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Zhu C, Wei WP, An JN, Hu JL, Gao CH, Yang M. SdrR, a LysR-type regulator, responds to the mycobacterial antioxidant defense. J Biochem 2024; 176:43-54. [PMID: 38444151 DOI: 10.1093/jb/mvae026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Revised: 01/26/2024] [Accepted: 02/27/2024] [Indexed: 03/07/2024] Open
Abstract
Protection against oxidative stress is a vital defense mechanism for Mycobacterium tuberculosis within the host. However, few transcription factors that control bacterial antioxidant defense are known. Here, we present evidence that SdrR, encoded by the MSMEG_5712 (Ms5712) gene, functions as an oxidative stress response regulator in Mycobacterium smegmatis. SdrR recognizes an 11-bp motif sequence in the operon's upstream regulatory region and negatively regulates the expression of short-chain dehydrogenases/reductases (SDR). Overexpressing sdrR inhibited SDR expression, which rendered the strain oxidative more stress-sensitive. Conversely, sdrR knockout alleviates SDR repression, which increases its oxidative stress tolerance. Thus, SdrR responds to oxidative stress by negatively regulating sdr expression. Therefore, this study elucidated an underlying regulatory mechanism behind mycobacterial oxidative stress adaptation.
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Affiliation(s)
- Chen Zhu
- School of Basic Medicine, Guizhou University of Traditional Chinese Medicine, Guiyang, 550025, China
| | - Wen-Ping Wei
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China
| | - Jing-Ning An
- State Key Laboratory of Agricultural Microbiology, College of Resources and Environment, Huazhong Agricultural University, Wuhan, 430070, China
| | - Jia-Ling Hu
- State Key Laboratory of Agricultural Microbiology, College of Resources and Environment, Huazhong Agricultural University, Wuhan, 430070, China
| | - Chun-Hui Gao
- State Key Laboratory of Agricultural Microbiology, College of Resources and Environment, Huazhong Agricultural University, Wuhan, 430070, China
| | - Min Yang
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China
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Chaturvedi M, Patel M, Tiwari A, Dwivedi N, Mondal DP, Srivastava AK, Dhand C. An insight to the recent advancements in detection of Mycobacterium tuberculosis using biosensors: A systematic review. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2024; 186:14-27. [PMID: 38052326 DOI: 10.1016/j.pbiomolbio.2023.10.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Revised: 07/31/2023] [Accepted: 10/01/2023] [Indexed: 12/07/2023]
Abstract
Since ancient times, Tuberculosis (TB) has been a severe invasive illness that has been prevalent for thousands of years and is also known as "consumption" or phthisis. TB is the most common chronic lung bacterial illness in the world, killing over 2 million people each year, caused by Mycobacterium tuberculosis (MTB). As per the reports of WHO, in spite of technology advancements, the average rate of decline in global TB infections from 2000-2018 was only 1.6% per year, and the worldwide reduction in TB deaths was only 11%. In addition, COVID-19 pandemic has reversed years of global progress in tackling TB with fewer diagnosed cases. The majority of undiagnosed patients of TB are found in low- and middle-income countries where the GeneXpert MTB/RIF assay and sputum smear microscopy have been approved by the WHO as reference procedures for quickly detecting TB. Biosensors, like other cutting-edge technologies, have piqued researchers' interest since they offer a quick and accurate way to identify MTB. Modern integrated technologies allow for the rapid, low-cost, and highly precise detection of analytes in extremely little amounts of sample by biosensors. Here in this review, we outlined the severity of tuberculosis (TB) and the most recent developments in the biosensors sector, as well as their various kinds and benefits for TB detection. The review also emphasizes how widespread TB is and how it needs accurate diagnosis and effective treatment.
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Affiliation(s)
- Mansi Chaturvedi
- CSIR-Advanced Materials and Processes Research Institute, Hoshangabad Road, Bhopal, 462026, India; School of Biomolecular Engineering & Biotechnology UTD RGPV, Bhopal, 462033, India
| | - Monika Patel
- CSIR-Advanced Materials and Processes Research Institute, Hoshangabad Road, Bhopal, 462026, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Archana Tiwari
- School of Biomolecular Engineering & Biotechnology UTD RGPV, Bhopal, 462033, India
| | - Neeraj Dwivedi
- CSIR-Advanced Materials and Processes Research Institute, Hoshangabad Road, Bhopal, 462026, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - D P Mondal
- CSIR-Advanced Materials and Processes Research Institute, Hoshangabad Road, Bhopal, 462026, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Avanish Kumar Srivastava
- CSIR-Advanced Materials and Processes Research Institute, Hoshangabad Road, Bhopal, 462026, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Chetna Dhand
- CSIR-Advanced Materials and Processes Research Institute, Hoshangabad Road, Bhopal, 462026, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India.
