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Valencia J, Rubio V, Puerto G, Vasquez L, Bernal A, Mora JR, Cuesta SA, Paz JL, Insuasty B, Abonia R, Quiroga J, Insuasty A, Coneo A, Vidal O, Márquez E, Insuasty D. QSAR Studies, Molecular Docking, Molecular Dynamics, Synthesis, and Biological Evaluation of Novel Quinolinone-Based Thiosemicarbazones against Mycobacterium tuberculosis. Antibiotics (Basel) 2022; 12:antibiotics12010061. [PMID: 36671262 PMCID: PMC9854539 DOI: 10.3390/antibiotics12010061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Revised: 12/21/2022] [Accepted: 12/22/2022] [Indexed: 12/31/2022] Open
Abstract
In this study, a series of novel quinolinone-based thiosemicarbazones were designed in silico and their activities tested in vitro against Mycobacterium tuberculosis (M. tuberculosis). Quantitative structure-activity relationship (QSAR) studies were performed using quinolinone and thiosemicarbazide as pharmacophoric nuclei; the best model showed statistical parameters of R2 = 0.83; F = 47.96; s = 0.31, and was validated by several different methods. The van der Waals volume, electron density, and electronegativity model results suggested a pivotal role in antituberculosis (anti-TB) activity. Subsequently, from this model a new series of quinolinone-thiosemicarbazone 11a-e was designed and docked against two tuberculosis protein targets: enoyl-acyl carrier protein reductase (InhA) and decaprenylphosphoryl-β-D-ribose-2'-oxidase (DprE1). Molecular dynamics simulation over 200 ns showed a binding energy of -71.3 to -12.7 Kcal/mol, suggesting likely inhibition. In vitro antimycobacterial activity of quinolinone-thiosemicarbazone for 11a-e was evaluated against M. bovis, M. tuberculosis H37Rv, and six different strains of drug-resistant M. tuberculosis. All compounds exhibited good to excellent activity against all the families of M. tuberculosis. Several of the here synthesized compounds were more effective than the standard drugs (isoniazid, oxafloxacin), 11d and 11e being the most active products. The results suggest that these compounds may contribute as lead compounds in the research of new potential antimycobacterial agents.
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Affiliation(s)
- Jhesua Valencia
- Grupo de Investigación en Química y Biología, Universidad del Norte, Km 5 vía Puerto Colombia, Barranquilla 081007, Colombia
| | - Vivian Rubio
- Grupo de Micobacterias, Red TB Colombia, Dirección de Investigación en Salud Pública, Instituto Nacional de Salud, Bogotá 111321, Colombia
| | - Gloria Puerto
- Grupo de Micobacterias, Red TB Colombia, Dirección de Investigación en Salud Pública, Instituto Nacional de Salud, Bogotá 111321, Colombia
| | - Luisa Vasquez
- Grupo de Micobacterias, Red TB Colombia, Dirección de Investigación en Salud Pública, Instituto Nacional de Salud, Bogotá 111321, Colombia
| | - Anthony Bernal
- Grupo de Investigación en Química y Biología, Universidad del Norte, Km 5 vía Puerto Colombia, Barranquilla 081007, Colombia
| | - José R. Mora
- Grupo de Química Computacional y Teórica (QCT-USFQ), Departamento de Ingeniería Química, Universidad San Francisco de Quito, Diego de Robles y Vía Interoceánica, Quito 170157, Ecuador
| | - Sebastian A. Cuesta
- Grupo de Química Computacional y Teórica (QCT-USFQ), Departamento de Ingeniería Química, Universidad San Francisco de Quito, Diego de Robles y Vía Interoceánica, Quito 170157, Ecuador
- Department of Chemistry, Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester M1 7DN, UK
| | - José Luis Paz
- Departamento Académico de Química Inorgánica, Facultad de Química e Ingeniería Química, Universidad Nacional Mayor de San Marcos, Cercado de Lima 15081, Peru
| | - Braulio Insuasty
- Research Group of Heterocyclic Compounds, Department of Chemistry, Universidad del Valle, A. A., Cali 25360, Colombia
| | - Rodrigo Abonia
- Research Group of Heterocyclic Compounds, Department of Chemistry, Universidad del Valle, A. A., Cali 25360, Colombia
| | - Jairo Quiroga
- Research Group of Heterocyclic Compounds, Department of Chemistry, Universidad del Valle, A. A., Cali 25360, Colombia
| | - Alberto Insuasty
- Grupo de Investigación en Materiales Funcionales Nanoestructurados, Universidad CESMAG, Pasto 520003, Colombia
| | - Andres Coneo
- Medicine Department, Division of Health Sciences, Universidad del Norte, Barranquilla 081007, Colombia
| | - Oscar Vidal
- Medicine Department, Division of Health Sciences, Universidad del Norte, Barranquilla 081007, Colombia
| | - Edgar Márquez
- Grupo de Investigación en Química y Biología, Universidad del Norte, Km 5 vía Puerto Colombia, Barranquilla 081007, Colombia
- Correspondence: (E.M.); (D.I.)
