLP were performed for genotypic analysis. RESULTS A single copy of IS6110 was found in 30% of isolates with 90.5% of them harboring characteristic 1.5-Kb IS6110 restriction fragment.IS6110RFLP identified 51 different types, FAFLP 41 types, and spoligotyping 31 types. Combination of all three techniques identified 67 different types.IS6110 RFLP analysis was found sensitive for genotyping isolates with more than one copy of IS6110 (Hunter Gaston Discriminatory Index (HGDI-1) while, neither spoligotyping (HGI-0.89) nor FAFLP (HGDI-0.92) or their combinations were as good. The discriminatory power of spoligotyping (HGDI- 0.89) in isolates with a single copy of IS6110 was higher than IS6110-RFLP.Clustering was reduced to 67% using spoligotyping and to 38% with FAFLP. CONCLUSION Combination of FAFLP and Spoligotyping may prove to be valuable in studying the epidemiology of M. tuberculosis strains harboring few copies of IS6110 element.
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Affiliation(s)
- Jyoti Arora
- Department of Microbiology, All India Institute of Medical Sciences,New Delhi, India
| | - Naga Suresh
- Department of Microbiology, All India Institute of Medical Sciences,New Delhi, India
| | - Chhavi Porwal
- Department of Microbiology, All India Institute of Medical Sciences,New Delhi, India
| | - Pooja Pandey
- Department of Microbiology, All India Institute of Medical Sciences,New Delhi, India
| | | | - Urvashi Balbir Singh
- Department of Microbiology, All India Institute of Medical Sciences,New Delhi, India.
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MIRU-VNTR genotyping of Mycobacterium tuberculosis in a population of patients in Cali, Colombia, 2013-2015. BIOMEDICA 2019; 39:71-85. [PMID: 31529850 DOI: 10.7705/biomedica.v39i2.3924] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2017] [Indexed: 11/21/2022]
Abstract
Introduction: Tuberculosis continues to be one of the main public health problems in the world. Together with the HIV infection, it is one of the main causes of death due to infections worldwide. In 2016, 6.3 million new cases of the disease were reported.
Objective: To describe the genetic patterns determined by genotyping using variable-number tandem repeats of mycobacterial interspersed repetitive units (MIRU-VNTR) in the study population and compare them with other studies carried out in Cali, Colombia, and the world.
Materials and methods: We genotyped a total of 105 DNA samples extracted from sputum or culture isolates of the Mycobacterium tuberculosis complex, which were obtained from pulmonary tuberculosis diagnosed patients over the period 2013-2015, in Cali. We performed PCR amplification of 24 loci by MIRU-VNTR on the DNA extracted from the samples. The amplicons were visualized in agarose gel electrophoresis (2%) with SYBR Safe™ staining. Then, the alleles were designated by graphical analysis using the GelAnalyzer 2010 software. These results were analyzed using the UPGMA logarithm and compared with the registers from the MIRU-VNTR plus and SITVITWEB databases.
Results: We genotyped 62 of the samples completely and we obtained 58 different MIRU-VNTR profiles. By comparing with the international databases, we determined the following distributions per lineage: LAM, 54.8%; Haarlem,25.8%; S, 14.5%; Beijing, 3.2%, and Cameroon, 1.6%. The MIRU-VNTR patterns corresponded to 17 different MITs; the most frequent were MIT 190 and MIT 110, with 22.6% and 6.5%, respectively.
Conclusions: These results demonstrated previous observations about the predominance of the LAM and Haarlem lineages in the city, and the presence of the MITs found in another city of Colombia.
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The Evolution of Genotyping Strategies To Detect, Analyze, and Control Transmission of Tuberculosis. Microbiol Spectr 2019; 6. [PMID: 30338753 DOI: 10.1128/microbiolspec.mtbp-0002-2016] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The introduction of genotypic tools to analyze Mycobacterium tuberculosis isolates has transformed our knowledge of the transmission dynamics of this pathogen. We discuss the development of the laboratory methods that have been applied in recent years to study the epidemiology of M. tuberculosis. This review integrates two approaches: on the one hand, it considers how genotyping techniques have evolved over the years; and on the other, it looks at how the way we think these techniques should be applied has changed. We begin by examining the application of fingerprinting tools to suspected outbreaks only, before moving on to universal genotyping schemes, and finally we describe the latest real-time strategies used in molecular epidemiology. We also analyze refined approaches to obtaining epidemiological data from patients and to increasing the discriminatory power of genotyping by techniques based on genomic characterization. Finally, we review the development of integrative solutions to reconcile the speed of PCR-based methods with the high discriminatory power of whole-genome sequencing in easily implemented formats adapted to low-resource settings. Our analysis of future considerations highlights the need to bring together the three key elements of high-quality surveillance of transmission in tuberculosis, namely, speed, precision, and ease of implementation.
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Koster KJ, Largen A, Foster JT, Drees KP, Qian L, Desmond E, Wan X, Hou S, Douglas JT. Genomic sequencing is required for identification of tuberculosis transmission in Hawaii. BMC Infect Dis 2018; 18:608. [PMID: 30509214 PMCID: PMC6276198 DOI: 10.1186/s12879-018-3502-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2018] [Accepted: 11/02/2018] [Indexed: 02/08/2023] Open
Abstract
Background Tuberculosis (TB) caused an estimated 1.4 million deaths and 10.4 million new cases globally in 2015. TB rates in the United States continue to steadily decline, yet rates in the State of Hawaii are perennially among the highest in the nation due to a continuous influx of immigrants from the Western Pacific and Asia. TB in Hawaii is composed of a unique distribution of genetic lineages, with the Beijing and Manila families of Mycobacterium tuberculosis (Mtb) comprising over two-thirds of TB cases. Standard fingerprinting methods (spoligotyping plus 24-loci Mycobacterial Interspersed Repetitive Units-Variable Number Tandem Repeats [MIRU-VNTR] fingerprinting) perform poorly when used to identify actual transmission clusters composed of isolates from these two families. Those typing methods typically group isolates from these families into large clusters of non-linked isolates with identical fingerprints. Next-generation whole-genome sequencing (WGS) provides a new tool for molecular epidemiology that can resolve clusters of isolates with identical spoligotyping and MIRU-VNTR fingerprints. Methods We performed WGS and SNP analysis and evaluated epidemiological data to investigate 19 apparent TB transmission clusters in Hawaii from 2003 to 2017 in order to assess WGS’ ability to resolve putative Mtb clusters from the Beijing and Manila families. This project additionally investigated MIRU-VNTR allele prevalence to determine why standard Mtb fingerprinting fails to usefully distinguish actual transmission clusters from these two Mtb families. Results WGS excluded transmission events in seven of these putative clusters, confirmed transmission in eight, and identified both transmission-linked and non-linked isolates in four. For epidemiologically identified clusters, while the sensitivity of MIRU-VNTR fingerprinting for identifying actual transmission clusters was found to be 100%, its specificity was only 28.6% relative to WGS. We identified that the Beijing and Manila families’ significantly lower Shannon evenness of MIRU-VNTR allele distributions than lineage 4 was the cause of standard fingerprinting’s poor performance when identifying transmission in Beijing and Manila family clusters. Conclusions This study demonstrated that WGS is necessary for epidemiological investigation of TB in Hawaii and the Pacific. Electronic supplementary material The online version of this article (10.1186/s12879-018-3502-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | - Angela Largen
- Hawaii State Department of Health, Honolulu, HI, USA
| | - Jeffrey T Foster
- University of New Hampshire, Durham, NH, USA.,Present Address: Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA
| | | | - Lishi Qian
- University of Hawaii at Manoa, Honolulu, HI, USA
| | - Ed Desmond
- California Department of Public Health, Richmond, CA, USA
| | - Xuehua Wan
- Advanced Studies in Genomics, Proteomics and Bioinformatics, Honolulu, HI, USA
| | - Shaobin Hou
- Advanced Studies in Genomics, Proteomics and Bioinformatics, Honolulu, HI, USA
| | - James T Douglas
- University of Hawaii at Manoa, Honolulu, HI, USA. .,Present Address: Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA.
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Genetic diversity of Mycobacterium tuberculosis isoniazid monoresistant and multidrug-resistant in Rio Grande do Sul, a tuberculosis high-burden state in Brazil. Tuberculosis (Edinb) 2018; 110:36-43. [DOI: 10.1016/j.tube.2018.02.009] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2017] [Revised: 02/09/2018] [Accepted: 02/26/2018] [Indexed: 11/19/2022]
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Risk factors associated with cluster size of Mycobacterium tuberculosis (Mtb) of different RFLP lineages in Brazil. BMC Infect Dis 2018; 18:71. [PMID: 29422032 PMCID: PMC5806441 DOI: 10.1186/s12879-018-2969-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2016] [Accepted: 01/17/2018] [Indexed: 12/15/2022] Open
Abstract
Background Tuberculosis (TB) transmission is influenced by patient-related risk, environment and bacteriological factors. We determined the risk factors associated with cluster size of IS6110 RFLP based genotypes of Mycobacterium tuberculosis (Mtb) isolates from Vitoria, Espirito Santo, Brazil. Methods Cross-sectional study of new TB cases identified in the metropolitan area of Vitoria, Brazil between 2000 and 2010. Mtb isolates were genotyped by the IS6110 RFLP, spoligotyping and RDRio. The isolates were classified according to genotype cluster sizes by three genotyping methods and associated patient epidemiologic characteristics. Regression Model was performed to identify factors associated with cluster size. Results Among 959 Mtb isolates, 461 (48%) cases had an isolate that belonged to an RFLP cluster, and six clusters with ten or more isolates were identified. Of the isolates spoligotyped, 448 (52%) were classified as LAM and 412 (48%) as non-LAM. Our regression model found that 6–9 isolates/RFLP cluster were more likely belong to the LAM family, having the RDRio genotype and to be smear-positive (adjusted OR = 1.17, 95% CI 1.08–1.26; adjusted OR = 1.25, 95% CI 1.14–1.37; crude OR = 2.68, 95% IC 1.13–6.34; respectively) and living in a Serra city neighborhood decrease the risk of being in the 6–9 isolates/RFLP cluster (adjusted OR = 0.29, 95% CI, 0.10–0.84), than in the others groups. Individuals aged 21 to 30, 31 to 40 and > 50 years were less likely of belonging the 2–5 isolates/RFLP cluster than unique patterns compared to individuals < 20 years of age (adjusted OR = 0.49, 95% CI 0.28–0.85, OR = 0.43 95% CI 0.24–0.77and OR = 0. 49, 95% CI 0.26–0.91), respectively. The extrapulmonary disease was less likely to occur in those infected with strains in the 2–5 isolates/cluster group (adjustment OR = 0.45, 95% CI 0.24–0.85) than unique patterns. Conclusions We found that a large proportion of new TB infections in Vitoria is caused by prevalent Mtb genotypes belonging to the LAM family and RDRio genotypes. Such information demonstrates that some genotypes are more likely to cause recent transmission. Targeting interventions such as screening in specific areas and social risk groups, should be a priority for reducing transmission.
