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Roychowdhury T, Singh VK, Bhattacharya A. Classification of pathogenic microbes using a minimal set of single nucleotide polymorphisms derived from whole genome sequences. Genomics 2018; 111:205-211. [PMID: 29432978 DOI: 10.1016/j.ygeno.2018.02.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2017] [Revised: 02/04/2018] [Accepted: 02/08/2018] [Indexed: 11/16/2022]
Abstract
In a context specific manner, Intra-species genomic variation plays an important role in phenotypic diversity observed among pathogenic microbes. Efficient classification of these pathogens is important for diagnosis and treatment of several infectious diseases. NGS technologies have provided access to wealth of data that can be utilized to discover important markers for pathogen classification. In this paper, we described three different approaches (Jensen-Shannon divergence, random forest and Shewhart control chart) for identification of a minimal set of SNPs that can be used for classification of organisms. These methods are generic and can be implemented for analysis of any organism. We have shown usefulness of these approaches for analysis of Mycobacterium tuberculosis and Escherichia coli isolates. We were able to identify a minimal set of 18 SNPs that can be used as molecular markers for phylogroup based classification and 8 SNPs for pathogroup based classification of E. coli.
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Affiliation(s)
- Tanmoy Roychowdhury
- School of Computational & Integrative Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Vinod Kumar Singh
- School of Computational & Integrative Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Alok Bhattacharya
- School of Computational & Integrative Sciences, Jawaharlal Nehru University, New Delhi, India; School of Life Sciences, Jawaharlal Nehru University, New Delhi, India.
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152
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Zachariah A, Pandiyan J, Madhavilatha GK, Mundayoor S, Chandramohan B, Sajesh PK, Santhosh S, Mikota SK. Mycobacterium tuberculosis in Wild Asian Elephants, Southern India. Emerg Infect Dis 2018; 23:504-506. [PMID: 28221104 PMCID: PMC5382741 DOI: 10.3201/eid2303.161741] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
We tested 3 ild Asian elephants (Elephas maximus) in southern India and confirmed infection in 3 animals with Mycobacterium tuberculosis, an obligate human pathogen, by PCR and genetic sequencing. Our results indicate that tuberculosis may be spilling over from humans (reverse zoonosis) and emerging in wild elephants.
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153
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Peres RL, Vinhas SA, Ribeiro FKC, Palaci M, do Prado TN, Reis-Santos B, Zandonade E, Suffys PN, Golub JE, Riley LW, Maciel EL. 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] [MESH Headings] [Grants] [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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Affiliation(s)
- Renata Lyrio Peres
- Núcleo de Doenças Infecciosas, Universidade Federal do Espírito Santo, Vitória, Espirito Santo, Brazil
- Laboratório de Epidemiologia da Universidade Federal do Espírito Santo, Av. Marechal Campos, 1468- Maruípe-, Vitória, ES Brazil
| | - Solange Alves Vinhas
- Núcleo de Doenças Infecciosas, Universidade Federal do Espírito Santo, Vitória, Espirito Santo, Brazil
| | | | - Moisés Palaci
- Núcleo de Doenças Infecciosas, Universidade Federal do Espírito Santo, Vitória, Espirito Santo, Brazil
| | - Thiago Nascimento do Prado
- Laboratório de Epidemiologia da Universidade Federal do Espírito Santo, Av. Marechal Campos, 1468- Maruípe-, Vitória, ES Brazil
| | - Bárbara Reis-Santos
- Laboratório de Epidemiologia da Universidade Federal do Espírito Santo, Av. Marechal Campos, 1468- Maruípe-, Vitória, ES Brazil
- Programa de Pós-Graduação em Epidemiologia, Universidade Federal de Pelotas, Pelotas, Brazil
| | - Eliana Zandonade
- Laboratório de Epidemiologia da Universidade Federal do Espírito Santo, Av. Marechal Campos, 1468- Maruípe-, Vitória, ES Brazil
| | - Philip Noel Suffys
- Laboratório de Biologia Molecular Aplicada a Micobactérias, Instituto Oswaldo Cruz – FioCruz, Rio de Janeiro, Brazil
| | | | - Lee W. Riley
- Division of Infectious Disease and Vaccinology, School of Public Health, University of California, Berkeley, CA USA
| | - Ethel Leonor Maciel
- Laboratório de Epidemiologia da Universidade Federal do Espírito Santo, Av. Marechal Campos, 1468- Maruípe-, Vitória, ES Brazil
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Sieniawska E, Sawicki R, Swatko-Ossor M, Napiorkowska A, Przekora A, Ginalska G, Augustynowicz-Kopec E. The Effect of Combining Natural Terpenes and Antituberculous Agents against Reference and Clinical Mycobacterium tuberculosis Strains. Molecules 2018; 23:E176. [PMID: 29342972 PMCID: PMC6017631 DOI: 10.3390/molecules23010176] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Revised: 12/28/2017] [Accepted: 01/06/2018] [Indexed: 11/17/2022] Open
Abstract
Background: On account of emergence of multi- and extensively drug-resistant Mycobacterium tuberculosis (Mtb) strains, combinations of drugs with natural compounds were tested to search for antibiotic activity enhancers. In this work we studied terpenes (α-pinene, bisabolol, β-elemene, (R)-limonene, (S)-limonene, myrcene, sabinene), which are the main constituents of essential oil obtained from Mutellina purpurea L., a plant with described antitubercular activity, to investigate their interactions with antibiotics against reference Mtb strains and multidrug-resistant clinical isolates. Methods: The serial dilution method was used to evaluate the minimal inhibitory concentration (MIC) of tested compounds, while the fractional inhibitory concentration index (FICI) was calculated for characterization of interactions. Moreover, IC50 values of tested compounds were determined using monkey kidney epithelial cell line (GMK). Results: The combinations of all studied terpenes with ethambutol or rifampicin resulted in a synergistic interaction. Bisabolol and (R)-limonene decreased the MIC for rifampicin at least two-fold for all tested strains, however no synergistic action was observed against virulent strains. The tested terpenes showed slight (bisabolol) or no cytotoxic effect against normal eukaryotic cells in vitro. Conclusions: The obtained enhanced activity (FICI < 0.5) of ethambutol and rifampicin against H37Ra strain under the influence of the studied terpenes may be correlated to the capability of essential oil constituents to modify bacterial resistance mechanisms in general. The observed differences in avirulent and virulent bacteria susceptibility to terpenes tested separately and in combinations with antibiotics can be correlated with the differences in the cell wall structure between H37Ra mutant and all virulent strains.
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Affiliation(s)
- Elwira Sieniawska
- Department of Pharmacognosy with Medicinal Plant Unit, Medical University of Lublin, 20-093 Lublin, Poland.
| | - Rafal Sawicki
- Department of Biochemistry and Biotechnology, Medical University of Lublin, 20-093 Lublin, Poland.
| | - Marta Swatko-Ossor
- Department of Biochemistry and Biotechnology, Medical University of Lublin, 20-093 Lublin, Poland.
| | - Agnieszka Napiorkowska
- Department of Microbiology, National Tuberculosis and Lung Diseases Research Institute, 01-138 Warsaw, Poland.
| | - Agata Przekora
- Department of Biochemistry and Biotechnology, Medical University of Lublin, 20-093 Lublin, Poland.
| | - Grazyna Ginalska
- Department of Biochemistry and Biotechnology, Medical University of Lublin, 20-093 Lublin, Poland.
| | - Ewa Augustynowicz-Kopec
- Department of Microbiology, National Tuberculosis and Lung Diseases Research Institute, 01-138 Warsaw, Poland.
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155
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Conceição EC, Rastogi N, Couvin D, Lopes ML, Furlaneto IP, Gomes HM, Vasconcellos SEG, Suffys PN, Schneider MPC, de Sousa MS, Sola C, de Paula Souza e Guimarães RJ, Duarte RS, Batista Lima KV. Genetic diversity of Mycobacterium tuberculosis from Pará, Brazil, reveals a higher frequency of ancestral strains than previously reported in South America. INFECTION GENETICS AND EVOLUTION 2017; 56:62-72. [DOI: 10.1016/j.meegid.2017.10.021] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2017] [Revised: 10/20/2017] [Accepted: 10/23/2017] [Indexed: 01/24/2023]
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Hoffner S, Sahebi L, Ansarin K, Sabour S, Mohajeri P. Mycobacterium tuberculosis of the Beijing Genotype in Iran and the World Health Organization Eastern Mediterranean Region: A Meta-Analysis. Microb Drug Resist 2017; 24:693-698. [PMID: 29058526 DOI: 10.1089/mdr.2017.0160] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
Abstract
OBJECTIVE The Beijing genotype is a distinct genetic lineage of Mycobacterium tuberculosis, which is distributed worldwide, and may cause large outbreaks of multidrug resistance-tuberculosis (MDR-TB). The distribution of such strains in the Eastern Mediterranean region (EMR) is unclear, and clarifying the data is our purpose apart from the presence of Beijing TB in Iran. METHODS We searched Published literature from CINAHL Cochrane Library, Current Contents, Database of Abstracts of Reviews of Effects (DARE), ProQuest Google Scholar PubMed, PsycINFO, Thomson Reuters, (SID), and Medical Library (MedLib) to detect relevant studies from the year 2000 to July 2015 with the following keywords: M. tuberculosis, Beijing genotype, EMR, and drug resistance. Random-effect models were used to estimate the proportion of Beijing strains in STATA 14. Heterogeneity was investigated by subgroup analysis and meta-regression. RESULTS AND CONCLUSION The meta-prevalence of Beijing strains was 4% (CI 95% = 3-5). The prevalence was different based on types of detection techniques (spoligotyping = 4% vs. other techniques = 6%; p = 0.003) and years of study (before the year 2000 = 2% vs. after year 2000 = 4%, p = 0.004). The Beijing family was most prevalent in Iran and Pakistan. A strong relationship with drug resistance was reported in Pakistan and Iran, and an increasing trend was seen in Pakistan. Additional studies of drug-resistant TB distribution among Beijing strains in EMR countries are needed as well as a time-trend analysis of the Beijing strain infection in the region.
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Affiliation(s)
- Sven Hoffner
- 1 Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet , Stockholm, Sweden
| | - Leyla Sahebi
- 2 Maternal/Fetal and Neonatal Research Center, Tehran University of Medical Sciences , Tehran, Iran .,3 Department of Epidemiology, Tuberculosis and Lung Disease Research Center, Tabriz University of Medical Science , Tabriz, Iran
| | - Khalil Ansarin
- 4 Department of Medicine, Tuberculosis and Lung Disease Research Center, Tabriz University of Medical Science, Tabriz, Iran
| | - Siamak Sabour
- 5 Department of Clinical Epidemiology, Safety Promotion and Injury Prevention Research Center, School of Health, Shahid Beheshti University of Medical Sciences , Tehran, Iran
| | - Parviz Mohajeri
- 6 Department of Microbiology, Faculty of Medicine, Kermanshah University of Medical Sciences , Kermanshah, Iran
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Hijikata M, Keicho N, Duc LV, Maeda S, Hang NTL, Matsushita I, Kato S. Spoligotyping and whole-genome sequencing analysis of lineage 1 strains of Mycobacterium tuberculosis in Da Nang, Vietnam. PLoS One 2017; 12:e0186800. [PMID: 29049400 PMCID: PMC5648229 DOI: 10.1371/journal.pone.0186800] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2017] [Accepted: 10/06/2017] [Indexed: 11/18/2022] Open
Abstract
Background Spacer oligonucleotide typing (spoligotyping), a widely used, classical genotyping method for Mycobacterium tuberculosis complex (MTBC), is a PCR-based dot-blot hybridization technique to detect the genetic diversity of the direct repeat (DR) region. Of the seven major MTBC lineages in the world, lineage 1 (Indo-Oceanic) mostly corresponds to the East African–Indian (EAI) spoligotype family in East Africa and Southeast Asia. Objectives We investigated the genomic features of Vietnamese lineage 1 strains, comparing spoligotype patterns using whole-genome sequencing (WGS) data. Methods M. tuberculosis strains isolated in Da Nang, Vietnam were subjected to conventional spoligotyping, followed by WGS analysis using a high-throughput sequencer. Vietnamese lineage 1 strains were further analyzed with other lineage 1 strains obtained from a public database. Results Indicating a major spoligotype in Da Nang, 86 (46.2%) of the 186 isolates belonged to the EAI family or lineage 1. Although typical EAI4-VNM strains are characterized by the deletion of spacers 26 and 27, 65 (75.6%) showed ambiguous signals on spacer 26. De novo assembly of the entire DR region and in silico spoligotyping analysis suggested the absence of spacer 26, and direct sequencing revealed that the 17th spacer sequence not used for conventional typing, was cross-hybridized to the spacer 26 probe. Vietnamese EAI4-VNM, other EAI-like strains, and those showing a non-EAI pattern lacking many spacers formed a monophyletic group separate from other EAI families in the world. Conclusion Information about the alignment of spacers in the entire DR region obtained from WGS data provides a clue for the determination of experimentally ambiguous spoligo patterns. WGS data also helped to analyze the hidden relationships between apparently distinct spoligo patterns.
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Affiliation(s)
- Minako Hijikata
- Department of Pathophysiology and Host Defense, The Research Institute of Tuberculosis, Japan Anti-Tuberculosis Association, Kiyose, Tokyo, Japan
| | - Naoto Keicho
- The Research Institute of Tuberculosis, Japan Anti-Tuberculosis Association, Kiyose, Tokyo, Japan
- * E-mail:
| | | | - Shinji Maeda
- Hokkaido Pharmaceutical University School of Pharmacy, Sapporo, Hokkaido, Japan
| | | | - Ikumi Matsushita
- Department of Pathophysiology and Host Defense, The Research Institute of Tuberculosis, Japan Anti-Tuberculosis Association, Kiyose, Tokyo, Japan
| | - Seiya Kato
- The Research Institute of Tuberculosis, Japan Anti-Tuberculosis Association, Kiyose, Tokyo, Japan
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158
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Tarazona D, Jaramillo L, Borda V, Levano K, Galarza M, Guio H. A Genomic Signature for Genotyping Mycobacterium tuberculosis. Bioinformation 2017; 13:224-230. [PMID: 28943727 PMCID: PMC5602289 DOI: 10.6026/97320630013224] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2017] [Revised: 07/13/2017] [Accepted: 07/23/2017] [Indexed: 11/30/2022] Open
Abstract
Mycobacterium tuberculosis (MTB), the causative agent of tuberculosis (TB), has a vast diversity of genotypes including Beijing, CAS,
EAI, Haarlem, LAM, X, Ural, T, AFRI1 and AFRI2. However, genotyping can be expensive, time consuming and in some cases, results
may vary depending on methodology used. Here, we proposed a new set of 10 SNPs using a total of 249 MTB genomes, and selected
by first the inclusion/ exclusion (IE) criteria using spoligotyping and phylogenies, followed by the selection of the nonsynonymous
SNPs present in the most conserved cluster of orthologous groups (COG) of each genotype of MTB. Genotype assignment of the new
set of 10 SNPs was validated using an additional of 34 MTB genomes and results showed 100% correlation with their known
genotypes. Our set of 10 SNPs have not been previously reported and cover the MTB genotypes that are prevalent worldwide. This set
of SNPs could be used for molecular epidemiology with drug resistant markers.