| | - Daniel Insuasty
- Grupo de Investigación en Química y Biología, Universidad del Norte, Km 5 vía Puerto Colombia, Barranquilla 081007, Colombia
- Correspondence: (E.M.); (D.I.)
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Castaño LF, Quiroga J, Abonia R, Insuasty D, Vidal OM, Seña R, Rubio V, Puerto G, Nogueras M, Cobo J, Guzman J, Insuasty A, Insuasty B. Synthesis, Anticancer and Antitubercular Properties of New Chalcones and Their Nitrogen-Containing Five-Membered Heterocyclic Hybrids Bearing Sulfonamide Moiety. Int J Mol Sci 2022; 23:ijms232012589. [PMID: 36293443 PMCID: PMC9604400 DOI: 10.3390/ijms232012589] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Revised: 10/10/2022] [Accepted: 10/11/2022] [Indexed: 11/16/2022] Open
Abstract
A new series of sulfonamides, 8a-b, 10, 12, and 14a-b, were synthesized by N-sulfonation reaction with sulfonyl chlorides 6a-b. Five new series of chalcone-sulfonamide hybrids (16-20)a-f were prepared via Claisen–Schmidt condensation of the newly obtained sulfonamides with aromatic aldehydes 15a-f in basic medium. Chalcones substituted with chlorine at position 4 of each series were used as precursors for the generation of their five-membered heterocyclic pyrazoline (22-23)a-d, (24-25)a-b and carbothioamide 27a-f derivatives. The synthesized compounds were evaluated for their anticancer and antituberculosis activities. To determine their anticancer activity, compounds were screened against sixty human cancer cell lines at a single dose (10 μM). Compounds 17a-c were highly active against LOX IMVI (melanoma), with IC50 values of 0.34, 0.73 and 0.54 μM, respectively. Chalcone 18e showed remarkable results against the entire panel of leukemia cell lines with IC50 values between 0.99–2.52 μM. Moreover, compounds 20e and 20f displayed growth inhibition of Mycobacterium tuberculosis H37Rv at concentrations below 10 μM. Although they showed low selectivity in cytotoxicity tests against the Vero cell line, further optimization could advance the potential biological activity of the selected compounds.
