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Sundararajan S, Muniyan R. Latent tuberculosis: interaction of virulence factors in Mycobacterium tuberculosis. Mol Biol Rep 2021; 48:6181-6196. [PMID: 34351540 DOI: 10.1007/s11033-021-06611-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Accepted: 07/29/2021] [Indexed: 11/28/2022]
Abstract
Tuberculosis (TB) remains a prominent health concern worldwide. Besides extensive research and vaccinations available, attempts to control the pandemic are cumbersome due to the complex physiology of Mycobacterium tuberculosis (Mtb). Alongside the emergence of drug-resistant TB, latent TB has worsened the condition. The tubercle bacilli are unusually behaved and successful with its strategies to modulate genes to evade host immune system and persist within macrophages. Under latent/unfavorable conditions, Mtb conceals itself from immune system and modulates its genes. Among many intracellular modulated genes, important are those involved in cell entry, fatty acid degradation, mycolic acid synthesis, phagosome acidification inhibition, inhibition of phagosome-lysosome complex and chaperon protein modulation. Though the study on these genes date back to early times of TB, an insight on their inter-relation within and to newly evolved genes are still required. This review focuses on the findings and discussions on these genes, possible mechanism, credibility as target for novel drugs and repurposed drugs and their interaction that enables Mtb in survival, pathogenesis, resistance and latency.
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Affiliation(s)
- Sadhana Sundararajan
- School of Biosciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu, 632014, India
| | - Rajiniraja Muniyan
- School of Biosciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu, 632014, India.
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2
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Yassine E, Galiwango R, Ssengooba W, Ashaba F, Joloba ML, Zalwango S, Whalen CC, Quinn F. Assessing a transmission network of Mycobacterium tuberculosis in an African city using single nucleotide polymorphism threshold analysis. Microbiologyopen 2021; 10:e1211. [PMID: 34180596 PMCID: PMC8209283 DOI: 10.1002/mbo3.1211] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Revised: 05/18/2021] [Accepted: 05/26/2021] [Indexed: 11/08/2022] Open
Abstract
Tuberculosis (TB) is the leading cause of death in humans by a single infectious agent worldwide with approximately two billion humans latently infected with the bacterium Mycobacterium tuberculosis. Currently, the accepted method for controlling the disease is Tuberculosis Directly Observed Treatment Shortcourse (TB-DOTS). This program is not preventative and individuals may transmit disease before diagnosis, thus better understanding of disease transmission is essential. Using whole-genome sequencing and single nucleotide polymorphism analysis, we analyzed genomes of 145 M. tuberculosis clinical isolates from active TB cases from the Rubaga Division of Kampala, Uganda. We established that these isolates grouped into M. tuberculosis complex (MTBC) lineages 1, 2, 3, and 4, with the most isolates grouping into lineage 4. Possible transmission pairs containing ≤12 SNPs were identified in lineages 1, 3, and 4 with the prevailing transmission in lineages 3 and 4. Furthermore, investigating DNA codon changes as a result of specific SNPs in prominent virulence genes including plcA and plcB could indicate potentially important modifications in protein function. Incorporating this analysis with corresponding epidemiological data may provide a blueprint for the integration of public health interventions to decrease TB transmission in a region.
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Affiliation(s)
- Edriss Yassine
- Department of Infectious DiseasesCollege of Veterinary MedicineUniversity of GeorgiaAthensGAUSA
| | - Ronald Galiwango
- Department of Epidemiology and BiostatisticsCollege of Public HealthUniversity of GeorgiaAthensGAUSA
| | - Willy Ssengooba
- Makerere University Lung InstituteCollege of Health SciencesMakerere UniversityKampalaUganda
- Mycobacteriology (BSL‐3) LaboratoryDepartment of Medical MicrobiologyMakerere UniversityKampalaUganda
| | - Fred Ashaba
- Uganda‐CWRU Research CollaborationMakerere University and Mulago HospitalKampalaUganda
| | - Moses L. Joloba
- Uganda‐CWRU Research CollaborationMakerere University and Mulago HospitalKampalaUganda
| | - Sarah Zalwango
- Uganda‐CWRU Research CollaborationMakerere University and Mulago HospitalKampalaUganda
| | - Christopher C. Whalen
- Department of Epidemiology and BiostatisticsCollege of Public HealthUniversity of GeorgiaAthensGAUSA
| | - Frederick Quinn
- Department of Infectious DiseasesCollege of Veterinary MedicineUniversity of GeorgiaAthensGAUSA