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Affiliation(s)
- David Tarazona
- Laboratorio de Biotecnología y Biología Molecular, Centro Nacional de Salud Pública, Instituto Nacional de Salud, Lima, Perú
| | - Luis Jaramillo
- Laboratorio de Biotecnología y Biología Molecular, Centro Nacional de Salud Pública, Instituto Nacional de Salud, Lima, Perú
| | - Victor Borda
- Laboratorio de Biotecnología y Biología Molecular, Centro Nacional de Salud Pública, Instituto Nacional de Salud, Lima, Perú
| | - Kelly Levano
- Laboratorio de Biotecnología y Biología Molecular, Centro Nacional de Salud Pública, Instituto Nacional de Salud, Lima, Perú
| | - Marco Galarza
- Laboratorio de Biotecnología y Biología Molecular, Centro Nacional de Salud Pública, Instituto Nacional de Salud, Lima, Perú
| | - Heinner Guio
- Laboratorio de Biotecnología y Biología Molecular, Centro Nacional de Salud Pública, Instituto Nacional de Salud, Lima, Perú
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159
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The predominance of Ethiopian specific Mycobacterium tuberculosis families and minimal contribution of Mycobacterium bovis in tuberculous lymphadenitis patients in Southwest Ethiopia. INFECTION GENETICS AND EVOLUTION 2017; 55:251-259. [PMID: 28919549 DOI: 10.1016/j.meegid.2017.09.016] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2017] [Revised: 09/12/2017] [Accepted: 09/13/2017] [Indexed: 11/20/2022]
Abstract
BACKGROUND Ethiopia has an extremely high rate of extrapulmonary tuberculosis, dominated by tuberculous lymphadenitis (TBLN). However, little is known about Mycobacterium tuberculosis complex (MTBc) lineages responsible for TBLN in Southwest Ethiopia. METHODS A total of 304 MTBc isolates from TBLN patients in Southwest Ethiopia were genotyped primarily by spoligotyping. Isolates of selected spoligotypes were further analyzed by 15-loci mycobacterial interspersed repetitive unit-variable number tandem repeat (MIRU-VNTR) (n=167) and qPCR-based single nucleotide polymorphism (n=38). Isolates were classified into main phylogenetic lineages and families by using the reference strain collections and identification tools available at MIRU-VNTRplus data base. Resistance to rifampicin was determined by Xpert MTB/RIF. RESULTS The majority of isolates (248; 81.6%) belonged to the Euro-American lineage (Lineage 4), with the ill-defined T and Haarlem as largest families comprising 116 (38.2%) and 43 (14.1%) isolates respectively. Of the T family, 108 isolates were classified as being part of the newly described Ethiopian families, namely Ethiopia_2 (n=44), Ethiopia_3 (n=34) and Ethiopia_H37Rv-like (n=30). Other sub-lineages included URAL (n=18), S (n=17), Uganda I (n=16), LAM (n=13), X (n=5), TUR (n=5), Uganda II (n=4) and unknown (n=19). Lineage 3 (Delhi/CAS) was the second most common lineage comprising 44 (14.5%) isolates. Interestingly, six isolates (2%) were belonged to Lineage 7, unique to Ethiopia. Lineage 1 (East-African Indian) and Lineage 2 (Beijing) were represented by 3 and 1 isolates respectively. M. bovis was identified in only two (0.7%) TBLN cases. The cluster rate was highest for Ethiopia_3 isolates showing clonal similarity with isolates from North Ethiopia. Lineage 3 was significantly associated with rifampicin resistance. CONCLUSIONS In TBLN in Southwest Ethiopia, the recently described Ethiopia specific Lineage 4 families were predominant, followed by Lineage 3 and Lineage 4-Haarlem. The contribution of M. bovis in TBLN infection is minimal.
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Shaping the niche in macrophages: Genetic diversity of the M. tuberculosis complex and its consequences for the infected host. Int J Med Microbiol 2017; 308:118-128. [PMID: 28969988 DOI: 10.1016/j.ijmm.2017.09.009] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2017] [Revised: 09/09/2017] [Accepted: 09/11/2017] [Indexed: 12/12/2022] Open
Abstract
Pathogenic mycobacteria of the Mycobacterium tuberculosis complex (MTBC) have co-evolved with their individual hosts and are able to transform the hostile environment of the macrophage into a permissive cellular habitat. The impact of MTBC genetic variability has long been considered largely unimportant in TB pathogenesis. Members of the MTBC can now be distinguished into three major phylogenetic groups consisting of 7 phylogenetic lineages and more than 30 so called sub-lineages/subgroups. MTBC genetic diversity indeed influences the transmissibility and virulence of clinical MTBC isolates as well as the immune response and the clinical outcome. Here we review the genetic diversity and epidemiology of MTBC strains and describe the current knowledge about the host immune response to infection with MTBC clinical isolates using human and murine experimental model systems in vivo and in vitro. We discuss the role of innate cytokines in detail and portray two in our group recently developed approaches to characterize the intracellular niches of MTBC strains. Characterizing the niches and deciphering the strategies of MTBC strains to transform an antibacterial effector cell into a permissive cellular habitat offers the opportunity to identify strain- and lineage-specific key factors which may represent targets for novel antimicrobial or host directed therapies for tuberculosis.
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161
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Blanco-Guillot F, Delgado-Sánchez G, Mongua-Rodríguez N, Cruz-Hervert P, Ferreyra-Reyes L, Ferreira-Guerrero E, Yanes-Lane M, Montero-Campos R, Bobadilla-del-Valle M, Torres-González P, Ponce-de-León A, Sifuentes-Osornio J, Garcia-Garcia L. Molecular clustering of patients with diabetes and pulmonary tuberculosis: A systematic review and meta-analysis. PLoS One 2017; 12:e0184675. [PMID: 28902922 PMCID: PMC5597214 DOI: 10.1371/journal.pone.0184675] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2017] [Accepted: 08/24/2017] [Indexed: 11/18/2022] Open
Abstract
Introduction Many studies have explored the relationship between diabetes mellitus (DM) and tuberculosis (TB) demonstrating increased risk of TB among patients with DM and poor prognosis of patients suffering from the association of DM/TB. Owing to a paucity of studies addressing this question, it remains unclear whether patients with DM and TB are more likely than TB patients without DM to be grouped into molecular clusters defined according to the genotype of the infecting Mycobacterium tuberculosis bacillus. That is, whether there is convincing molecular epidemiological evidence for TB transmission among DM patients. Objective: We performed a systematic review and meta-analysis to quantitatively evaluate the propensity for patients with DM and pulmonary TB (PTB) to cluster according to the genotype of the infecting M. tuberculosis bacillus. Materials and methods We conducted a systematic search in MEDLINE and LILACS from 1990 to June, 2016 with the following combinations of key words “tuberculosis AND transmission” OR “tuberculosis diabetes mellitus” OR “Mycobacterium tuberculosis molecular epidemiology” OR “RFLP-IS6110” OR “Spoligotyping” OR “MIRU-VNTR”. Studies were included if they met the following criteria: (i) studies based on populations from defined geographical areas; (ii) use of genotyping by IS6110- restriction fragment length polymorphism (RFLP) analysis and spoligotyping or mycobacterial interspersed repetitive unit-variable number of tandem repeats (MIRU-VNTR) or other amplification methods to identify molecular clustering; (iii) genotyping and analysis of 50 or more cases of PTB; (iv) study duration of 11 months or more; (v) identification of quantitative risk factors for molecular clustering including DM; (vi) > 60% coverage of the study population; and (vii) patients with PTB confirmed bacteriologically. The exclusion criteria were: (i) Extrapulmonary TB; (ii) TB caused by nontuberculous mycobacteria; (iii) patients with PTB and HIV; (iv) pediatric PTB patients; (v) TB in closed environments (e.g. prisons, elderly homes, etc.); (vi) diabetes insipidus and (vii) outbreak reports. Hartung-Knapp-Sidik-Jonkman method was used to estimate the odds ratio (OR) of the association between DM with molecular clustering of cases with TB. In order to evaluate the degree of heterogeneity a statistical Q test was done. The publication bias was examined with Begg and Egger tests. Review Manager 5.3.5 CMA v.3 and Biostat and Software package R were used. Results Selection criteria were met by six articles which included 4076 patients with PTB of which 13% had DM. Twenty seven percent of the cases were clustered. The majority of cases (48%) were reported in a study in China with 31% clustering. The highest incidence of TB occurred in two studies from China. The global OR for molecular clustering was 0.84 (IC 95% 0.40–1.72). The heterogeneity between studies was moderate (I2 = 55%, p = 0.05), although there was no publication bias (Beggs test p = 0.353 and Eggers p = 0.429). Conclusion There were very few studies meeting our selection criteria. The wide confidence interval indicates that there is not enough evidence to draw conclusions about the association. Clustering of patients with DM in TB transmission chains should be investigated in areas where both diseases are prevalent and focus on specific contexts.
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Affiliation(s)
- Francles Blanco-Guillot
- Doctorado en Ciencias en Enfermedades Infecciosas, Centro de Investigación sobre Enfermedades Infecciosas, Instituto Nacional de Salud Pública, Cuernavaca, Morelos, México
| | - Guadalupe Delgado-Sánchez
- Centro de Investigación sobre Enfermedades Infecciosas, Instituto Nacional de Salud Pública, Cuernavaca, Morelos, México
| | - Norma Mongua-Rodríguez
- Centro de Investigación sobre Enfermedades Infecciosas, Instituto Nacional de Salud Pública, Cuernavaca, Morelos, México
- Maestría en Ciencias Médicas con énfasis en Epidemiología, Facultad de Medicina, Universidad Nacional Autónoma de México, Distrito Federal, México
| | - Pablo Cruz-Hervert
- Centro de Investigación sobre Enfermedades Infecciosas, Instituto Nacional de Salud Pública, Cuernavaca, Morelos, México
| | - Leticia Ferreyra-Reyes
- Centro de Investigación sobre Enfermedades Infecciosas, Instituto Nacional de Salud Pública, Cuernavaca, Morelos, México
| | - Elizabeth Ferreira-Guerrero
- Centro de Investigación sobre Enfermedades Infecciosas, Instituto Nacional de Salud Pública, Cuernavaca, Morelos, México
| | - Mercedes Yanes-Lane
- Centro de Investigación sobre Enfermedades Infecciosas, Instituto Nacional de Salud Pública, Cuernavaca, Morelos, México
- Facultad de Medicina, Universidad Autónoma de San Luis Potosí, San Luis Potosí, San Luis Potosí, México
| | - Rogelio Montero-Campos
- Centro de Investigación sobre Enfermedades Infecciosas, Instituto Nacional de Salud Pública, Cuernavaca, Morelos, México
| | - Miriam Bobadilla-del-Valle
- Laboratorio de Microbiología, Instituto Nacional de Ciencias Médicas y Nutrición “Salvador Zubirán”, México, Distrito Federal, México
| | - Pedro Torres-González
- Laboratorio de Microbiología, Instituto Nacional de Ciencias Médicas y Nutrición “Salvador Zubirán”, México, Distrito Federal, México
| | - Alfredo Ponce-de-León
- Laboratorio de Microbiología, Instituto Nacional de Ciencias Médicas y Nutrición “Salvador Zubirán”, México, Distrito Federal, México
| | - José Sifuentes-Osornio
- Dirección Médica, Instituto Nacional de Ciencias Médicas y Nutrición “Salvador Zubirán”, México, Distrito Federal, México
| | - Lourdes Garcia-Garcia
- Centro de Investigación sobre Enfermedades Infecciosas, Instituto Nacional de Salud Pública, Cuernavaca, Morelos, México
- * E-mail:
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Abstract
The tuberculosis agent Mycobacterium tuberculosis has undergone a long and selective evolution toward human infection and represents one of the most widely spread pathogens due to its efficient aerosol-mediated human-to-human transmission. With the availability of more and more genome sequences, the evolutionary trajectory of this obligate pathogen becomes visible, which provides us with new insights into the molecular events governing evolution of the bacterium and its ability to accumulate drug-resistance mutations. In this review, we summarize recent developments in mycobacterial research related to this matter that are important for a better understanding of the current situation and future trends and developments in the global epidemiology of tuberculosis, as well as for possible public health intervention possibilities.
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163
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Ratovonirina NH, Rakotosamimanana N, Razafimahatratra SL, Raherison MS, Refrégier G, Sola C, Rakotomanana F, Rasolofo Razanamparany V. Assessment of tuberculosis spatial hotspot areas in Antananarivo, Madagascar, by combining spatial analysis and genotyping. BMC Infect Dis 2017; 17:562. [PMID: 28806916 PMCID: PMC5557477 DOI: 10.1186/s12879-017-2653-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2017] [Accepted: 07/30/2017] [Indexed: 11/17/2022] Open
Abstract
Background Tuberculosis (TB) remains a public health problem in Madagascar. A crucial element of TB control is the development of an easy and rapid method for the orientation of TB control strategies in the country. Our main objective was to develop a TB spatial hotspot identification method by combining spatial analysis and TB genotyping method in Antananarivo. Methods Sputa of new pulmonary TB cases from 20 TB diagnosis and treatment centers (DTCs) in Antananarivo were collected from August 2013 to May 2014 for culture. Mycobacterium tuberculosis complex (MTBC) clinical isolates were typed by spoligotyping on a Luminex® 200 platform. All TB patients were respectively localized according to their neighborhood residence and the spatial distribution of all pulmonary TB patients and patients with genotypic clustered isolates were scanned respectively by the Kulldorff spatial scanning method for identification of significant spatial clustering. Areas exhibiting spatial clustering of patients with genotypic clustered isolates were considered as hotspot TB areas for transmission. Results Overall, 467 new cases were included in the study, and 394 spoligotypes were obtained (84.4%). New TB cases were distributed in 133 of the 192 Fokontany (administrative neighborhoods) of Antananarivo (1 to 15 clinical patients per Fokontany) and patients with genotypic clustered isolates were distributed in 127 of the 192 Fokontany (1 to 13 per Fokontany). A single spatial focal point of epidemics was detected when ignoring genotypic data (p = 0.039). One Fokontany of this focal point and three additional ones were detected to be spatially clustered when taking genotypes into account (p < 0.05). These four areas were declared potential TB transmission hotspots in Antananarivo and will be considered as priority targets for surveillance in the future. Conclusion This method, combining spatial analysis and TB genotyping will now be used for further focused clinical and epidemiological studies in Madagascar and will allow better TB control strategies by public health authorities. Electronic supplementary material The online version of this article (doi:10.1186/s12879-017-2653-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Noël Harijaona Ratovonirina
- Unité des Mycobactéries, Institut Pasteur de Madagascar, Antananarivo, Madagascar.,Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette cedex, France
| | | | | | - Mamy Serge Raherison
- Unité des Mycobactéries, Institut Pasteur de Madagascar, Antananarivo, Madagascar.,Programme National de Lutte contre la Tuberculose (PNLT), Ministère de la Santé, Antananarivo, Madagascar
| | - Guislaine Refrégier
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette cedex, France
| | - Christophe Sola
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette cedex, France
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164
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Mycobacterium tuberculosis genotypes and predominant clones among the multidrug-resistant isolates in Spain 1998-2005. INFECTION GENETICS AND EVOLUTION 2017; 55:117-126. [PMID: 28789982 DOI: 10.1016/j.meegid.2017.08.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2017] [Revised: 07/31/2017] [Accepted: 08/03/2017] [Indexed: 11/23/2022]
Abstract
Although the incidence of tuberculosis (TB) is gradually decreasing in Spain, there is an increase in the proportion of foreign-born cases. This changing scenario is slowly shifting the local TB epidemiology from endemic to imported cases with an increased risk for multidrug-resistant (MDR) and extensively drug resistant (XDR) strains of Mycobacterium tuberculosis complex. MDR/XDR strains from Spain (n=366 MTBC isolates, 1 strain per patient) isolated between 1998 and 2005 were retained for this retrospective analysis. All strains were analyzed by spoligotyping, while 12-loci MIRU-VNTR data were available for 106 isolates from 2003 to 2005. Demographic, phylogenetic, and epidemiologic analyses using anonymized data were collected and analyzed using the SITVIT2 database. Our study provides with a first snapshot of genetic diversity of MDR/XDR-TB in several autonomous regions of Spain. It highlights significantly more of SIT1/Beijing and SIT66/BOV MDR isolates (5.7% and 7.38% respectively) and increasingly more foreign-born cases from Eastern Europe. Future studies should focus on shared genotypes between Spanish and foreign-born patients to decipher the modes of transmission and risk factors involved, and decipher the proportion of imported cases of active disease versus cases of reactivation of latent TB infection among foreign-born individuals.