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Rasoahanitralisoa R, Rakotosamimanana N, Stucki D, Sola C, Gagneux S, Rasolofo Razanamparany V. Evaluation of spoligotyping, SNPs and customised MIRU-VNTR combination for genotyping Mycobacterium tuberculosis clinical isolates in Madagascar. PLoS One 2017; 12:e0186088. [PMID: 29053711 PMCID: PMC5650158 DOI: 10.1371/journal.pone.0186088] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2017] [Accepted: 09/25/2017] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Combining different molecular typing methods for Mycobacterium tuberculosis complex (MTBC) can be a powerful tool for molecular epidemiology-based investigation of TB. However, the current standard method that provides high discriminatory power for such a combination, mycobacterial interspersed repetitive units-variable numbers of tandem repeats typing (MIRU-VNTR), is laborious, time-consuming and often too costly for many resource-limited laboratories. We aimed to evaluate a reduced set of loci for MIRU-VNTR typing in combination with spoligotyping and SNP-typing for routine molecular epidemiology of TB. METHOD Spoligotyping and SNP-typing, in combination with the 15 loci MIRU-VNTR typing, were first used to type clinical MTBC isolates (n = 158) from Madagascar. A step by step reduction of MIRU-VNTR loci number was then performed according to the Hunter and Gaston Discriminatory Index (HGDI) and to the Principal component analysis (PCA) correlation with the spoligotype profiles to evaluate the discrimination power inside the generated spoligotype clusters. The 15 MIRU-VNTR was used as reference and SNP-typing was used to determine the main MTBC lineages. RESULTS Of the 158 clinical isolates studied, the SNP-typing classified 23 into Lineage 1 (14.6%), 31 into Lineage 2 (19.6%), 23 into Lineage 3 (14.6%) and 81 into Lineage 4 strains (51.3%). 37 different spoligotypes profiles were obtained, 15 of which were unique and 20 in clusters. 15-loci MIRU-VNTR typing revealed 144 different genotypes: 132 isolates had a unique MIRU-VNTR profile and 27 isolates were grouped into 12 clusters. After a stepwise reduction of the MIRU-VNTR loci number within each main spoligotype families, three different sets composed of 5 customised MIRU-VNTR loci had a similar discrimination level to the reference 15 loci MIRU-VNTR in lineage 1, lineage 2 and lineage 3. For lineage 4, a set of 4 and 3 MIRU-VNTR loci were proposed to subtype the Harleem and LAM spoligotype families, respectively. For the T spoligotype family, a set of 5 MIRU-VNTR loci was proposed. CONCLUSION According to the lineages and the spoligotype families, the number of MIRU-VNTR loci can be reduced to get an optimal classification of MTBC. These customized sets of MIRU-VNTR loci reduce workload and save resources while maintaining optimal discriminatory power.
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Affiliation(s)
- Rondroarivelo Rasoahanitralisoa
- Mycobacteria Unit, Institut Pasteur of Madagascar, Antananarivo, Madagascar, Ecole Doctorale Science de la Vie et de l'Environnement, Faculté des Sciences, Université d'Antananarivo, Antananarivo, Madagascar
| | | | - David Stucki
- Department of Medical Parasitology and infection Biology, Swiss Tropical and Public Health Institute, Basel, Switzerland.,University of Basel, Basel, Switzerland
| | | | - Sebastien Gagneux
- Department of Medical Parasitology and infection Biology, Swiss Tropical and Public Health Institute, Basel, Switzerland.,Institut for Integrative Cell Biology, I2BC, UMR9198 CEA-CNRS-UP Saclay, Orsay, France
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Séraphin MN, Doggett R, Johnston L, Zabala J, Gerace AM, Lauzardo M. Association between Mycobacterium tuberculosis lineage and site of disease in Florida, 2009-2015. INFECTION GENETICS AND EVOLUTION 2017; 55:366-371. [PMID: 28993293 DOI: 10.1016/j.meegid.2017.10.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2017] [Revised: 10/01/2017] [Accepted: 10/03/2017] [Indexed: 01/05/2023]
Abstract
BACKGROUND Mycobacterium tuberculosis is characterized into four global lineages with strong geographical restriction. To date one study in the United States has investigated M. tuberculosis lineage association with tuberculosis (TB) disease presentation (extra-pulmonary versus pulmonary). We update this analysis using recent (2009-2015) data from the State of Florida to measure lineage association with pulmonary TB, the infectious form of the disease. METHODS M. tuberculosis lineage was assigned based on the spacer oligonucleotide typing (spoligotyping) patterns. TB disease site was defined as exclusively pulmonary or extra-pulmonary. We used ORs to measure the association between M. tuberculosis lineages and pulmonary compared to extra-pulmonary TB. The final multivariable model was adjusted for patient socio-demographics, HIV and diabetes status. RESULTS We analyzed 3061 cases, 83.4% were infected with a Euro-American lineage, 8.4% Indo-Oceanic and 8.2% East-Asian lineage. The majority of the cases (86.0%) were exclusively pulmonary. Compared to the Indo-Oceanic lineage, infection with a Euro-American (AOR=1.87, 95% CI: 1.21, 2.91) or an East-Asian (AOR=2.11, 95% CI: 1.27, 3.50) lineage favored pulmonary disease compared to extra-pulmonary. In a sub-analysis among pulmonary cases, strain lineage was not associated with sputum smear positive status, indicating that the observed association with pulmonary disease is independent of host contagiousness. CONCLUSION As an obligate pathogen, M. tuberculosis' fitness is directly correlated to its transmission potential. In this analysis, we show that M. tuberculosis lineage is associated with pulmonary disease presentation. This association may explain the predominance in a region of certain lineages compared to others.
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Affiliation(s)
- Marie Nancy Séraphin
- Division of Infectious Diseases and Global Medicine, University of Florida, College of Medicine, 2055 Mowry Road, P.O. Box 103600, Gainesville, FL 32610, USA; Emerging Pathogen Institute, University of Florida, 2055 Mowry Road, P.O. Box 100009, Gainesville, FL 32610, USA.
| | - Richard Doggett
- Florida Department of Health, Bureau of Public Health Laboratories, 1217 N. Pearl Street, Jacksonville, FL, 32202, USA.
| | - Lori Johnston
- Florida Department of Health, Bureau of Tuberculosis Control, 4052 Bald Cypress Way, Bin A-20, Tallahassee, FL 32399.
| | - Jose Zabala
- Florida Department of Health, Bureau of Tuberculosis Control, 4052 Bald Cypress Way, Bin A-20, Tallahassee, FL 32399.
| | - Alexandra M Gerace
- Division of Infectious Diseases and Global Medicine, University of Florida, College of Medicine, 2055 Mowry Road, P.O. Box 103600, Gainesville, FL 32610, USA; Emerging Pathogen Institute, University of Florida, 2055 Mowry Road, P.O. Box 100009, Gainesville, FL 32610, USA.
| | - Michael Lauzardo
- Division of Infectious Diseases and Global Medicine, University of Florida, College of Medicine, 2055 Mowry Road, P.O. Box 103600, Gainesville, FL 32610, USA; Emerging Pathogen Institute, University of Florida, 2055 Mowry Road, P.O. Box 100009, Gainesville, FL 32610, USA.
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13
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Molecular typing of Mycobacterium tuberculosis complex isolated from pulmonary tuberculosis patients in central Ethiopia. BMC Infect Dis 2017; 17:184. [PMID: 28249607 PMCID: PMC5333391 DOI: 10.1186/s12879-017-2267-2] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2015] [Accepted: 02/15/2017] [Indexed: 11/25/2022] Open
Abstract
Background Identification of the types of strains of Mycobacterium tuberculosis (M. tuberculosis) complex causing tuberculosis (TB) could contribute to TB control program of specific geographic region as well as it could add knowledge onto the existing literature on TB worldwide. The objective of the present study was to identify the species and strains of M. tuberculosis complex causing pulmonary tuberculosis in central Ethiopia. Methods A health institution- based cross-sectional study was conducted on 338 smear positive TB cases visiting three hospitals between October 2012 and September 2013. Morning and spot sputum samples were collected before the starting of treatment regimens. Thus, a total of 338 pooled sputum samples collected from these cases. Samples were cultured on Löwenstein Jensen media and the isolates were identified by the region of difference (RD) 9 based polymerase chain reaction (PCR) and spoligotyping. Result Of the total isolates 98.6% of the isolates were identified to be M. tuberculosis while the remaining 1.4% were identified as M. africanum. Further, typing of M. tuberculosis using spoligotyping lead to the identification of 90 different strains of M. tuberculosis. Of these strains, 32 were clustered consisting of more than one isolate while the remaining 58 strains were unique consisting of single isolate. Thus, 79.3% (223/281) of the isolates were found in the clustered while only 20.6% (58/281) of the strains were unique. Forty-five of the spolgotyping patterns were registeredin the SITVIT2 or SpolDB4 database in while the remaining 45 were notfound in the database and hence were orphan strains. The dominant strains were SIT53, SIT149, and SIT54, consisting of 43, 37 and 34 isolates, respectively. Classification of the spoligotype patterns using TB-insight RUN TB-Lineage showed that 86.8, 6.4, 5, 1.4% ofthe isolatesbelonged to the Euro-American lineage, East-African-Indian, Indo-oceanic and M. africanum, respectively. Conclusion The identification of clustered and new strains using spolygotyping in present study does not give conclusive finding as spoligotyping has low discriminatory power. Thus, further identification of these isolates using mycobacterial interspersed repetitive unit-variable number tandem repeat (MIRU-VENTR) and or whole genome sequencing (WGS) recommended.
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Genotypic Diversity of Mycobacterium tuberculosis Clinical Isolates in the Multiethnic Area of the Xinjiang Uygur Autonomous Region in China. BIOMED RESEARCH INTERNATIONAL 2017; 2017:3179535. [PMID: 28337447 PMCID: PMC5350424 DOI: 10.1155/2017/3179535] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 08/11/2016] [Revised: 10/28/2016] [Accepted: 01/04/2017] [Indexed: 12/05/2022]
Abstract
Objectives. We studied the genetic diversity of clinical isolates from patients with tuberculosis in the multiethnic area of Xinjiang autonomous region in China. A total of 311 clinical M. tuberculosis isolates were collected in 2006 and 2011 and genotyped by two genotyping methods. All isolates were grouped into 68 distinct spoligotypes using the spoligotyping method. The Beijing family was dominant, followed by T1 and CAS. MIRU-VNTR results showed that a total of 195 different VNTR types were identified. Ten of the 15 loci were highly or moderately discriminant according to their HGDI scores, and 13 loci had good discriminatory power in non-Beijing family strains, whereas only two loci had good discriminatory power in Beijing family strains. Chi-square tests demonstrated that there were no correlations between four characteristics (sex, age, type of case, and treatment history) and the Beijing family. In summary, Beijing family strains were predominant in Xinjiang, and the VNTR-15China locus-set was suitable for genotyping all Xinjiang strains, but not for the Beijing family strains. Thus, these data suggested that different genotype distributions may exist in different regions; MLVA locus-sets should be adjusted accordingly, with newly added loci to increase resolution if necessary.
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The Evolution of Strain Typing in the Mycobacterium tuberculosis Complex. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017; 1019:43-78. [PMID: 29116629 DOI: 10.1007/978-3-319-64371-7_3] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Tuberculosis (TB) is a contagious disease with a complex epidemiology. Therefore, molecular typing (genotyping) of Mycobacterium tuberculosis complex (MTBC) strains is of primary importance to effectively guide outbreak investigations, define transmission dynamics and assist global epidemiological surveillance of the disease. Large-scale genotyping is also needed to get better insights into the biological diversity and the evolution of the pathogen. Thanks to its shorter turnaround and simple numerical nomenclature system, mycobacterial interspersed repetitive unit-variable-number tandem repeat (MIRU-VNTR) typing, based on 24 standardized plus 4 hypervariable loci, optionally combined with spoligotyping, has replaced IS6110 DNA fingerprinting over the last decade as a gold standard among classical strain typing methods for many applications. With the continuous progress and decreasing costs of next-generation sequencing (NGS) technologies, typing based on whole genome sequencing (WGS) is now increasingly performed for near complete exploitation of the available genetic information. However, some important challenges remain such as the lack of standardization of WGS analysis pipelines, the need of databases for sharing WGS data at a global level, and a better understanding of the relevant genomic distances for defining clusters of recent TB transmission in different epidemiological contexts. This chapter provides an overview of the evolution of genotyping methods over the last three decades, which culminated with the development of WGS-based methods. It addresses the relative advantages and limitations of these techniques, indicates current challenges and potential directions for facilitating standardization of WGS-based typing, and provides suggestions on what method to use depending on the specific research question.