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Comin J, Chaure A, Cebollada A, Ibarz D, Viñuelas J, Vitoria MA, Iglesias MJ, Samper S. Investigation of a rapidly spreading tuberculosis outbreak using whole-genome sequencing. INFECTION GENETICS AND EVOLUTION 2020; 81:104184. [PMID: 31931260 DOI: 10.1016/j.meegid.2020.104184] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Revised: 12/17/2019] [Accepted: 01/06/2020] [Indexed: 12/01/2022]
Abstract
This paper describes the application of whole-genome sequencing (WGS) to investigate an outbreak of Mycobacterium tuberculosis occurring in Aragon, Spain, where strains have been submitted to genotyping since 2004. The responsible outbreak strain appeared in our region first in 2014 and it spread to 14 patients in the following three years. WGS found low variability between the isolates with none of the SNPs differences detected more than once, all of which were attributed to a recent transmission. Although two ambiguous bases linked two cases with those who presented the SNP in the same position, the establishment of a definitive transmission route was not possible. The epidemiological data supported the existence of a super-spreader, probably responsible for the majority of the cases involved since there was a two-year delay in diagnoses among cases. This fact would also help explaining the low variability found. The index case was not identified, possibly because it was not diagnosed in Aragon. In addition WGS characterised the strain as a Linage 4.3.3/LAM family and corroborated the susceptibility to anti-tuberculosis drugs observed by the clinical laboratories. This work shows the need to have epidemiological data to support the genomic data in order to clarify the evolution of tuberculosis outbreaks.
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Affiliation(s)
- Jessica Comin
- Instituto Aragonés de Ciencias de la Salud, Zaragoza, Spain
| | | | | | | | - Jesús Viñuelas
- Hospital Universitario Miguel Servet, Zaragoza, Spain; Sociedad Española de Enfermedades Infecciosas y Microbiología Clínica, Madrid, Spain
| | - María Asunción Vitoria
- Hospital Clínico Universitario Lozano Blesa, Zaragoza, Spain; Sociedad Española de Enfermedades Infecciosas y Microbiología Clínica, Madrid, Spain
| | - María José Iglesias
- Universidad de Zaragoza, Zaragoza, Spain; CIBER de enfermedades respiratorias, Madrid, Spain; Fundación IIS Aragón, Zaragoza, Spain
| | - Sofía Samper
- Instituto Aragonés de Ciencias de la Salud, Zaragoza, Spain; CIBER de enfermedades respiratorias, Madrid, Spain; Fundación IIS Aragón, Zaragoza, Spain.
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4
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Wang X, Huang K, Zeng X, Liu Z, Liao X, Yang C, Yu T, Han C, Zhu G, Qin W, Peng T. Diagnostic and prognostic value of mRNA expression of phospholipase C β family genes in hepatitis B virus‑associated hepatocellular carcinoma. Oncol Rep 2019; 41:2855-2875. [PMID: 30896816 PMCID: PMC6448089 DOI: 10.3892/or.2019.7066] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2018] [Accepted: 03/05/2019] [Indexed: 02/07/2023] Open
Abstract
Four phospholipase C β (PLCB) isoforms, PLCB1, PLCB2, PLCB3 and PLCB4, have been previously investigated regarding their roles in the metabolism of inositol lipids and cancer. The present study aimed to explore the association between PLCB1-4 and hepatocellular carcinoma (HCC). Data from 212 patients with hepatitis B virus-associated HCC were used to analyze the diagnostic and prognostic significance of PLCB genes in. A nomogram predicted the survival probability. Gene set enrichment analysis explored gene ontology terms and the metabolic pathways associated with PLCB genes. Validation of the prognostic values of PLCB genes was performed using the Gene Expression Profiling Interactive Analysis website. PLCB1 and PLCB2 were revealed to have diagnostic value for HCC (0.869 and 0.836 area under the curve, respectively; both P≤0.05). The combination analysis of these genes had an advantage over each alone (0.905 PLCB1 and PLCB2, and 0.877 PLCB1 and PLCB3 area under the curve; P≤0.05). PLCB1 was associated with overall survival (OS) and recurrence-free survival (RFS; adjusted P=0.002 and P=0.001, respectively). A nomogram predicted survival probability of patients with HCC at 1, 3- and 5-years. Gene set enrichment analysis indicated that PLCB1 and PLCB2 are involved in the cell cycle, cell division and the PPAR signaling pathway, among other functions. Validation using GEPIA revealed that PLCB1 and PLCB2 were associated with OS and PLCB1 and PLCB4 were associated with RFS. PLCB1 and PLCB2 exhibited diagnostic value for HCC and their combination had an advantage over each individually. PLCB1 has OS and RFS prognostic value for patients with HCC.