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Affiliation(s)
- Lina Fernanda Castaño
- Heterocyclic Compounds Research Group, Department of Chemistry, Universidad del Valle, A.A., Cali 25360, Colombia
| | - Jairo Quiroga
- Heterocyclic Compounds Research Group, Department of Chemistry, Universidad del Valle, A.A., Cali 25360, Colombia
- Centre for Bioinformatics and Photonics-CIBioFI, Universidad del Valle, A.A., Cali 25360, Colombia
| | - Rodrigo Abonia
- Heterocyclic Compounds Research Group, Department of Chemistry, Universidad del Valle, A.A., Cali 25360, Colombia
- Centre for Bioinformatics and Photonics-CIBioFI, Universidad del Valle, A.A., Cali 25360, Colombia
| | - Daniel Insuasty
- Department of Chemistry and Biology, Basic Sciences Division, Universidad del Norte, Barranquilla 081007, Colombia
| | - Oscar M. Vidal
- Department of Medicine, Health Division, Universidad del Norte, Barranquilla 081007, Colombia
| | - Rosalia Seña
- Department of Chemistry and Biology, Basic Sciences Division, Universidad del Norte, Barranquilla 081007, Colombia
- Department of Medicine, Health Division, Universidad del Norte, Barranquilla 081007, Colombia
| | - Vivian Rubio
- Grupo de Micobacterias, Red TB. Dirección de Investigación en Salud Pública, Instituto Nacional de Salud, Bogotá 111321, Colombia
| | - Gloria Puerto
- Grupo de Micobacterias, Red TB. Dirección de Investigación en Salud Pública, Instituto Nacional de Salud, Bogotá 111321, Colombia
| | - Manuel Nogueras
- Department of Inorganic and Organic Chemistry, Universidad de Jaén, 23071 Jaén, Spain
| | - Justo Cobo
- Department of Inorganic and Organic Chemistry, Universidad de Jaén, 23071 Jaén, Spain
| | - Juan Guzman
- Department of Bioresources, Fraunhofer Institute for Molecular Biology and Applied Ecology, 35392 Giessen, Germany
| | - Alberto Insuasty
- Nanostructured Functional Materials Research Group, Universidad CESMAG, Pasto 520003, Colombia
- Correspondence: (A.I.); (B.I.)
| | - Braulio Insuasty
- Heterocyclic Compounds Research Group, Department of Chemistry, Universidad del Valle, A.A., Cali 25360, Colombia
- Centre for Bioinformatics and Photonics-CIBioFI, Universidad del Valle, A.A., Cali 25360, Colombia
- Correspondence: (A.I.); (B.I.)
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BCGΔBCG1419c increased memory CD8 + T cell-associated immunogenicity and mitigated pulmonary inflammation compared with BCG in a model of chronic tuberculosis. Sci Rep 2022; 12:15824. [PMID: 36138053 PMCID: PMC9499934 DOI: 10.1038/s41598-022-20017-w] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Accepted: 09/07/2022] [Indexed: 12/18/2022] Open
Abstract
Previously, we reported that a hygromycin resistant version of the BCGΔBCG1419c vaccine candidate reduced tuberculosis (TB) disease in BALB/c, C57BL/6, and B6D2F1 mice infected with Mycobacterium tuberculosis (Mtb) H37Rv. Here, the second-generation version of BCGΔBCG1419c (based on BCG Pasteur ATCC 35734, without antibiotic resistance markers, and a complete deletion of BCG1419c) was compared to its parental BCG for immunogenicity and protective efficacy against the Mtb clinical isolate M2 in C57BL/6 mice. Both BCG and BCGΔBCG1419c induced production of IFN-γ, TNF-α, and/or IL-2 by effector memory (CD44+CD62L-), PPD-specific, CD4+ T cells, and only BCGΔBCG1419c increased effector memory, PPD-specific CD8+ T cell responses in the lungs and spleens compared with unvaccinated mice before challenge. BCGΔBCG1419c increased levels of central memory (CD62L+CD44+) T CD4+ and CD8+ cells compared to those of BCG-vaccinated mice. Both BCG strains elicited Th1-biased antigen-specific polyfunctional effector memory CD4+/CD8+ T cell responses at 10 weeks post-infection, and both vaccines controlled Mtb M2 growth in the lung and spleen. Only BCGΔBCG1419c significantly ameliorated pulmonary inflammation and decreased neutrophil infiltration into the lung compared to BCG-vaccinated and unvaccinated mice. Both BCG strains reduced pulmonary TNF-α, IFN-γ, and IL-10 levels. Taken together, BCGΔBCG1419c increased memory CD8+T cell-associated immunogenicity and mitigated pulmonary inflammation compared with BCG.