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Ndungu PW, Kariuki S, Revathi G, Ng’ang’a Z, Niemann S. Mycobacteria Interspersed Repetitive Units-Variable Number of Tandem Repeat, Spoligotyping and Drug Resistance of Isolates from Pulmonary Tuberculosois Patients in Kenya. ACTA ACUST UNITED AC 2017. [DOI: 10.4236/aim.2017.73017] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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17
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Lewinsohn DM, Leonard MK, LoBue PA, Cohn DL, Daley CL, Desmond E, Keane J, Lewinsohn DA, Loeffler AM, Mazurek GH, O'Brien RJ, Pai M, Richeldi L, Salfinger M, Shinnick TM, Sterling TR, Warshauer DM, Woods GL. Official American Thoracic Society/Infectious Diseases Society of America/Centers for Disease Control and Prevention Clinical Practice Guidelines: Diagnosis of Tuberculosis in Adults and Children. Clin Infect Dis 2016; 64:e1-e33. [PMID: 27932390 DOI: 10.1093/cid/ciw694] [Citation(s) in RCA: 258] [Impact Index Per Article: 32.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2016] [Accepted: 10/14/2016] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND Individuals infected with Mycobacterium tuberculosis (Mtb) may develop symptoms and signs of disease (tuberculosis disease) or may have no clinical evidence of disease (latent tuberculosis infection [LTBI]). Tuberculosis disease is a leading cause of infectious disease morbidity and mortality worldwide, yet many questions related to its diagnosis remain. METHODS A task force supported by the American Thoracic Society, Centers for Disease Control and Prevention, and Infectious Diseases Society of America searched, selected, and synthesized relevant evidence. The evidence was then used as the basis for recommendations about the diagnosis of tuberculosis disease and LTBI in adults and children. The recommendations were formulated, written, and graded using the Grading, Recommendations, Assessment, Development and Evaluation (GRADE) approach. RESULTS Twenty-three evidence-based recommendations about diagnostic testing for latent tuberculosis infection, pulmonary tuberculosis, and extrapulmonary tuberculosis are provided. Six of the recommendations are strong, whereas the remaining 17 are conditional. CONCLUSIONS These guidelines are not intended to impose a standard of care. They provide the basis for rational decisions in the diagnosis of tuberculosis in the context of the existing evidence. No guidelines can take into account all of the often compelling unique individual clinical circumstances.
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Affiliation(s)
| | | | - Philip A LoBue
- Centers for Disease Control and Prevention, Atlanta, Georgia
| | - David L Cohn
- Denver Public Health Department, Denver, Colorado
| | - Charles L Daley
- National Jewish Health and the University of Colorado Denver, and
| | - Ed Desmond
- California Department of Public Health, Richmond
| | | | | | - Ann M Loeffler
- Francis J. Curry International TB Center, San Francisco, California
| | | | | | - Madhukar Pai
- McGill University and McGill International TB Centre, Montreal, Canada
| | | | | | | | - Timothy R Sterling
- Vanderbilt University School of Medicine, Vanderbilt Institute for Global Health, Nashville, Tennessee
| | | | - Gail L Woods
- University of Arkansas for Medical Sciences, Little Rock
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18
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Methodological and Clinical Aspects of the Molecular Epidemiology of Mycobacterium tuberculosis and Other Mycobacteria. Clin Microbiol Rev 2016; 29:239-90. [PMID: 26912567 DOI: 10.1128/cmr.00055-15] [Citation(s) in RCA: 97] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Molecular typing has revolutionized epidemiological studies of infectious diseases, including those of a mycobacterial etiology. With the advent of fingerprinting techniques, many traditional concepts regarding transmission, infectivity, or pathogenicity of mycobacterial bacilli have been revisited, and their conventional interpretations have been challenged. Since the mid-1990s, when the first typing methods were introduced, a plethora of other modalities have been proposed. So-called molecular epidemiology has become an essential subdiscipline of modern mycobacteriology. It serves as a resource for understanding the key issues in the epidemiology of tuberculosis and other mycobacterial diseases. Among these issues are disclosing sources of infection, quantifying recent transmission, identifying transmission links, discerning reinfection from relapse, tracking the geographic distribution and clonal expansion of specific strains, and exploring the genetic mechanisms underlying specific phenotypic traits, including virulence, organ tropism, transmissibility, or drug resistance. Since genotyping continues to unravel the biology of mycobacteria, it offers enormous promise in the fight against and prevention of the diseases caused by these pathogens. In this review, molecular typing methods for Mycobacterium tuberculosis and nontuberculous mycobacteria elaborated over the last 2 decades are summarized. The relevance of these methods to the epidemiological investigation, diagnosis, evolution, and control of mycobacterial diseases is discussed.
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Riyahi Zaniani F, Moghim S, Mirhendi H, Ghasemian Safaei H, Fazeli H, Salehi M, Nasr Esfahani B. Genetic Lineages of Mycobacterium tuberculosis Isolates in Isfahan, Iran. Curr Microbiol 2016; 74:14-21. [PMID: 27743106 DOI: 10.1007/s00284-016-1145-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2016] [Accepted: 10/06/2016] [Indexed: 11/29/2022]
Abstract
In this study, we aimed to identify the genetic lineages of Mycobacterium tuberculosis isolates in Isfahan via the mycobacterial interspersed repetitive-unit-variable number tandem repeat typing method based on 15 loci. Forty-nine M. tuberculosis isolates were collected between 2013 and 2015 from Tuberculosis patients in Mollahadi Sabzevari Tuberculosis Center in Isfahan. All isolates were typed by 15-locus MIRU-VNTR typing. The highest percentage of isolates, 44.89 % (22/49), belonged to the Euro-American lineage, while the frequencies of the East-African-Indian, East-Asian, and Indo-Oceanic lineages were 28.57 % (14/49), 24.4 % (12/49), and 2.04 % (1/49), respectively. Among the 22 isolates of the Euro-American lineage, those belonging to the NEW-1 sub-lineage were most prevalent (24.4 %). Approximately, the same proportion of isolates belonging to the Delhi/CAS, Beijing, and NEW-1 sub-lineages were identified in Iranian and Afghan immigrant patients. The Delhi/CAS and Beijing sub-lineage isolates were prevalent among patients who had been previously treated for TB. Results showed that all of the 49 MIRU-VNTR patterns were unique and the clustering rate of the 15-locus MIRU-VNTR was 0.0 (minimum recent transmission). The results of this study show that the lineages of M. tuberculosis isolates in Isfahan are similar to those reported in the Eastern Mediterranean region (indicative of the epidemiological relationship between the countries in the region). The low clustering rate in our results reveals that transmission of tuberculosis in Isfahan is, in most cases, a reactivation of previous tuberculosis infection and the role of recently transmitted disease is minor.
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Affiliation(s)
- Fatemeh Riyahi Zaniani
- Department of Microbiology, Faculty of Medicine, Isfahan University of Medical Sciences, Esfahān, Iran
| | - Sharareh Moghim
- Department of Microbiology, Faculty of Medicine, Isfahan University of Medical Sciences, Esfahān, Iran
| | - Hossein Mirhendi
- Department of Medical Parasitology and Mycology, Faculty of Medicine, Isfahan University of Medical Sciences, Esfahān, Iran
| | - Hajieh Ghasemian Safaei
- Department of Microbiology, Faculty of Medicine, Isfahan University of Medical Sciences, Esfahān, Iran
| | - Hossein Fazeli
- Department of Microbiology, Faculty of Medicine, Isfahan University of Medical Sciences, Esfahān, Iran
| | - Mahshid Salehi
- Regional Tuberculosis Reference Laboratories in Esfahan, Esfahān, Iran
| | - Bahram Nasr Esfahani
- Department of Microbiology, Faculty of Medicine, Isfahan University of Medical Sciences, Esfahān, Iran.
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20
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Scott C, Cavanaugh JS, Pratt R, Silk BJ, LoBue P, Moonan PK. Human Tuberculosis Caused by Mycobacterium bovis in the United States, 2006-2013. Clin Infect Dis 2016; 63:594-601. [PMID: 27298329 DOI: 10.1093/cid/ciw371] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2016] [Accepted: 05/12/2016] [Indexed: 11/12/2022] Open
Abstract
BACKGROUND Using genotyping techniques that have differentiated Mycobacterium bovis from Mycobacterium tuberculosis since 2005, we review the epidemiology of human tuberculosis caused by M. bovis in the United States and validate previous findings nationally. METHODS All tuberculosis cases with a genotyped M. tuberculosis complex isolate reported during 2006-2013 in the United States were eligible for analysis. We used binomial regression to identify characteristics independently associated with M. bovis disease using adjusted prevalence ratios (aPRs) and corresponding 95% confidence intervals (CIs). RESULTS During 2006-2013, the annual percentages of tuberculosis cases attributable to M. bovis remained consistent nationally (range, 1.3%-1.6%) among all tuberculosis cases (N = 59 273). Compared with adults 25-44 years of age, infants aged 0-4 years (aPR, 1.9 [95% CI, 1.4-2.8]) and children aged 5-14 years (aPR, 4.0 [95% CI, 3.1-5.3]) had higher prevalences of M. bovis disease. Patients who were foreign-born (aPR, 1.4 [95% CI, 1.2-1.7]), Hispanic (aPR, 3.9 [95% CI, 3.0-5.0]), female (aPR, 1.4 [95% CI, 1.3-1.6]), and resided in US-Mexico border counties (aPR, 2.0 [95% CI, 1.7-2.4]) also had higher M. bovis prevalences. Exclusively extrapulmonary disease (aPR, 3.7 [95% CI, 3.3-4.2]) or disease that was both pulmonary and extrapulmonary (aPR, 2.4 [95% CI, 2.1-2.9]) were associated with a higher prevalence of M. bovis disease. CONCLUSIONS Children, foreign-born persons, Hispanics, and females are disproportionately affected by M. bovis, which was independently associated with extrapulmonary disease. Targeted prevention efforts aimed at Hispanic mothers and caregivers are warranted.
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Affiliation(s)
- Colleen Scott
- Epidemic Intelligence Service, Division of Applied Sciences Division of Global HIV and TB
| | | | - Robert Pratt
- Division of Tuberculosis Elimination, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Benjamin J Silk
- Division of Tuberculosis Elimination, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Philip LoBue
- Division of Tuberculosis Elimination, Centers for Disease Control and Prevention, Atlanta, Georgia
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Hoza AS, Mfinanga SG, Moser I, König B. Molecular characterization of Mycobacterium tuberculosis isolates from Tanga, Tanzania: First insight of MIRU-VNTR and microarray-based spoligotyping in a high burden country. Tuberculosis (Edinb) 2016; 98:116-24. [PMID: 27156627 DOI: 10.1016/j.tube.2016.02.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2015] [Revised: 02/12/2016] [Accepted: 02/13/2016] [Indexed: 11/26/2022]
Abstract
Molecular typing of Mycobacterium tuberculosis(MTB) has greatly enhanced the understanding of the population structure of MTB isolates and epidemiology of tuberculosis (TB). To characterize prevalent genotypes of MTB, microarrays‑based spoligotyping and mycobacterial interspersed repetitive unit‑variable number of tandem repeats (MIRU‑VNTR) were applied on 80 isolates collected from primary health care facilities in Tanga, North‑eastern Tanzania. A total of 18 distinct spoligotypes were identified. The lineages by order of their predominance were EAI and CAS families (26.25%, 21 isolates each), LAM family and T super‑family (10%, 8 isolates each), MANU family (3.75%, 3 isolates), Beijing family (2.5%, 2 isolates) and S family (1.25%, 1 isolate). Overall, sixteen (20%) strains could not be allocated to any lineage according to the SITVIT_WEB database. The allelic diversity (h) for specific MIRU‑VNTR loci showed a considerable variation ranging from 0.826 of VNTR locus 3192 to 0.141 of VNTR locus 2059. The allelic diversity for 11 loci (VNTR 3192, 2996, 2165, 960, 4052, 424, 4156, 2531, 1644, 802 and 3690) exceeded 0.6, indicating highly discriminatory power. Seven loci (VNTR 2163b, 2401, 1955, 577, 4348, 2687 and 580) showed moderate discrimination (0.3 ≤ h ≥ 0.6), and three loci (VNTR3007, 154 and 2059) were less polymorphic. The present study suggests that the TB cases in Tanga might be caused by a diverse array of MTB strain families that may be indicative of a cosmopolitan population with frequent migration and travel. Microarray‑based spoligotyping and MIRU‑VNTR could be reliable tools in detecting different MTB genotypes in high burden settings.