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Affiliation(s)
- Xiangkun Wang
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region 530021, P.R. China
| | - Ketuan Huang
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region 530021, P.R. China
| | - Xianmin Zeng
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region 530021, P.R. China
| | - Zhengqian Liu
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region 530021, P.R. China
| | - Xiwen Liao
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region 530021, P.R. China
| | - Chengkun Yang
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region 530021, P.R. China
| | - Tingdong Yu
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region 530021, P.R. China
| | - Chuangye Han
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region 530021, P.R. China
| | - Guangzhi Zhu
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region 530021, P.R. China
| | - Wei Qin
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region 530021, P.R. China
| | - Tao Peng
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region 530021, P.R. China
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Beijing clades of Mycobacterium tuberculosis are associated with differential survival in HIV-negative Russian patients. INFECTION GENETICS AND EVOLUTION 2015; 36:517-523. [PMID: 26319998 DOI: 10.1016/j.meegid.2015.08.028] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2015] [Revised: 08/01/2015] [Accepted: 08/23/2015] [Indexed: 11/24/2022]
Abstract
We conducted a prospective study to establish factors associated with survival in tuberculosis patients in Russia including social, clinical and pathogen-related genetic parameters. Specifically we wished to determine whether different strains/clades of the Beijing lineage exerted a differential effect of survival. HIV-negative culture-confirmed cases were recruited during 2008-2010 across Samara Oblast and censored in December 2011. Molecular characterization was performed by a combination of spoligotyping, multilocus VNTR typing and whole genome sequencing (WGS). We analyzed 2602 strains and detected a high prevalence of Beijing family (n=1933; 74%) represented largely by two highly homogenous dominant clades A (n=794) and B (n=402) and non-A/non-B (n=737). Multivariable analysis of 1366 patients with full clinical and genotyping data showed that multi- and extensive drug resistance (HR=1.86; 95%CI: 1.52, 2.28 and HR=2.19; 95%CI: 1.55, 3.11) had the largest impact on survival. In addition older age, extensive lung damage, shortness of breath, treatment in the past and alcohol abuse reduced survival time. After adjustment for clinical and demographic predictors there was evidence that clades A and B combined were associated with poorer survival than other Beijing strains (HR=0.48; 95%CI 0.34, 0.67). All other pathogen-related factors (polymorphisms in genes plcA, plcB, plcC, lipR, dosT and pks15/1) had no effect on survival. In conclusion, drug resistance exerted the greatest effect on survival of TB patients. Nevertheless we provide evidence for the independent biological effect on survival of different Beijing family strains even within the same defined geographical population. Better understanding of the role of different strain factors in active disease and their influence on outcome is essential.
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6
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Niu C, Yu D, Wang Y, Ren H, Jin Y, Zhou W, Li B, Cheng Y, Yue J, Gao Z, Liang L. Common and pathogen-specific virulence factors are different in function and structure. Virulence 2013; 4:473-82. [PMID: 23863604 PMCID: PMC5359729 DOI: 10.4161/viru.25730] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
In the process of host–pathogen interactions, bacterial pathogens always employ some special genes, e.g., virulence factors (VFs) to interact with host and cause damage or diseases to host. A number of VFs have been identified in bacterial pathogens that confer upon bacterial pathogens the ability to cause various types of damage or diseases. However, it has been clarified that some of the identified VFs are also encoded in the genomes of nonpathogenic bacteria, and this finding gives rise to considerable controversy about the definition of virulence factor.
Here 1988 virulence factors of 51 sequenced pathogenic bacterial genomes from the virulence factor database (VFDB) were collected, and an orthologous comparison to a non-pathogenic bacteria protein database was conducted using the reciprocal-best-BLAST-hits approach. Six hundred and twenty pathogen-specific VFs and 1368 common VFs (present in both pathogens and nonpathogens) were identified, which account for 31.19% and 68.81% of the total VFs, respectively. The distribution of pathogen-specific VFs and common VFs in pathogenicity islands (PAIs) was systematically investigated, and pathogen-specific VFs were more likely to be located in PAIs than common VFs. The function of the two classes of VFs were also analyzed and compared in depth. Our results indicated that most but not all T3SS proteins are pathogen-specific. T3SS effector proteins tended to be distributed in pathogen-specific VFs, whereas T3SS translocation proteins, apparatus proteins, and chaperones were inclined to be distributed in common VFs. We also observed that exotoxins were located in both pathogen-specific and common VFs. In addition, the architecture of the two classes of VFs was compared, and the results indicated that common VFs had a higher domain number and lower domain coverage value, revealed that common VFs tend to be more complex and less compact proteins.