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165
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Bhembe NL, Jaja IF, Nwodo UU, Okoh AI, Green E. Prevalence of tuberculous lymphadenitis in slaughtered cattle in Eastern Cape, South Africa. Int J Infect Dis 2017; 61:27-37. [DOI: 10.1016/j.ijid.2017.05.005] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2017] [Revised: 04/29/2017] [Accepted: 05/09/2017] [Indexed: 11/29/2022] Open
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166
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Abstract
Tuberculosis (TB) remains the most deadly bacterial infectious disease worldwide. Its treatment and control are threatened by increasing numbers of multidrug-resistant (MDR) or nearly untreatable extensively drug-resistant (XDR) strains. New concepts are therefore urgently needed to understand the factors driving the TB epidemics and the spread of different strain populations, especially in association with drug resistance. Classical genotyping and, more recently, whole-genome sequencing (WGS) revealed that the world population of tubercle bacilli is more diverse than previously thought. Several major phylogenetic lineages can be distinguished, which are associated with their sympatric host population. Distinct clonal (sub)populations can even coexist within infected patients. WGS is now used as the ultimate approach for differentiating clinical isolates and for linking phenotypic to genomic variation from lineage to strain levels. Multiple lines of evidence indicate that the genetic diversity of TB strains translates into pathobiological consequences, and key molecular mechanisms probably involved in differential pathoadaptation of some main lineages have recently been identified. Evidence also accumulates on molecular mechanisms putatively fostering the emergence and rapid expansion of particular MDR and XDR strain groups in some world regions. However, further integrative studies will be needed for complete elucidation of the mechanisms that allow the pathogen to infect its host, acquire multidrug resistance, and transmit so efficiently. Such knowledge will be key for the development of the most effective new diagnostics, drugs, and vaccination strategies.
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167
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Zheng C, Reynaud Y, Zhao C, Zozio T, Li S, Luo D, Sun Q, Rastogi N. New Mycobacterium tuberculosis Beijing clonal complexes in China revealed by phylogenetic and Bayesian population structure analyses of 24-loci MIRU-VNTRs. Sci Rep 2017; 7:6065. [PMID: 28729708 PMCID: PMC5519585 DOI: 10.1038/s41598-017-06346-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2016] [Accepted: 06/12/2017] [Indexed: 11/09/2022] Open
Abstract
Beijing lineage of Mycobacterium tuberculosis constitutes the most predominant lineage in East Asia. Beijing epidemiology, evolutionary history, genetics are studied in details for years revealing probable origin from China followed by worldwide expansion, partially linked to higher mutation rate, hypervirulence, drug-resistance, and association with cases of mixed infections. Considering huge amount of data available for 24-loci Mycobacterial Interspersed Repetitive Units-Variable Number of Tandem Repeats, we performed detailed phylogenetic and Bayesian population structure analyses of Beijing lineage strains in mainland China and Taiwan using available 24-loci MIRU-VNTR data extracted from publications or the SITVIT2 database (n = 1490). Results on genetic structuration were compared to previously published data. A total of three new Beijing clonal complexes tentatively named BSP1, BPS2 and BSP3 were revealed with surprising phylogeographical specificities to previously unstudied regions in Sichuan, Chongqing and Taiwan, proving the need for continued investigations with extended datasets. Such geographical restriction could correspond to local adaptation of these “ecological specialist” Beijing isolates to local human host populations in contrast with “generalist pathogens” able to adapt to several human populations and to spread worldwide.
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Affiliation(s)
- Chao Zheng
- Key Laboratory of Bio-resources and Eco-environment of the Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, 610065, PR China.,WHO Supranational TB Reference Laboratory, Tuberculosis and Mycobacteria Unit, Institut Pasteur de la Guadeloupe, Morne Jolivière, 97183, Abymes, Guadeloupe, France
| | - Yann Reynaud
- WHO Supranational TB Reference Laboratory, Tuberculosis and Mycobacteria Unit, Institut Pasteur de la Guadeloupe, Morne Jolivière, 97183, Abymes, Guadeloupe, France.
| | - Changsong Zhao
- Key Laboratory of Bio-resources and Eco-environment of the Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, 610065, PR China
| | - Thierry Zozio
- WHO Supranational TB Reference Laboratory, Tuberculosis and Mycobacteria Unit, Institut Pasteur de la Guadeloupe, Morne Jolivière, 97183, Abymes, Guadeloupe, France
| | - Song Li
- Key Laboratory of Bio-resources and Eco-environment of the Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, 610065, PR China
| | - Dongxia Luo
- Public Health Clinical Center of Chengdu, Chengdu, Sichuan, 610000, PR China
| | - Qun Sun
- Key Laboratory of Bio-resources and Eco-environment of the Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, 610065, PR China.
| | - Nalin Rastogi
- WHO Supranational TB Reference Laboratory, Tuberculosis and Mycobacteria Unit, Institut Pasteur de la Guadeloupe, Morne Jolivière, 97183, Abymes, Guadeloupe, France.
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168
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Rodríguez-Castillo JG, Pino C, Niño LF, Rozo JC, Llerena-Polo C, Parra-López CA, Tauch A, Murcia-Aranguren MI. Comparative genomic analysis of Mycobacterium tuberculosis Beijing-like strains revealed specific genetic variations associated with virulence and drug resistance. INFECTION GENETICS AND EVOLUTION 2017; 54:314-323. [PMID: 28734764 DOI: 10.1016/j.meegid.2017.07.022] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2017] [Revised: 07/14/2017] [Accepted: 07/18/2017] [Indexed: 12/30/2022]
Abstract
Isolates of the Mycobacterium tuberculosis lineage 2/East-Asian are considered one of the most successful strains due to their increased pathogenicity, hyper-virulence associated with drug resistance, and high transmission. Recent studies in Colombia have shown that the Beijing-like genotype is associated with multidrug-resistance and high prevalence in the southwest of the country, but the genetic basis of its success in dissemination is unknown. In contribution to this matter, we obtained the whole sequences of six genomes of clinical isolates assigned to the Beijing-like genotype. The genomes were compared with the reference genome of M. tuberculosis H37Rv and 53 previously published M. tuberculosis genomes. We found that the six Beijing-like isolates belong to a modern Beijing sub-lineage and share specific genomic variants: i.e. deletion in the PPE8 gene, in Rv3806c (ubiA) responsible of high ethambutol resistance and in Rv3862c (whiB6) which is involved in granuloma formation and virulence, are some of them. Moreover, each isolated has exclusively single nucleotide polymorphisms (SNPs) in genes related with cell wall processes and cell metabolism. We identified polymorphisms in genes related to drug resistance that could explain the drug-resistant phenotypes found in the six isolates from Colombia. We hypothesize that changes due to these genetic variations contribute to the success of these strains. Finally, we analyzed the IS6110 insertion sequences finding very low variance between them, suggesting that SNPs is the major cause of variability found in Beijing-like strains circulating in Colombia.
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Affiliation(s)
- Juan Germán Rodríguez-Castillo
- Departamento de Microbiología, Grupo MICOBACUN, Facultad de Medicina, Universidad Nacional de Colombia, Bogotá 111321, Colombia
| | - Camilo Pino
- Facultad de Ingeniería, Grupo BioLISI, Universidad Nacional de Colombia, Bogotá 111321, Colombia
| | - Luis Fernando Niño
- Facultad de Ingeniería, Grupo BioLISI, Universidad Nacional de Colombia, Bogotá 111321, Colombia
| | - Juan Carlos Rozo
- Centro Internacional de Entrenamiento e Investigaciones Médicas (CIDEIM), Cali 760031, Colombia
| | | | - Carlos A Parra-López
- Departamento de Microbiología, Grupo MICOBACUN, Facultad de Medicina, Universidad Nacional de Colombia, Bogotá 111321, Colombia
| | - Andreas Tauch
- Centrum für Biotechnologie (CeBiTec), Universität Bielefeld, 33615 Bielefeld, Germany
| | - Martha Isabel Murcia-Aranguren
- Departamento de Microbiología, Grupo MICOBACUN, Facultad de Medicina, Universidad Nacional de Colombia, Bogotá 111321, Colombia.
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169
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Chen YY, Chang JR, Wu CD, Yeh YP, Yang SJ, Hsu CH, Lin MC, Tsai CF, Lin MS, Su IJ, Dou HY. Combining molecular typing and spatial pattern analysis to identify areas of high tuberculosis transmission in a moderate-incidence county in Taiwan. Sci Rep 2017; 7:5394. [PMID: 28710410 PMCID: PMC5511213 DOI: 10.1038/s41598-017-05674-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2017] [Accepted: 06/01/2017] [Indexed: 11/08/2022] Open
Abstract
In total, 303 randomly selected clinical Mycobacterium tuberculosis (MTB) isolates from 303 patients (collected January to December 2012) in central Taiwan were examined. The major lineages found were Beijing (N = 114, 37.62%), Haarlem (N = 76, 25.08%) and East African-Indian (EAI) (N = 42, 13.86%). Notably, younger persons (≤30 years old) were 6.58 times more likely to be infected with a Beijing genotype compared to older persons (>70 years) (p < 0.05). Combining molecular typing methods and geographical information system (GIS) analysis, we uncovered a twofold higher incidence of Beijing strains in a hotspot area (33%) compared to non-hotspot areas (17%). By 24 MIRU-VNTR typing, persons in clustered groups were 1.96 times more likely to be infected with a Beijing strain compared with non-clustered persons, suggesting recent spread and emergence of MTB. Finally, we observed a trend in which TB incidence increased as the density/concentration of analyzed environmental factors increased, suggesting that environmental factors are associated with TB transmission; however, only population density was found to be significantly associated with increased risk of TB (p < 0.05). Molecular typing methods combined with spatial analysis suggest possible TB transmission. Early intervention to interrupt transmission may be most effective if targeted to hot zones of TB.
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Affiliation(s)
- Yih-Yuan Chen
- Department of Biochemical Science and Technology, National Chiayi University, Chiai-Yi, Taiwan
| | - Jia-Ru Chang
- National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Zhunan, Miaoli, Taiwan
| | - Chih-Da Wu
- Department of Forestry and Natural Resources, National Chiayi University, Chia-Yi, Taiwan
- The Center for Health and the Global Environment, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Yen-Po Yeh
- Chang-Hua County Public Health Bureau, Changhua City, Taiwan
| | - Shiu-Ju Yang
- National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Zhunan, Miaoli, Taiwan
| | - Chih-Hao Hsu
- National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Zhunan, Miaoli, Taiwan
| | - Ming-Ching Lin
- National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Zhunan, Miaoli, Taiwan
| | - Ching-Fang Tsai
- Department of Medical Research, Ditmanson Medical Foundation, Chia-Yi Christian Hospital, Chia-Yi, Taiwan
| | - Ming-Shian Lin
- Department of Internal Medicine, Ditmanson Medical Foundation, Chia-Yi Christian Hospital, Chia-Yi, Taiwan
| | - Ih-Jen Su
- National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Zhunan, Miaoli, Taiwan
| | - Horng-Yunn Dou
- National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Zhunan, Miaoli, Taiwan.
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170
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Comparative study of genotypes of Mycobacterium tuberculosis from a Northern Indian setting with strains reported from other parts of India and neighboring countries. Tuberculosis (Edinb) 2017; 105:60-72. [DOI: 10.1016/j.tube.2017.04.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2016] [Revised: 04/03/2017] [Accepted: 04/08/2017] [Indexed: 01/11/2023]
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171
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Development of a One-Step Multiplex PCR Assay for Differential Detection of Major Mycobacterium Species. J Clin Microbiol 2017; 55:2736-2751. [PMID: 28659320 DOI: 10.1128/jcm.00549-17] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2017] [Accepted: 06/20/2017] [Indexed: 12/17/2022] Open
Abstract
The prevalence of tuberculosis continues to be high, and nontuberculous mycobacterial (NTM) infection has also emerged worldwide. Moreover, differential and accurate identification of mycobacteria to the species or subspecies level is an unmet clinical need. Here, we developed a one-step multiplex PCR assay using whole-genome analysis and bioinformatics to identify novel molecular targets. The aims of this assay were to (i) discriminate between the Mycobacterium tuberculosis complex (MTBC) and NTM using rv0577 or RD750, (ii) differentiate M. tuberculosis (M. tuberculosis) from MTBC using RD9, (iii) selectively identify the widespread M. tuberculosis Beijing genotype by targeting mtbk_20680, and (iv) simultaneously detect five clinically important NTM (M. avium, M. intracellulare, M. abscessus, M. massiliense, and M. kansasii) by targeting IS1311, DT1, mass_3210, and mkan_rs12360 An initial evaluation of the multiplex PCR assay using reference strains demonstrated 100% specificity for the targeted Mycobacterium species. Analytical sensitivity ranged from 1 to 10 pg for extracted DNA and was 103 and 104 CFU for pure cultures and nonhomogenized artificial sputum cultures, respectively, of the targeted species. The accuracy of the multiplex PCR assay was further evaluated using 55 reference strains and 94 mycobacterial clinical isolates. Spoligotyping, multilocus sequence analysis, and a commercial real-time PCR assay were employed as standard assays to evaluate the multiplex PCR assay with clinical M. tuberculosis and NTM isolates. The PCR assay displayed 100% identification agreement with the standard assays. Our multiplex PCR assay is a simple, convenient, and reliable technique for differential identification of MTBC, M. tuberculosis, M. tuberculosis Beijing genotype, and major NTM species.