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Affiliation(s)
- Abubakar S Hoza
- Department of Medical Microbiology and Epidemiology of Infectious Diseases, Medical Faculty, University of Leipzig, Liebig Str. 21, 04103 Leipzig, Germany; Department of Veterinary Microbiology and Parasitology, Sokoine University of Agriculture, P.O. Box 3019, Morogoro, Tanzania.
| | - Sayoki G Mfinanga
- National Institute for Medical Research, Muhimbili Medical Research Centre, P.O. Box 3436 Dar es Salaam, Tanzania
| | - Irmgard Moser
- Friedrich Loeffler Institut, Institute of Molecular Pathogenesis, Naumburger Str. 96a, 07743 Jena, Germany
| | - Brigitte König
- Department of Medical Microbiology and Epidemiology of Infectious Diseases, Medical Faculty, University of Leipzig, Liebig Str. 21, 04103 Leipzig, Germany
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22
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Garfein RS, Catanzaro DG, Rodwell TC, Avalos E, Jackson RL, Kaping J, Evasco H, Rodrigues C, Crudu V, Lin SYG, Groessl E, Groessel E, Hillery N, Trollip A, Ganiats T, Victor TC, Eisenach K, Valafar F, Channick J, Qian L, Catanzaro A. Phenotypic and genotypic diversity in a multinational sample of drug-resistant Mycobacterium tuberculosis isolates. Int J Tuberc Lung Dis 2016; 19:420-7. [PMID: 25859997 DOI: 10.5588/ijtld.14.0488] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
OBJECTIVE To develop and evaluate rapid, molecular-based drug susceptibility testing (DST) for extensively drug-resistant tuberculosis (XDR-TB), we assembled a phenotypically and genotypically diverse collection of Mycobacterium tuberculosis isolates from patients evaluated for drug resistance in four high-burden countries. METHODS M. tuberculosis isolates from India (n = 111), Moldova (n = 90), the Philippines (n = 96), and South Africa (n = 103) were selected from existing regional and national repositories to maximize phenotypic diversity for resistance to isoniazid, rifampin (RMP), moxifloxacin, ofloxacin, amikacin, kanamycin, and capreomycin. MGIT™ 960 was performed on viable isolates in one laboratory using standardized procedures and drug concentrations. Genetic diversity within drug resistance phenotypes was assessed. RESULTS Nineteen distinct phenotypes were observed among 400 isolates with complete DST results. Diversity was greatest in the Philippines (14 phenotypes), and least in South Africa (9 phenotypes). Nearly all phenotypes included multiple genotypes. All sites provided isolates resistant to injectables but susceptible to fluoroquinolones. Many patients were taking drugs to which their disease was resistant. DISCUSSION Diverse phenotypes for XDR-TB-defining drugs, including resistance to fluoroquinolones and/or injectable drugs in RMP-susceptible isolates, indicate that RMP susceptibility does not ensure effectiveness of a standard four-drug regimen. Rapid, low-cost DST assays for first- and second-line drugs are thus needed.
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Affiliation(s)
- R S Garfein
- Department of Medicine, University of California, San Diego, California, USA
| | - D G Catanzaro
- University of Arkansas, Department of Biological Sciences, Fayetteville, Arkansas, USA
| | - T C Rodwell
- Department of Medicine, University of California, San Diego, California, USA
| | - E Avalos
- Department of Family Medicine and Public Health, University of California, San Diego, California, USA
| | - R L Jackson
- Department of Medicine, University of California, San Diego, California, USA
| | - J Kaping
- Department of Medicine, University of California, San Diego, California, USA
| | - H Evasco
- Tropical Disease Foundation, Inc, Philippine Institute of Tuberculosis Building, Makati City, Philippines
| | | | - V Crudu
- Microbiology and Morphology Laboratory, Institute of Phthisiopneumology, Chisinau, Moldova
| | - S-Y G Lin
- California Department of Public Health, Richmond, California, USA
| | | | - E Groessel
- Department of Family Medicine and Public Health, University of California, San Diego, California, USA
| | - N Hillery
- Department of Family Medicine and Public Health, University of California, San Diego, California, USA
| | - A Trollip
- Department of Biomedical Sciences, Stellenbosch University, Cape Town, South Africa
| | - T Ganiats
- Department of Family Medicine and Public Health, University of California, San Diego, California, USA
| | - T C Victor
- Department of Biomedical Sciences, Stellenbosch University, Cape Town, South Africa
| | - K Eisenach
- Department of Pathology, University of Arkansas for Medical Sciences, Little Rock, Arkansas, USA
| | - F Valafar
- University of Arkansas, Department of Biological Sciences, Fayetteville, Arkansas, USA
| | - J Channick
- Department of Medicine, University of California, San Diego, California, USA
| | - L Qian
- Department of Microbiology, University of Hawaii, Honolulu, Hawaii, USA
| | - A Catanzaro
- Department of Medicine, University of California, San Diego, California, USA
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Baker BJ, Moonan PK. Characterizing tuberculosis genotype clusters along the United States-Mexico border. Int J Tuberc Lung Dis 2015; 18:289-91. [PMID: 24670563 DOI: 10.5588/ijtld.13.0684] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
We examined the growth of tuberculosis (TB) genotype clusters during 2005-2010 in the United States, categorized by country of origin and ethnicity of the index case and geographic proximity to the US-Mexico border at the time of TB diagnosis. Nationwide, 38.9% of cases subsequent to Mexico-born index cases were US-born. Among clusters following US-born Hispanic and US-born non-Hispanic index cases, respectively 29.2% and 5.3% of subsequent cluster members were Mexico-born. In border areas, the majority of subsequent cases were Mexico-born following US-born Hispanic (56.4%) and US-born non-Hispanic (55.6%) index cases. These findings suggest that TB transmission commonly occurs between US-born and Mexico-born persons. Along the US-Mexico border, prioritizing TB genotype clusters following US-born index cases for investigation may prevent subsequent cases among both US-born and Mexico-born persons.
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Affiliation(s)
- B J Baker
- Epidemic Intelligence Service, and Division of Tuberculosis Elimination, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - P K Moonan
- Division of Tuberculosis Elimination, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
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24
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Reynaud Y, Millet J, Rastogi N. Genetic Structuration, Demography and Evolutionary History of Mycobacterium tuberculosis LAM9 Sublineage in the Americas as Two Distinct Subpopulations Revealed by Bayesian Analyses. PLoS One 2015; 10:e0140911. [PMID: 26517715 PMCID: PMC4627653 DOI: 10.1371/journal.pone.0140911] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2015] [Accepted: 10/01/2015] [Indexed: 02/06/2023] Open
Abstract
Tuberculosis (TB) remains broadly present in the Americas despite intense global efforts for its control and elimination. Starting from a large dataset comprising spoligotyping (n = 21183 isolates) and 12-loci MIRU-VNTRs data (n = 4022 isolates) from a total of 31 countries of the Americas (data extracted from the SITVIT2 database), this study aimed to get an overview of lineages circulating in the Americas. A total of 17119 (80.8%) strains belonged to the Euro-American lineage 4, among which the most predominant genotypic family belonged to the Latin American and Mediterranean (LAM) lineage (n = 6386, 30.1% of strains). By combining classical phylogenetic analyses and Bayesian approaches, this study revealed for the first time a clear genetic structuration of LAM9 sublineage into two subpopulations named LAM9C1 and LAM9C2, with distinct genetic characteristics. LAM9C1 was predominant in Chile, Colombia and USA, while LAM9C2 was predominant in Brazil, Dominican Republic, Guadeloupe and French Guiana. Globally, LAM9C2 was characterized by higher allelic richness as compared to LAM9C1 isolates. Moreover, LAM9C2 sublineage appeared to expand close to twenty times more than LAM9C1 and showed older traces of expansion. Interestingly, a significant proportion of LAM9C2 isolates presented typical signature of ancestral LAM-RDRio MIRU-VNTR type (224226153321). Further studies based on Whole Genome Sequencing of LAM strains will provide the needed resolution to decipher the biogeographical structure and evolutionary history of this successful family.
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Affiliation(s)
- Yann Reynaud
- WHO Supranational TB Reference Laboratory, Tuberculosis and Mycobacteria Unit, Institut Pasteur de la Guadeloupe, Abymes, Guadeloupe, France
- * E-mail: (YR); (NR)
| | - Julie Millet
- WHO Supranational TB Reference Laboratory, Tuberculosis and Mycobacteria Unit, Institut Pasteur de la Guadeloupe, Abymes, Guadeloupe, France
| | - Nalin Rastogi
- WHO Supranational TB Reference Laboratory, Tuberculosis and Mycobacteria Unit, Institut Pasteur de la Guadeloupe, Abymes, Guadeloupe, France
- * E-mail: (YR); (NR)
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Novel katG mutations causing isoniazid resistance in clinical M. tuberculosis isolates. Emerg Microbes Infect 2015; 4:e42. [PMID: 26251830 PMCID: PMC4522615 DOI: 10.1038/emi.2015.42] [Citation(s) in RCA: 73] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2014] [Revised: 04/08/2015] [Accepted: 05/19/2015] [Indexed: 12/16/2022]
Abstract
We report the discovery and confirmation of 23 novel mutations with previously undocumented role in isoniazid (INH) drug resistance, in catalase-peroxidase (katG) gene of Mycobacterium tuberculosis (Mtb) isolates. With these mutations, a synonymous mutation in fabG1g609a, and two canonical mutations, we were able to explain 98% of the phenotypic resistance observed in 366 clinical Mtb isolates collected from four high tuberculosis (TB)-burden countries: India, Moldova, Philippines, and South Africa. We conducted overlapping targeted and whole-genome sequencing for variant discovery in all clinical isolates with a variety of INH-resistant phenotypes. Our analysis showed that just two canonical mutations (katG 315AGC-ACC and inhA promoter-15C-T) identified 89.5% of resistance phenotypes in our collection. Inclusion of the 23 novel mutations reported here, and the previously documented point mutation in fabG1, increased the sensitivity of these mutations as markers of INH resistance to 98%. Only six (2%) of the 332 resistant isolates in our collection did not harbor one or more of these mutations. The third most prevalent substitution, at inhA promoter position -8, present in 39 resistant isolates, was of no diagnostic significance since it always co-occurred with katG 315. 79% of our isolates harboring novel mutations belong to genetic group 1 indicating a higher tendency for this group to go down an uncommon evolutionary path and evade molecular diagnostics. The results of this study contribute to our understanding of the mechanisms of INH resistance in Mtb isolates that lack the canonical mutations and could improve the sensitivity of next generation molecular diagnostics.