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Tafess K, Beyen TK, Girma S, Girma A, Siu G. Spatial clustering and genetic diversity of Mycobacterium tuberculosis isolate among pulmonary tuberculosis suspected patients, Arsi Zone, Ethiopia. BMC Pulm Med 2021; 21:206. [PMID: 34193091 PMCID: PMC8244181 DOI: 10.1186/s12890-021-01567-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2020] [Accepted: 06/10/2021] [Indexed: 11/20/2022] Open
Abstract
BACKGROUND Tuberculosis remains a serious public health concern globally. The enormous social, economic, and health impacts of the diseases are attributed to the lack of updated data on the prevalence, geospatial distribution, population structures, and genotypic variants of the circulating M. tuberculosis. METHODS Structured questionnaire, mycobacterial culture, and standard 24-Mycobacterial Interspersed Repeated Units-Variable Number Tandem Repeats (MIRU-VNTR) were employed to collect sociodemographic characters, residence linked information, and genotype the isolates. The retrospective discrete Bernoulli model was used to identify the hot spot districts of sputum smear positivity, and Web-based Miru-VNTRPlus were used for the identification of lineages and sublineages. RESULTS Out of 832 presumptive pulmonary tuberculosis (PTB) suspects, 119 (14.3%) were smear-positive. In the multivariate binary logistic model, PTB suspected patients in the age groups of 7-25 and 25-34 and those from rural residents were 4.53 (AOR = 4.53; 95% CI 2.25-9.13), 3.00 (AOR = 3.00; 95% CI 1.41-6.35) and 1.65 (AOR = 1.65; 95% CI 1.01-2.70) times at higher risk of turning smear-positive. Eleven (47.8%) districts of Arsi Zone were shown to have a high rate of clustering (RR = 2.27; 95% CI 1.62-3.2) of smear-positive PTB. Of 72 isolates queried for the lineage assignment, 59 (81.9%) were classified into the previously known lineages and 13 (18.1%) were not assigned to any known lineages. Overall, 42 (58.3%) belong to M. tuberculosis lineage 4 (Euro-American), 16 (22.2%) M. tuberculosis lineage 3 (Delhi/CAS), and 1 (1.4%) M. tuberculosis Lineage 1 (Indo-Oceanic/ East Africa Indian). Further classification to the sublineage indicates that the predominant lineage was Delhi/CAS comprising 16 (22.2%) isolates followed by 15 (20.8%) isolates belonging to Haarlem. The remaining isolates were distributed as 13 (18.1%) TUR, 6 (8.3%) LAM, 4 (5.5%) URAL, 4 (4.5%) NEW-1 and 1 (1.4%) EAI. CONCLUSION Our study showed higher smear-positive results among PTB suspected patients and remarkable spatial variation across districts of Arsi Zone in smear-positive PTB. This information together with the genotypic features could be used as input for the efforts of designing control strategies.
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Affiliation(s)
- Ketema Tafess
- Institute of Pharmaceutical Science, School of Applied Natural Science, Adama Science and Technology University, Adama, Ethiopia
| | - Teresa Kisi Beyen
- Department of Public Health, College of Health Sciences, Arsi University, Asella, Ethiopia
| | - Sisay Girma
- Department of Clinical Study, College of Veterinary Medicine and Agriculture, Addis Ababa University, P. O. Box 34, Bishoftu, Ethiopia
| | - Asnakech Girma
- Disease Prevention, Training and Research Division, Federal Prison General Hospital, Addis Ababa, Ethiopia
| | - Gilman Siu
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hung Hom, Hong Kong
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Gomes B, Molina-Correa G, Neves-Reina L, Oliveira AC, Macedo R, Carvalho C, Correia AM. Poly-resistant tuberculosis outbreak in Northern Portugal: a nine year tale. Pulmonology 2020; 26:412-414. [PMID: 32238328 DOI: 10.1016/j.pulmoe.2020.02.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Revised: 02/06/2020] [Accepted: 02/10/2020] [Indexed: 10/24/2022] Open
Affiliation(s)
- B Gomes
- Entre Douro e Vouga I Public Health Unit, Northern Regional Health Administration, Santa Maria da Feira, Portugal; Department of Public Health, Northern Regional Health Administration, Porto, Portugal; Instituto de Saúde Pública da Universidade do Porto, EPIUnit, Porto, Portugal.
