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Shitikov E, Bespiatykh D. A revised SNP-based barcoding scheme for typing Mycobacterium tuberculosis complex isolates. mSphere 2023; 8:e0016923. [PMID: 37314207 PMCID: PMC10449489 DOI: 10.1128/msphere.00169-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Accepted: 04/28/2023] [Indexed: 06/15/2023] Open
Abstract
The development of whole-genome sequencing technologies is gradually leading to a more detailed description of the population structure of the Mycobacterium tuberculosis complex (MTBC). In this study, we correlated previously published classifications on a collection of more than 10,000 genomes and proposed a new, comprehensive nomenclature that unifies the existing ones. In total, we identified 169 lineages and sublineages of M. tuberculosis/M. africanum and 9 animal-adapted species. For the purpose of organizing these genotypes in a more streamlined manner, we stratified them into five hierarchical levels. To represent the classification and compare it with the reference, we compiled a confirmatory data set of 670 high-quality isolates, which includes all genotypes and species of MTBC, and this confirmatory data set can serve as a basis for further studies. We proposed a set of 213 robust barcoding single-nucleotide polymorphisms and a suitable workflow for reliable differentiation of genotypes and species within the complex. This work integrates the results of all the major systematized studies to date to provide an understanding of the global diversity of the MTBC population structure. The results of this work may ultimately help to reliably determine the pathogen genotype and associate it with traits that reflect its prevalence, virulence, vaccination, and treatment efficiency, as well as to reliably find natural features revealed during its spread. IMPORTANCE Through years of research into the Mycobacterium tuberculosis complex (MTBC), a number of ambiguous phylogenetic classifications have emerged, which often overlap with one another. In the present study, we have combined all major studies on MTBC classification and inferred a unified, most complete to date classification and accompanying SNP barcodes.
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Affiliation(s)
- Egor Shitikov
- Department of biomedicine and genomics, Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, Russia
| | - Dmitry Bespiatykh
- Department of biomedicine and genomics, Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, Russia
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Kornienko M, Bespiatykh D, Gorodnichev R, Abdraimova N, Shitikov E. Transcriptional Landscapes of Herelleviridae Bacteriophages and Staphylococcus aureus during Phage Infection: An Overview. Viruses 2023; 15:1427. [PMID: 37515114 PMCID: PMC10383478 DOI: 10.3390/v15071427] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 06/16/2023] [Accepted: 06/22/2023] [Indexed: 07/30/2023] Open
Abstract
The issue of antibiotic resistance in healthcare worldwide has led to a pressing need to explore and develop alternative approaches to combat infectious diseases. Among these methods, phage therapy has emerged as a potential solution to tackle this growing challenge. Virulent phages of the Herelleviridae family, known for their ability to cause lysis of Staphylococcus aureus, a clinically significant pathogen frequently associated with multidrug resistance, have proven to be one of the most effective viruses utilized in phage therapy. In order to utilize phages for therapeutic purposes effectively, a thorough investigation into their physiology and mechanisms of action on infected cells is essential. The use of omics technologies, particularly total RNA sequencing, is a promising approach for analyzing the interaction between phages and their hosts, allowing for the assessment of both the behavior of the phage during infection and the cell's response. This review aims to provide a comprehensive overview of the physiology of the Herelleviridae family, utilizing existing analyses of their total phage transcriptomes. Additionally, it sheds light on the changes that occur in the metabolism of S. aureus when infected with virulent bacteriophages, contributing to a deeper understanding of the phage-host interaction.