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Peñuelas-Urquides K, Martínez-Rodríguez HG, Enciso-Moreno JA, Molina-Salinas GM, Silva-Ramírez B, Padilla-Rivas GR, Vera-Cabrera L, Torres-de-la-Cruz VM, Martínez-Martínez YB, Ortega-García JL, Garza-Treviño EN, Enciso-Moreno L, Saucedo-Cárdenas O, Becerril-Montes P, Said-Fernández S. Correlations between major risk factors and closely related Mycobacterium tuberculosis isolates grouped by three current genotyping procedures: a population-based study in northeast Mexico. Mem Inst Oswaldo Cruz 2015; 109:814-9. [PMID: 25317710 PMCID: PMC4238775 DOI: 10.1590/0074-0276130550] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2013] [Accepted: 08/06/2014] [Indexed: 12/02/2022] Open
Abstract
The characteristics of tuberculosis (TB) patients related to a chain of recent TB
transmissions were investigated. Mycobacterium tuberculosis (MTB) isolates (120) were
genotyped using the restriction fragment length polymorphism-IS6110 (R), spacer
oligotyping (S) and mycobacterial interspersed repetitive units-variable number of
tandem repeats (M) methods. The MTB isolates were clustered and the clusters were
grouped according to the similarities of their genotypes. Spearman’s rank correlation
coefficients between the groups of MTB isolates with similar genotypes and those
patient characteristics indicating a risk for a pulmonary TB (PTB) chain transmission
were ana- lysed. The isolates showing similar genotypes were distributed as follows:
SMR (5%), SM (12.5%), SR (1.67%), MR (0%), S (46.67%), M (5%) and R (0%). The
remaining 35 cases were orphans. SMR exhibited a significant correlation (p <
0.05) with visits to clinics, municipalities and comorbidities (primarily diabetes
mellitus). S correlated with drug consumption and M with comorbidities. SMR is needed
to identify a social network in metropolitan areas for PTB transmission and S and M
are able to detect risk factors as secondary components of a transmission chain of
TB.
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Affiliation(s)
- Katia Peñuelas-Urquides
- División de Biología Celular y Molecular, Centro de Investigación Biomédica del Noreste, Zacatecas, ZC, México
| | - Herminia Guadalupe Martínez-Rodríguez
- Departamento de Bioquímica y Medicina Molecula, Hospital Universitario, Facultad de Medicina, Universidad Autónoma de Nuevo León, Monterrey, NL, México
| | - José Antonio Enciso-Moreno
- Unidad de Investigación Médica de Zacatecas, Instituto Mexicano del Seguro Social, Zacatecas, ZC, México
| | - Gloria María Molina-Salinas
- División de Biología Celular y Molecular, Centro de Investigación Biomédica del Noreste, Zacatecas, ZC, México
| | - Beatriz Silva-Ramírez
- División de Biología Celular y Molecular, Centro de Investigación Biomédica del Noreste, Zacatecas, ZC, México
| | - Gerardo Raymundo Padilla-Rivas
- Departamento de Bioquímica y Medicina Molecula, Hospital Universitario, Facultad de Medicina, Universidad Autónoma de Nuevo León, Monterrey, NL, México
| | - Lucio Vera-Cabrera
- Servicio de Dermatología, Hospital Universitario, Facultad de Medicina, Universidad Autónoma de Nuevo León, Monterrey, NL, México
| | | | - Yazmin Berenice Martínez-Martínez
- Departamento de Bioquímica y Medicina Molecula, Hospital Universitario, Facultad de Medicina, Universidad Autónoma de Nuevo León, Monterrey, NL, México
| | - Jorge Luis Ortega-García
- Departamento de Bioquímica y Medicina Molecula, Hospital Universitario, Facultad de Medicina, Universidad Autónoma de Nuevo León, Monterrey, NL, México
| | - Elsa Nancy Garza-Treviño
- Departamento de Bioquímica y Medicina Molecula, Hospital Universitario, Facultad de Medicina, Universidad Autónoma de Nuevo León, Monterrey, NL, México
| | - Leonor Enciso-Moreno
- División de Biología Celular y Molecular, Centro de Investigación Biomédica del Noreste, Zacatecas, ZC, México
| | - Odila Saucedo-Cárdenas
- División de Biología Celular y Molecular, Centro de Investigación Biomédica del Noreste, Zacatecas, ZC, México
| | - Pola Becerril-Montes
- División de Biología Celular y Molecular, Centro de Investigación Biomédica del Noreste, Zacatecas, ZC, México
| | - Salvador Said-Fernández
- División de Biología Celular y Molecular, Centro de Investigación Biomédica del Noreste, Zacatecas, ZC, México
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Mears J, Abubakar I, Cohen T, McHugh TD, Sonnenberg P. Effect of study design and setting on tuberculosis clustering estimates using Mycobacterial Interspersed Repetitive Units-Variable Number Tandem Repeats (MIRU-VNTR): a systematic review. BMJ Open 2015; 5:e005636. [PMID: 25609667 PMCID: PMC4305070 DOI: 10.1136/bmjopen-2014-005636] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
OBJECTIVES To systematically review the evidence for the impact of study design and setting on the interpretation of tuberculosis (TB) transmission using clustering derived from Mycobacterial Interspersed Repetitive Units-Variable Number Tandem Repeats (MIRU-VNTR) strain typing. DATA SOURCES MEDLINE, EMBASE, CINHAL, Web of Science and Scopus were searched for articles published before 21st October 2014. REVIEW METHODS Studies in humans that reported the proportion of clustering of TB isolates by MIRU-VNTR were included in the analysis. Univariable meta-regression analyses were conducted to assess the influence of study design and setting on the proportion of clustering. RESULTS The search identified 27 eligible articles reporting clustering between 0% and 63%. The number of MIRU-VNTR loci typed, requiring consent to type patient isolates (as a proxy for sampling fraction), the TB incidence and the maximum cluster size explained 14%, 14%, 27% and 48% of between-study variation, respectively, and had a significant association with the proportion of clustering. CONCLUSIONS Although MIRU-VNTR typing is being adopted worldwide there is a paucity of data on how study design and setting may influence estimates of clustering. We have highlighted study design variables for consideration in the design and interpretation of future studies.
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Affiliation(s)
- Jessica Mears
- Department of Infection and Population Health, University College London, London, UK
| | - Ibrahim Abubakar
- Department of Infection and Population Health, University College London, London, UK
- Centre for Infectious Disease Surveillance and Control, Public Health England, London, UK
- Clinical Trials Unit, Medical Research Council, London, UK
| | - Theodore Cohen
- Division of Global Health Equity, Brigham and Women's Hospital and Department of Epidemiology, Harvard School of Public Health, Harvard University, Boston, USA
| | - Timothy D McHugh
- Department of Infection, Centre for Clinical Microbiology, University College London, London, UK
| | - Pam Sonnenberg
- Department of Infection and Population Health, University College London, London, UK
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Pouseele H, Supply P. Accurate Whole-Genome Sequencing-Based Epidemiological Surveillance of Mycobacterium Tuberculosis. METHODS IN MICROBIOLOGY 2015. [DOI: 10.1016/bs.mim.2015.04.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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Thabet S, Karboul A, Dekhil N, Mardassi H. IS6110-5'3'FP: an automated typing approach for Mycobacterium tuberculosis complex strains simultaneously targeting and resolving IS6110 5' and 3' polymorphisms. Int J Infect Dis 2014; 29:211-8. [PMID: 25447727 DOI: 10.1016/j.ijid.2014.10.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2014] [Revised: 10/18/2014] [Accepted: 10/18/2014] [Indexed: 01/28/2023] Open
Abstract
OBJECTIVES Fingerprinting of Mycobacterium tuberculosis complex strains based on the IS6110 insertion sequence would considerably gain in terms of discriminatory power and versatility if both 5' and 3' polymorphisms were simultaneously targeted, and if it benefited from automated capillary electrophoresis. In response to these requirements, we developed IS6110-5'3'FP (IS6110 5' and 3' fluorescent polymorphisms). METHODS IS6110-5'3'FP involves the construction of an M. tuberculosis genomic library in a plasmid vector using HincII endonuclease, which cuts within the IS6110 sequence. After amplification in Escherichia coli, the library is subjected to selective and simultaneous PCR amplification of IS6110 5' and 3' polymorphic fragments, using differentially labeled fluorescent primers. The resulting amplicons are then fractionated on a capillary sequencer and the signal peaks analyzed as digital data. RESULTS IS6110-5'3'FP consistently detected and resolved both 5' and 3' IS6110 polymorphic fragments (35% and 65%, respectively) with a high level of reproducibility. The method differentiated all M. tuberculosis strains, as did IS6110 restriction fragment length polymorphism (RFLP), the gold standard of IS6110-based typing. Strikingly, the potential of IS6110-5'3'FP to resolve more polymorphic fragments than IS6110 RFLP was demonstrated. CONCLUSIONS IS6110-5'3'FP demonstrated sufficient potential to be a promising automated alternative to IS6110 RFLP, amenable to high throughput analysis and inter-laboratory comparison.
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Affiliation(s)
- Sara Thabet
- Unit of Typing and Genetics of Mycobacteria, LR11IPT01 Laboratory of Molecular Microbiology, Vaccinology, and Biotechnology Development, Institut Pasteur de Tunis, Université de Tunis El Manar, 13 Place Pasteur, BP 74, 1002, Tunis-Belvédère, Tunis, Tunisia
| | - Anis Karboul
- Unit of Typing and Genetics of Mycobacteria, LR11IPT01 Laboratory of Molecular Microbiology, Vaccinology, and Biotechnology Development, Institut Pasteur de Tunis, Université de Tunis El Manar, 13 Place Pasteur, BP 74, 1002, Tunis-Belvédère, Tunis, Tunisia
| | - Neira Dekhil
- Unit of Typing and Genetics of Mycobacteria, LR11IPT01 Laboratory of Molecular Microbiology, Vaccinology, and Biotechnology Development, Institut Pasteur de Tunis, Université de Tunis El Manar, 13 Place Pasteur, BP 74, 1002, Tunis-Belvédère, Tunis, Tunisia
| | - Helmi Mardassi
- Unit of Typing and Genetics of Mycobacteria, LR11IPT01 Laboratory of Molecular Microbiology, Vaccinology, and Biotechnology Development, Institut Pasteur de Tunis, Université de Tunis El Manar, 13 Place Pasteur, BP 74, 1002, Tunis-Belvédère, Tunis, Tunisia.
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Vasconcellos SEG, Acosta CC, Gomes LL, Conceição EC, Lima KV, de Araujo MI, Leite MDL, Tannure F, Caldas PCDS, Gomes HM, Santos AR, Gomgnimbou MK, Sola C, Couvin D, Rastogi N, Boechat N, Suffys PN. Strain classification of Mycobacterium tuberculosis isolates in Brazil based on genotypes obtained by spoligotyping, mycobacterial interspersed repetitive unit typing and the presence of large sequence and single nucleotide polymorphism. PLoS One 2014; 9:e107747. [PMID: 25314118 PMCID: PMC4196770 DOI: 10.1371/journal.pone.0107747] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2014] [Accepted: 08/21/2014] [Indexed: 11/26/2022] Open
Abstract
Rio de Janeiro is endemic for tuberculosis (TB) and presents the second largest prevalence of the disease in Brazil. Here, we present the bacterial population structure of 218 isolates of Mycobacterium tuberculosis, derived from 186 patients that were diagnosed between January 2008 and December 2009. Genotypes were generated by means of spoligotyping, 24 MIRU-VNTR typing and presence of fbpC103, RDRio and RD174. The results confirmed earlier data that predominant genotypes in Rio de Janeiro are those of the Euro American Lineages (99%). However, we observed differences between the classification by spoligotyping when comparing to that of 24 MIRU-VNTR typing, being respectively 43.6% vs. 62.4% of LAM, 34.9% vs. 9.6% of T and 18.3% vs. 21.5% of Haarlem. Among isolates classified as LAM by MIRU typing, 28.0% did not present the characteristic spoligotype profile with absence of spacers 21 to 24 and 32 to 36 and we designated these conveniently as “LAM-like”, 79.3% of these presenting the LAM-specific SNP fbpC103. The frequency of RDRio and RD174 in the LAM strains, as defined both by spoligotyping and 24 MIRU-VNTR loci, were respectively 11% and 15.4%, demonstrating that RD174 is not always a marker for LAM/RDRio strains. We conclude that, although spoligotyping alone is a tool for classification of strains of the Euro-American lineage, when combined with MIRU-VNTRs, SNPs and RD typing, it leads to a much better understanding of the bacterial population structure and phylogenetic relationships among strains of M. tuberculosis in regions with high incidence of TB.