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Affiliation(s)
- Chao Niu
- Tianjin Institute of Health & Environmental Medicine, Tianjin, People's Republic of China
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7
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Goudarzi H, Mirsamadi ES, Farnia P, Jahani Sherafat S, Esfahani M, Faramarzi N. Phospholipase C in Beijing strains of Mycobacterium tuberculosis. IRANIAN JOURNAL OF MICROBIOLOGY 2010; 2:194-7. [PMID: 22347572 PMCID: PMC3279787] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 10/29/2022]
Abstract
BACKGROUND AND OBJECTIVES Phospholipase of Mycobacterium tuberculosis plays an important role in pathogenesis through breaking up phospholipids and production of diacylglycerol. In this study, we examined the Beijing strains of Mycobacterium tuberculosis isolated from Iranian patients for the genes encoding this enzyme. MATERIALS AND METHODS DNA extraction was performed using CTAB (cetyltrimethylammonium bromide) from positive culture specimens in tuberculosis patients. PCR was then used to amplify the plcA, plcB, plcC genes of Beijing strain, and non-Beijing strains were identified by spoligotyping. RESULTS Of 200 specimens, 19 (9.5%) were Beijing strain and 181 (90.5%) were non-Beijing strains. The results of PCR for Beijing strains were as follows: 16 strains (84.2%) were positive for plcA, 17 (89.4%) were positive for plcB and 17 (89.4%) were positive for plcC genes. The standard strain (H37RV) was used as control. CONCLUSION The majority of Beijing strains have phospholipase C genes which can contribute to their pathogenesis but we need complementary studies to confirm the role of phospholipase C in pathogenecity of Mycobacterium tuberculosis.
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Affiliation(s)
- H Goudarzi
- Department of Microbiology, Faculty of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - ES Mirsamadi
- Department of Microbiology, Faculty of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran,Mycobacterium Research Center (MRC) National Research Institute of Tuberculosis and Lung Disease (NRITLD), Tehran, Iran
| | - P Farnia
- Mycobacterium Research Center (MRC) National Research Institute of Tuberculosis and Lung Disease (NRITLD), Tehran, Iran
| | - S Jahani Sherafat
- Department of Microbiology, Faculty of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran,Mycobacterium Research Center (MRC) National Research Institute of Tuberculosis and Lung Disease (NRITLD), Tehran, Iran
| | - M Esfahani
- School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - N Faramarzi
- School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
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8
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9
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Caws M, Thwaites G, Dunstan S, Hawn TR, Lan NTN, Thuong NTT, Stepniewska K, Huyen MNT, Bang ND, Loc TH, Gagneux S, van Soolingen D, Kremer K, van der Sande M, Small P, Anh PTH, Chinh NT, Quy HT, Duyen NTH, Tho DQ, Hieu NT, Torok E, Hien TT, Dung NH, Nhu NTQ, Duy PM, van Vinh Chau N, Farrar J. The influence of host and bacterial genotype on the development of disseminated disease with Mycobacterium tuberculosis. PLoS Pathog 2008; 4:e1000034. [PMID: 18369480 PMCID: PMC2268004 DOI: 10.1371/journal.ppat.1000034] [Citation(s) in RCA: 358] [Impact Index Per Article: 22.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2007] [Accepted: 02/26/2008] [Indexed: 12/13/2022] Open
Abstract
The factors that govern the development of tuberculosis disease are incompletely understood. We hypothesized that some strains of Mycobacterium tuberculosis (M. tuberculosis) are more capable of causing disseminated disease than others and may be associated with polymorphisms in host genes responsible for the innate immune response to infection. We compared the host and bacterial genotype in 187 Vietnamese adults with tuberculous meningitis (TBM) and 237 Vietnamese adults with uncomplicated pulmonary tuberculosis. The host genotype of tuberculosis cases was also compared with the genotype of 392 cord blood controls from the same population. Isolates of M. tuberculosis were genotyped by large sequence polymorphisms. The hosts were defined by polymorphisms in genes encoding Toll-interleukin 1 receptor domain containing adaptor protein (TIRAP) and Toll-like receptor-2 (TLR-2). We found a significant protective association between the Euro-American lineage of