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Affiliation(s)
- Maria Kornienko
- Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency Medicine, Moscow 119435, Russia
| | - Dmitry Bespiatykh
- Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency Medicine, Moscow 119435, Russia
| | - Roman Gorodnichev
- Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency Medicine, Moscow 119435, Russia
| | - Narina Abdraimova
- Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency Medicine, Moscow 119435, Russia
| | - Egor Shitikov
- Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency Medicine, Moscow 119435, Russia
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3
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Mokrousov I, Vyazovaya A, Shitikov E, Badleeva M, Belopolskaya O, Bespiatykh D, Gerasimova A, Ioannidis P, Jiao W, Khromova P, Masharsky A, Naizabayeva D, Papaventsis D, Pasechnik O, Perdigão J, Rastogi N, Shen A, Sinkov V, Skiba Y, Solovieva N, Tafaj S, Valcheva V, Kostyukova I, Zhdanova S, Zhuravlev V, Ogarkov O. Insight into pathogenomics and phylogeography of hypervirulent and highly-lethal Mycobacterium tuberculosis strain cluster. BMC Infect Dis 2023; 23:426. [PMID: 37353765 DOI: 10.1186/s12879-023-08413-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2023] [Accepted: 06/21/2023] [Indexed: 06/25/2023] Open
Abstract
BACKGROUND . The Mycobacterium tuberculosis Beijing genotype is globally spread lineage with important medical properties that however vary among its subtypes. M. tuberculosis Beijing 14717-15-cluster was recently discovered as both multidrug-resistant, hypervirulent, and highly-lethal strain circulating in the Far Eastern region of Russia. Here, we aimed to analyze its pathogenomic features and phylogeographic pattern. RESULTS . The study collection included M. tuberculosis DNA collected between 1996 and 2020 in different world regions. The bacterial DNA was subjected to genotyping and whole genome sequencing followed by bioinformatics and phylogenetic analysis. The PCR-based assay to detect specific SNPs of the Beijing 14717-15-cluster was developed and used for its screening in the global collections. Phylogenomic and phylogeographic analysis confirmed endemic prevalence of the Beijing 14717-15-cluster in the Asian part of Russia, and distant common ancestor with isolates from Korea (> 115 SNPs). The Beijing 14717-15-cluster isolates had two common resistance mutations RpsL Lys88Arg and KatG Ser315Thr and belonged to spoligotype SIT269. The Russian isolates of this cluster were from the Asian Russia while 4 isolates were from the Netherlands and Spain. The cluster-specific SNPs that significantly affect the protein function were identified in silico in genes within different categories (lipid metabolism, regulatory proteins, intermediary metabolism and respiration, PE/PPE, cell wall and cell processes). CONCLUSIONS . We developed a simple method based on real-time PCR to detect clinically significant MDR and hypervirulent Beijing 14717-15-cluster. Most of the identified cluster-specific mutations were previously unreported and could potentially be associated with increased pathogenic properties of this hypervirulent M. tuberculosis strain. Further experimental study to assess the pathobiological role of these mutations is warranted.
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Affiliation(s)
- Igor Mokrousov
- Laboratory of Molecular Epidemiology and Evolutionary Genetics, St. Petersburg Pasteur Institute, St. Petersburg, Russia.
- Henan International Joint Laboratory of Children's Infectious Diseases, Henan Children's Hospital, Children's Hospital, Zhengzhou University, Zhengzhou Children's Hospital, Zhengzhou, China.
| | - Anna Vyazovaya
- Laboratory of Molecular Epidemiology and Evolutionary Genetics, St. Petersburg Pasteur Institute, St. Petersburg, Russia
| | - Egor Shitikov
- Department of Biomedicine and Genomics, Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, 119435, Russia
| | - Maria Badleeva
- Department of Infectious Diseases, Dorji Banzarov Buryat State University, Ulan-Ude, Buryatia, Russia
| | - Olesya Belopolskaya
- Resource Center Bio-bank Center, Research Park of St. Petersburg State University, St. Petersburg, Russia
- Laboratory of Genogeography, Vavilov Institute of General Genetics Russian Academy of Sciences Moscow, Moscow, Russia
| | - Dmitry Bespiatykh
- Department of Biomedicine and Genomics, Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, 119435, Russia
| | - Alena Gerasimova
- Laboratory of Molecular Epidemiology and Evolutionary Genetics, St. Petersburg Pasteur Institute, St. Petersburg, Russia
| | - Panayotis Ioannidis
- National Reference Laboratory for Mycobacteria, Sotiria Chest Diseases Hospital, Athens, Greece
| | - Weiwei Jiao
- National Clinical Research Center for Respiratory Diseases, Beijing Key Laboratory of Pediatric Respiratory Infection Disease, Beijing Children's Hospital, Beijing Pediatric Research Institute, Capital Medical University, National Center for Children's Health, Beijing, China
| | - Polina Khromova
