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Bespyatykh J, Shitikov E, Guliaev A, Smolyakov A, Klimina K, Veselovsky V, Malakhova M, Arapidi G, Dogonadze M, Manicheva O, Bespiatykh D, Mokrousov I, Zhuravlev V, Ilina E, Govorun V. System OMICs analysis of Mycobacterium tuberculosis Beijing B0/W148 cluster. Sci Rep 2019; 9:19255. [PMID: 31848428 PMCID: PMC6917788 DOI: 10.1038/s41598-019-55896-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Accepted: 12/04/2019] [Indexed: 11/30/2022] Open
Abstract
Mycobacterium tuberculosis Beijing B0/W148 is one of the most widely distributed clusters in the Russian Federation and in some countries of the former Soviet Union. Recent studies have improved our understanding of the reasons for the “success” of the cluster but this area remains incompletely studied. Here, we focused on the system omics analysis of the RUS_B0 strain belonging to the Beijing B0/W148 cluster. Completed genome sequence of RUS_B0 (CP020093.1) and a collection of WGS for 394 cluster strains were used to describe the main genetic features of the population. In turn, proteome and transcriptome studies allowed to confirm the genomic data and to identify a number of finds that have not previously been described. Our results demonstrated that expression of the whiB6 which contains cluster-specific polymorphism (a151c) increased almost 40 times in RUS_B0. Additionally, the level of ethA transcripts in RUS_B0 was increased by more than 7 times compared to the H37Rv. Start sites for 10 genes were corrected based on the combination of proteomic and transcriptomic data. Additionally, based on the omics approach, we identified 5 new genes. In summary, our analysis allowed us to summarize the available results and also to obtain fundamentally new data.
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Affiliation(s)
- Julia Bespyatykh
- Federal Research and Clinical Centre of Physical-Chemical Medicine, Moscow, Russian Federation.
| | - Egor Shitikov
- Federal Research and Clinical Centre of Physical-Chemical Medicine, Moscow, Russian Federation
| | - Andrei Guliaev
- Federal Research and Clinical Centre of Physical-Chemical Medicine, Moscow, Russian Federation
| | - Alexander Smolyakov
- Federal Research and Clinical Centre of Physical-Chemical Medicine, Moscow, Russian Federation.,Moscow Institute of Physics and Technology (State University), Dolgoprudny, Russian Federation
| | - Ksenia Klimina
- Federal Research and Clinical Centre of Physical-Chemical Medicine, Moscow, Russian Federation
| | - Vladimir Veselovsky
- Federal Research and Clinical Centre of Physical-Chemical Medicine, Moscow, Russian Federation
| | - Maya Malakhova
- Federal Research and Clinical Centre of Physical-Chemical Medicine, Moscow, Russian Federation
| | - Georgij Arapidi
- Federal Research and Clinical Centre of Physical-Chemical Medicine, Moscow, Russian Federation.,Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow, Russian Federation.,Moscow Institute of Physics and Technology (State University), Dolgoprudny, Russian Federation
| | - Marine Dogonadze
- Research Institute of Phtisiopulmonology, St. Petersburg, Russian Federation
| | - Olga Manicheva
- Research Institute of Phtisiopulmonology, St. Petersburg, Russian Federation
| | - Dmitry Bespiatykh
- Federal Research and Clinical Centre of Physical-Chemical Medicine, Moscow, Russian Federation
| | - Igor Mokrousov
- St. Petersburg Pasteur Institute, St. Petersburg, Russian Federation
| | | | - Elena Ilina
- Federal Research and Clinical Centre of Physical-Chemical Medicine, Moscow, Russian Federation
| | - Vadim Govorun
- Federal Research and Clinical Centre of Physical-Chemical Medicine, Moscow, Russian Federation
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Saleh S, Staes A, Deborggraeve S, Gevaert K. Targeted Proteomics for Studying Pathogenic Bacteria. Proteomics 2019; 19:e1800435. [DOI: 10.1002/pmic.201800435] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Revised: 06/04/2019] [Indexed: 02/04/2023]
Affiliation(s)
- Sara Saleh
- Department of Biomedical SciencesInstitute of Tropical Medicine B‐2000 Antwerp Belgium
- VIB Center for Medical Biotechnology B‐9000 Ghent Belgium
- Department of Biomolecular MedicineGhent University B‐9000 Ghent Belgium
| | - An Staes
- VIB Center for Medical Biotechnology B‐9000 Ghent Belgium
- Department of Biomolecular MedicineGhent University B‐9000 Ghent Belgium
| | - Stijn Deborggraeve
- Department of Biomedical SciencesInstitute of Tropical Medicine B‐2000 Antwerp Belgium
| | - Kris Gevaert
- VIB Center for Medical Biotechnology B‐9000 Ghent Belgium
- Department of Biomolecular MedicineGhent University B‐9000 Ghent Belgium
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Bespyatykh J, Smolyakov A, Guliaev A, Shitikov E, Arapidi G, Butenko I, Dogonadze M, Manicheva O, Ilina E, Zgoda V, Govorun V. Proteogenomic analysis of Mycobacterium tuberculosis Beijing B0/W148 cluster strains. J Proteomics 2019; 192:18-26. [DOI: 10.1016/j.jprot.2018.07.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2018] [Revised: 06/29/2018] [Accepted: 07/10/2018] [Indexed: 10/28/2022]
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Antonova AV, Gryadunov DA, Zimenkov DV. Molecular Mechanisms of Drug Tolerance in Mycobacterium tuberculosis. Mol Biol 2018. [DOI: 10.1134/s0026893318030020] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Banaei-Esfahani A, Nicod C, Aebersold R, Collins BC. Systems proteomics approaches to study bacterial pathogens: application to Mycobacterium tuberculosis. Curr Opin Microbiol 2017; 39:64-72. [PMID: 29032348 DOI: 10.1016/j.mib.2017.09.013] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2017] [Revised: 09/15/2017] [Accepted: 09/26/2017] [Indexed: 12/13/2022]
Abstract
Significant developments and improvements in basic and clinical research notwithstanding, infectious diseases still claim at least 13 million lives annually. Classical research approaches have deciphered many molecular mechanisms underlying infection. Today it is increasingly recognized that multiple molecular mechanisms cooperate to constitute a complex system that is used by a given pathogen to interfere with the biochemical processes of the host. Therefore, systems-level approaches now complement the standard molecular biology techniques to investigate pathogens and their interactions with the human host. Here we review omic studies in Mycobacterium tuberculosis, the causative agent of tuberculosis, with a particular focus on proteomic methods and their application to the bacilli. Likewise, the discussed methods are directly portable to other bacterial pathogens.