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3
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Bhargavi G, Singh AK, Patil SA, Palaniyandi K. A putative short-chain dehydrogenase Rv0148 of Mycobacterium tuberculosis affects bacterial survival and virulence. CURRENT RESEARCH IN MICROBIAL SCIENCES 2022; 3:100113. [PMID: 35243448 PMCID: PMC8861579 DOI: 10.1016/j.crmicr.2022.100113] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Revised: 01/27/2022] [Accepted: 02/10/2022] [Indexed: 12/17/2022] Open
Affiliation(s)
- Gunapati Bhargavi
- ICMR-National Institute for Research in Tuberculosis, Chennai, India
| | - Amit Kumar Singh
- ICMR- National JALMA Institute for Leprosy & Other Mycobacterial Diseases, Agra, India
| | - Shripad A. Patil
- ICMR- National JALMA Institute for Leprosy & Other Mycobacterial Diseases, Agra, India
| | - Kannan Palaniyandi
- ICMR-National Institute for Research in Tuberculosis, Chennai, India
- Corresponding author.
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4
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Shang Y, Ye Q, Wu Q, Pang R, Zhou B, Wang C, Xiang X, Li F, Wang J, Zhang Y, Wang J, Sun X, Zhang J. PCR and multiplex PCR assays for the detection of Cronobacter species using specific targets obtained by a bioinformatics approach. Food Control 2021. [DOI: 10.1016/j.foodcont.2021.107896] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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5
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Shang Y, Ye Q, Wu Q, Pang R, Xiang X, Wang C, Li F, Zhou B, Xue L, Zhang Y, Sun X, Zhang J. PCR identification of Salmonella serovars for the E serogroup based on novel specific targets obtained by pan-genome analysis. Lebensm Wiss Technol 2021. [DOI: 10.1016/j.lwt.2020.110535] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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6
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Loop-mediated isothermal amplification (LAMP) for rapid detection of Salmonella in foods based on new molecular targets. Lebensm Wiss Technol 2021. [DOI: 10.1016/j.lwt.2021.110999] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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7
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Ye Q, Shang Y, Chen M, Pang R, Li F, Xiang X, Zhou B, Wang C, Zhang S, Zhang J, Wang J, Xue L, Ding Y, Wu Q. Mining and evaluating novel serovar-specific Salmonella C1 serogroup genes by polymerase chain reaction analysis. Lebensm Wiss Technol 2021. [DOI: 10.1016/j.lwt.2020.110821] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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8
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Li F, Ye Q, Chen M, Zhou B, Xiang X, Wang C, Shang Y, Zhang J, Pang R, Wang J, Xue L, Cai S, Ding Y, Wu Q. Mining of novel target genes through pan-genome analysis for multiplex PCR differentiation of the major Listeria monocytogenes serotypes. Int J Food Microbiol 2020; 339:109026. [PMID: 33360877 DOI: 10.1016/j.ijfoodmicro.2020.109026] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Revised: 12/06/2020] [Accepted: 12/08/2020] [Indexed: 02/08/2023]
Abstract
The abundant information provided by the pan-genome analysis approach reveals the diversity among Listeria monocytogenes serotypes. The objective of this study was to mine novel target genes using pan-genome analysis for multiplex PCR detection and differentiation of the major L. monocytogenes serotypes present in food. Pan-genome analysis and PCR validation revealed a total of 10 specific targets: one for lineage I, two for serogroup I.1, one for serogroup I.2, two for lineage II, one for serogroup II.1, three for lineage III. Primers for the novel targets were highly specific in individual reactions. The detection limits were 103-104 colony-forming units (CFU)/mL in pure bacterial cultures, meeting the requirements of molecular detection. Based on these novel targets, two new "lineage" multiplex PCR assays were developed to simultaneously distinguish between three lineages (I, II, and III) and five major serotypes (1/2a, 1/2b, 1/2c, 4b, and 4c) of L. monocytogenes. The detection limits of lineage I and lineage II&III mPCRs were 0.771 pg/μL and 1.76 pg/μL genomic DNA, respectively. The specificity of the mPCRs was robustly verified using other L. monocytogenes and non-L. monocytogenes serotypes. These results suggest that the two "lineage" multiplex PCRs based on novel targets offer a promising approach for accurate, sensitive, and rapid identification of L. monocytogenes serotypes.