| | - G Molina-Correa
- Entre Douro e Vouga I Public Health Unit, Northern Regional Health Administration, Santa Maria da Feira, Portugal
| | - L Neves-Reina
- Entre Douro e Vouga I Public Health Unit, Northern Regional Health Administration, Santa Maria da Feira, Portugal
| | - A C Oliveira
- Entre Douro e Vouga I Public Health Unit, Northern Regional Health Administration, Santa Maria da Feira, Portugal
| | - R Macedo
- Head of the National Reference Laboratory for Mycobacteria, National Institute of Health Dr. Ricardo Jorge, Lisbon, Portugal
| | - C Carvalho
- Department of Public Health, Northern Regional Health Administration, Porto, Portugal; Multidisciplinary Unit for Biomedical Research (UMIB), Institute of Biomedical Sciences Abel Salazar, University of Porto, Porto, Portugal
| | - A M Correia
- Department of Public Health, Northern Regional Health Administration, Porto, Portugal
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Phylogenetic Analysis of Mycobacterium tuberculosis Strains in Wales by Use of Core Genome Multilocus Sequence Typing To Analyze Whole-Genome Sequencing Data. J Clin Microbiol 2019; 57:JCM.02025-18. [PMID: 30944195 DOI: 10.1128/jcm.02025-18] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Accepted: 03/27/2019] [Indexed: 01/08/2023] Open
Abstract
An inability to standardize the bioinformatic data produced by whole-genome sequencing (WGS) has been a barrier to its widespread use in tuberculosis phylogenetics. The aim of this study was to carry out a phylogenetic analysis of tuberculosis in Wales, United Kingdom, using Ridom SeqSphere software for core genome multilocus sequence typing (cgMLST) analysis of whole-genome sequencing data. The phylogenetics of tuberculosis in Wales have not previously been studied. Sixty-six Mycobacterium tuberculosis isolates (including 42 outbreak-associated isolates) from south Wales were sequenced using an Illumina platform. Isolates were assigned to principal genetic groups, single nucleotide polymorphism (SNP) cluster groups, lineages, and sublineages using SNP-calling protocols. WGS data were submitted to the Ridom SeqSphere software for cgMLST analysis and analyzed alongside 179 previously lineage-defined isolates. The data set was dominated by the Euro-American lineage, with the sublineage composition being dominated by T, X, and Haarlem family strains. The cgMLST analysis successfully assigned 58 isolates to major lineages, and the results were consistent with those obtained by traditional SNP mapping methods. In addition, the cgMLST scheme was used to resolve an outbreak of tuberculosis occurring in the region. This study supports the use of a cgMLST method for standardized phylogenetic assignment of tuberculosis isolates and for outbreak resolution and provides the first insight into Welsh tuberculosis phylogenetics, identifying the presence of the Haarlem sublineage commonly associated with virulent traits.
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Tarashi S, Fateh A, Jamnani FR, Siadat SD, Vaziri F. Prevalence of Beijing and Haarlem genotypes among multidrug-resistant Mycobacterium tuberculosis in Iran: Systematic review and meta-analysis. Tuberculosis (Edinb) 2017; 107:31-37. [PMID: 29050769 DOI: 10.1016/j.tube.2017.03.005] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2016] [Revised: 02/03/2017] [Accepted: 03/23/2017] [Indexed: 10/19/2022]
Abstract
Antimicrobial drug resistance creates major problems in the control of tuberculosis (TB). Beijing and Haarlem genotypes of Mycobacterium tuberculosis are the prevalent genotypes responsible for multidrug resistant (MDR) TB worldwide. The aim of this study was to conduct a systematic review using meta-analysis to indicate the prevalence of Beijing and Haarlem genotypes among MDR-TB cases in Iran. Data sources of current study were 311 original articles (2006-2016) that were searched in several databases including Medline, Scopus, Embase, Cochrane library, and Iranian databases. Sixteen articles were selected for the prevalence of Beijing and Haarlem families among MDR-TB strains. Data were evaluated using meta-analysis and random effects models with the Meta-Analysis Software package Version 2.2 (Biostat, Englewood, NJ). Final investigation indicated 856 MDR samples in the 16 articles. Overall, the prevalence of Beijing and Haarlem genotypes among MDR-TB isolates in Iran was estimated to be 19.3% (95% CI, 13.1-27.5) and 18.7% (95% CI, 11.9-28.3) respectively. The studies conducted in northern Iran showing a significant association between Haarlem genotype and MDR is of particular concern. Certain refugee migration flows make this genotype of particular epidemiological and clinical concern because of its potential ability to endanger TB control programs in Iran.