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Affiliation(s)
- Sidra E. G. Vasconcellos
- Laboratory of Molecular Biology Applied to Mycobacteria, Oswaldo Cruz Institute, FIOCRUZ, Rio de Janeiro, Rio de Janeiro, Brazil
- Multidisciplinary Research Laboratory, University Hospital Clementino Fraga Filho – HUCFF, Federal University of Rio de Janeiro, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Chyntia Carolina Acosta
- Laboratory of Cellular Microbiology, Oswaldo Cruz Institute, FIOCRUZ, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Lia Lima Gomes
- Laboratory of Molecular Biology Applied to Mycobacteria, Oswaldo Cruz Institute, FIOCRUZ, Rio de Janeiro, Rio de Janeiro, Brazil
| | | | - Karla Valéria Lima
- Instituto Evandro Chagas, Section of Bacteriology and Mycology, Belém, Pará, Brazil
| | - Marcelo Ivens de Araujo
- Laboratory of Molecular Biology Applied to Mycobacteria, Oswaldo Cruz Institute, FIOCRUZ, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Maria de Lourdes Leite
- Hospital Municipal Rafael de Paula Souza, Municipal Secretary of Health, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Flávio Tannure
- Hospital Municipal Rafael de Paula Souza, Municipal Secretary of Health, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Paulo Cesar de Souza Caldas
- Centro de Referência Professor Hélio Fraga, Escola Nacional de Saúde Publica Sergio Arouca, FIOCRUZ, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Harrison M. Gomes
- Laboratory of Molecular Biology Applied to Mycobacteria, Oswaldo Cruz Institute, FIOCRUZ, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Adalberto Rezende Santos
- Laboratory of Molecular Biology Applied to Mycobacteria, Oswaldo Cruz Institute, FIOCRUZ, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Michel K. Gomgnimbou
- CNRS–Université Paris–Sud, Institut de Génétique et Microbiologie–Infection Genetics Emerging Pathogens Evolution Team, Orsay, France
| | - Christophe Sola
- CNRS–Université Paris–Sud, Institut de Génétique et Microbiologie–Infection Genetics Emerging Pathogens Evolution Team, Orsay, France
| | - David Couvin
- Supranational TB Reference Laboratory, Unité de la Tuberculose et des Mycobactéries, Institut Pasteur de Guadeloupe, Abymes, Guadeloupe, France
| | - Nalin Rastogi
- Supranational TB Reference Laboratory, Unité de la Tuberculose et des Mycobactéries, Institut Pasteur de Guadeloupe, Abymes, Guadeloupe, France
| | - Neio Boechat
- Multidisciplinary Research Laboratory, University Hospital Clementino Fraga Filho – HUCFF, Federal University of Rio de Janeiro, Rio de Janeiro, Rio de Janeiro, Brazil
- Graduate Program in Clinical Medicine, Faculty of Medicine, University Hospital Clementino Fraga Filho, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Philip Noel Suffys
- Laboratory of Molecular Biology Applied to Mycobacteria, Oswaldo Cruz Institute, FIOCRUZ, Rio de Janeiro, Rio de Janeiro, Brazil
- * E-mail:
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Use of the VNTR typing technique to determine the origin of Mycobacterium tuberculosis strains isolated from Filipino patients in Korea. World J Microbiol Biotechnol 2014; 30:1625-31. [DOI: 10.1007/s11274-013-1588-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2013] [Accepted: 12/19/2013] [Indexed: 10/25/2022]
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Asante-Poku A, Nyaho MS, Borrell S, Comas I, Gagneux S, Yeboah-Manu D. Evaluation of customised lineage-specific sets of MIRU-VNTR loci for genotyping Mycobacterium tuberculosis complex isolates in Ghana. PLoS One 2014; 9:e92675. [PMID: 24667333 PMCID: PMC3965448 DOI: 10.1371/journal.pone.0092675] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2013] [Accepted: 02/25/2014] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Different combinations of variable number of tandem repeat (VNTR) loci have been proposed for genotyping Mycobacterium tuberculosis complex (MTBC). Existing VNTR schemes show different discriminatory capacity among the six human MTBC lineages. Here, we evaluated the discriminatory power of a "customized MIRU12" loci format proposed previously by Comas et al. based on the standard 24 loci defined by Supply et al. for VNTR-typing of MTBC in Ghana. METHOD One hundred and fifty-eight MTBC isolates classified into Lineage 4 and Lineage 5 were used to compare a customized lineage-specific panel of 12 MIRU-VNTR loci ("customized MIRU-12") to the standard MIRU-15 genotyping scheme. The resolution power of each typing method was determined based on the Hunter-Gaston- Discriminatory Index (HGDI). A minimal set of customized MIRU-VNTR loci for typing Lineages 4 (Euro-American) and 5 (M. africanum West African 1) strains from Ghana was defined based on the cumulative HGDI. RESULTS AND CONCLUSION Among the 106 Lineage 4 strains, the customized MIRU-12 identified a total of 104 distinct genotypes consisting of 2 clusters of 2 isolates each (clustering rate 1.8%), and 102 unique strains while standard MIRU-15 yielded a total of 105 different genotypes, including 1 cluster of 2 isolates (clustering rate: 0.9%) and 104 singletons. Among, 52 Lineage 5 isolates, customized MIRU-12 genotyping defined 51 patterns with 1 cluster of 2 isolates (clustering rate: 0.9%) and 50 unique strains whereas MIRU-15 classified all 52 strains as unique. Cumulative HGDI values for customized MIRU-12 for Lineages 4 and 5 were 0.98 respectively whilst that of standard MIRU-15 was 0.99. A union of loci from the customised MIRU-12 and standard MIRU-15 revealed a set of customized eight highly discriminatory loci: 4052, 2163B, 40, 4165, 2165, 10,16 and 26 with a cumulative HGDI of 0.99 for genotyping Lineage 4 and 5 strains from Ghana.
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Affiliation(s)
- Adwoa Asante-Poku
- Bacteriology Department, Noguchi Memorial institute For Medical Research, University of Ghana, Legon, Ghana
- Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Michael Selasi Nyaho
- Bacteriology Department, Noguchi Memorial institute For Medical Research, University of Ghana, Legon, Ghana
- Biochemistry Department, University of Ghana, Legon, Ghana
| | - Sonia Borrell
- Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Iñaki Comas
- Genomics and Health Unit, Centre for Public Health Research, Valencia, Spain
- CIBER (Centros de Investigación Biomédica en Red) in Epidemiology and Public Health, Madrid, Spain
| | - Sebastien Gagneux
- Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Dorothy Yeboah-Manu
- Bacteriology Department, Noguchi Memorial institute For Medical Research, University of Ghana, Legon, Ghana
- * E-mail:
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Lee J, Kang H, Kim S, Yoo H, Kim HJ, Park YK. Optimal Combination of VNTR Typing for Discrimination of Isolated Mycobacterium tuberculosis in Korea. Tuberc Respir Dis (Seoul) 2014; 76:59-65. [PMID: 24624214 PMCID: PMC3948853 DOI: 10.4046/trd.2014.76.2.59] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2013] [Revised: 11/04/2013] [Accepted: 11/07/2013] [Indexed: 12/04/2022] Open
Abstract
Background Variable-number tandem repeat (VNTR) typing is a promising method to discriminate the Mycobacterium tuberculosis isolates in molecular epidemiology. The purpose of this study is to determine the optimal VNTR combinations for discriminating isolated M. tuberculosis strains in Korea. Methods A total of 317 clinical isolates collected throughout Korea were genotyped by using the IS6110 restriction fragment length polymorphism (RFLP), and then analysed for the number of VNTR copies from 32 VNTR loci. Results The results of discriminatory power according to diverse combinations were as follows: 25 clusters in 83 strains were yielded from the internationally standardized 15 VNTR loci (Hunter-Gaston discriminatory index [HGDI], 0.9958), 25 clusters in 65 strains by using IS6110 RFLP (HGDI, 0.9977), 14 clusters in 32 strains in 12 hyper-variable VNTR loci (HGDI, 0.9995), 6 clusters in 13 strains in 32 VNTR loci (HDGI, 0.9998), and 7 clusters in 14 strains of both the 12 hyper-variable VNTR and IS6110 RFLP (HDGI, 0.9999). Conclusion The combination of 12 hyper-variable VNTR typing can be an effective tool for genotyping Korean M. tuberculosis isolates where the Beijing strains are predominant.
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Affiliation(s)
- Jihye Lee
- Korean Institute of Tuberculosis, Cheongwon, Korea
| | - Heeyoon Kang
- Korean Institute of Tuberculosis, Cheongwon, Korea
| | - Sarang Kim
- Korean Institute of Tuberculosis, Cheongwon, Korea
| | - Heekyung Yoo
- Korean Institute of Tuberculosis, Cheongwon, Korea
| | - Hee Jin Kim
- Korean Institute of Tuberculosis, Cheongwon, Korea
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Molecular epidemiology and genotyping of Mycobacterium tuberculosis isolated in Baghdad. BIOMED RESEARCH INTERNATIONAL 2014; 2014:580981. [PMID: 24719873 PMCID: PMC3955663 DOI: 10.1155/2014/580981] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/07/2013] [Revised: 01/17/2014] [Accepted: 01/18/2014] [Indexed: 12/17/2022]
Abstract
Tuberculosis (TB) remains a major health problem in Iraq but the strains responsible for the epidemic have been poorly characterized. Our aim was to characterize the TB strains circulating in Bagdad (Iraq). A total of 270 Mycobacterium tuberculosis complex (MTBC) strains isolated between 2010 and 2011 from TB patients attending the Center of Chest and Respiratory diseases in Baghdad were analyzed by Spoligotyping. The analysis indicated that 94.1% of the isolates belong to known genotype clades: CAS 39.6%, ill-defined T clade 29.6%, Manu 7.4%, Haarlem 7%, Ural 4.1%, LAM 3.3%, X 0.7%, LAM7-TUR 0.7%, EAI 0.7%, S 0.7%, and unknown 5.9%. Comparison with the international multimarker database SITVIT2 showed that SIT 309 (CAS1-Delhi) and SIT1144 (T1) were the most common types. In addition, 44 strains were included in SITVIT2 database under 16 new Spoligotype International Types (SITs); of these, 6 SITs (SIT3346, SIT3497, SIT3708, SIT3790, SIT3791, and SIT3800) (n = 32 strains) were created within the present study and 10 were created after a match with an orphan in the database. By using 24-loci MIRU-VNTR-typing on a subset of 110 samples we found a high recent transmission index (RTI) of 33.6%. In conclusion, we present the first unifying framework for both epidemiology and evolutionary analysis of M. tuberculosis in Iraq.
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Comparison of ligation-mediated PCR methods in differentiation of Mycobacterium tuberculosis strains. BIOMED RESEARCH INTERNATIONAL 2014; 2014:782071. [PMID: 24696162 PMCID: PMC3947874 DOI: 10.1155/2014/782071] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 11/20/2013] [Accepted: 01/08/2014] [Indexed: 11/17/2022]
Abstract
Fast and inexpensive identification of epidemiological links between limited number of Mycobacterium tuberculosis strains is required to initially evaluate hospital outbreaks, laboratory crosscontaminations, and family or small community transmissions. The ligation-mediated PCR methods (LM-PCR) appear sufficiently discriminative and reproducible to be considered as a good candidate for such initial, epidemiological analysis. Here, we compared the discriminative power of the recently developed in our laboratory fast ligation amplification polymorphism (FLAP) method with fast ligation-mediated PCR (FLiP). Verification of the results was based on analyzing a set of reference strains and RFLP-IS6110 typing. The HGDI value was very similar for both LM-PCR methods and RFLP-IS6110 typing. However, only 52% of strains were correspondingly grouped by both FLiP and FLAP methods. Differentiation by FLAP method demonstrated a limited similarity to IS6110-RFLP (37,7%). As much as 78,7% of strains were grouped identically when differentiated by FLiP and IS6110-RFLP methods. The analysis differentiated 31, 35, and 36 groups when using FLAP, FLiP, and RFLP-IS6110 methods, respectively.