- Department of Epidemiology and Microbiology, Scientific Centre of the Family Health and Human Reproduction Problems, Irkutsk, Russia
| | - Aleksey Masharsky
- Resource Center Bio-bank Center, Research Park of St. Petersburg State University, St. Petersburg, Russia
| | - Dinara Naizabayeva
- Laboratory of Molecular Biology, Almaty Branch of National Center for Biotechnology in Central Reference Laboratory, Almaty, Kazakhstan
- Department of Biotechnology, Al-Farabi Kazakh National University, Almaty, Kazakhstan
| | - Dimitrios Papaventsis
- National Reference Laboratory for Mycobacteria, Sotiria Chest Diseases Hospital, Athens, Greece
| | - Oksana Pasechnik
- Department of Public Health, Omsk State Medical University, Omsk, Russia
| | - João Perdigão
- iMed.ULisboa - Instituto de Investigação do Medicamento, Faculdade de Farmácia, Universidade de Lisboa, Lisbon, Portugal
| | - Nalin Rastogi
- WHO Supranational TB Reference Laboratory, Unité de la Tuberculose et des Mycobactéries, Institut Pasteur de la Guadeloupe, Abymes, Guadeloupe, France
| | - Adong Shen
- National Clinical Research Center for Respiratory Diseases, Beijing Key Laboratory of Pediatric Respiratory Infection Disease, Beijing Children's Hospital, Beijing Pediatric Research Institute, Capital Medical University, National Center for Children's Health, Beijing, China
- Henan Children's Hospital, Children's Hospital Affiliated to Zhengzhou University, Zhengzhou Children's Hospital, Zhengzhou, China
| | - Viacheslav Sinkov
- Department of Epidemiology and Microbiology, Scientific Centre of the Family Health and Human Reproduction Problems, Irkutsk, Russia
| | - Yuriy Skiba
- Laboratory of Molecular Biology, Almaty Branch of National Center for Biotechnology in Central Reference Laboratory, Almaty, Kazakhstan
| | - Natalia Solovieva
- St. Petersburg Research Institute of Phthisiopulmonology, St. Petersburg, Russia
| | - Silva Tafaj
- National Mycobacteria Reference Laboratory, University Hospital Shefqet Ndroqi, Tirana, Albania
| | - Violeta Valcheva
- Laboratory of Molecular Genetics of Mycobacteria, The Stephan Angeloff Institute of Microbiology, Bulgarian Academy of Sciences, Sofia, Bulgaria
| | - Irina Kostyukova
- Bacteriology laboratory, Clinical Tuberculosis Dispensary, Omsk, Russia
| | - Svetlana Zhdanova
- Department of Epidemiology and Microbiology, Scientific Centre of the Family Health and Human Reproduction Problems, Irkutsk, Russia
| | - Viacheslav Zhuravlev
- St. Petersburg Research Institute of Phthisiopulmonology, St. Petersburg, Russia
| | - Oleg Ogarkov
- Department of Epidemiology and Microbiology, Scientific Centre of the Family Health and Human Reproduction Problems, Irkutsk, Russia
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Merker M, Rasigade JP, Barbier M, Cox H, Feuerriegel S, Kohl TA, Shitikov E, Klaos K, Gaudin C, Antoine R, Diel R, Borrell S, Gagneux S, Nikolayevskyy V, Andres S, Crudu V, Supply P, Niemann S, Wirth T. Transcontinental spread and evolution of Mycobacterium tuberculosis W148 European/Russian clade toward extensively drug resistant tuberculosis. Nat Commun 2022; 13:5105. [PMID: 36042200 PMCID: PMC9426364 DOI: 10.1038/s41467-022-32455-1] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Accepted: 08/01/2022] [Indexed: 11/09/2022] Open
Abstract
Transmission-driven multi-/extensively drug resistant (M/XDR) tuberculosis (TB) is the largest single contributor to human mortality due to antimicrobial resistance. A few major clades of the Mycobacterium tuberculosis complex belonging to lineage 2, responsible for high prevalence of MDR-TB in Eurasia, show outstanding transnational distributions. Here, we determined factors underlying the emergence and epidemic spread of the W148 clade by genome sequencing and Bayesian demogenetic analyses of 720 isolates from 23 countries. We dated a common ancestor around 1963 and identified two successive epidemic expansions in the late 1980s and late 1990s, coinciding with major socio-economic changes in the post-Soviet Era. These population expansions favored accumulation of resistance mutations to up to 11 anti-TB drugs, with MDR evolving toward additional resistances to fluoroquinolones and second-line injectable drugs within 20 years on average. Timescaled haplotypic density analysis revealed that widespread acquisition of compensatory mutations was associated with transmission success of XDR strains. Virtually all W148 strains harbored a hypervirulence-associated ppe38 gene locus, and incipient recurrent emergence of prpR mutation-mediated drug tolerance was detected. The outstanding genetic arsenal of this geographically widespread M/XDR strain clade represents a “perfect storm” that jeopardizes the successful introduction of new anti-M/XDR-TB antibiotic regimens. An outbreak of the multidrug-resistant Mycobacterium tuberculosis lineage W148 has spread widely across Russia, Central Asia and Europe. Here, the authors use whole genome sequences of ~700 isolates of this lineage collected over ~20 years to analyze its spread, evolution of drug resistance, and impact of compensatory mutations.