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Affiliation(s)
- Fan Li
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China; Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Qinghua Ye
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Moutong Chen
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Baoqing Zhou
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Xinran Xiang
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Chufang Wang
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Yuting Shang
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Jumei Zhang
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Rui Pang
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Juan Wang
- College of Food Science, South China Agricultural University, Guangzhou, China
| | - Liang Xue
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Shuzhen Cai
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Yu Ding
- Department of Food Science and Technology, Jinan University, Guangzhou, China.
| | - Qingping Wu
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China.
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Tuberculosis, human immunodeficiency viruses and TB/HIV co-infection in pregnant women: A meta-analysis. CLINICAL EPIDEMIOLOGY AND GLOBAL HEALTH 2020. [DOI: 10.1016/j.cegh.2020.05.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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10
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Bakhshi M, Zandi H, Bafghi MF, Astani A, Ranjbar VR, Vakili M. A survey for phylogenetic relationship; presence of virulence genes and antibiotic resistance patterns of avian pathogenic and uropathogenic Escherichia coli isolated from poultry and humans in Yazd, Iran. GENE REPORTS 2020. [DOI: 10.1016/j.genrep.2020.100725] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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11
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Sayadi M, Zare H, Jamedar SA, Hashemy SI, Meshkat Z, Soleimanpour S, Hoffner S, Ghazvini K. Genotypic and phenotypic characterization of Mycobacterium tuberculosis resistance against fluoroquinolones in the northeast of Iran. BMC Infect Dis 2020; 20:390. [PMID: 32487030 PMCID: PMC7268510 DOI: 10.1186/s12879-020-05112-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2019] [Accepted: 05/20/2020] [Indexed: 11/24/2022] Open
Abstract
BACKGROUND Fluoroquinolones are broad-spectrum antibiotics that are recommended, and increasingly important, for the treatment of multidrug-resistant tuberculosis (MDR-TB). Resistance to fluoroquinolones is caused by mutations in the Quinolone Resistance Determining Region (QRDR) of gyrA and gyrB genes of Mycobacterium tuberculosis. In this study, we characterized the phenotypic and genotypic resistance to fluoroquinolones for the first time in northeast Iran. METHODS A total of 123 Mycobacterium tuberculosis isolates, including 111 clinical and 12 collected multidrug-resistant isolates were studied. Also, 19 WHO quality control strains were included in the study. The phenotypic susceptibility was determined by the proportion method on Löwenstein-Jensen medium. The molecular cause of resistance to the fluoroquinolone drugs ofloxacin and levofloxacin was investigated by sequencing of the QRDR region of the gyrA and gyrB genes. RESULTS Among 123 isolates, six (4.8%) were fluoroquinolone-resistant according to phenotypic methods, and genotypically three of them had a mutation at codon 94 of the gyrA gene (Asp→ Gly) which was earlier reported to cause resistance. All three remaining phenotypically resistant isolates had a nucleotide change in codon 95. No mutations were found in the gyrB gene. Five of the 19 WHO quality control strains, were phenotypically fluoroquinolone-resistant, four of them were genotypically resistant with mutations at codon 90, 91 of the gyrA gene and one resistant strain had no detected mutation. CONCLUSIONS Mutation at codon 94 of the gyrA gene, was the main cause of fluoroquinolone resistance among M. tuberculosis isolates in our region. In 3/6 fluoroquinolone-resistant isolates, no mutations were found in either gyrA or gyrB. Therefore, it can be concluded that various other factors may lead to fluoroquinolone resistance, such as active efflux pumps, decreased cell wall permeability, and drug inactivation.