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Click ES, Moonan PK, Winston CA, Cowan LS, Oeltmann JE. Relationship between Mycobacterium tuberculosis phylogenetic lineage and clinical site of tuberculosis. Clin Infect Dis 2014; 54:211-9. [PMID: 22198989 DOI: 10.1093/cid/cir788] [Citation(s) in RCA: 79] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Genotyping of Mycobacterium tuberculosis has revealed 4 major phylogenetic lineages with differential distribution worldwide. It is not clear whether different lineages are associated with different sites of infection (eg, pulmonary tuberculosis versus extrapulmonary tuberculosis). We sought to determine whether M. tuberculosis lineage is associated with the site of tuberculosis disease. METHODS We conducted a cross-sectional analysis of all culture-confirmed cases of tuberculosis with routinely determined M. tuberculosis spoligotype-defined lineage reported to the US National Tuberculosis Surveillance System from 2004 through 2008. Odds ratios (ORs) were used to assess the relation between disease site and M. tuberculosis lineage, after adjustment for age, sex, human immunodeficiency virus infection status, region of birth, and race/ethnicity. RESULTS Of 53972 reported culture-positive tuberculosis cases, 32000 (59.3%) were cases of M. tuberculosis that included complete spoligotype-based data on lineage. Of these, 23844 (74.5%) were exclusively pulmonary, 5085 (15.9%) were exclusively extrapulmonary, and 3071 (9.6%) were combined pulmonary and extrapulmonary. The percentages of tuberculosis cases that were exclusively extrapulmonary differed by lineage: East Asian, 13.0%; Euro-American, 13.8%; Indo-Oceanic, 22.6%; and East-African Indian, 34.3%. Compared with East Asian lineage, the odds of exclusively extrapulmonary tuberculosis relative to exclusively pulmonary tuberculosis were greater for Euro-American (adjusted OR, 1.3; 95% confidence interval [CI], 1.1-1.4), Indo-Oceanic (adjusted OR, 1.7; 95% CI, 1.5-1.9), and East-African Indian (adjusted OR, 1.6; 95% CI, 1.4-1.9) lineages. CONCLUSIONS Phylogenetic lineage of M. tuberculosis is associated with the site of tuberculosis disease.
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Affiliation(s)
- Eleanor S Click
- Epidemic Intelligence Service , Division of Tuberculosis Elimination, Centers for Disease Control and Prevention, Atlanta, Georgia 30333, USA.
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Shea KM, Kammerer JS, Winston CA, Navin TR, Horsburgh CR. Estimated rate of reactivation of latent tuberculosis infection in the United States, overall and by population subgroup. Am J Epidemiol 2014; 179:216-25. [PMID: 24142915 DOI: 10.1093/aje/kwt246] [Citation(s) in RCA: 141] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We estimated the rate of reactivation tuberculosis (TB) in the United States, overall and by population subgroup, using data on TB cases and Mycobacterium tuberculosis isolate genotyping reported to the Centers for Disease Control and Prevention during 2006-2008. The rate of reactivation TB was defined as the number of non-genotypically clustered TB cases divided by the number of person-years at risk for reactivation due to prevalent latent TB infection (LTBI). LTBI was ascertained from tuberculin skin tests given during the 1999-2000 National Health and Nutrition Examination Survey. Clustering of TB cases was determined using TB genotyping data collected by the Centers for Disease Control and Prevention and analyzed via spatial scan statistic. Of the 39,920 TB cases reported during 2006-2008, 79.7% were attributed to reactivation. The overall rate of reactivation TB among persons with LTBI was estimated as 0.084 (95% confidence interval (CI): 0.083, 0.085) cases per 100 person-years. Rates among persons with and without human immunodeficiency virus coinfection were 1.82 (95% CI: 1.74, 1.89) and 0.073 (95% CI: 0.070, 0.075) cases per 100 person-years, respectively. The rate of reactivation TB among persons with LTBI was higher among foreign-born persons (0.098 cases/100 person-years; 95% CI: 0.096, 0.10) than among persons born in the United States (0.082 cases/100 person-years; 95% CI: 0.080, 0.083). Differences in rates of TB reactivation across subgroups support current recommendations for targeted testing and treatment of LTBI.
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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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Lu W, Lu B, Liu Q, Dong H, Shao Y, Jiang Y, Song H, Chen C, Li G, Xu W, Zhao X, Wan K, Zhu L. Genotypes of Mycobacterium tuberculosis isolates in rural China: using MIRU-VNTR and spoligotyping methods. ACTA ACUST UNITED AC 2013; 46:98-106. [PMID: 24359517 DOI: 10.3109/00365548.2013.858182] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
BACKGROUND The genotypes of Mycobacterium tuberculosis (MTB) have been found to be related to the risk of transmission and the development of drug resistance of this pathogen. Thus, exploring the molecular characteristics of MTB is helpful for understanding and controlling the spread of strains in areas with a high incidence of tuberculosis. METHODS We recruited 512 sputum smear-positive tuberculosis patients from 30 counties from 1 April to 30 June 2010; 503 MTB strains were isolated and 497 were successfully genotyped. We genotyped the strains based on a new 15-locus mycobacterial interspersed repetitive unit-variable number of tandem repeats (MIRU-VNTR) method in combination with spacer-oligonucleotide typing (spoligotyping) technology. RESULTS Based on spoligotyping, 487 strains displayed known patterns, and 10 were absent from the current global spoligotyping database (SpolDB4). The predominant spoligotypes belonged to the Beijing or Beijing-like family (81.1%). When we used the new 15-locus (MIRU-15) set for the MIRU-VNTR analysis, 388 different patterns were identified, including 46 clusters and 342 unique patterns. The combination of spoligotyping and MIRU-15 demonstrated a high discriminatory power. The proportion of clusters varied significantly between the Beijing and non-Beijing family strains, but no significant association was observed between multidrug resistance and Beijing family strains. CONCLUSIONS The present study demonstrated that the Beijing family strains are the most prevalent in rural China. Spoligotyping in combination with the new MIRU-15 technique is useful for the epidemiological analysis of MTB transmission and could be used as a first-line method for the large-scale genotyping of MTB.
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Affiliation(s)
- Wei Lu
- From the Department of Chronic Communicable Disease, Center for Disease Control and Prevention of Jiangsu Province , Nanjing
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Genotyping of clinical Mycobacterium tuberculosis isolates based on IS6110 and MIRU-VNTR polymorphisms. BIOMED RESEARCH INTERNATIONAL 2013; 2013:865197. [PMID: 24455734 PMCID: PMC3877603 DOI: 10.1155/2013/865197] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/07/2013] [Accepted: 11/20/2013] [Indexed: 11/18/2022]
Abstract
In this study, 155 clinical Mycobacterium tuberculosis isolates were subject to genotyping with fast ligation-mediated PCR (FLiP). This typing method is a modified mixed-linker PCR, a rapid approach based on the PCR amplification of HhaI restriction fragments of genomic DNA containing the 3' end of IS6110 and resolving the amplicons by polyacrylamide gel electrophoresis. The results were compared with previous data of the more commonly used methods, 15-locus mycobacterial interspersed repetitive unit-variable number tandem repeat (MIRU-VNTR) typing and, to verify combined FLiP/MIRU-VNTR clusters, the reference IS6110 restriction fragment length polymorphism (RFLP). FLiP banding patterns were highly reproducible and polymorphic. This method differentiated 119 types among the study set compared to 108 distinct MIRU-VNTR profiles. The discriminatory power of FLiP was slightly higher than that of MIRU-VNTR analysis (Hunter-Gaston Discriminatory Index = 0.991 and 0.990, resp.). Detailed comparison of the clusters defined by each of the methods revealed, however, a more apparent difference in the discriminatory abilities that favored FLiP. Clustering of strains by using combined results of these two PCR-based methods correlated well with IS6110 RFLP-defined clusters, further confirming high discriminatory potential of FLiP typing. These results indicate that FLiP could be an attractive and valuable secondary typing technique for verification of MIRU-VNTR clusters of M. tuberculosis strains.
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Sia IG, Buckwalter SP, Doerr KA, Lugos S, Kramer R, Orillaza-Chi R, Quelapio MI, Tupasi TE, Wengenack NL. Genotypic characteristics of Mycobacterium tuberculosis isolated from household contacts of tuberculosis patients in the Philippines. BMC Infect Dis 2013; 13:571. [PMID: 24308751 PMCID: PMC4028849 DOI: 10.1186/1471-2334-13-571] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2013] [Accepted: 11/27/2013] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The Philippines has an extremely high rate of tuberculosis but little is known about M. tuberculosis genotypes and transmission dynamics in this country. The aim of this study was to determine the proportion of household contacts who develop active TB due to direct transmission from an index case in that household. METHODS Mycobacterium tuberculosis isolates from household contacts of tuberculosis patients in the Philippines were characterized using restriction-fragment-length polymorphism analysis, spoligotyping, and mycobacterial interspersed repetitive units - variable number tandem repeats typing (12-loci) to determine their utility in elucidating transmission in an area of high tuberculosis prevalence. Drug susceptibility patterns for these isolates were also determined. RESULTS Spoligotyping and MIRU-VNTR typing results matched in 10 (62.5%) of 16 index patient-household contact pairs while IS6110 fingerprints matched in only six (37.5%) pairs. Only 3/16 (18.8%) index patient-household contact pairs had identical drug susceptibility results. CONCLUSIONS Strain typing of M. tuberculosis isolates from household contacts in the Philippines indicates that transmission of strains does not necessarily occur directly from the index patient living in close proximity in the same household but rather that community-based transmission also frequently occurs. Accurate susceptibility testing of all isolates is necessary to insure optimal care of both the index patients and any culture-positive household contacts.
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Affiliation(s)
- Irene G Sia
- Department of Laboratory Medicine and Pathology, Mayo Clinic, 200 First Street SW, Rochester, MN 55905, USA.
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Soares RO, de Macedo MB, von Groll A, da Silva PEA. Mycobacterium tuberculosis belonging to family LAM and sublineage RD(Rio): common strains in Southern Brazil for over 10 years. Braz J Microbiol 2013; 44:1251-5. [PMID: 24688519 PMCID: PMC3958195 DOI: 10.1590/s1517-83822013000400032] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2011] [Accepted: 04/04/2013] [Indexed: 11/21/2022] Open
Abstract
A sublineage of Mycobacterium tuberculosis called RD(Rio) was described in 2007. Although only recently described, this strain may have been present previously in the population, and its identification in clinical isolates will elucidate bacterial transmission dynamics and host-pathogen interactions. This study evaluated the clonal diversity of the RD(Rio) sublineage in clinical isolates from Rio Grande-RS obtained between 1998 and 2001. Among the 45 samples analyzed by the MIRU-VNTR method, there were six clusters with two samples each and 33 orphan strains with unique pattern. The strains were distributed across several different lineages including LAM (34.04%), × (14.89%), Haarlem (12.77%), UgandaI (10.64%), S (4.26%), NEW-1 (2.13%) and Cameroon (2.13%); 14.89% of the strains matched to multiple lineages. RD(Rio) strains were present in 28.9% of the samples and 81.25% of the identified strains belonged to the LAM family. The high clonal diversity observed in this study is a constant feature in this region. The RD(Rio) sublineage has been in Rio Grande-RS since 1998. The continued monitoring of RD(Rio) in clinical isolates will enhance the understanding of its epidemiological significance.
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Lindquist S, Allen S, Field K, Ghosh S, Haddad MB, Narita M, Oren E. Prioritizing tuberculosis clusters by genotype for public health action, Washington, USA. Emerg Infect Dis 2013; 19:493-6. [PMID: 23621956 PMCID: PMC3647672 DOI: 10.3201/eid1903.121453] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Groups of tuberculosis cases with indistinguishable Mycobacterium tuberculosis genotypes (clusters) might represent recent transmission. We compared geospatial concentration of genotype clusters with independent priority rankings determined by local public health officials; findings were highly correlated. Routine use of geospatial statistics could help health departments identify recent disease transmission.