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Affiliation(s)
- Matthias Merker
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Germany.,German Center for Infection Research, Partner site Hamburg-Lübeck-Borstel-Riems, Borstel, Germany.,Evolution of the Resistome, Research Center Borstel, Borstel, Germany
| | - Jean-Philippe Rasigade
- EPHE, PSL University, Paris, France.,Institut de Systématique, Evolution, Biodiversité, ISYEB, Muséum national d'Histoire naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, Paris, France.,Centre International de Recherche en Infectiologie, INSERM U1111, CNRS UMR5308, Université Lyon 1, ENS de Lyon, Lyon, France
| | - Maxime Barbier
- EPHE, PSL University, Paris, France.,Institut de Systématique, Evolution, Biodiversité, ISYEB, Muséum national d'Histoire naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, Paris, France
| | - Helen Cox
- Division of Medical Microbiology and Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Silke Feuerriegel
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Germany.,German Center for Infection Research, Partner site Hamburg-Lübeck-Borstel-Riems, Borstel, Germany
| | - Thomas A Kohl
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Germany.,German Center for Infection Research, Partner site Hamburg-Lübeck-Borstel-Riems, Borstel, Germany
| | - Egor Shitikov
- Federal Research and Clinical Centre of Physical-Chemical Medicine, Moscow, Russian Federation
| | - Kadri Klaos
- SA TUH United Laboratories, Mycobacteriology, Tartu, Estonia
| | | | - Rudy Antoine
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019 - UMR 9017 - CIIL - Centre d'Infection et d'Immunité de Lille, F-59000, Lille, France
| | - Roland Diel
- Institute for Epidemiology, Schleswig-Holstein University Hospital, Kiel, Germany.,Lung Clinic Grosshansdorf, German Center for Lung Research (DZL), Airway Research Center North (ARCN), 22927, Großhansdorf, Germany
| | - Sonia Borrell
- Swiss Tropical and Public Health Institute, Allschwil, Switzerland.,University of Basel, Basel, Switzerland
| | - Sebastien Gagneux
- Swiss Tropical and Public Health Institute, Allschwil, Switzerland.,University of Basel, Basel, Switzerland
| | | | - Sönke Andres
- National and WHO Supranational Reference Center for Mycobacteria, Research Center Borstel, Borstel, Germany
| | - Valeriu Crudu
- National TB Reference Laboratory, Institute of Phthisiopneumology, Chisinau, Moldova
| | - Philip Supply
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019 - UMR 9017 - CIIL - Centre d'Infection et d'Immunité de Lille, F-59000, Lille, France.
| | - Stefan Niemann
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Germany. .,German Center for Infection Research, Partner site Hamburg-Lübeck-Borstel-Riems, Borstel, Germany.
| | - Thierry Wirth
- EPHE, PSL University, Paris, France. .,Institut de Systématique, Evolution, Biodiversité, ISYEB, Muséum national d'Histoire naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, Paris, France.