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Affiliation(s)
- Samira Tarashi
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran
| | - Abolfazl Fateh
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran; Microbiology Research Center (MRC), Pasteur Institute of Iran, Tehran, Iran
| | - Fatemeh Rahimi Jamnani
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran; Microbiology Research Center (MRC), Pasteur Institute of Iran, Tehran, Iran
| | - Seyed Davar Siadat
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran; Microbiology Research Center (MRC), Pasteur Institute of Iran, Tehran, Iran
| | - Farzam Vaziri
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran; Microbiology Research Center (MRC), Pasteur Institute of Iran, Tehran, Iran.
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Ramazanzadeh R, Roshani D, Shakib P, Rouhi S. Prevalence and occurrence rate of Mycobacterium tuberculosis Haarlem family multi-drug resistant in the worldwide population: A systematic review and meta-analysis. JOURNAL OF RESEARCH IN MEDICAL SCIENCES : THE OFFICIAL JOURNAL OF ISFAHAN UNIVERSITY OF MEDICAL SCIENCES 2015; 20:78-88. [PMID: 25767526 PMCID: PMC4354070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/16/2014] [Revised: 03/03/2014] [Accepted: 10/14/2014] [Indexed: 11/05/2022]
Abstract
BACKGROUND Transmission of Mycobacterium tuberculosis (M. tuberculosis) can occur in different ways. Furthermore, drug resistant in M. tuberculosis family is a major problem that creates obstacles in treatment and control of tuberculosis (TB) in the world. One of the most prevalent families of M. tuberculosis is Haarlem, and it is associated with drug resistant. Our objectives of this study were to determine the prevalence and occurrence rate of M. tuberculosis Haarlem family multi-drug resistant (MDR) in the worldwide using meta-analysis based on a systematic review that performed on published articles. MATERIALS AND METHODS Data sources of this study were 78 original articles (2002-2012) that were published in the literatures in several databases including PubMed, Science Direct, Google Scholar, Biological abstracts, ISI web of knowledge and IranMedex. The articles were systematically reviewed for prevalence and rate of MDR. Data were analyzed using meta-analysis and random effects models with the software package Meta R, Version 2.13 (P < 0.10). RESULTS Final analysis included 28601 persons in 78 articles. The highest and lowest occurrence rate of Haarlem family in M. tuberculosis was in Hungary in 2006 (66.20%) with negative MDR-TB and in China in 2010 (0.8%), respectively. From 2002 to 2012, the lowest rate of prevalence was in 2010, and the highest prevalence rate was in 2012. Also 1.076% were positive for MDR and 9.22% were negative (confidence interval: 95%).0020. CONCLUSION Many articles and studies are performed in this field globally, and we only chose some of them. Further studies are needed to be done in this field. Our study showed that M. tuberculosis Haarlem family is prevalent in European countries. According to the presence of MDR that was seen in our results, effective control programs are needed to control the spread of drug-resistant strains, especially Haarlem family.