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172
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Toyo‐oka L, Mahasirimongkol S, Yanai H, Mushiroda T, Wattanapokayakit S, Wichukchinda N, Yamada N, Smittipat N, Juthayothin T, Palittapongarnpim P, Nedsuwan S, Kantipong P, Takahashi A, Kubo M, Sawanpanyalert P, Tokunaga K. Strain‐based
HLA
association analysis identified
HLA‐DRB1
*09:01
associated with modern strain tuberculosis. HLA 2017; 90:149-156. [DOI: 10.1111/tan.13070] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2017] [Revised: 05/18/2017] [Accepted: 05/22/2017] [Indexed: 01/08/2023]
Affiliation(s)
- L. Toyo‐oka
- Medical Genetics Center, Medical Life Science Institute Department of Medical Sciences, Ministry of Public Health Nonthaburi Thailand
- Department of Human Genetics, Graduate School of Medicine The University of Tokyo Tokyo Japan
| | - S. Mahasirimongkol
- Medical Genetics Center, Medical Life Science Institute Department of Medical Sciences, Ministry of Public Health Nonthaburi Thailand
| | - H. Yanai
- Fukujuji Hospital Japan Anti‐Tuberculosis Association (JATA) Kiyose Japan
- Research Institute of Tuberculosis Japan Anti‐Tuberculosis Association (JATA) Kiyose Japan
| | - T. Mushiroda
- Laboratory for Pharmacogenomics RIKEN Center for Integrative Medical Sciences Yokohama Japan
| | - S. Wattanapokayakit
- Medical Genetics Center, Medical Life Science Institute Department of Medical Sciences, Ministry of Public Health Nonthaburi Thailand
| | - N. Wichukchinda
- Medical Genetics Center, Medical Life Science Institute Department of Medical Sciences, Ministry of Public Health Nonthaburi Thailand
| | - N. Yamada
- Research Institute of Tuberculosis Japan Anti‐Tuberculosis Association (JATA) Kiyose Japan
| | - N. Smittipat
- Tuberculosis Research Laboratory, National Center for Genetic Engineering and Biotechnology National Science and Technology Development Agency, Thailand Science Park (TSP) Pathum Thani Thailand
| | - T. Juthayothin
- Tuberculosis Research Laboratory, National Center for Genetic Engineering and Biotechnology National Science and Technology Development Agency, Thailand Science Park (TSP) Pathum Thani Thailand
| | - P. Palittapongarnpim
- Department of Microbiology, Faculty of Science Mahidol University Bangkok Thailand
| | - S. Nedsuwan
- Chiangrai Prachanukroh Hospital Ministry of Public Health Chiang Rai Thailand
| | - P. Kantipong
- Chiangrai Prachanukroh Hospital Ministry of Public Health Chiang Rai Thailand
| | - A. Takahashi
- Laboratory for Statistical Analysis RIKEN Center for Integrative Medical Sciences Yokohama Japan
| | - M. Kubo
- Laboratory for Genotyping Development RIKEN Center for Integrative Medical Sciences Yokohama Japan
| | - P. Sawanpanyalert
- Health Technical Office Ministry of Public Health Nonthaburi Thailand
| | - K. Tokunaga
- Department of Human Genetics, Graduate School of Medicine The University of Tokyo Tokyo Japan
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173
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Abaye GE, Abebe T, Worku A, Tolessa D, Ameni G, Mihret A. Detection of Mycobacterium tuberculosis from the stool of HIV sero-positive individuals suspected of pulmonary tuberculosis. PLoS One 2017; 12:e0177529. [PMID: 28542255 PMCID: PMC5438117 DOI: 10.1371/journal.pone.0177529] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2016] [Accepted: 04/29/2017] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND The impact of tuberculosis (TB) is exacerbated in Africa because of the human immunodeficiency virus (HIV) pandemic. Pulmonary tuberculosis (PTB) diagnosis is difficult in HIV-infected patients and negative sputum results are more common which leads to diagnostic delay and increases morbidity and mortality. Extra-pulmonary samples such as stool may be easier to obtain and our approach may therefore significantly improve PTB detection in people living with HIV. OBJECTIVE To detect Mycobacterium tuberculosis from the stool of HIV sero-positive individuals suspected of pulmonary TB. METHOD A total of 117 HIV-infected individuals from three public health facilities in Addis Ababa, Ethiopia were enrolled consecutively in the study. Paired morning sputum and stool samples were simultaneously collected from anti-retroviral therapy (ART) naïve individuals living with HIV and suspected for PTB. The diagnostic accuracy of the smear microscopy, culture and region of difference (RD)9-based polymerase chain reaction (PCR) in stool was compared with the accuracy of sputum testing. Chi-square test and kappa value were used to compare different method used. RESULTS Sputum culture positivity for mycobacteria was confirmed in 33(28.2%) of the study subjects. Of 33 individuals positive for sputa culture, 10 individuals were observed to be stools culture positive. Of the 84 individuals negative for mycobacteria by sputum culture, three (3.6%) were stool culture positive and thus, the sensitivity and agreement between stool culture as compare to sputum culture were 30.3% and 0.33, respectively. Of 117 individuals, 11(9.4%) were sputum smear positive and of 11 sputum smear positive three were also stool smear positive. While of the 106 sputum smear negative individuals', only one was stool smear positive resulting in 12.1% sensitivity and 0.18 agreements against sputum culture. On the other hand, the sensitivity of RD9-based PCR directly on stool was 69.7% by considering sputum culture as a reference standard. Moreover, RD9-based PCR directly on sputum detected 7(6.0%) individuals who were sputum culture negative for M. tuberculosis. CONCLUSION M. tuberculosis was detected in stool of individuals living with HIV who were negative for sputum smear microscopy and culture. Hence, examination of stool samples alongside with sputum samples increases the detection of PTB in individuals living with HIV.
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Affiliation(s)
- Gizaw E. Abaye
- Department of Medical Laboratory Science, College of Health Sciences, Arsi University, Asella, Ethiopia
| | - Tamrat Abebe
- Department of Microbiology, Immunology and Parasitology, College of Health Sciences, Faculty of Medicine, Addis Ababa University, Addis Ababa, Ethiopia
| | - Adane Worku
- Aklilu Lemma Institute of Patho-biology, Addis Ababa University, Addis Ababa, Ethiopia
| | - Debela Tolessa
- Department of Biomedical Science, College of Health Sciences, Arsi University, Asella, Ethiopia
| | - Gobena Ameni
- Aklilu Lemma Institute of Patho-biology, Addis Ababa University, Addis Ababa, Ethiopia
| | - Adane Mihret
- Department of Microbiology, Immunology and Parasitology, College of Health Sciences, Faculty of Medicine, Addis Ababa University, Addis Ababa, Ethiopia
- Armauer Hansen Research Institute, Addis Ababa, Ethiopia
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174
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Bashir G, Wani T, Sharma P, Katoch VM, Lone R, Shah A, Katoch K, Kakru DK, Chauhan DS. Predominance of Central Asian and European families among Mycobacterium tuberculosis isolates in Kashmir Valley, India. Indian J Tuberc 2017; 64:302-308. [PMID: 28941853 DOI: 10.1016/j.ijtb.2017.05.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2016] [Revised: 04/03/2017] [Accepted: 05/11/2017] [Indexed: 10/19/2022]
Abstract
BACKGROUND As there are no data available regarding the strains of Mycobacterium tuberculosis circulating in Kashmir Valley, India, the current study aimed at describing the genetic diversity of M. tuberculosis strains in this region, by spoligotyping and 12-locus-based MIRU-VNTR typing (Mycobacterial Interspersed Repetitive Unit-Variable Number Tandem Repeat). METHODS Sputa from 207 smear positive cases with newly diagnosed pulmonary tuberculosis were subjected to culture for M. tuberculosis. Eighty-five isolates confirmed as M. tuberculosis were subjected to drug susceptibility testing and molecular typing by spoligotyping and MIRU-VNTRs. RESULTS Drug susceptibility results of 72 isolates revealed 76.3% as fully sensitive while 5.5% as multidrug resistant (MDR). Spoligotyping of 85 isolates detected 42 spoligotypes with 50 isolates (58.8%) clustered into seven spoligotypes. SIT26/CAS1_Del was the major spoligotype (23, 27%) followed by SIT127/H4 (12, 14.1%); CAS lineage (37.6%) was predominant, followed by Haarlem (25.8%) and ill-defined T clade (23.5%). MIRU-VNTR analysis displayed 82 MIRU patterns from 85 strains, including 3 small clusters and 79 unique. MIRU 26 was found to be the most discriminatory locus. CONCLUSIONS Kashmir Valley has CAS as the predominant lineage of M. tuberculosis similar to the rest of the Indian sub-continent, while it is peculiar in having Euro American lineages such as Haarlem and ill-defined T clade.
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Affiliation(s)
- Gulnaz Bashir
- Department of Microbiology, Sher-i-Kashmir Institute of Medical Sciences, Soura, Srinagar, India.
| | - Tehmeena Wani
- Department of Microbiology, Sher-i-Kashmir Institute of Medical Sciences, Soura, Srinagar, India
| | - Pragya Sharma
- Department of Microbiology and Molecular Biology, NJIL& OMD (ICMR), Tajganj, Agra, India
| | - V M Katoch
- NASI-ICMR Chair on Public Health Research, Rajasthan University of Health Sciences, Jaipur, India; Former Secretary, Former Director General, Department of Health Research (Ministry of Health and Family Welfare), Indian Council of Medical Research, New Delhi, India
| | - Rubina Lone
- Department of Microbiology, SKIMS Medical College, Bemina, Srinagar, India
| | - Azra Shah
- Department of Pathology, Sher-i-Kashmir Institute of Medical Sciences, Soura, Srinagar, India
| | - Kiran Katoch
- Department of Microbiology and Molecular Biology, NJIL& OMD (ICMR), Tajganj, Agra, India
| | - D K Kakru
- Department of Microbiology, Sher-i-Kashmir Institute of Medical Sciences, Soura, Srinagar, India
| | - Devendra Singh Chauhan
- Department of Microbiology and Molecular Biology, NJIL& OMD (ICMR), Tajganj, Agra, India
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175
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Zhao J, Matsuba T, Zhang X, Leano S, Nakajima C, Chagan-Yasutan H, Telan EF, Suzuki Y, Hattori T. Comparison of antibody responses against Mycobacterium tuberculosis antigen Rv0679c in tuberculosis patients from the endemic and non-endemic regions of the Beijing genotype: a case control study. BMC Infect Dis 2017; 17:344. [PMID: 28506215 PMCID: PMC5433171 DOI: 10.1186/s12879-017-2442-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2017] [Accepted: 05/04/2017] [Indexed: 11/10/2022] Open
Abstract
Background Strains of the Beijing genotype of Mycobacterium tuberculosis (MTB) are reportedly associated with the virulence of tuberculosis (TB) infection, unfavorable outcomes of anti-TB treatment, and the global TB pandemic. Rv0679c, a hypothetical membrane protein related to host cell invasion, has a Beijing genotype-specific mutation at residue 142 (Asn142Lys). Antigenicity differences between Rv0679c-Asn142 (N-type) and Rv0679c-Lys142 (K-type) have been previously observed in mice antigen-antibody responses. However, the immune response to Rv0679c in humans remains unknown. Therefore, we aimed to investigate the anti-Rv0679c immune response in TB patients from the endemic and non-endemic regions of the Beijing MTB genotype. Methods We analyzed the Rv0679c-specific antibody responses in 84 subjects from the endemic region of the Beijing genotype MTB in China, including 45 pulmonary TB patients (C-PTB) and 39 healthy controls (C-HC), and 81 subjects from the Philippines (the endemic region of the non-Beijing genotype), including 51 pulmonary TB patients (P-PTB) and 30 healthy controls (P-HC). Anti-tuberculous-glycolipid (TBGL) antigen was used as the control antibody. Results TBGL IgG titers were higher in both C-PTB and P-PTB than those in their corresponding HC (C-PTB median 4.2, P-PTB median 11.2; C-PTB vs. P-PTB, p > 0.05), suggesting immune response comparability in PTB from two different countries. C-PTB showed a higher response compared to C-HC for anti-K-type IgG (53.3%) than anti-N-type IgG (6.67%); this response was not observed in P-PTB (both N-type and K-type 9.80%). Conclusion Dimorphic antigen Rv0679c was found to be associated with distinct immune response patterns, indicating the role of Beijing/non-Beijing genotype of MTB in stimulating specific responses in TB patients from the endemic region of Beijing MTB. Meanwhile, reactions to Rv0679c in patients and HC from non-endemic regions of the Beijing MTB may be caused by the response to the common epitope of Rv0679c N/K-type.
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Affiliation(s)
- Jingge Zhao
- Laboratory of Disaster Medicine, International Research Institute of Disaster Science, Tohoku University, Sendai, Miyagi, 980-8574, Japan
| | - Takashi Matsuba
- Division of Bacteriology, Department of Microbiology and Immunology, Faculty of Medicine, Tottori University, Yonago, Tottori, 683-8503, Japan
| | - Xiaoyan Zhang
- Shanghai Public Health Clinical Center, Fudan Univeristy, Shanghai, 201508, China
| | - Susan Leano
- STD AIDS Cooperative Central Laboratory, San Lazaro Hospital, Quiricada Street, 1003, Manila, Philippines
| | - Chie Nakajima
- Division of Global Epidemiology, Hokkaido University Research Center for Zoonosis Control, Sapporo, Hokkaido, 001-0020, Japan.,The Global Station for Zoonosis Control, Hokkaido University Global Institution for Collaborative Research and Education, Sapporo, Hokkaido, 001-0020, Japan
| | - Haorile Chagan-Yasutan
- Laboratory of Disaster Medicine, International Research Institute of Disaster Science, Tohoku University, Sendai, Miyagi, 980-8574, Japan
| | - Elizabeth Freda Telan
- STD AIDS Cooperative Central Laboratory, San Lazaro Hospital, Quiricada Street, 1003, Manila, Philippines
| | - Yasuhiko Suzuki
- Division of Global Epidemiology, Hokkaido University Research Center for Zoonosis Control, Sapporo, Hokkaido, 001-0020, Japan.,The Global Station for Zoonosis Control, Hokkaido University Global Institution for Collaborative Research and Education, Sapporo, Hokkaido, 001-0020, Japan
| | - Toshio Hattori
- Graduate School of Health Science Studies, Kibi International University, 8 Igamachi, Takahashi, 716-8508, Japan.
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176
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Dou HY, Lin CH, Chen YY, Yang SJ, Chang JR, Wu KM, Chen YT, Chin PJ, Liu YM, Su IJ, Tsai SF. Lineage-specific SNPs for genotyping of Mycobacterium tuberculosis clinical isolates. Sci Rep 2017; 7:1425. [PMID: 28469152 PMCID: PMC5431204 DOI: 10.1038/s41598-017-01580-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2016] [Accepted: 03/29/2017] [Indexed: 11/09/2022] Open
Abstract
Tuberculosis (TB) is a severe infectious disease worldwide. Genetic variation of the causative agent, Mycobacterium tuberculosis (MTB), determines the outcomes of infection and anti-TB treatment. Until recently, there has been no effective and convenient way for classifying clinical isolates based on the DNA sequences of the divergent lineages of MTB infecting human populations. Here, we identified single nucleotide polymorphisms (SNPs) of six representative strains from Taiwan by whole-genome sequencing and comparing the results to the sequence of the H37Rv reference strain. One hundred and ten SNPs, each unique to one of the six strains, were used to genotype 150 additional isolates by applying DNA mass spectrometry. Lineage-specific SNPs were identified that could distinguish the major lineages of the clinical isolates. A subset including 32 SNPs was found to be sufficient to type four major groups of MTB isolates in Taiwan (ancient Beijing, modern Beijing, East African–Indian, and Latin-American Mediterranean). However, there was high genetic homozygosity within the Euro-American lineage, which included spoligotype-classified Haarlem and T strains. By whole-genome sequencing of 12 representative Euro-American isolates, we identified multiple subtype-specific SNPs which allowed us to distinguish two major branches within the Euro-American lineage.