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5
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Shitikov E, Bespiatykh D, Malakhova M, Bespyatykh J, Bodoev I, Vedekhina T, Zaychikova M, Veselovsky V, Klimina K, Ilina E, Varizhuk A. Genome-Wide Transcriptional Response of Mycobacterium smegmatis MC2155 to G-Quadruplex Ligands BRACO-19 and TMPyP4. Front Microbiol 2022; 13:817024. [PMID: 35308348 PMCID: PMC8931766 DOI: 10.3389/fmicb.2022.817024] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Accepted: 02/15/2022] [Indexed: 12/13/2022] Open
Abstract
G-quadruplexes (G4s) are non-canonical DNA structures that could be considered as potential therapeutic targets for antimicrobial compounds, also known as G4-stabilizing ligands. While some of these ligands are shown in vitro to have a stabilizing effect, the precise mechanism of antibacterial action has not been fully investigated. Here, we employed genome-wide RNA-sequencing to analyze the response of Mycobacterium smegmatis to inhibitory concentrations of BRACO-19 and TMPyP4 G4 ligands. The expression profile changed (FDR < 0.05, log2FC > |1|) for 822 (515↑; 307↓) genes in M. smegmatis in response to BRACO-19 and for 680 (339↑; 341↓) genes in response to TMPyP4. However, the analysis revealed no significant ligand-induced changes in the expression levels of G4-harboring genes, genes under G4-harboring promoters, or intergenic regions located on mRNA-like or template strands. Meanwhile, for the BRACO-19 ligand, we found significant changes in the replication and repair system genes, as well as in iron metabolism genes which is, undoubtedly, evidence of the induced stress. For the TMPyP4 compound, substantial changes were found in transcription factors and the arginine biosynthesis system, which may indicate multiple biological targets for this compound.
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Bodoev I, Malakhova M, Bespyatykh J, Bespiatykh D, Arapidi G, Pobeguts O, Zgoda V, Shitikov E, Ilina E. Substitutions in SurA and BamA Lead to Reduced Susceptibility to Broad Range Antibiotics in Gonococci. Genes (Basel) 2021; 12:1312. [PMID: 34573293 PMCID: PMC8467665 DOI: 10.3390/genes12091312] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Revised: 08/18/2021] [Accepted: 08/24/2021] [Indexed: 11/29/2022] Open
Abstract
There is growing concern about the emergence and spread of multidrug-resistant Neisseria gonorrhoeae. To effectively control antibiotic-resistant bacterial pathogens, it is necessary to develop new antimicrobials and to understand the resistance mechanisms to existing antibiotics. In this study, we discovered the unexpected onset of drug resistance in N. gonorrhoeae caused by amino acid substitutions in the periplasmic chaperone SurA and the β-barrel assembly machinery component BamA. Here, we investigated the i19.05 clinical isolate with mutations in corresponding genes along with reduced susceptibility to penicillin, tetracycline, and azithromycin. The mutant strain NG05 (surAmut bamAmut, and penAmut) was obtained using the pan-susceptible n01.08 clinical isolate as a recipient in the transformation procedure. Comparative proteomic analysis of NG05 and n01.08 strains revealed significantly increased levels of other chaperones, Skp and FkpA, and some transport proteins. Efflux pump inhibition experiments demonstrated that the reduction in sensitivity was achieved due to the activity of efflux pumps. We hypothesize that the described mutations in the surA and bamA genes cause the qualitative and quantitative changes of periplasmic chaperones, which in turn alters the function of synthesized cell envelope proteins.
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Affiliation(s)
- Ivan Bodoev
- Federal Research and Clinical Center of Physical-Chemical Medicine, 119435 Moscow, Russia; (M.M.); (J.B.); (D.B.); (G.A.); (O.P.); (E.S.); (E.I.)
| | - Maja Malakhova
- Federal Research and Clinical Center of Physical-Chemical Medicine, 119435 Moscow, Russia; (M.M.); (J.B.); (D.B.); (G.A.); (O.P.); (E.S.); (E.I.)
| | - Julia Bespyatykh
- Federal Research and Clinical Center of Physical-Chemical Medicine, 119435 Moscow, Russia; (M.M.); (J.B.); (D.B.); (G.A.); (O.P.); (E.S.); (E.I.)
| | - Dmitry Bespiatykh
- Federal Research and Clinical Center of Physical-Chemical Medicine, 119435 Moscow, Russia; (M.M.); (J.B.); (D.B.); (G.A.); (O.P.); (E.S.); (E.I.)
| | - Georgij Arapidi
- Federal Research and Clinical Center of Physical-Chemical Medicine, 119435 Moscow, Russia; (M.M.); (J.B.); (D.B.); (G.A.); (O.P.); (E.S.); (E.I.)