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Affiliation(s)
- Rashid Ramazanzadeh
- Department of Microbiology, Cellular and Molecular Research Center, Faculty of Medicine, Kurdistan University of Medical Sciences, Sanandaj, Iran
| | - Daem Roshani
- Department of Epidemiology and Biostatistics, Medical School, Kurdistan University of Medical Sciences, Sanandaj, Iran,Kurdistan Research Center for Social Determinants of Health, Medical School, Kurdistan University of Medical Sciences, Sanandaj, Iran
| | - Pegah Shakib
- Department of Microbiology, Cellular and Molecular Research Center, Student Research Committee, Kurdistan University of Medical Sciences, Sanandaj, Iran
| | - Samaneh Rouhi
- Department of Microbiology, Cellular and Molecular Research Center, Student Research Committee, Kurdistan University of Medical Sciences, Sanandaj, Iran,Address for correspondence: Dr. Samaneh Rouhi, Department of Microbiology, Cellular and Molecular Research Center, Member of Student Research Committee, Kurdistan University of Medical Sciences, Sanandaj, Iran. E-mail:
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Doughty EL, Sergeant MJ, Adetifa I, Antonio M, Pallen MJ. Culture-independent detection and characterisation of Mycobacterium tuberculosis and M. africanum in sputum samples using shotgun metagenomics on a benchtop sequencer. PeerJ 2014; 2:e585. [PMID: 25279265 PMCID: PMC4179564 DOI: 10.7717/peerj.585] [Citation(s) in RCA: 92] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2014] [Accepted: 08/28/2014] [Indexed: 01/27/2023] Open
Abstract
Tuberculosis remains a major global health problem. Laboratory diagnostic methods that allow effective, early detection of cases are central to management of tuberculosis in the individual patient and in the community. Since the 1880s, laboratory diagnosis of tuberculosis has relied primarily on microscopy and culture. However, microscopy fails to provide species- or lineage-level identification and culture-based workflows for diagnosis of tuberculosis remain complex, expensive, slow, technically demanding and poorly able to handle mixed infections. We therefore explored the potential of shotgun metagenomics, sequencing of DNA from samples without culture or target-specific amplification or capture, to detect and characterise strains from the Mycobacterium tuberculosis complex in smear-positive sputum samples obtained from The Gambia in West Africa. Eight smear- and culture-positive sputum samples were investigated using a differential-lysis protocol followed by a kit-based DNA extraction method, with sequencing performed on a benchtop sequencing instrument, the Illumina MiSeq. The number of sequence reads in each sputum-derived metagenome ranged from 989,442 to 2,818,238. The proportion of reads in each metagenome mapping against the human genome ranged from 20% to 99%. We were able to detect sequences from the M. tuberculosis complex in all eight samples, with coverage of the H37Rv reference genome ranging from 0.002X to 0.7X. By analysing the distribution of large sequence polymorphisms (deletions and the locations of the insertion element IS6110) and single nucleotide polymorphisms (SNPs), we were able to assign seven of eight metagenome-derived genomes to a species and lineage within the M. tuberculosis complex. Two metagenome-derived mycobacterial genomes were assigned to M. africanum, a species largely confined to West Africa; the others that could be assigned belonged to lineages T, H or LAM within the clade of "modern" M. tuberculosis strains. We have provided proof of principle that shotgun metagenomics can be used to detect and characterise M. tuberculosis sequences from sputum samples without culture or target-specific amplification or capture, using an accessible benchtop-sequencing platform, the Illumina MiSeq, and relatively simple DNA extraction, sequencing and bioinformatics protocols. In our hands, sputum metagenomics does not yet deliver sufficient depth of coverage to allow sequence-based sensitivity testing; it remains to be determined whether improvements in DNA extraction protocols alone can deliver this or whether culture, capture or amplification steps will be required. Nonetheless, we can foresee a tipping point when a unified automated metagenomics-based workflow might start to compete with the plethora of methods currently in use in the diagnostic microbiology laboratory.