M. tuberculosis and pulmonary rather than meningeal tuberculosis (Odds ratio (OR) for causing TBM 0.395, 95% confidence intervals (C.I.) 0.193–0.806, P = 0.009), suggesting these strains are less capable of extra-pulmonary dissemination than others in the study population. We also found that individuals with the C allele of TLR-2 T597C allele were more likely to have tuberculosis caused by the East-Asian/Beijing genotype (OR = 1.57 [95% C.I. 1.15–2.15]) than other individuals. The study provides evidence that M. tuberculosis genotype influences clinical disease phenotype and demonstrates, for the first time, a significant interaction between host and bacterial genotypes and the development of tuberculosis. Tuberculosis, caused by the bacterium Mycobacterium tuberculosis, kills over 2 million people each year. It is estimated that approximately one-third of the world population is infected with M. tuberculosis, though the majority will never develop active disease. The most severe form of tuberculosis occurs when the bacterium spreads to the brain to cause meningitis. We examined whether the genetic variation of the person and the bacteria influenced the type of disease a person develops. We have previously shown that certain mutations in genes of the human immune system can predispose adults in Vietnam to developing tuberculous meningitis. In this study we show that some strains of M. tuberculosis commonly found in Europe and America are less likely to cause tuberculous meningitis in Vietnamese adults than strains predominantly found in Asia. We then looked at the interaction between M. tuberculosis strains and mutations in human immune genes and show that a particular mutation, TLR2 T597C, is more commonly found in patients infected with the East-Asian/Beijing strains of M. tuberculosis. This is the first study to look at both the host and pathogen genotypes together in tuberculosis infection, and the findings suggest that the outcome of exposure to M. tuberculosis can depend on both the human genotype and the bacterial genotype.
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Affiliation(s)
- Maxine Caws
- Oxford University Clinical Research Unit, Hospital for Tropical Diseases, District 5, Ho Chi Minh City, Vietnam.
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Pinto H, Bica CG, Palaci M, Dietze R, Basso LA, Santos DS. Using polymerase chain reaction with primers based on the plcB-plcC intergenic region to detect Mycobacterium tuberculosis in clinical samples. J Bras Pneumol 2008; 33:437-42. [PMID: 17982536 DOI: 10.1590/s1806-37132007000400013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2006] [Accepted: 11/28/2006] [Indexed: 11/22/2022] Open
Abstract
OBJECTIVE To develop a system for the molecular diagnosis of tuberculosis by polymerase chain reaction (PCR), constructing primers based on the difference in gene organization of the intergenic region of phospholipase C (plcB-plcC region), which differentiates Mycobacterium tuberculosis from other mycobacteria. METHODS A PCR product of the expected size (432 bp) was obtained from M. tuberculosis and M. africanum only. A total of 33 mycobacterial isolates and 273 clinical samples from patients suspected of having tuberculosis were examined. These were used in the comparative study of the PCR technique versus culture. RESULTS For PCR versus culture, the data showed 93.8% accuracy (p < 0.0001), 93.1% sensitivity (CI: 88.7-96.0), and 96.4% specificity (CI: 96.1-99.4). The Kappa value (0.82) shows that there was a near-perfect concordance between the two tests. CONCLUSION The use of the plcB-plcC region in PCR amplification was found to be an important and reliable tool for the specific diagnosis of tuberculosis in the samples analyzed.
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Molecular characteristics of the Mycobacterium tuberculosis LAM-RUS family prevalent in Central Russia. J Clin Microbiol 2007; 45:4036-8. [PMID: 17942651 DOI: 10.1128/jcm.01217-07] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We analyzed IS6110-associated polymorphisms in the phospholipase C genes of 107 isolates of Mycobacterium tuberculosis selected to be representative of isolates circulating in central Russia. We found that the majority of Latin American-Mediterranean family strains contained an insertion in a unique position in the plcA gene, suggesting a common ancestor. This insertion can serve as a specific genetic marker for this group, which we designate the LAM-RUS family.