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Affiliation(s)
- Mahdieh Sayadi
- Antimicrobial Resistance Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
- Department of Microbiology and Virology, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Hosna Zare
- Antimicrobial Resistance Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
- Department of Microbiology and Virology, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
- Student Research Committee, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Saeed Amel Jamedar
- Antimicrobial Resistance Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
- Department of Microbiology and Virology, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Seyed Isaac Hashemy
- Department of Clinical Biochemistry, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Zahra Meshkat
- Antimicrobial Resistance Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
- Department of Microbiology and Virology, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Saman Soleimanpour
- Antimicrobial Resistance Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
- Department of Microbiology and Virology, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Sven Hoffner
- Department of Global Public Health, Karolinska Institute, Stockholm, Sweden
| | - Kiarash Ghazvini
- Antimicrobial Resistance Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
- Department of Microbiology and Virology, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
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12
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COVID-19 target: A specific target for novel coronavirus detection. GENE REPORTS 2020; 20:100740. [PMID: 32510005 PMCID: PMC7261075 DOI: 10.1016/j.genrep.2020.100740] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2020] [Revised: 05/24/2020] [Accepted: 05/28/2020] [Indexed: 11/21/2022]
Abstract
An ongoing outbreak of pneumonia associated with a novel coronavirus has been reported worldwide and become a global health problem; hence, the diagnosis and differentiation of this virus from other types of coronavirus is essential to control of the disease. To this end, the analysis of genomics data plays a vital role in introducing a stronger target and consequently provides better results in laboratory examinations. The modified comparative genomics approach helps us to find novel specific targets by comparing two or more sequences on the nucleotide collection database. We, for the first time, detected ORF8 gene as a potential target for the detection of the novel coronavirus. Unlike previous reported genes (RdRP, E and N genes), ORF8 is entirely specific to the novel coronavirus (COVID-19) and has no cross-reactivity with other kinds of coronavirus. Accordingly, ORF8 gene can be used as an additional confirmatory assay.
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13
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Kamali Kakhki R, Najafzadeh MJ, Kachuei R, Ghazvini K. Targeting novel genes for simultaneous detection of five fungal and bacterial agents from BAL samples using multiplex PCR assay. Eur J Clin Microbiol Infect Dis 2020; 39:1535-1542. [PMID: 32253622 DOI: 10.1007/s10096-020-03879-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Accepted: 03/24/2020] [Indexed: 12/26/2022]
Abstract
The main purpose of our study was to evaluate multiplex PCR assay targeting novel genes for detection of five fungal and bacterial agents in BAL samples; because many fungi and bacteria that cause respiratory infections have similar clinical symptoms, diagnosing and differentiating them are therefore essential to controlling and treating them. A total of 100 BAL specimens from a mycobacterium and mycology laboratory were collected from patients suspected of having TB or other respiratory diseases. Novel DNA targets for Aspergillus, Nocardia, Cryptococcus, and Streptomyces were found using modified comparative genomic analysis. Afterward, the primers were designed based on novel targets, and the sensitivity and specificity of the newly designed primers were evaluated. These primers, along with specific primers for M. tuberculosis (SDR), were used in a multiplex PCR assay. The results showed the culture test to be more sensitive than the PCR assay in detecting M. tuberculosis. However, in the detection of Aspergillus, the PCR assay was more sensitive than the culture test. We also found one positive culture and two positive PCR assays for Nocardiosis. Cryptococcal infections and Streptomyces associated with lung diseases were not identified by the culture test nor by the PCR assay. The multiplex PCR is one of the cheapest molecular diagnostic tests readily available for BAL samples in clinical laboratories. This assay can be used for early reports of the causative agents and for treating patients with appropriate drugs at an early stage.
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Affiliation(s)
- Reza Kamali Kakhki
- Antimicrobial Resistance Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Mohammad Javad Najafzadeh
- Department of Parasitology and Mycology, School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Reza Kachuei
- Molecular Biology Research Center, Systems Biology and Poisonings Institute, Baqiyatallah University of Medical Sciences, Tehran, Iran.