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Affiliation(s)
- Horng-Yunn Dou
- Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Zhunan, Miaoli, Taiwan.
| | - Chien-Hsing Lin
- Institute of Molecular and Genomic Medicine, National Health Research Institutes, Zhunan, Miaoli, Taiwan
| | - Yih-Yuan Chen
- Department of Biochemical Science and Technology, National Chiayi University, Chia-Yi, Taiwan
| | - Shiu-Ju Yang
- Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Zhunan, Miaoli, Taiwan
| | - Jia-Ru Chang
- Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Zhunan, Miaoli, Taiwan
| | - Keh-Ming Wu
- Institute of Molecular and Genomic Medicine, National Health Research Institutes, Zhunan, Miaoli, Taiwan.,Genome Research Center, National Yang-Ming University, Taipei, Taiwan
| | - Ying-Tsong Chen
- Institute of Molecular and Genomic Medicine, National Health Research Institutes, Zhunan, Miaoli, Taiwan.,Institute of Bioinformatics, National Chung Hsing University, Taichung, Taiwan
| | - Pei-Ju Chin
- Institute of Molecular and Genomic Medicine, National Health Research Institutes, Zhunan, Miaoli, Taiwan.,Genome Research Center, National Yang-Ming University, Taipei, Taiwan
| | - Yen-Ming Liu
- Institute of Molecular and Genomic Medicine, National Health Research Institutes, Zhunan, Miaoli, Taiwan
| | - Ih-Jen Su
- Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Zhunan, Miaoli, Taiwan
| | - Shih-Feng Tsai
- Institute of Molecular and Genomic Medicine, National Health Research Institutes, Zhunan, Miaoli, Taiwan. .,Genome Research Center, National Yang-Ming University, Taipei, Taiwan. .,Institute of Biomedical Informatics, National Yang-Ming University, Taipei, Taiwan.
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177
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Elnaggar MM, Abdellrazeq GS, Elsisy A, Mahmoud AH, Shyboub A, Sester M, Khaliel SA, Singh M, Torky HA, Davis WC. Evaluation of antigen specific interleukin-1β as a biomarker to detect cattle infected with Mycobacterium bovis. Tuberculosis (Edinb) 2017; 105:53-59. [PMID: 28610788 DOI: 10.1016/j.tube.2017.04.009] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2017] [Revised: 04/04/2017] [Accepted: 04/21/2017] [Indexed: 01/01/2023]
Abstract
Bovine tuberculosis (bTB) is a major world-wide health problem that has been difficult to control, due to the lack of an effective vaccine and limited ability of the tuberculin skin test (TST) and the ancillary whole blood interferon-gamma (IFN-γ) release assay (IGRA) to detect all infected animals. A 6 h cytokine flow cytometric IFN-γ (CFC) assay was developed in effort to overcome these limitations and expand methods for studying the mechanisms of bTB immunopathogenesis. The present study was conducted to evaluate IL-1β as a biomarker to use in conjunction with the IFN-γ CFC assay to improve the diagnostic accuracy for bTB. Three animal groups with predefined Mbv infection status were used for analysis of IL-1β in plasma from whole blood cultures stimulated with ESAT-6/CFP-10 for 20-24 h. Parallel stimulations were performed for enumeration of IFN-γ producing T cells. Data analysis showed that Mbv infected animals have a higher frequency of IFN-γ producing CD4+ T cells and plasma IL-1β than animals exposed to non-tuberculous mycobacteria (NTM) or uninfected control animals, with a significant correlation between the two readouts, thus allowing differentiation between the three animal groups. IL-1β has the potential to serve as an additional biomarker for detecting cattle infected with Mbv.
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Affiliation(s)
- Mahmoud M Elnaggar
- Department of Microbiology, Faculty of Veterinary Medicine, Alexandria University, Egypt; Department of Veterinary Microbiology and Pathology, College of Veterinary Medicine, Pullman, WA, USA.
| | - Gaber S Abdellrazeq
- Department of Microbiology, Faculty of Veterinary Medicine, Alexandria University, Egypt; Department of Veterinary Microbiology and Pathology, College of Veterinary Medicine, Pullman, WA, USA
| | - Alaa Elsisy
- Department of Microbiology, Faculty of Veterinary Medicine, Alexandria University, Egypt
| | - Asmaa H Mahmoud
- Department of Microbiology, Faculty of Veterinary Medicine, Alexandria University, Egypt
| | - Abdelrazeq Shyboub
- Department of Microbiology, Faculty of Veterinary Medicine, Alexandria University, Egypt
| | - Martina Sester
- Department of Transplant and Infection Immunology, Institutes for Infection Medicine, Saarland University, Homburg, Germany
| | - Samy A Khaliel
- Department of Microbiology, Faculty of Veterinary Medicine, Alexandria University, Egypt
| | - Mahavir Singh
- Lionex Diagnostics & Therapeutics, Braunschweig, Germany
| | - Helmy A Torky
- Department of Microbiology, Faculty of Veterinary Medicine, Alexandria University, Egypt
| | - William C Davis
- Department of Veterinary Microbiology and Pathology, College of Veterinary Medicine, Pullman, WA, USA
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178
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Rasigade JP, Barbier M, Dumitrescu O, Pichat C, Carret G, Ronnaux-Baron AS, Blasquez G, Godin-Benhaim C, Boisset S, Carricajo A, Jacomo V, Fredenucci I, Pérouse de Montclos M, Flandrois JP, Ader F, Supply P, Lina G, Wirth T. Strain-specific estimation of epidemic success provides insights into the transmission dynamics of tuberculosis. Sci Rep 2017; 7:45326. [PMID: 28349973 PMCID: PMC5368603 DOI: 10.1038/srep45326] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2016] [Accepted: 02/21/2017] [Indexed: 12/03/2022] Open
Abstract
The transmission dynamics of tuberculosis involves complex interactions of socio-economic and, possibly, microbiological factors. We describe an analytical framework to infer factors of epidemic success based on the joint analysis of epidemiological, clinical and pathogen genetic data. We derive isolate-specific, genetic distance-based estimates of epidemic success, and we represent success-related time-dependent concepts, namely epidemicity and endemicity, by restricting analysis to specific time scales. The method is applied to analyze a surveillance-based cohort of 1,641 tuberculosis patients with minisatellite-based isolate genotypes. Known predictors of isolate endemicity (older age, native status) and epidemicity (younger age, sputum smear positivity) were identified with high confidence (P < 0.001). Long-term epidemic success also correlated with the ability of Euro-American and Beijing MTBC lineages to cause active pulmonary infection, independent of patient age and country of origin. Our results demonstrate how important insights into the transmission dynamics of tuberculosis can be gained from active surveillance data.
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Affiliation(s)
- Jean-Philippe Rasigade
- Institut de Systématique, Evolution, Biodiversité, UMR-CNRS 7205, Muséum National d'Histoire Naturelle, Université Pierre et Marie Curie, Ecole Pratique des Hautes Etudes, Sorbonne Universités, Paris, France.,Laboratoire Biologie Intégrative des Populations, Ecole Pratique des Hautes Etudes, PSL Research University, Paris, France.,Centre International de Recherche en Infectiologie, CIRI, University of Lyon, France.,Institut des Agents Infectieux, Hospices Civils de Lyon, Lyon, France
| | - Maxime Barbier
- Institut de Systématique, Evolution, Biodiversité, UMR-CNRS 7205, Muséum National d'Histoire Naturelle, Université Pierre et Marie Curie, Ecole Pratique des Hautes Etudes, Sorbonne Universités, Paris, France.,Laboratoire Biologie Intégrative des Populations, Ecole Pratique des Hautes Etudes, PSL Research University, Paris, France
| | - Oana Dumitrescu
- Centre International de Recherche en Infectiologie, CIRI, University of Lyon, France.,Institut des Agents Infectieux, Hospices Civils de Lyon, Lyon, France
| | - Catherine Pichat
- Institut des Agents Infectieux, Hospices Civils de Lyon, Lyon, France
| | - Gérard Carret
- Institut des Agents Infectieux, Hospices Civils de Lyon, Lyon, France
| | | | | | | | - Sandrine Boisset
- Laboratoire de Bactériologie, Institut de Biologie et de Pathologie, CHU de Grenoble, Grenoble, France.,Laboratoire TIMC-IMAG, UMR 5525 CNRS-UJF, UFR de Médecine, Université Grenoble Alpes, Grenoble, France
| | - Anne Carricajo
- Laboratoire des Agents Infectieux et d'Hygiène, CHU de Saint-Etienne, Saint-Etienne, France
| | | | | | | | - Jean-Pierre Flandrois
- Institut des Agents Infectieux, Hospices Civils de Lyon, Lyon, France.,Laboratoire de Biométrie et Biologie Evolutive, UMR CNRS 5558, University of Lyon, France
| | - Florence Ader
- Centre International de Recherche en Infectiologie, CIRI, University of Lyon, France.,Service des Maladies Infectieuses et Tropicales, Hôpital de la Croix-Rousse, Hospices Civils de Lyon, Lyon, France
| | - Philip Supply
- INSERM U1019, CNRS-UMR 8204, Center for Infection and Immunity of Lille, Institut Pasteur de Lille, Université de Lille, Lille, France
| | - Gérard Lina
- Centre International de Recherche en Infectiologie, CIRI, University of Lyon, France.,Institut des Agents Infectieux, Hospices Civils de Lyon, Lyon, France
| | - Thierry Wirth
- Institut de Systématique, Evolution, Biodiversité, UMR-CNRS 7205, Muséum National d'Histoire Naturelle, Université Pierre et Marie Curie, Ecole Pratique des Hautes Etudes, Sorbonne Universités, Paris, France.,Laboratoire Biologie Intégrative des Populations, Ecole Pratique des Hautes Etudes, PSL Research University, Paris, France
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179
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Panwalkar N, Chauhan DS, Desikan P. Spoligotype defined lineages of Mycobacterium tuberculosis and drug resistance: Merely a casual correlation? Indian J Med Microbiol 2017; 35:27-32. [PMID: 28303814 DOI: 10.4103/0255-0857.202327] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
Drug-resistant tuberculosis (TB) is a major challenge to TB control strategy worldwide. Analysis of genetic polymorphism among drug resistant Mycobacterium tuberculosis (MTB) strains may help provide some insight into the transmission dynamics of these strains. Spoligotyping is a widely used technique to identify genetic polymorphism, based on 43 known spacers interspersed between direct repeat regions. Considerable work has been done in various parts of the world using this technique to identify and analyse the polymorphic nature of MTB. Many studies have been carried out to determine the association of drug resistance with spoligotype defined lineages, and much data has been produced over the years. New information continues to be generated. This review aims to put together the findings of relevant studies in an attempt to understand the correlation of drug resistance with spoligotype defined lineages of MTB. This would help provide a perspective of the available data that can be used as a starting point to understand the molecular epidemiology of drug resistant TB.
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Affiliation(s)
- Nikita Panwalkar
- Department of Microbiology and NRL, Bhopal Memorial Hospital and Research Centre, Bhopal, Madhya Pradesh, India
| | - Devendra S Chauhan
- National JALMA Institute for Leprosy and Other Mycobacterial Diseases, Indian Council of Medical Research, Agra, Uttar Pradesh, India
| | - Prabha Desikan
- Department of Microbiology and NRL, Bhopal Memorial Hospital and Research Centre, Bhopal, Madhya Pradesh, India
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180
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Vinhas SA, Jones-López EC, Ribeiro Rodrigues R, Gaeddert M, Peres RL, Marques-Rodrigues P, de Aguiar PPL, White LF, Alland D, Salgame P, Hom D, Ellner JJ, Dietze R, Collins LF, Shashkina E, Kreiswirth B, Palaci M. Strains of Mycobacterium tuberculosis transmitting infection in Brazilian households and those associated with community transmission of tuberculosis. Tuberculosis (Edinb) 2017; 104:79-86. [PMID: 28454653 DOI: 10.1016/j.tube.2017.03.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2016] [Revised: 03/08/2017] [Accepted: 03/10/2017] [Indexed: 12/16/2022]
Abstract
Molecular epidemiologic studies have shown that the dynamics of tuberculosis transmission varies geographically. We sought to determine which strains of Mycobacterium tuberculosis (MTB) were infecting household contacts (HHC), and which were causing clusters of tuberculosis (TB) disease in Vitoria-ES, Brazil. A total of 741 households contacts (445 TST +) and 139 index cases were characterized according to the proportion of contacts in each household that had a tuberculin skin test positive: low (LT) (≤40% TST+), high (HT) (≥70% TST+) and (40-70% TST+) intermediate (IT) transmission. IS6110-RFLP and spoligotyping analysis were performed only 139 MTB isolates from index cases and 841 community isolates. Clustering occurred in 45% of the entire study population. There was no statistically significant association between MTB household transmission category and clustering. Within the household study population, the proportion of clusters in HT and LT groups was similar (31% and 36%, respectively; p = 0.82). Among index cases isolates associated with households demonstrating TST conversion, the frequency of unique pattern genotypes was higher for index cases of the LT compared to HT households (p = 0.03). We concluded that clusters and lineages associated with MTB infection in HT households had no proclivity for increased transmission of TB in the community.
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Affiliation(s)
- Solange Alves Vinhas
- Núcleo de Doenças Infecciosas (NDI), Universidade Federal do Espírito Santo (UFES), Vitória, Brazil
| | - Edward C Jones-López
- Section of Infectious Diseases, Department of Medicine, Boston Medical Center and Boston University School of Medicine, Boston, MA, USA
| | | | - Mary Gaeddert
- Section of Infectious Diseases, Department of Medicine, Boston Medical Center and Boston University School of Medicine, Boston, MA, USA
| | - Renata Lyrio Peres
- Núcleo de Doenças Infecciosas (NDI), Universidade Federal do Espírito Santo (UFES), Vitória, Brazil
| | | | | | - Laura Forsberg White
- Section of Infectious Diseases, Department of Medicine, Boston Medical Center and Boston University School of Medicine, Boston, MA, USA
| | - David Alland
- Division of Infectious Diseases, Department of Medicine, New Jersey Medical School - Rutgers, The State University of New Jersey, Newark, NJ, USA
| | - Padmini Salgame
- Division of Infectious Diseases, Department of Medicine, New Jersey Medical School - Rutgers, The State University of New Jersey, Newark, NJ, USA
| | - David Hom
- Section of Infectious Diseases, Department of Medicine, Boston Medical Center and Boston University School of Medicine, Boston, MA, USA
| | - Jerrold J Ellner
- Section of Infectious Diseases, Department of Medicine, Boston Medical Center and Boston University School of Medicine, Boston, MA, USA
| | - Reynaldo Dietze
- Núcleo de Doenças Infecciosas (NDI), Universidade Federal do Espírito Santo (UFES), Vitória, Brazil
| | - Lauren F Collins
- Department of Medicine, Duke University Medical Center, Durham, NC, USA
| | - Elena Shashkina
- Public Health Research Institute Center, New Jersey Medical School - Rutgers, The State University of New Jersey, Newark, NJ, USA
| | - Barry Kreiswirth
- Public Health Research Institute Center, New Jersey Medical School - Rutgers, The State University of New Jersey, Newark, NJ, USA
| | - Moisés Palaci
- Núcleo de Doenças Infecciosas (NDI), Universidade Federal do Espírito Santo (UFES), Vitória, Brazil.