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Kong Y, Cave MD, Zhang L, Foxman B, Marrs CF, Bates JH, Yang ZH. Association between Mycobacterium tuberculosis Beijing/W lineage strain infection and extrathoracic tuberculosis: Insights from epidemiologic and clinical characterization of the three principal genetic groups of M. tuberculosis clinical isolates. J Clin Microbiol 2006; 45:409-14. [PMID: 17166963 PMCID: PMC1829078 DOI: 10.1128/jcm.01459-06] [Citation(s) in RCA: 108] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Clinical strains of Mycobacterium tuberculosis can be divided into three principal genetic groups based on the single-nucleotide polymorphisms at the katG gene codon 463 and the gyrA gene codon 95. One subgroup of genetic group 1, the Beijing/W lineage, has been widely studied because of its worldwide distribution and association with outbreaks. In order to increase our understanding of the clinical and epidemiological relevance of the genetic grouping of M. tuberculosis clinical strains and the Beijing/W lineage, we investigated the genetic grouping of 679 clinical isolates of M. tuberculosis, representing 96.3% of culture-confirmed tuberculosis cases diagnosed in Arkansas between January 1996 and December 2000 using PCR and DNA sequencing. We assessed the associations of infections by different genetic groups of M. tuberculosis strains and infection by the Beijing/W lineage strains with the clinical and epidemiological characteristics of the patients using chi-square tests and multivariate logistic regression analysis. Of the 679 study isolates, 676 fell into one of the three principal genetic groups, with 63 (9.3%) in group 1, 438 (64.8%) in group 2, and 175 (25.9%) in group 3. After adjusting for potential confounding of age, gender, race/ethnicity, human immunodeficiency virus serostatus, and plcD genotype in a multivariate logistic regression model, patients infected by the Beijing/W lineage isolates were nearly three times as likely as patients infected with the non-Beijing/W lineage isolates to have an extrathoracic involvement (odds ratio [95% confidence interval], 2.85 [1.33, 6.12]). Thus, the Beijing/W lineage strains may have some special biological features that facilitate the development of extrathoracic tuberculosis.
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Affiliation(s)
- Y Kong
- Epidemiology Department, School of Public Health, University of Michigan, 109 S. Observatory Street, Ann Arbor, MI 48109-2029, USA
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13
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Affiliation(s)
- Wing Wai Yew
- Grantham Hospital Tuberculosis and Chest Unit, 125 Wong Chuk Hang Road, Hong Kong, China.
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14
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Viana-Niero C, Rodriguez CAR, Bigi F, Zanini MS, Ferreira-Neto JS, Cataldi A, Leão SC. Identification of an IS6110 insertion site in plcD, the unique phospholipase C gene of Mycobacterium bovis. J Med Microbiol 2006; 55:451-457. [PMID: 16533994 DOI: 10.1099/jmm.0.46364-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The IS6110 repetitive element is present in multiple copies in most Mycobacterium tuberculosis complex bacteria, except for Mycobacterium bovis strains, which usually contain a single copy of IS6110 located on a 1·9 kb PvuII fragment of the direct repeat region. IS6110 transposition can disrupt coding regions and is a major force of genomic variation. In a previous work it was demonstrated that phospholipase C genes are preferential loci for IS6110 transposition in M. tuberculosis clinical strains. Bacterial phospholipase C enzymes participate in pathogenic mechanisms used by different organisms, and have been implicated in intracellular survival, cytolysis and cell-to-cell spread. Four phospholipase C genes (plcA, plcB, plcC and plcD) were detected in the genomes of M. tuberculosis, Mycobacterium africanum, Mycobacterium microti and ‘Mycobacterium canettii’. M. bovis and the vaccine strain M. bovis Bacillus Calmette–Guérin contain only the plcD gene. In the present work, the existence of IS6110 insertions within plcD, the unique phospholipase C gene of M. bovis, has been investigated by PCR, Southern blot hybridization and sequencing analysis. In 18 (7·3 %) of 245 isolates analysed, the plcD gene was interrupted by the insertion of one copy of IS6110, which in all cases was transposed in the same orientation and at the same position, 1 972 894, relative to the genome of M. bovis AF2122/97. These 18 isolates were distributed in 6 different spoligotype patterns and contained 4 to 8 IS6110 copies. In contrast, strains showing an intact plcD gene contained one (87 %), two (9·4 %) or three (2·4 %) IS6110 copies, and only a single isolate (1·2 %) had four IS6110 copies. The implications of plcD gene disruption in M. bovis have not been fully investigated, but no differences in the organ distribution of the disease were detected when animals infected with strains from the same spoligotype patterns bearing plcD : : IS6110 and intact plcD were compared.