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Affiliation(s)
- Amir Banaei-Esfahani
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland; PhD Program in Systems Biology, Life Science Zurich Graduate School, University of Zurich and ETH Zurich, Zurich, Switzerland
| | - Charlotte Nicod
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland; PhD Program in Systems Biology, Life Science Zurich Graduate School, University of Zurich and ETH Zurich, Zurich, Switzerland
| | - Ruedi Aebersold
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland; Faculty of Science, University of Zurich, Zurich, Switzerland.
| | - Ben C Collins
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland.
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Anthony RM. Sputum Microscopy and Mycobacterium tuberculosis Infectiousness. J Infect Dis 2017; 216:507-508. [PMID: 28510701 DOI: 10.1093/infdis/jix231] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2017] [Accepted: 05/09/2017] [Indexed: 11/14/2022] Open
Affiliation(s)
- Richard M Anthony
- Center for Infectious Disease Research, Diagnostics, and Perinatal Screening, National Institute for Public Health and the Environment, Bilthoven, The Netherlands
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de Knegt GJ, Dickinson L, Pertinez H, Evangelopoulos D, McHugh TD, Bakker-Woudenberg IAJM, Davies GR, de Steenwinkel JEM. Assessment of treatment response by colony forming units, time to culture positivity and the molecular bacterial load assay compared in a mouse tuberculosis model. Tuberculosis (Edinb) 2017; 105:113-118. [PMID: 28610782 DOI: 10.1016/j.tube.2017.05.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2016] [Revised: 05/01/2017] [Accepted: 05/07/2017] [Indexed: 01/03/2023]
Abstract
The aim of the study is to compare counting of colony forming units (CFU), the time to positivity (TTP) assay and the molecular bacterial load (MBL) assay, and explore whether the last assays can detect a subpopulation which is unable to grown on solid media. CFU counting, TTP and the MBL assay were used to determine the mycobacterial load in matched lung samples of a murine tuberculosis model. Mice were treated for 24 weeks with 4 treatment arms: isoniazid (H) - rifampicin (R) - pyrazinamide (Z), HRZ-Streptomycin (S), HRZ - ethambutol (E) or ZES. Inverse relationships were observed when comparing TPP with CFU or MBL. Positive associations were observed when comparing CFU with MBL. Description of the net elimination of bacteria was performed for CFU vs. time, MBL vs. time and 1/TTP vs. time and fitted by nonlinear regression. CFU vs. time and 1/TTP vs. time showed bi-phasic declines with the exception of HRZE. A similar rank order, based on the alpha slope, was found comparing CFU vs. time and TTP vs. time, respectively HRZE, HRZ, HRZS and ZES. In contrast, MBL vs. time showed a mono-phasic decline with a flat gradient of elimination and a different rank order respectively, ZES, HRZ, HRZE and HRZS. The correlations found between methods reflects the ability of each to discern the general mycobacterial load. Based on the description of net elimination, we conclude that the MBL assay can detect a subpopulation of Mycobacterium tuberculosis which is not detected by the CFU or TTP assays.
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Affiliation(s)
- Gerjo J de Knegt
- Erasmus MC, University Medical Centre Rotterdam, Department of Medical Microbiology & Infectious Diseases, Rotterdam, The Netherlands.
| | - Laura Dickinson
- Department of Molecular & Clinical Pharmacology, University of Liverpool, Liverpool, United Kingdom
| | - Henry Pertinez
- Department of Molecular & Clinical Pharmacology, University of Liverpool, Liverpool, United Kingdom
| | | | - Timothy D McHugh
- Centre for Clinical Microbiology, University College London, London, United Kingdom
| | - Irma A J M Bakker-Woudenberg
- Erasmus MC, University Medical Centre Rotterdam, Department of Medical Microbiology & Infectious Diseases, Rotterdam, The Netherlands
| | - Gerry R Davies
- Department of Molecular & Clinical Pharmacology, University of Liverpool, Liverpool, United Kingdom
| | - Jurriaan E M de Steenwinkel
- Erasmus MC, University Medical Centre Rotterdam, Department of Medical Microbiology & Infectious Diseases, Rotterdam, The Netherlands
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