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181
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Kahaliw W, Aseffa A, Abebe M, Teferi M, Engidawork E. Evaluation of the antimycobacterial activity of crude extracts and solvent fractions of selected Ethiopian medicinal plants. BMC COMPLEMENTARY AND ALTERNATIVE MEDICINE 2017; 17:143. [PMID: 28274226 PMCID: PMC5343536 DOI: 10.1186/s12906-017-1563-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 10/09/2016] [Accepted: 01/06/2017] [Indexed: 01/08/2023]
Abstract
BACKGROUND Tuberculosis (TB) is a global health problem complicated by drug resistance and human immunodeficiency virus that has dramatically increased active TB. Several medicinal plants are used traditionally to treat TB in Ethiopia and investigating these plants is required as plants are an alternative source for development of new anti-TB drugs. The purpose of this study was to investigate antimycobacterial activity of crude extract of Carissa edulis, Otostegia integrifolia, Persea americana, Pterolobium stellatum and Vernonia amygdalina as well as fractions of the most active crude extract. METHODS The effect of various doses of the crude extracts as well as solvent fractions on M. tuberculosis H37Rv and/or MDR-TB clinical isolate was determined using broth microdilution and microtiter resazurin assay methods. Minimum inhibitory concentration was determined by CFU count and resazurin color change observation. RESULTS Chloroform and 80% methanol extracts of P. stellatum and O. integrifolia as well as 80% methanol and acetone extracts of P. americana had significant antimycobacterial activity (p < 0.001) against M. tuberculosis H37Rv. Chloroform extract of V. amygdalina and C. edulis didn't, however, show any significant activity compared to negative controls. P. stellatum chloroform extract was the most active on M. tuberculosis H37Rv (MIC 0.039 mg/ml) and AOZ8W-4 (MDR-TB clinical isolate) (MIC = 0.078 mg/ml). Ethyl acetate fraction of P. stellatum chloroform extract was the most active fraction. CONCLUSION P. stellatum, O. integrifolia and P. americana were found to be endowed with antimycobacterial activity. However, P. stellatum appears to be the most promising plant based on criteria set by different studies. Ethyl acetate fraction of P. stellatum was found to be the most active and future studies should involve this fraction.
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Affiliation(s)
- Wubayehu Kahaliw
- Department of Pharmacology, School of Pharmacy, College of Medicine and Health Sciences, University of Gondar, P. O. Box: 196, Gondar, Ethiopia
| | - Abraham Aseffa
- Armauer Hanson Research Institute, P. O. Box: 1005, Addis Ababa, Ethiopia
| | - Markos Abebe
- Armauer Hanson Research Institute, P. O. Box: 1005, Addis Ababa, Ethiopia
| | - Mekonen Teferi
- Armauer Hanson Research Institute, P. O. Box: 1005, Addis Ababa, Ethiopia
| | - Ephrem Engidawork
- Department of Pharmacology and Clinical Pharmacy, School of Pharmacy, College of Health Sciences, Addis Ababa University, P. O. Box: 1176, Addis Ababa, Ethiopia
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182
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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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183
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Moraes EB, Slompo L, Finardi AJ, Silveira HPPD, Ruiz L, Gomes HM, Richini VB, Suffys P, Fortaleza CMCB, Cavalcanti R, Baptista IMFD. Tuberculosis associated factors caused by Mycobacterium tuberculosis of the RDRio genotype. Mem Inst Oswaldo Cruz 2017; 112:182-187. [PMID: 28225901 PMCID: PMC5319367 DOI: 10.1590/0074-02760160347] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2016] [Accepted: 11/07/2016] [Indexed: 11/22/2022] Open
Affiliation(s)
- Eloise Brasil Moraes
- Instituto Lauro de Souza Lima, Brasil; Universidade Estadual Paulista Júlio de Mesquita Filho, Brasil
| | | | - Amanda Juliane Finardi
- Instituto Lauro de Souza Lima, Brasil; Universidade Estadual Paulista Júlio de Mesquita Filho, Brasil
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184
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Freidlin PJ, Nissan I, Luria A, Goldblatt D, Schaffer L, Kaidar-Shwartz H, Chemtob D, Dveyrin Z, Head SR, Rorman E. Structure and variation of CRISPR and CRISPR-flanking regions in deleted-direct repeat region Mycobacterium tuberculosis complex strains. BMC Genomics 2017; 18:168. [PMID: 28201993 PMCID: PMC5310062 DOI: 10.1186/s12864-017-3560-6] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2016] [Accepted: 02/07/2017] [Indexed: 12/16/2022] Open
Abstract
Background CRISPR and CRISPR-flanking genomic regions are important for molecular epidemiology of Mycobacterium tuberculosis complex (MTBC) strains, and potentially for adaptive immunity to phage and plasmid DNA, and endogenous roles in the bacterium. Genotyping in the Israel National Mycobacterium Reference Center Tel-Aviv of over 1500 MTBC strains from 2008–2013 showed three strains with validated negative 43-spacer spoligotypes, that is, with putatively deleted direct repeat regions (deleted-DR/CRISPR regions). Two isolates of each of three negative spoligotype MTBC (a total of 6 isolates) were subjected to Next Generation Sequencing (NGS). As positive controls, NGS was performed for three intact-DR isolates belonging to T3_Eth, the largest multiple-drug-resistant (MDR)-containing African-origin cluster in Israel. Other controls consisted of NGS reads and complete whole genome sequences from GenBank for 20 intact-DR MTBC and for 1 deleted-DR MTBC strain recognized as CAS by its defining RD deletion. Results NGS reads from negative spoligotype MTBC mapped to reference H37Rv NC_000962.3 suggested that the DR/CRISPR regions were completely deleted except for retention of the middle IS6110 mobile element. Clonally specific deletion of CRISPR-flanking genes also was observed, including deletion of at least cas2 and cas1 genes. Genomic RD deletions defined lineages corresponding to the major spoligotype families Beijing, EAI, and Haarlem, consistent with 24 loci MIRU-VNTR profiles. Analysis of NGS reads, and analysis of contigs obtained by manual PCR confirmed that all 43 gold standard DR/CRISPR spacers were missing in the deleted-DR genomes. Conclusions Although many negative spoligotype strains are recorded as spoligotype-international-type (SIT) 2669 in the SITVIT international database, this is the first time to our knowledge that it has been shown that negative spoligotype strains are found in at least 4 different 24 loci MIRU-VNTR and RD deletion families. We report for the first time negative spoligotype-associated total loss of CRISPR region spacers and repeats, with accompanying clonally specific loss of flanking genes, including at least CRISPR-associated genes cas2 and cas1. Since cas1 deleted E.coli shows increased sensitivity to DNA damage and impaired chromosomal segregation, we discussed the possibility of a similar phenotype in the deleted-DR strains and Beijing family strains as both lack the cas1 gene. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-3560-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Paul Jeffrey Freidlin
- National Mycobacterium Reference Center, National Public Health Laboratory Tel Aviv, Ministry of Health, Tel Aviv, Israel.
| | - Israel Nissan
- National Mycobacterium Reference Center, National Public Health Laboratory Tel Aviv, Ministry of Health, Tel Aviv, Israel
| | - Anna Luria
- National Mycobacterium Reference Center, National Public Health Laboratory Tel Aviv, Ministry of Health, Tel Aviv, Israel.,current address: Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Drora Goldblatt
- National Mycobacterium Reference Center, National Public Health Laboratory Tel Aviv, Ministry of Health, Tel Aviv, Israel
| | | | - Hasia Kaidar-Shwartz
- National Mycobacterium Reference Center, National Public Health Laboratory Tel Aviv, Ministry of Health, Tel Aviv, Israel
| | - Daniel Chemtob
- Department of Tuberculosis and AIDS, Ministry of Health, Jerusalem, Israel
| | - Zeev Dveyrin
- National Public Health Laboratory Tel Aviv, Ministry of Health, Tel Aviv, Israel
| | | | - Efrat Rorman
- National Public Health Laboratory Tel Aviv, Ministry of Health, Tel Aviv, Israel
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185
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Reynaud Y, Zheng C, Wu G, Sun Q, Rastogi N. Bayesian population structure analysis reveals presence of phylogeographically specific sublineages within previously ill-defined T group of Mycobacterium tuberculosis. PLoS One 2017; 12:e0171584. [PMID: 28166309 PMCID: PMC5293260 DOI: 10.1371/journal.pone.0171584] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2016] [Accepted: 01/22/2017] [Indexed: 11/23/2022] Open
Abstract
Mycobacterium tuberculosis genetic structure, and evolutionary history have been studied for years by several genotyping approaches, but delineation of a few sublineages remains controversial and needs better characterization. This is particularly the case of T group within lineage 4 (L4) which was first described using spoligotyping to pool together a number of strains with ill-defined signatures. Although T strains were not traditionally considered as a real phylogenetic group, they did contain a few phylogenetically meaningful sublineages as shown using SNPs. We therefore decided to investigate if this observation could be corroborated using other robust genetic markers. We consequently made a first assessment of genetic structure using 24-loci MIRU-VNTRs data extracted from the SITVIT2 database (n = 607 clinical isolates collected in Russia, Albania, Turkey, Iraq, Brazil and China). Combining Minimum Spanning Trees and Bayesian population structure analyses (using STRUCTURE and TESS softwares), we distinctly identified eight tentative phylogenetic groups (T1-T8) with a remarkable correlation with geographical origin. We further compared the present structure observed with other L4 sublineages (n = 416 clinical isolates belonging to LAM, Haarlem, X, S sublineages), and showed that 5 out of 8 T groups seemed phylogeographically well-defined as opposed to the remaining 3 groups that partially mixed with other L4 isolates. These results provide with novel evidence about phylogeographically specificity of a proportion of ill-defined T group of M. tuberculosis. The genetic structure observed will now be further validated on an enlarged worldwide dataset using Whole Genome Sequencing (WGS).
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Affiliation(s)
- Yann Reynaud
- WHO Supranational TB Reference Laboratory, Tuberculosis and Mycobacteria Unit, Institut Pasteur de la Guadeloupe, Morne Jolivière Abymes, Guadeloupe, France
| | - Chao Zheng
- WHO Supranational TB Reference Laboratory, Tuberculosis and Mycobacteria Unit, Institut Pasteur de la Guadeloupe, Morne Jolivière Abymes, Guadeloupe, France
- College of Life Sciences, Sichuan University, Chengdu, Sichuan, China
| | - Guihui Wu
- Chengdu Public Health Clinical Center, Chengdu, Sichuan, China
| | - Qun Sun
- College of Life Sciences, Sichuan University, Chengdu, Sichuan, China
| | - Nalin Rastogi
- WHO Supranational TB Reference Laboratory, Tuberculosis and Mycobacteria Unit, Institut Pasteur de la Guadeloupe, Morne Jolivière Abymes, Guadeloupe, France
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186
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Difference in Antibody Responses to Mycobacterium tuberculosis Antigens in Japanese Tuberculosis Patients Infected with the Beijing/Non-Beijing Genotype. J Immunol Res 2017; 2017:4797856. [PMID: 28182078 PMCID: PMC5274661 DOI: 10.1155/2017/4797856] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2016] [Accepted: 12/08/2016] [Indexed: 01/25/2023] Open
Abstract
The Beijing genotype Mycobacterium tuberculosis (MTB), notorious for its virulence and predisposition to relapse, could be identified by spoligotyping based on genetic heterogeneity. The plasma samples from 20 cases of Beijing and 16 cases of non-Beijing MTB infected individuals and 24 healthy controls (HCs) were collected, and antibodies against 11 antigens (Rv0679c142Asn, Rv0679c142Lys, Ag85B, Ag85A, ARC, TDM-M, TDM-K, HBHA, MDP-1, LAM, and TBGL) were measured by ELISA. Compared to the HCs, the MTB infected subjects showed higher titers of anti-Ag85B IgG (positivity 58.2%) and anti-ACR IgG (positivity 48.2%). Of note, anti-ACR IgG showed higher titer in Beijing MTB infected tuberculosis (TB) patients than in HC (Kruskal–Wallis test, p < 0.05), while the levels of anti-Ag85B, anti-TBGL, anti-TDM-K, and anti-TDM-M IgG were higher in non-Beijing TB patients than in HC. Moreover, anti-Ag85B IgG showed higher response in non-Beijing TB patients than in Beijing TB patients (p < 0.05; sensitivity, 76.9% versus 44.4%). The sensitivity and specificity analysis showed that 78.8% Beijing infected individuals were negative in anti-TBGL-IgG or/and anti-Ag85B-IgG, while 75.0% of those were positive in anti-TBGL-IgA or/and anti-ACR-IgG tests. These results indicate the possibility of developing antibody-based test to identify Beijing MTB.
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187
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Mycobacterium caprae transmission to free-living grey wolves (Canis lupus) in the Bieszczady Mountains in Southern Poland. EUR J WILDLIFE RES 2017. [DOI: 10.1007/s10344-017-1079-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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188
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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: 36] [Impact Index Per Article: 5.1] [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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189
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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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190
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What Do We Know about Anthracofibrosis? A Literature Review. TANAFFOS 2017; 16:175-189. [PMID: 29849671 PMCID: PMC5960222] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Recently, the significance of anthracosis in the tracheobronchial tree, lung parenchyma, and even non-respiratory organs has been postulated and discussed in association with other diseases, especially tuberculosis. We reviewed the current literature by using the following key words in Medline/PubMed, Embase, and Google Scholar databases: anthracosis, anthracofibrosis, anthracotic bronchitis, biomass fuels, and mixed-dust pneumoconiosis. The bibliographies of eligible papers were also reviewed for further relevant articles. A total of 37 studies were assessed. The content of these studies was then divided into specific categories. Considering the pathogenesis, along with histopathological, radiological, and bronchoscopic results regarding anthracotic lesions, we suggest these findings be defined as "ANTHRACOSIS SYNDROME". For the first time, we describe a syndrome involving black pigmentation, which was previously thought to involve only the tracheobronchial tree. Until recently, it was not considered to be a single syndrome with different sites of involvement.
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191
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Genetic Structure and Drug Susceptibility Patterns of Mycobacterium tuberculosis Complex Strains Responsible of Human Pulmonary Tuberculosis in the Major Rearing Region in Cameroon. BIOMED RESEARCH INTERNATIONAL 2016; 2016:2904832. [PMID: 28119925 PMCID: PMC5227118 DOI: 10.1155/2016/2904832] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 08/24/2016] [Revised: 11/15/2016] [Accepted: 12/07/2016] [Indexed: 11/17/2022]
Abstract
Background. Cameroon this last decade continues to present a low contribution of M. africanum and M. bovis in human tuberculosis (TB), while M. bovis was prevalent in cattle but all these pieces of information only concerned West and Center regions. Methods. We carried out the first study in Adamaoua, one of the most rearing regions of Cameroon, on the genetic structure and drug susceptibility of the MTBC strains isolated from newly diagnosed sputum smear-positive patients aged 15 years and above. For that purpose, spoligotyping, a modified 15 standard MIRU/VNTR loci typing, and the proportion method were used. Results. Four hundred and thirty-seven MTBC isolates were analyzed by spoligotyping. Of these, 423 were identified as M. tuberculosis, within the Cameroon family being dominant with 278 (65.7%) isolates; twelve (2.75%) isolates were classified as M. africanum and two as M. bovis. MIRU/VNTR typing of the most prevalent sublineage (SIT 61) suggested that this lineage is not a unique clone as thought earlier but could constitute a group of strains implicated to different pocket of TB transmission. Only M. tuberculosis sublineages were associated with antituberculosis drug resistance. Conclusion. These results showed the weak contribution of M. africanum and M. bovis to human active pulmonary tuberculosis in Cameroon even in the rearing region.