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Affiliation(s)
- Cristina Viana-Niero
- Departamento de Microbiologia, Imunologia e Parasitologia, Universidade Federal de São Paulo, Rua Botucatu 862 3° andar, São Paulo, CEP 04023-062, Brazil
| | - Cesar Alejandro Rosales Rodriguez
- Faculdade de Medicina Veterinária e Zootecnia, Universidade de São Paulo, Av. Professor Dr Orlando Marques de Paiva 87, São Paulo, CEP 05508-900, Brazil
| | - Fabiana Bigi
- Instituto de Microbiología y Zoología Agrícola del CICVyA - Instituto Nacional de Tecnología Agropecuaria (INTA), Castelar, Buenos Aires, Argentina
| | - Marcos Santos Zanini
- Centro de Ciências Agrárias, Universidade Federal do Espírito Santo, PO Box 16, Alegre, Espírito Santo, Brazil
| | - José Soares Ferreira-Neto
- Faculdade de Medicina Veterinária e Zootecnia, Universidade de São Paulo, Av. Professor Dr Orlando Marques de Paiva 87, São Paulo, CEP 05508-900, Brazil
| | - Angel Cataldi
- Instituto de Microbiología y Zoología Agrícola del CICVyA - Instituto Nacional de Tecnología Agropecuaria (INTA), Castelar, Buenos Aires, Argentina
| | - Sylvia Cardoso Leão
- Departamento de Microbiologia, Imunologia e Parasitologia, Universidade Federal de São Paulo, Rua Botucatu 862 3° andar, São Paulo, CEP 04023-062, Brazil
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Kong Y, Cave MD, Yang D, Zhang L, Marrs CF, Foxman B, Bates JH, Wilson F, Mukasa LN, Yang ZH. Distribution of insertion- and deletion-associated genetic polymorphisms among four Mycobacterium tuberculosis phospholipase C genes and associations with extrathoracic tuberculosis: a population-based study. J Clin Microbiol 2006; 43:6048-53. [PMID: 16333097 PMCID: PMC1317199 DOI: 10.1128/jcm.43.12.6048-6053.2005] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The Mycobacterium tuberculosis genome contains four phospholipase C (PLC)-encoding genes, designated plcA, plcB, plcC, and plcD, respectively. Each of the four genes contributes to the overall PLC activity of M. tuberculosis. PLC is hypothesized to contribute to M. tuberculosis virulence. Infection of M. tuberculosis strains carrying a truncated plcD gene is associated with the occurrence of extrathoracic tuberculosis. However, whether the other three plc genes are also associated with extrathoracic tuberculosis remains to be assessed. We investigated the insertion- and deletion-associated genetic diversity in all four plc genes among 682 epidemiologically and clinically well-characterized M. tuberculosis clinical isolates using PCR, DNA sequencing, and Southern hybridization. Two hundred sixty-six (39%) of the 682 isolates had an interruption in at least one of the four plc genes, most often associated with an IS6110 insertion. The plcD gene interruption was the most common: it was observed in 233 (34%) of the isolates, compared to 4.7%, 4.1%, and 5.9% for plcA, plcB, and plcC gene interruption, respectively. The association between the plc gene genotypes and disease presentation was adjusted for clustering using generalized estimating equations for both bivariate and multivariate analyses. After controlling for the genotypes of the plcABC genes and the host-related risk factors, interruption in the plcD gene remained significantly associated with extrathoracic tuberculosis (odds ratio, 3.27; 95% confidence interval, 1.32 to 8.14). The data suggest that the plcD gene might play a more important role in the pathogenesis of thoracic TB than it does in the pathogenesis of extrathoracic TB.
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Affiliation(s)
- Y Kong
- Epidemiology Department, School of Public Health, University of Michigan, 109 S. Observatory Street, Ann Arbor, MI 48109-2029, USA
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16
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Azhikina T, Gvozdevsky N, Botvinnik A, Fushan A, Shemyakin I, Stepanshina V, Lipin M, Barry C, Sverdlov E. A genome-wide sequence-independent comparative analysis of insertion-deletion polymorphisms in multiple Mycobacterium tuberculosis strains. Res Microbiol 2005; 157:282-90. [PMID: 16239096 DOI: 10.1016/j.resmic.2005.08.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2005] [Revised: 07/20/2005] [Accepted: 08/12/2005] [Indexed: 11/30/2022]
Abstract
We applied an enhanced version of subtractive hybridization for comparative analyses of indel differences between genomes of several Mycobacterium tuberculosis strains widespread in Russian regions, and the H37Rv reference strain. A number of differences were detected and partially analyzed, thus demonstrating the practicality of the approach. A majority of the insertions found were shared by all Russian strains, except for strain 1540 that revealed the highest virulence in animal tests. This strain possesses a number of genes absent from other clinical strains. Two of the differential genes were found to encode putative membrane proteins and are presumed to affect mycobacterial interaction with the host cell, thus enhancing virulent properties of the isolate. The method used is of general application, and enables the elaboration of a catalogue of indel polymorphic genomic differences between closely related strains.
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Affiliation(s)
- Tatyana Azhikina
- Laboratory of Structure and Functions of Human Genes, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Science, Moscow, Russia.