- Moscow Institute of Physics and Technology, State University, 141701 Dolgoprudny, Russia
| | - Olga Pobeguts
- Federal Research and Clinical Center of Physical-Chemical Medicine, 119435 Moscow, Russia; (M.M.); (J.B.); (D.B.); (G.A.); (O.P.); (E.S.); (E.I.)
| | - Victor Zgoda
- Orekhovich Institute of Biomedical Chemistry, Russian Academy of Medical Sciences, 119121 Moscow, Russia;
| | - Egor Shitikov
- Federal Research and Clinical Center of Physical-Chemical Medicine, 119435 Moscow, Russia; (M.M.); (J.B.); (D.B.); (G.A.); (O.P.); (E.S.); (E.I.)
| | - Elena Ilina
- Federal Research and Clinical Center of Physical-Chemical Medicine, 119435 Moscow, Russia; (M.M.); (J.B.); (D.B.); (G.A.); (O.P.); (E.S.); (E.I.)
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Abstract
Recent advances in MS/MS technology have made it possible to use proteomic data to predict protein-coding sequences. This approach is called proteogenomics, and it allows to correctly translate start and stop sites and to reveal new open reading frames. Here, we focus on using proteogenomics to improve the annotation of Mycobacteriumtuberculosis strains. We also describe detail procedures of the extraction of proteins and their further preparation for LC-MS/MS analysis and outline the main steps of data analysis.
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Affiliation(s)
- Julia Bespyatykh
- Federal Research and Clinical Center of Physical-Chemical Medicine, Moscow, Russia.
| | - Georgij Arapidi
- Federal Research and Clinical Center of Physical-Chemical Medicine, Moscow, Russia
| | - Egor Shitikov
- Federal Research and Clinical Center of Physical-Chemical Medicine, Moscow, Russia
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8
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Kornienko M, Fisunov G, Bespiatykh D, Kuptsov N, Gorodnichev R, Klimina K, Kulikov E, Ilina E, Letarov A, Shitikov E. Transcriptional Landscape of Staphylococcus aureus Kayvirus Bacteriophage vB_SauM-515A1. Viruses 2020; 12:E1320. [PMID: 33213043 PMCID: PMC7698491 DOI: 10.3390/v12111320] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Revised: 11/09/2020] [Accepted: 11/16/2020] [Indexed: 12/15/2022] Open
Abstract
The Twort-like myoviruses (Kayvirus genus) of S. aureus are promising agents for bacteriophage therapy due to a broad host range and high killing activity against clinical isolates. This work improves the current understanding of the phage infection physiology by transcriptome analysis. The expression profiles of a typical member of the Kayvirus genus (vB_SauM-515A1) were obtained at three time-points post-infection using RNA sequencing. A total of 35 transcription units comprising 238 ORFs were established. The sequences for 58 early and 12 late promoters were identified in the phage genome. The early promoters represent the strong sigma-70 promoters consensus sequence and control the host-dependent expression of 26 transcription units (81% of genes). The late promoters exclusively controlled the expression of four transcription units, while the transcription of the other five units was directed by both types of promoters. The characteristic features of late promoters were long -10 box of TGTTATATTA consensus sequence and the absence of -35 boxes. The data obtained are also of general interest, demonstrating a strategy of the phage genome expression with a broad overlap of the early and late transcription phases without any middle transcription, which is unusual for the large phage genomes (>100 kbp).