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192
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Sahebi L, Ansarin K, Hoffner S, Mohajeri P, Mohammadi A. Beijing strains of Mycobacterium tuberculosis in smear-positive tuberculosis patients in North-West and West of Iran. Adv Biomed Res 2016; 5:181. [PMID: 28028521 PMCID: PMC5157006 DOI: 10.4103/2277-9175.190982] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2015] [Accepted: 05/31/2016] [Indexed: 11/04/2022] Open
Abstract
BACKGROUND Tuberculosis (TB) is the leading cause of morbidity and mortality among chronic infectious diseases. The goal of this cross-sectional study (2012-2014) was to examine the prevalence of Mycobacterium TB (MTB) Beijing strains in regions near the Iranian border and to identify any epidemiological links. MATERIALS AND METHODS To this end, MTB isolates were harvested, from 64 HIV-negative, pulmonary smear-positive TB patients from the Iranian border provinces of East Azerbaijan (North-West), Kurdistan (West), and Kermanshah (West) (2012-2014). Isolates were subjected to restriction fragment length polymorphism (RFLP) analysis, using the insertion sequence IS6110 as a probe (IS6110 RFLP), and drug susceptibility testing by the proportion method. We gathered demographic and clinical data using a questionnaire and reviewing patient records. Results were analyzed with Gel Compare II 6.6 and SPSS-18. RESULTS The mean age of the patients was 54.4 years and 46.9% were male. The prevalence of Beijing strains among the isolates was 9.4% (17.6% in the Western provinces and 0% in East Azerbaijan). There was a statistically significant relationship between the Beijing strains and drug resistance and also between these strains, and the recurrence of TB in patients that had previously received treatment (P = 0.02 and P = 0.04, respectively). CONCLUSIONS Finally, the prevalence of Beijing strains in Western Iran was greater than expected. Our results therefore indicate that regional and cross-border tracing may be necessary to control spread of this organism.
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Affiliation(s)
- Leyla Sahebi
- Department of Tuberculosis and Lung Disease, Tuberculosis and Lung Disease Research Centre, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Khalil Ansarin
- Department of Tuberculosis and Lung Disease, Tuberculosis and Lung Disease Research Centre, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Sven Hoffner
- Department of Microbiology, Karolinska Institute, The Public Health Agency of Sweden, Stockholm, Sweden
| | - Parviz Mohajeri
- Department of Microbiology, Faculty of Medicine, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Abolghasem Mohammadi
- Department of Plant Breeding and Biotechnology, School of Agriculture, University of Tabriz, Tabriz, Iran
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193
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Rahim Z, Thapa J, Fukushima Y, van der Zanden AGM, Gordon SV, Suzuki Y, Nakajima C. Tuberculosis Caused by Mycobacterium orygis in Dairy Cattle and Captured Monkeys in Bangladesh: a New Scenario of Tuberculosis in South Asia. Transbound Emerg Dis 2016; 64:1965-1969. [PMID: 27888587 DOI: 10.1111/tbed.12596] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2016] [Indexed: 11/28/2022]
Abstract
Mycobacterium orygis, commonly known as the oryx bacillus and a newly proposed Mycobacterium tuberculosis complex subspecies, was isolated from 18 cattle in a dairy farm and two captured rhesus monkeys in a zoo in Bangladesh. All the infected animals had tuberculosis lesions in their lungs, suggesting transmission and infection with M. orygis by an airborne route. The 20 isolates were analysed using a range of conventional and molecular typing methods, and RD-deletion typing and sequencing of selected genes confirmed the isolates as M. orygis. Multiple-locus variable-number tandem repeat analysis (MLVA) allowed the isolates to be divided into three clusters based on the relatedness of their MLVA profiles. The two monkey isolates shared the same MLVA pattern with 15 of the cattle isolates, whereas the remaining three cattle isolates had different patterns, even though the latter animals had been kept in the same dairy farm. The diversity observed among isolates may suggest the bacteria have been established in this area for a long period. This study along with other recent findings that report the detection of M. orygis from animals as well as humans originating from South Asia potentially indicate endemic distribution of M. orygis in South Asia.
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Affiliation(s)
- Z Rahim
- Tuberculosis Laboratory, International Centre for Diarrhoeal Disease Research, Bangladesh, Mohakhali, Dhaka, Bangladesh
| | - J Thapa
- Division of Bioresources, Hokkaido University Research Center for Zoonosis Control, Sapporo, Hokkaido, Japan
| | - Y Fukushima
- Division of Bioresources, Hokkaido University Research Center for Zoonosis Control, Sapporo, Hokkaido, Japan
| | - A G M van der Zanden
- Laboratory for Medical Microbiology and Public Health, Enschede, The Netherlands
| | - S V Gordon
- UCD School of Veterinary Medicine, University College Dublin, Dublin, Ireland
| | - Y Suzuki
- Division of Bioresources, Hokkaido University Research Center for Zoonosis Control, Sapporo, Hokkaido, Japan.,The Global Station for Zoonosis Control, Hokkaido University Global Institution for Collaborative Research and Education, Sapporo, Japan
| | - C Nakajima
- Division of Bioresources, Hokkaido University Research Center for Zoonosis Control, Sapporo, Hokkaido, Japan.,The Global Station for Zoonosis Control, Hokkaido University Global Institution for Collaborative Research and Education, Sapporo, Japan
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194
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Ei PW, Aung WW, Lee JS, Choi GE, Chang CL. Molecular Strain Typing of Mycobacterium tuberculosis: a Review of Frequently Used Methods. J Korean Med Sci 2016; 31:1673-1683. [PMID: 27709842 PMCID: PMC5056196 DOI: 10.3346/jkms.2016.31.11.1673] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/15/2016] [Accepted: 08/06/2016] [Indexed: 11/20/2022] Open
Abstract
Tuberculosis, caused by the bacterium Mycobacterium tuberculosis, remains one of the most serious global health problems. Molecular typing of M. tuberculosis has been used for various epidemiologic purposes as well as for clinical management. Currently, many techniques are available to type M. tuberculosis. Choosing the most appropriate technique in accordance with the existing laboratory conditions and the specific features of the geographic region is important. Insertion sequence IS6110-based restriction fragment length polymorphism (RFLP) analysis is considered the gold standard for the molecular epidemiologic investigations of tuberculosis. However, other polymerase chain reaction-based methods such as spacer oligonucleotide typing (spoligotyping), which detects 43 spacer sequence-interspersing direct repeats (DRs) in the genomic DR region; mycobacterial interspersed repetitive units-variable number tandem repeats, (MIRU-VNTR), which determines the number and size of tandem repetitive DNA sequences; repetitive-sequence-based PCR (rep-PCR), which provides high-throughput genotypic fingerprinting of multiple Mycobacterium species; and the recently developed genome-based whole genome sequencing methods demonstrate similar discriminatory power and greater convenience. This review focuses on techniques frequently used for the molecular typing of M. tuberculosis and discusses their general aspects and applications.
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Affiliation(s)
- Phyu Win Ei
- Advanced Molecular Research Centre, Department of Medical Research, Yangon, Myanmar
| | - Wah Wah Aung
- Advanced Molecular Research Centre, Department of Medical Research, Yangon, Myanmar
| | - Jong Seok Lee
- International Tuberculosis Research Center, Changwon, Korea
| | - Go Eun Choi
- Institute of Convergence Bio-Health, Dong-A University, Busan, Korea
| | - Chulhun L Chang
- Department of Laboratory Medicine, Pusan National University Yangsan Hospital, Yangsan, Korea.
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195
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Stucki D, Brites D, Jeljeli L, Coscolla M, Liu Q, Trauner A, Fenner L, Rutaihwa L, Borrell S, Luo T, Gao Q, Kato-Maeda M, Ballif M, Egger M, Macedo R, Mardassi H, Moreno M, Tudo Vilanova G, Fyfe J, Globan M, Thomas J, Jamieson F, Guthrie JL, Asante-Poku A, Yeboah-Manu D, Wampande E, Ssengooba W, Joloba M, Henry Boom W, Basu I, Bower J, Saraiva M, Vaconcellos SEG, Suffys P, Koch A, Wilkinson R, Gail-Bekker L, Malla B, Ley SD, Beck HP, de Jong BC, Toit K, Sanchez-Padilla E, Bonnet M, Gil-Brusola A, Frank M, Penlap Beng VN, Eisenach K, Alani I, Wangui Ndung'u P, Revathi G, Gehre F, Akter S, Ntoumi F, Stewart-Isherwood L, Ntinginya NE, Rachow A, Hoelscher M, Cirillo DM, Skenders G, Hoffner S, Bakonyte D, Stakenas P, Diel R, Crudu V, Moldovan O, Al-Hajoj S, Otero L, Barletta F, Jane Carter E, Diero L, Supply P, Comas I, Niemann S, Gagneux S. Mycobacterium tuberculosis lineage 4 comprises globally distributed and geographically restricted sublineages. Nat Genet 2016; 48:1535-1543. [PMID: 27798628 PMCID: PMC5238942 DOI: 10.1038/ng.3704] [Citation(s) in RCA: 248] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2016] [Accepted: 09/27/2016] [Indexed: 12/30/2022]
Abstract
Generalist and specialist species differ in the breadth of their ecological niches. Little is known about the niche width of obligate human pathogens. Here we analyzed a global collection of Mycobacterium tuberculosis lineage 4 clinical isolates, the most geographically widespread cause of human tuberculosis. We show that lineage 4 comprises globally distributed and geographically restricted sublineages, suggesting a distinction between generalists and specialists. Population genomic analyses showed that, whereas the majority of human T cell epitopes were conserved in all sublineages, the proportion of variable epitopes was higher in generalists. Our data further support a European origin for the most common generalist sublineage. Hence, the global success of lineage 4 reflects distinct strategies adopted by different sublineages and the influence of human migration.
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Affiliation(s)
- David Stucki
- Swiss Tropical and Public Health Institute, Basel, Switzerland.,University of Basel, Switzerland
| | - Daniela Brites
- Swiss Tropical and Public Health Institute, Basel, Switzerland.,University of Basel, Switzerland
| | - Leïla Jeljeli
- Forschungszentrum Borstel, Germany.,Institut Pasteur de Tunis, Université de Tunis El Manar, Tunis, Tunisia
| | - Mireia Coscolla
- Swiss Tropical and Public Health Institute, Basel, Switzerland.,University of Basel, Switzerland
| | - Qingyun Liu
- The Key Laboratory of Medical Molecular Virology of Ministries of Education and Health, Institutes of Biomedical Sciences and Institute of Medical Microbiology, School of Basic Medical Science of Fudan University, Shanghai, China
| | - Andrej Trauner
- Swiss Tropical and Public Health Institute, Basel, Switzerland.,University of Basel, Switzerland
| | - Lukas Fenner
- Swiss Tropical and Public Health Institute, Basel, Switzerland.,University of Basel, Switzerland.,Institute for Social and Preventive Medicine, University of Bern, Switzerland
| | - Liliana Rutaihwa
- Swiss Tropical and Public Health Institute, Basel, Switzerland.,University of Basel, Switzerland
| | - Sonia Borrell
- Swiss Tropical and Public Health Institute, Basel, Switzerland.,University of Basel, Switzerland
| | - Tao Luo
- Laboratory of Infection and Immunity, School of Basic Medical Science, West China Center of Medical Sciences, Sichuan University, Chengdu, Sichuan 610041, China
| | - Qian Gao
- The Key Laboratory of Medical Molecular Virology of Ministries of Education and Health, Institutes of Biomedical Sciences and Institute of Medical Microbiology, School of Basic Medical Science of Fudan University, Shanghai, China
| | | | - Marie Ballif
- Swiss Tropical and Public Health Institute, Basel, Switzerland.,University of Basel, Switzerland.,Institute for Social and Preventive Medicine, University of Bern, Switzerland
| | - Matthias Egger
- Institute for Social and Preventive Medicine, University of Bern, Switzerland
| | - Rita Macedo
- Laboratòrio de Saùde Publica, Lisbon, Portugal
| | - Helmi Mardassi
- Institut Pasteur de Tunis, Université de Tunis El Manar, Tunis, Tunisia
| | | | | | - Janet Fyfe
- Victorian Infectious Diseases Reference Laboratory, Victoria, Australia
| | - Maria Globan
- Victorian Infectious Diseases Reference Laboratory, Victoria, Australia
| | | | | | | | - Adwoa Asante-Poku
- Noguchi Memorial Institute for Medical Research, University of Ghana, Accra, Ghana
| | - Dorothy Yeboah-Manu
- Noguchi Memorial Institute for Medical Research, University of Ghana, Accra, Ghana
| | - Eddie Wampande
- Department of Medical Microbiology, Makerere University, Kampala, Uganda
| | - Willy Ssengooba
- Department of Medical Microbiology, Makerere University, Kampala, Uganda.,Department of Global Health, University of Amsterdam, Amsterdam, the Netherlands
| | - Moses Joloba
- Department of Medical Microbiology, Makerere University, Kampala, Uganda
| | - W Henry Boom
- Department of Molecular Biology and Microbiology, Case Western Reserve University, Cleveland, USA
| | - Indira Basu
- LabPlus, Auckland City Hospital, Auckland, New Zealand
| | - James Bower
- LabPlus, Auckland City Hospital, Auckland, New Zealand
| | - Margarida Saraiva
- Life and Health Sciences Research Institute (ICVS), School of Health Sciences, University of Minho, Braga, Portugal.,ICVS/3B's - PT Government Associate Laboratory, Braga/Guimarães, Portugal
| | | | | | - Anastasia Koch
- Institute of Infectious Disease and Molecular Medicine and Department of Clinical Laboratory Sciences, University of Cape Town, South Africa
| | - Robert Wilkinson
- Institute of Infectious Disease and Molecular Medicine and Department of Clinical Laboratory Sciences, University of Cape Town, South Africa.,Department of Medicine, Imperial College London, UK.,The Francis Crick Institute Mill Hill Laboratory, London, UK
| | - Linda Gail-Bekker
- Institute of Infectious Disease and Molecular Medicine and Department of Clinical Laboratory Sciences, University of Cape Town, South Africa
| | - Bijaya Malla
- Swiss Tropical and Public Health Institute, Basel, Switzerland.,University of Basel, Switzerland
| | - Serej D Ley
- Swiss Tropical and Public Health Institute, Basel, Switzerland.,University of Basel, Switzerland.,Papua New Guinea Institute of Medical Research, Goroka, PNG
| | - Hans-Peter Beck
- Swiss Tropical and Public Health Institute, Basel, Switzerland.,University of Basel, Switzerland
| | | | - Kadri Toit
- Tartu University Hospital United Laboratories, Mycobacteriology, Tartu, Estonia
| | | | | | - Ana Gil-Brusola
- Department of Microbiology, University Hospital La Fe, Valencia, Spain
| | - Matthias Frank
- Institute of Tropical Medicine, University of Tübingen, Tübingen, Germany
| | - Veronique N Penlap Beng
- Institute Laboratory for Tuberculosis Research (LTR), Biotechnology Center (BTC), University of Yaoundé I, Yaoundé, Cameroon
| | - Kathleen Eisenach
- Department of Pathology, University of Arkansas for Medical Sciences, Little Rock, Arkansas, USA
| | - Issam Alani
- Department of Medical Laboratory Technology, Faculty of Medical Technology, Baghdad, Iraq
| | - Perpetual Wangui Ndung'u