| | - Kiarash Ghazvini
- Antimicrobial Resistance Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
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14
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Goig GA, Torres-Puente M, Mariner-Llicer C, Villamayor LM, Chiner-Oms Á, Gil-Brusola A, Borrás R, Comas Espadas I. Towards next-generation diagnostics for tuberculosis: identification of novel molecular targets by large-scale comparative genomics. Bioinformatics 2020; 36:985-989. [PMID: 31580405 PMCID: PMC7703747 DOI: 10.1093/bioinformatics/btz729] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2019] [Revised: 09/02/2019] [Accepted: 09/25/2019] [Indexed: 02/01/2023] Open
Abstract
MOTIVATION Tuberculosis (TB) remains one of the main causes of death worldwide. The long and cumbersome process of culturing Mycobacterium tuberculosis complex (MTBC) bacteria has encouraged the development of specific molecular tools for detecting the pathogen. Most of these tools aim to become novel TB diagnostics, and big efforts and resources are invested in their development, looking for the endorsement of the main public health agencies. Surprisingly, no study has been conducted where the vast amount of genomic data available is used to identify the best MTBC diagnostic markers. RESULTS In this work, we used large-scale comparative genomics to identify 40 MTBC-specific loci. We assessed their genetic diversity and physiological features to select 30 that are good targets for diagnostic purposes. Some of these markers could be used to assess the physiological status of the bacilli. Remarkably, none of the most used MTBC markers is in our catalog. Illustrating the translational potential of our work, we develop a specific qPCR assay for quantification and identification of MTBC DNA. Our rational design of targeted molecular assays for TB could be used in many other fields of clinical and basic research. AVAILABILITY AND IMPLEMENTATION The database of non-tuberculous mycobacteria assemblies can be accessed at: 10.5281/zenodo.3374377. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Galo A Goig
- Tuberculosis Genomics Unit, Institute of Biomedicine of Valencia (CSIC), Valencia 46010, Spain
| | - Manuela Torres-Puente
- Tuberculosis Genomics Unit, Institute of Biomedicine of Valencia (CSIC), Valencia 46010, Spain
| | - Carla Mariner-Llicer
- Tuberculosis Genomics Unit, Institute of Biomedicine of Valencia (CSIC), Valencia 46010, Spain
| | - Luis M Villamayor
- Genomics and Health Unit, FISABIO Public Health (CSISP), Valencia 46035, Spain
| | - Álvaro Chiner-Oms
- Tuberculosis Genomics Unit, Institute of Biomedicine of Valencia (CSIC), Valencia 46010, Spain
| | - Ana Gil-Brusola
- Microbiology Service, La Fe University and Polytechnic Hospital, Valencia 46026, Spain
| | - Rafael Borrás
- Microbiology Service, University Clinic Hospital, Valencia 46010, Spain
- Microbiology Department, School of Medicine, University of Valencia, Valencia 46010, Spain
| | - Iñaki Comas Espadas
- Tuberculosis Genomics Unit, Institute of Biomedicine of Valencia (CSIC), Valencia 46010, Spain
- CIBER in Epidemiology and Public Health, Madrid 28029, Spain
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15
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Host and Mycobacterium tuberculosis interaction; expression of iNOS and Tbet genes from the host and virulence factors of the bacteria. GENE REPORTS 2019. [DOI: 10.1016/j.genrep.2019.100503] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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16
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Golichenari B, Nosrati R, Farokhi-Fard A, Faal Maleki M, Gheibi Hayat SM, Ghazvini K, Vaziri F, Behravan J. Electrochemical-based biosensors for detection of Mycobacterium tuberculosis and tuberculosis biomarkers. Crit Rev Biotechnol 2019; 39:1056-1077. [DOI: 10.1080/07388551.2019.1668348] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Behrouz Golichenari
- Biotechnology Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran
- Department of Pharmaceutical Biotechnology, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Rahim Nosrati
- Cellular and Molecular Research Center, Faculty of Medicine, Guilan University of Medical Sciences, Rasht, Iran
| | - Aref Farokhi-Fard
- Medical Biotechnology Department, Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran
| | - Mahdi Faal Maleki
- Department of Pharmaceutical Chemistry, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran
| | | | - Kiarash Ghazvini
- Department of Microbiology and Virology, School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Farzam Vaziri
- Microbiology Research Center (MRC), Pasteur Institute of Iran, Tehran, Iran
- Center for Bioengineering and Biotechnology, University of Waterloo, Waterloo, Canada
| | - Javad Behravan
- Biotechnology Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran
- Center for Bioengineering and Biotechnology, University of Waterloo, Waterloo, Canada
- School of Pharmacy, University of Waterloo, Waterloo, Canada
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