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Gilbert GL, Sintchenko V. The use of mycobacterial interspersed repetitive unit typing and whole genome sequencing to inform tuberculosis prevention and control activities. NEW SOUTH WALES PUBLIC HEALTH BULLETIN 2013; 24:10-14. [PMID: 23849021 DOI: 10.1071/nb12106] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Molecular strain typing of Mycobacterium tuberculosis has been possible for only about 20 years; it has significantly improved our understanding of the evolution and epidemiology of Mycobacterium tuberculosis and tuberculosis disease. Mycobacterial interspersed repetitive unit typing, based on 24 variable number tandem repeat unit loci, is highly discriminatory, relatively easy to perform and interpret and is currently the most widely used molecular typing system for tuberculosis surveillance. Nevertheless, clusters identified by mycobacterial interspersed repetitive unit typing sometimes cannot be confirmed or adequately defined by contact tracing and additional methods are needed. Recently, whole genome sequencing has been used to identify single nucleotide polymorphisms and other mutations, between genotypically indistinguishable isolates from the same cluster, to more accurately trace transmission pathways. Rapidly increasing speed and quality and reduced costs will soon make large scale whole genome sequencing feasible, combined with the use of sophisticated bioinformatics tools, for epidemiological surveillance of tuberculosis.
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Kammerer JS, Shang N, Althomsons SP, Haddad MB, Grant J, Navin TR. Using statistical methods and genotyping to detect tuberculosis outbreaks. Int J Health Geogr 2013; 12:15. [PMID: 23497235 PMCID: PMC3608068 DOI: 10.1186/1476-072x-12-15] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2012] [Accepted: 03/11/2013] [Indexed: 01/04/2023] Open
Abstract
Background Early identification of outbreaks remains a key component in continuing to reduce the burden of infectious disease in the United States. Previous studies have applied statistical methods to detect unexpected cases of disease in space or time. The objectives of our study were to assess the ability and timeliness of three spatio-temporal methods to detect known outbreaks of tuberculosis. Methods We used routinely available molecular and surveillance data to retrospectively assess the effectiveness of three statistical methods in detecting tuberculosis outbreaks: county-based log-likelihood ratio, cumulative sums, and a spatial scan statistic. Results Our methods identified 8 of the 9 outbreaks, and 6 outbreaks would have been identified 1–52 months (median = 10 months) before local public health authorities identified them. Assuming no delays in data availability, 46 (59.7%) of the 77 patients in the 9 outbreaks were identified after our statistical methods would have detected the outbreak but before local public health authorities became aware of the problem. Conclusions Statistical methods, when applied retrospectively to routinely collected tuberculosis data, can successfully detect known outbreaks, potentially months before local public health authorities become aware of the problem. The three methods showed similar results; no single method was clearly superior to the other two. Further study to elucidate the performance of these methods in detecting tuberculosis outbreaks will be done in a prospective analysis.
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Affiliation(s)
- J Steve Kammerer
- Division of Tuberculosis Elimination, Centers for Disease Control and Prevention, 1600 Clifton Rd NE, Atlanta, GA 30333, USA.
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Bamrah S, Desmond E, Ghosh S, France AM, Kammerer JS, Cowan LS, Heetderks A, Forbes A, Moonan PK. Molecular epidemiology of Mycobacterium tuberculosis in the United States-Affiliated Pacific Islands. Asia Pac J Public Health 2012; 26:77-84. [PMID: 23239749 DOI: 10.1177/1010539512469249] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The United States-Affiliated Pacific Islands (USAPI) are part of the US National Tuberculosis (TB) Surveillance System and use laboratory services contracted through a cooperative agreement with the Centers for Disease Control and Prevention (CDC). In 2004, the CDC established the National Tuberculosis Genotyping Service, a system to genotype 1 isolate from each culture-confirmed case of TB. To describe the molecular epidemiology of TB in the region, we examined all Mycobacterium tuberculosis isolates submitted for genotyping from January 1, 2004, to December 31, 2008. Over this time period, the USAPI jurisdictions reported 1339 verified TB cases to the National Tuberculosis Surveillance System. Among 419 (31%) reported culture-confirmed TB cases, 352 (84%) had complete genotype results. Routine TB genotyping allowed, for the first time, an exploration of the molecular epidemiology of TB in the USAPI.
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Affiliation(s)
- Sapna Bamrah
- 1Centers for Disease Control and Prevention, Atlanta, GA, USA
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Use of tuberculosis genotyping for postoutbreak monitoring. JOURNAL OF PUBLIC HEALTH MANAGEMENT AND PRACTICE 2012; 18:375-8. [PMID: 22635193 DOI: 10.1097/phh.0b013e31823680f4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
CONTEXT Review of routinely collected tuberculosis genotyping results following a known outbreak is a potential mechanism to examine the effectiveness of outbreak control measures. OBJECTIVE To assess differences in characteristics between outbreak and postoutbreak tuberculosis cases. DESIGN Retrospective. SETTING United States. PARTICIPANTS All tuberculosis cases identified as a result of >5-person outbreaks investigated by the Centers for Disease Control and Prevention during 2003 to 2007 (original outbreak cases), and subsequent culture-positive tuberculosis cases with matching Mycobacterium tuberculosis genotypes reported in the same county during 2004 to 2008 (postoutbreak cases). MAIN OUTCOME MEASURE Proportion of demographic, social, and clinical characteristics of tuberculosis outbreak cases compared to postoutbreak cases. SECONDARY: Proportion of demographic, social, and clinical characteristics of epidemiologically linked versus nonlinked cases. RESULTS Six outbreaks with 111 outbreak cases and 110 postoutbreak cases were identified. Differences between outbreak and postoutbreak cases were gender (69% vs 85% male; P < .01), birth origin (3% vs 11% foreign-born; P = .02), disease severity (48% vs 62% sputum smear-positive; P = .04), homelessness (38% vs 51%; P = .05), and injection drug use (4% vs 11%; P = .04). For 5 of the 6 outbreaks, the status of epidemiologic relationships among postoutbreak cases was available (n = 89). The postoutbreak cases with a known epidemiologic link to the original outbreak were in younger persons (aged 39 vs 47 years; P < .01), and a larger proportion reported injection drug use (18% vs 4%; P = .04) or noninjection drug use (44% vs 18%; P < .01) than those without a reported link. CONCLUSIONS Health jurisdictions can utilize genotyping data to monitor and define the characteristics of postoutbreak cases related to the original outbreak.
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Ouassa T, Borroni E, Loukou GY, Faye-Kette H, Kouakou J, Menan H, Cirillo DM. High prevalence of shared international type 53 among Mycobacterium tuberculosis complex strains in retreated patients from Côte d'Ivoire. PLoS One 2012; 7:e45363. [PMID: 23028962 PMCID: PMC3445461 DOI: 10.1371/journal.pone.0045363] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2011] [Accepted: 08/21/2012] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Genotyping methods are useful tools to provide information on tuberculosis epidemic. They can allow a better response from health authorities and the implementation of measures for tuberculosis control. This study aimed to identify the main lineages and clades of Mycobacterium tuberculosis complex strains circulating in Côte d'Ivoire. METHODS/MAIN FINDINGS Strains isolated from sputum samples of patients ongoing retreatment from all the country were characterized by spoligotyping and by MIRU-VNTR. Profiles obtained by spoligotyping were first compared to the SITVIT/SpolDB4 database for family assignment. Of 194 strains analysed, 146 (75.3%) belonged to the T lineage. The most predominant spoligotype was the shared international type 53 with 135 strains (69.6%). In contrast with neighbouring countries, LAM (11 strains, 5.7%) and H (9 strains 4.6%) lineages were slightly represented. Only 3 Beijing strains (1.5%) and 4 strains of Mycobacterium africanum (2%) were found. Analysis of the results obtained with MIRU-VNTR revealed also a high level of clustering. CONCLUSION/SIGNIFICANCE The population of Mycobacterium tuberculosis complex strains among retreatment cases in Côte d'Ivoire exhibits a low diversity, allowing to assume recent transmission and locally based infection.
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Affiliation(s)
- Timothée Ouassa
- Department of Bacteriology and Virology, Faculty of Pharmacy, University of Cocody, Abidjan, Côte d'Ivoire.
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Mycobacterium tuberculosis population in northwestern Russia: an update from Russian-EU/Latvian border region. PLoS One 2012; 7:e41318. [PMID: 22844457 PMCID: PMC3402494 DOI: 10.1371/journal.pone.0041318] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2012] [Accepted: 06/20/2012] [Indexed: 11/19/2022] Open
Abstract
This study aimed to characterize the population structure of Mycobacterium tuberculosis in Pskov oblast in northwestern Russia, to view it in the geographical context, to compare drug resistance properties across major genetic families. Ninety M. tuberculosis strains from tuberculosis (TB) patients, permanent residents in Pskov oblast were subjected to LAM-specific IS6110-PCR and spoligotyping, followed by comparison with SITVITWEB and MIRU-VNTRplus databases. The Beijing genotype (n = 40) was found the most prevalent followed by LAM (n = 18), T (n = 13), Haarlem (n = 10), Ural (n = 5), and Manu2 (n = 1); the family status remained unknown for 3 isolates. The high rate of Beijing genotype and prevalence of LAM family are similar to those in the other Russian settings. A feature specific for M. tuberculosis population in Pskov is a relatively higher rate of Haarlem and T types. Beijing strains were further typed with 12-MIRU (followed by comparison with proprietary global database) and 3 hypervariable loci QUB-3232, VNTR-3820, VNTR-4120. The 12-MIRU typing differentiated 40 Beijing strains into 14 types (HGI = 0.82) while two largest types were M2 (223325153533) prevalent throughout former USSR and M11 (223325173533) prevalent in Russia and East Asia. The use of 3 hypervariable loci increased a discrimination of the Beijing strains (18 profiles, HGI = 0.89). Both major families Beijing and LAM had similar rate of MDR strains (62.5 and 55.6%, respectively) that was significantly higher than in other strains (21.9%; P = 0.001 and 0.03, respectively). The rpoB531 mutations were more frequently found in Beijing strains while LAM drug resistant strains mainly harbored rpoB516 and inhA -15 mutations. Taken together with a high rate of multidrug resistance among Beijing strains from new TB cases (79.3% versus 44.4% in LAM), these findings suggest the critical impact of the Beijing genotype on the current situation with MDR-TB in the Pskov region in northwestern Russia.
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Moonan PK, Ghosh S, Oeltmann JE, Kammerer JS, Cowan LS, Navin TR. Using genotyping and geospatial scanning to estimate recent mycobacterium tuberculosis transmission, United States. Emerg Infect Dis 2012; 18:458-65. [PMID: 22377473 PMCID: PMC3309578 DOI: 10.3201/eid1803.111107] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
To determine the proportion of reported tuberculosis (TB) cases due to recent transmission in the United States, we conducted a cross-sectional study to examine culture-positive TB cases with complete genotype results (spoligotyping and 12-locus mycobacterial interspersed repetitive unit-variable-number tandem repeat typing) reported during January 2005-December 2009. Recently transmitted cases were defined as cases with matching results reported within statistically significant geospatial zones (identified by a spatial span statistic within a sliding 3-year window). Approximately 1 in 4 TB cases reported in the United States may be attributed to recent transmission. Groups at greatest risk for recent transmission appear to be men, persons born in the United States, members of a minority race or ethnic group, persons who abuse substances, and the homeless. Understanding transmission dynamics and establishing strategies for rapidly detecting recent transmission among these populations are essential for TB elimination in the United States.
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Affiliation(s)
- Patrick K Moonan
- US Centers for Disease Control and Prevention, Atlanta, GA 30333, USA.
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