- Institute of Tropical Medicine and Infectious Diseases (ITROMID), Jomo Kenyatta University of Agriculture and Technology (JKUAT), Nairobi, Kenya
| | - Gunturu Revathi
- Department of Pathology, Aga Khan University Hospital (AKUH), Nairobi, Kenya
| | - Florian Gehre
- Insitute of Tropical Medicine, Antwerp, Belgium.,Medical Research Council, Fajara, the Gambia
| | | | - Francine Ntoumi
- Institute of Tropical Medicine, University of Tübingen, Tübingen, Germany.,Fondation Congolaise pour la Recherche Médicale, Université Marien Gouabi, Brazzaville, Congo
| | - Lynsey Stewart-Isherwood
- Right to Care and the Clinical HIV Research Unit, University of the Witwatersrand, Johannesburg, South Africa
| | - Nyanda E Ntinginya
- National Institute of Medical Research, Mbeya Medical Research Centre (NIMR-MMRC), Mbeya, Tanzania
| | - Andrea Rachow
- Division of Infectious Diseases and Tropical Medicine, Medical Centre of the University of Munich, Munich, Germany; German Centre for Infection Research (DZIF), partner site Munich, Germany
| | - Michael Hoelscher
- Division of Infectious Diseases and Tropical Medicine, Medical Centre of the University of Munich, Munich, Germany; German Centre for Infection Research (DZIF), partner site Munich, Germany
| | - Daniela Maria Cirillo
- Emerging Bacterial Pathogens Unit, IRCCS, San Raffaele Scientific Institute, Milan, Italy
| | - Girts Skenders
- Riga East University Hospital, Centre of Tuberculosis and Lung Diseases, Riga, Latvia
| | - Sven Hoffner
- WHO Supranational TB Reference Laboratory, Department of Microbiology, The Public Health Agency of Sweden, Solna, Sweden
| | - Daiva Bakonyte
- Department of Immunology and Cell Biology, Institute of Biotechnology, Vilnius University, Vilnius, Lithuania
| | - Petras Stakenas
- Department of Immunology and Cell Biology, Institute of Biotechnology, Vilnius University, Vilnius, Lithuania
| | - Roland Diel
- Institute for Epidemiology, Schleswig-Holstein University Hospital, Kiel, Germany
| | - Valeriu Crudu
- National Tuberculosis Reference Laboratory, Phthysiopneumology Institute, Chisinau, Republic of Moldova
| | - Olga Moldovan
- 'Marius Nasta' Pneumophtisiology Institute, Bucharest, Romania
| | - Sahal Al-Hajoj
- Department of Infection and Immunity, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
| | - Larissa Otero
- Instituto de Medicina Tropical Alexander von Humboldt, Molecular Epidemiology Unit-Tuberculosis, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Francesca Barletta
- Instituto de Medicina Tropical Alexander von Humboldt, Molecular Epidemiology Unit-Tuberculosis, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - E Jane Carter
- Alpert School of Medicine at Brown University, Providence, Rhode Island, USA.,Moi University School of Medicine, Eldoret, Kenya
| | - Lameck Diero
- Moi University School of Medicine, Eldoret, Kenya
| | - Philip Supply
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019 - UMR 8204 - CIIL - Centre d'Infection et d'Immunité de Lille, F-59000 Lille, France
| | - Iñaki Comas
- Institute of Biomedicine of Valencia (IBV-CSIC), 46010, Valencia, Spain.,CIBER Epidemiology and Public Health, Madrid, Spain
| | - Stefan Niemann
- Forschungszentrum Borstel, Germany.,German Center for Infection Research, Borstel Site, Borstel, Germany
| | - Sebastien Gagneux
- Swiss Tropical and Public Health Institute, Basel, Switzerland.,University of Basel, Switzerland
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196
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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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197
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Dou HY, Chen YY, Chen YT, Chang JR, Lin CH, Wu KM, Lin MS, Su IJ, Tsai SF. Genomics Study of Mycobacterium tuberculosis Strains from Different Ethnic Populations in Taiwan. Evol Bioinform Online 2016; 12:213-221. [PMID: 27721649 PMCID: PMC5040422 DOI: 10.4137/ebo.s40152] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2016] [Revised: 07/31/2016] [Accepted: 08/01/2016] [Indexed: 01/18/2023] Open
Abstract
To better understand the transmission and evolution of Mycobacterium tuberculosis (MTB) in Taiwan, six different MTB isolates (representatives of the Beijing ancient sublineage, Beijing modern sublineage, Haarlem, East-African Indian, T1, and Latin-American Mediterranean (LAM)) were characterized and their genomes were sequenced. Discriminating among large sequence polymorphisms (LSPs) that occur once versus those that occur repeatedly in a genomic region may help to elucidate the biological roles of LSPs and to identify the useful phylogenetic relationships. In contrast to our previous LSP-based phylogeny, the sequencing data allowed us to determine actual genetic distances and to define precisely the phylogenetic relationships between the main lineages of the MTB complex. Comparative genomics analyses revealed more nonsynonymous substitutions than synonymous changes in the coding sequences. Furthermore, MTB isolate M7, a LAM-3 clinical strain isolated from a patient of Taiwanese aboriginal origin, is closely related to F11 (LAM), an epidemic tuberculosis strain isolated in the Western Cape of South Africa. The PE/PPE protein family showed a higher dn/ds ratio compared to that for all protein-coding genes. Finally, we found Haarlem-3 and LAM-3 isolates to be circulating in the aboriginal community in Taiwan, suggesting that they may have originated with post-Columbus Europeans. Taken together, our results revealed an interesting association with historical migrations of different ethnic populations, thus providing a good model to explore the global evolution and spread of MTB.
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Affiliation(s)
- Horng-Yunn Dou
- National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Zhunan, Miaoli, Taiwan
| | - Yih-Yuan Chen
- National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Zhunan, Miaoli, Taiwan.; Department of Internal Medicine, Ditmanson Medical Foundation Chia-Yi Christian Hospital, Chiayi City, Taiwan.; Department of Biochemical Science and Technology, National Chiayi University, Chiayi City, Taiwan
| | - Ying-Tsong Chen
- Institute of Genomics and Bioinformatics, National Chung Hsing University, Taichung City, Taiwan
| | - Jia-Ru Chang
- National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Zhunan, Miaoli, Taiwan
| | - Chien-Hsing Lin
- Institute of Molecular and Genomic Medicine, National Health Research Institutes, Zhunan, Miaoli City, Taiwan
| | - Keh-Ming Wu
- Institute of Molecular and Genomic Medicine, National Health Research Institutes, Zhunan, Miaoli City, Taiwan
| | - Ming-Shian Lin
- Department of Internal Medicine, Ditmanson Medical Foundation Chia-Yi Christian Hospital, Chiayi City, Taiwan
| | - Ih-Jen Su
- National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Zhunan, Miaoli, Taiwan
| | - Shih-Feng Tsai
- Institute of Molecular and Genomic Medicine, National Health Research Institutes, Zhunan, Miaoli City, Taiwan
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198
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Tun T, Aye KS, Nyunt WW, Crump JA, Nakajima C, Suzuki Y, Thinn KK, Cook GM, Aung HL. Genotypic diversity of Mycobacterium tuberculosis strains in Myanmar. Infect Dis (Lond) 2016; 49:237-239. [PMID: 27644269 DOI: 10.1080/23744235.2016.1231419] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
Affiliation(s)
- Thanda Tun
- a National Health Laboratory , Ministry of Health and Sports , Yangon , Myanmar
| | - Khin Saw Aye
- b Department of Medical Research , Ministry of Health and Sports , Yangon , Myanmar
| | - Wint Wint Nyunt
- c National Tuberculosis Reference Laboratory , Ministry of Health and Sports , Yangon , Myanmar
| | - John A Crump
- d Centre for International Health, Dunedin School of Medicine, University of Otago , Dunedin , New Zealand
| | - Chie Nakajima
- e Hokkaido University Research Centre for Zoonosis Control , Sapporo , Japan.,f Global Institution for Collaborative Research and Education (GI-CoRE), Hokkaido University , Sapporo , Japan
| | - Yasuhiko Suzuki
- e Hokkaido University Research Centre for Zoonosis Control , Sapporo , Japan.,f Global Institution for Collaborative Research and Education (GI-CoRE), Hokkaido University , Sapporo , Japan
| | - Kyi Kyi Thinn
- g Department of Microbiology , University of Medicine 1 , Yangon , Myanmar
| | - Gregory M Cook
- h Department of Microbiology and Immunology , Otago School of Medical Sciences, University of Otago , Dunedin , New Zealand
| | - Htin Lin Aung
- h Department of Microbiology and Immunology , Otago School of Medical Sciences, University of Otago , Dunedin , New Zealand
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199
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Varma-Basil M, Narang A, Chakravorty S, Garima K, Gupta S, Kumar Sharma N, Giri A, Zozio T, Couvin D, Hanif M, Bhatnagar A, Menon B, Niemann S, Rastogi N, Alland D, Bose M. A snapshot of the predominant single nucleotide polymorphism cluster groups of Mycobacterium tuberculosis clinical isolates in Delhi, India. Tuberculosis (Edinb) 2016; 100:72-81. [DOI: 10.1016/j.tube.2016.07.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2016] [Accepted: 07/10/2016] [Indexed: 11/25/2022]
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200
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Farhat MR, Sultana R, Iartchouk O, Bozeman S, Galagan J, Sisk P, Stolte C, Nebenzahl-Guimaraes H, Jacobson K, Sloutsky A, Kaur D, Posey J, Kreiswirth BN, Kurepina N, Rigouts L, Streicher EM, Victor TC, Warren RM, van Soolingen D, Murray M. Genetic Determinants of Drug Resistance in Mycobacterium tuberculosis and Their Diagnostic Value. Am J Respir Crit Care Med 2016; 194:621-30. [PMID: 26910495 PMCID: PMC5027209 DOI: 10.1164/rccm.201510-2091oc] [Citation(s) in RCA: 101] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2015] [Accepted: 02/22/2016] [Indexed: 11/16/2022] Open
Abstract
RATIONALE The development of molecular diagnostics that detect both the presence of Mycobacterium tuberculosis in clinical samples and drug resistance-conferring mutations promises to revolutionize patient care and interrupt transmission by ensuring early diagnosis. However, these tools require the identification of genetic determinants of resistance to the full range of antituberculosis drugs. OBJECTIVES To determine the optimal molecular approach needed, we sought to create a comprehensive catalog of resistance mutations and assess their sensitivity and specificity in diagnosing drug resistance. METHODS We developed and validated molecular inversion probes for DNA capture and deep sequencing of 28 drug-resistance loci in M. tuberculosis. We used the probes for targeted sequencing of a geographically diverse set of 1,397 clinical M. tuberculosis isolates with known drug resistance phenotypes. We identified a minimal set of mutations to predict resistance to first- and second-line antituberculosis drugs and validated our predictions in an independent dataset. We constructed and piloted a web-based database that provides public access to the sequence data and prediction tool. MEASUREMENTS AND MAIN RESULTS The predicted resistance to rifampicin and isoniazid exceeded 90% sensitivity and specificity but was lower for other drugs. The number of mutations needed to diagnose resistance is large, and for the 13 drugs studied it was 238 across 18 genetic loci. CONCLUSIONS These data suggest that a comprehensive M. tuberculosis drug resistance diagnostic will need to allow for a high dimension of mutation detection. They also support the hypothesis that currently unknown genetic determinants, potentially discoverable by whole-genome sequencing, encode resistance to second-line tuberculosis drugs.
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MESH Headings
- Antitubercular Agents/pharmacology
- Drug Resistance, Multiple, Bacterial/drug effects
- Drug Resistance, Multiple, Bacterial/genetics
- Genes, Bacterial/drug effects
- Genes, Bacterial/genetics
- Humans
- Molecular Diagnostic Techniques
- Mutation/drug effects
- Mutation/genetics
- Mycobacterium tuberculosis/drug effects
- Mycobacterium tuberculosis/genetics
- Mycobacterium tuberculosis/isolation & purification
- Sequence Analysis, DNA
- Tuberculosis, Multidrug-Resistant/drug therapy
- Tuberculosis, Multidrug-Resistant/genetics
- Tuberculosis, Multidrug-Resistant/microbiology
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Affiliation(s)
- Maha R. Farhat
- Division of Pulmonary and Critical Care Medicine, Massachusetts General Hospital, Boston, Massachusetts
- Department of Global Health and Social Medicine, Harvard Medical School, Boston, Massachusetts
| | - Razvan Sultana
- Genomics England, Queen Mary University, London, United Kingdom
| | - Oleg Iartchouk
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts
| | | | - James Galagan
- Department of Biomedical Engineering
- Department of Microbiology, and
- Bioinformatics Program, Boston University, Boston, Massachusetts
| | | | | | - Hanna Nebenzahl-Guimaraes
- National Institute for Public Health and the Environment, Bilthoven, the Netherlands
- Department of Pulmonary Diseases and
- Department of Medical Microbiology, Radboud University Nijmegen Medical Center, Nijmegen, the Netherlands
- Life and Health Sciences Research Institute, School of Health Sciences, University of Minho, Braga, Portugal
- Life and Health Sciences Research Institute/3Bs, PT Government Associate Laboratory, Braga/Guimaraes, Portugal
| | - Karen Jacobson
- Section of Infectious Diseases, Boston University School of Medicine, Boston, Massachusetts
- DST/NRF Center of Excellence for Biomedical TB Research/SAMRC Center for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, South Africa
| | - Alexander Sloutsky
- Department of Global Health and Social Medicine, Harvard Medical School, Boston, Massachusetts
- University of Massachusetts Medical School, Worcester, Massachusetts
| | - Devinder Kaur
- University of Massachusetts Medical School, Worcester, Massachusetts
| | - James Posey
- Division of Tuberculosis Elimination, National Center for HIV/AIDS, Viral Hepatitis, STD, and TB Prevention, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Barry N. Kreiswirth
- Public Health Research Institute Tuberculosis Center, Rutgers University, Newark, New Jersey
| | - Natalia Kurepina
- Public Health Research Institute Tuberculosis Center, Rutgers University, Newark, New Jersey
| | - Leen Rigouts
- Mycobacteriology, Institute of Tropical Medicine, Antwerp, Belgium
- Biomedical Sciences, Antwerp University, Antwerp, Belgium; and
| | - Elizabeth M. Streicher
- DST/NRF Center of Excellence for Biomedical TB Research/SAMRC Center for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, South Africa
| | - Tommie C. Victor
- DST/NRF Center of Excellence for Biomedical TB Research/SAMRC Center for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, South Africa
| | - Robin M. Warren
- DST/NRF Center of Excellence for Biomedical TB Research/SAMRC Center for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, South Africa
| | - Dick van Soolingen
- Department of Pulmonary Diseases and
- Department of Medical Microbiology, Radboud University Nijmegen Medical Center, Nijmegen, the Netherlands
- Life and Health Sciences Research Institute, School of Health Sciences, University of Minho, Braga, Portugal
| | - Megan Murray
- Department of Global Health and Social Medicine, Harvard Medical School, Boston, Massachusetts
- Department of Epidemiology, Harvard School of Public Health, Boston, Massachusetts
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