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17
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Zozio T, Allix C, Gunal S, Saribas Z, Alp A, Durmaz R, Fauville-Dufaux M, Rastogi N, Sola C. Genotyping of Mycobacterium tuberculosis clinical isolates in two cities of Turkey: description of a new family of genotypes that is phylogeographically specific for Asia Minor. BMC Microbiol 2005; 5:44. [PMID: 16045794 PMCID: PMC1192800 DOI: 10.1186/1471-2180-5-44] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2005] [Accepted: 07/26/2005] [Indexed: 11/30/2022] Open
Abstract
Background Population-based bacterial genetics using repeated DNA loci is an efficient approach to study the biodiversity and phylogeographical structure of human pathogens, such as Mycobacterium tuberculosis, the agent of tuberculosis. Indeed large genetic diversity databases are available for this pathogen and are regularly updated. No population-based polymorphism data were yet available for M. tuberculosis in Turkey, at the crossroads of Eurasia. Results A total of 245 DNAs from Mycobacterium tuberculosis clinical isolates from tuberculosis patients residing in Turkey (Malatya n = 147 or Ankara n = 98) were genotyped by spoligotyping, a high-throughput genotyping method based on the polymorphism of the Direct Repeat locus. Thirty-three spoligotyping-defined clusters including 206 patients and 39 unique patterns were found. The ST41 cluster, as designated according to the international SpolDB3 database project, represented one fourth and when gathered to three genotypes, ST53, ST50 and ST284, one half of all the isolates. Out of 34 clinical isolates harboring ST41 which were further genotyped by IS6110 and by MIRU-VNTR typing, a typical 2-copy IS6110-RFLP pattern and a "215125113322" MIRU-VNTR pattern were observed among 21 clinical isolates. Further search in various databases confirms the likely Turkish-phylogeographical specificity of this clonal complex. Conclusion We described a new phylogeographically-specific clone of M. tuberculosis, designated LAM7-TUR. Further investigations to assess its frequency within all regions of Turkey and its phylogeographical origin and phylogenetic position within the global M. tuberculosis phylogenetic tree will shed new light on its endemicity in Asia Minor.
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Affiliation(s)
- Thierry Zozio
- Unité de la Tuberculose et des Mycobactéries, Institut Pasteur de Guadeloupe
| | - Caroline Allix
- Laboratoire de la Tuberculose, Institut Pasteur de Bruxelles
| | - Selami Gunal
- Department of Clinical Microbiology, Faculty of Medicine, Inonu University, Malatya, Turkey
| | - Zeynep Saribas
- Department of Microbiology and Clinical Microbiology, Faculty of Medicine, Hacettepe University, Ankara, Turkey
| | - Alpaslan Alp
- Department of Microbiology and Clinical Microbiology, Faculty of Medicine, Hacettepe University, Ankara, Turkey
| | - Riza Durmaz
- Department of Clinical Microbiology, Faculty of Medicine, Inonu University, Malatya, Turkey
| | | | - Nalin Rastogi
- Unité de la Tuberculose et des Mycobactéries, Institut Pasteur de Guadeloupe
| | - Christophe Sola
- Unité de la Tuberculose et des Mycobactéries, Institut Pasteur de Guadeloupe
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Yang Z, Yang D, Kong Y, Zhang L, Marrs CF, Foxman B, Bates JH, Wilson F, Cave MD. Clinical relevance of Mycobacterium tuberculosis plcD gene mutations. Am J Respir Crit Care Med 2005; 171:1436-42. [PMID: 15805187 PMCID: PMC2718484 DOI: 10.1164/rccm.200408-1147oc] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
To identify Mycobacterium tuberculosis virulence factors, we integrated comparative genomics and epidemiologic data analysis to investigate the relationship between certain genomic insertions and deletions in the phospholipase-C gene D (plcD) with the clinical presentation of tuberculosis (TB). Four hundred ninety-six well-characterized M. tuberculosis clinical isolates were studied. Approximately 30% (147) of the isolates had an interruption of the plcD gene. Patients infected with the plcD mutant were twice as likely to have extrathoracic disease as those infected by a strain without an interruption (adjusted odds ratio, 2.19; 95% confidence interval, 1.27, 3.76). When we limited the analysis to the 275 isolates with distinct DNA fingerprint patterns, we observed the same association (adjusted odds ratio, 2.74; 95% confidence interval, 1.35, 5.56). Furthermore, the magnitude of the association appeared to differ with the type of extrathoracic TB. Our findings suggest that the plcD gene of M. tuberculosis is potentially involved in the pathogenesis of TB, and the clinical presentation of the disease may be influenced by the genetic variability of the plcD region.
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Affiliation(s)
- Zhenhua Yang
- Epidemiology Department, School of Public Health, University of Michigan, 109 S. Observatory Street, Ann Arbor, MI 48109-2029, USA.
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