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Affiliation(s)
- Emma L. Doughty
- Microbiology and Infection Unit, Warwick Medical School, University of Warwick, Coventry, United Kingdom
| | - Martin J. Sergeant
- Microbiology and Infection Unit, Warwick Medical School, University of Warwick, Coventry, United Kingdom
| | | | - Martin Antonio
- Microbiology and Infection Unit, Warwick Medical School, University of Warwick, Coventry, United Kingdom
- Medical Research Council Unit, Fajara, The Gambia
| | - Mark J. Pallen
- Microbiology and Infection Unit, Warwick Medical School, University of Warwick, Coventry, United Kingdom
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Cabal A, Strunk M, Domínguez J, Lezcano MA, Vitoria MA, Ferrero M, Martín C, Iglesias MJ, Samper S. Single nucleotide polymorphism (SNP) analysis used for the phylogeny of the Mycobacterium tuberculosis complex based on a pyrosequencing assay. BMC Microbiol 2014; 14:21. [PMID: 24491224 PMCID: PMC3922597 DOI: 10.1186/1471-2180-14-21] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2013] [Accepted: 01/27/2014] [Indexed: 12/14/2022] Open
Abstract
Background Different polymorphisms have been described as markers to classify the lineages of the Mycobacterium tuberculosis complex. The analysis of nine single nucleotide polymorphisms (SNPs) was used to describe seven SNPs cluster groups (SCGs). We attempted to classify those strains that could not been categorized into lineages by the genotyping methods used in the routine testing. Results The M. tuberculosis complex isolates collected in 2010 in our region were analysed. A new method based on multiplex-PCRs and pyrosequencing to analyse these SNPs was designed. For the pyrosequencing assay nine SNPs that defined the seven SCGs were selected from the literature: 1977, 74092, 105139, 232574, 311613, 913274, 2460626, 3352929 and gyrA95. In addition, SNPs in katG463, mgtC182, Ag85C103 and RDRio deletion were detected. Conclusions This work has permitted to achieve a better classification of Aragonian strains into SCGs and in some cases, to assign strains to its certain lineage. Besides, the description of a new pattern shared by two isolates “SCG-6c” reinforces the interest of SNPs to follow the evolution of M. tuberculosis complex.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Sofía Samper
- IIS Aragón, Hopsital Universitario Miguel Servet, Zaragoza, Spain.
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11
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Cui T, He Z. C-di-GMP signaling and implications for pathogenesis of Mycobacterium tuberculosis. CHINESE SCIENCE BULLETIN-CHINESE 2012. [DOI: 10.1007/s11434-012-5298-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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12
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Reyes A, Sandoval A, Cubillos-Ruiz A, Varley KE, Hernández-Neuta I, Samper S, Martín C, García MJ, Ritacco V, López L, Robledo J, Zambrano MM, Mitra RD, Del Portillo P. IS-seq: a novel high throughput survey of in vivo IS6110 transposition in multiple Mycobacterium tuberculosis genomes. BMC Genomics 2012; 13:249. [PMID: 22703188 PMCID: PMC3443423 DOI: 10.1186/1471-2164-13-249] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2011] [Accepted: 05/30/2012] [Indexed: 11/10/2022] Open
Abstract
Background The insertion element IS6110 is one of the main sources of genomic variability in Mycobacterium tuberculosis, the etiological agent of human tuberculosis. Although IS 6110 has been used extensively as an epidemiological marker, the identification of the precise chromosomal insertion sites has been limited by technical challenges. Here, we present IS-seq, a novel method that combines high-throughput sequencing using Illumina technology with efficient combinatorial sample multiplexing to simultaneously probe 519 clinical isolates, identifying almost all the flanking regions of the element in a single experiment. Results We identified a total of 6,976 IS6110 flanking regions on the different isolates. When validated using reference strains, the method had 100% specificity and 98% positive predictive value. The insertions mapped to both coding and non-coding regions, and in some cases interrupted genes thought to be essential for virulence or in vitro growth. Strains were classified into families using insertion sites, and high agreement with previous studies was observed. Conclusions This high-throughput IS-seq method, which can also be used to map insertions in other organisms, extends previous surveys of in vivo interrupted loci and provides a baseline for probing the consequences of disruptions in M. tuberculosis strains.
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Affiliation(s)
- Alejandro Reyes
- Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St, Louis, MO 63108, USA
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