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Affiliation(s)
- Maria Kornienko
- Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, 119435 Moscow, Russia; (G.F.); (D.B.); (N.K.); (R.G.); (K.K.); (E.I.); (E.S.)
| | - Gleb Fisunov
- Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, 119435 Moscow, Russia; (G.F.); (D.B.); (N.K.); (R.G.); (K.K.); (E.I.); (E.S.)
| | - Dmitry Bespiatykh
- Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, 119435 Moscow, Russia; (G.F.); (D.B.); (N.K.); (R.G.); (K.K.); (E.I.); (E.S.)
| | - Nikita Kuptsov
- Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, 119435 Moscow, Russia; (G.F.); (D.B.); (N.K.); (R.G.); (K.K.); (E.I.); (E.S.)
| | - Roman Gorodnichev
- Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, 119435 Moscow, Russia; (G.F.); (D.B.); (N.K.); (R.G.); (K.K.); (E.I.); (E.S.)
| | - Ksenia Klimina
- Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, 119435 Moscow, Russia; (G.F.); (D.B.); (N.K.); (R.G.); (K.K.); (E.I.); (E.S.)
| | - Eugene Kulikov
- Research Center of Biotechnology of the Russian Academy of Sciences, Winogradsky Institute of Microbiology, 117312 Moscow, Russia; (E.K.); (A.L.)
| | - Elena Ilina
- Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, 119435 Moscow, Russia; (G.F.); (D.B.); (N.K.); (R.G.); (K.K.); (E.I.); (E.S.)
| | - Andrey Letarov
- Research Center of Biotechnology of the Russian Academy of Sciences, Winogradsky Institute of Microbiology, 117312 Moscow, Russia; (E.K.); (A.L.)
| | - Egor Shitikov
- Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, 119435 Moscow, Russia; (G.F.); (D.B.); (N.K.); (R.G.); (K.K.); (E.I.); (E.S.)
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9
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Kornienko M, Kuptsov N, Gorodnichev R, Bespiatykh D, Guliaev A, Letarova M, Kulikov E, Veselovsky V, Malakhova M, Letarov A, Ilina E, Shitikov E. Contribution of Podoviridae and Myoviridae bacteriophages to the effectiveness of anti-staphylococcal therapeutic cocktails. Sci Rep 2020; 10:18612. [PMID: 33122703 PMCID: PMC7596081 DOI: 10.1038/s41598-020-75637-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Accepted: 10/09/2020] [Indexed: 02/06/2023] Open
Abstract
Bacteriophage therapy is considered one of the most promising therapeutic approaches against multi-drug resistant bacterial infections. Infections caused by Staphylococcus aureus are very efficiently controlled with therapeutic bacteriophage cocktails, containing a number of individual phages infecting a majority of known pathogenic S. aureus strains. We assessed the contribution of individual bacteriophages comprising a therapeutic bacteriophage cocktail against S. aureus in order to optimize its composition. Two lytic bacteriophages vB_SauM-515A1 (Myoviridae) and vB_SauP-436A (Podoviridae) were isolated from the commercial therapeutic cocktail produced by Microgen (Russia). Host ranges of the phages were established on the panel of 75 S. aureus strains. Phage vB_SauM-515A1 lysed 85.3% and vB_SauP-436A lysed 68.0% of the strains, however, vB_SauP-436A was active against four strains resistant to vB_SauM-515A1, as well as to the therapeutic cocktail per se. Suboptimal results of the therapeutic cocktail application were due to extremely low vB_SauP-436A1 content in this composition. Optimization of the phage titers led to an increase in overall cocktail efficiency. Thus, one of the effective ways to optimize the phage cocktails design was demonstrated and realized by using bacteriophages of different families and lytic spectra.
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Affiliation(s)
- Maria Kornienko
- Federal Research and Clinical Center of Physical-Chemical Medicine, Moscow, Russia.
| | - Nikita Kuptsov
- Federal Research and Clinical Center of Physical-Chemical Medicine, Moscow, Russia
| | - Roman Gorodnichev
- Federal Research and Clinical Center of Physical-Chemical Medicine, Moscow, Russia
| | - Dmitry Bespiatykh
- Federal Research and Clinical Center of Physical-Chemical Medicine, Moscow, Russia
| | - Andrei Guliaev
- Federal Research and Clinical Center of Physical-Chemical Medicine, Moscow, Russia
| | - Maria Letarova
- Research Center of Biotechnology of the Russian Academy of Sciences, Winogradsky Institute of Microbiology, Moscow, Russia
| | - Eugene Kulikov
- Research Center of Biotechnology of the Russian Academy of Sciences, Winogradsky Institute of Microbiology, Moscow, Russia
| | - Vladimir Veselovsky
- Federal Research and Clinical Center of Physical-Chemical Medicine, Moscow, Russia
| | - Maya Malakhova
- Federal Research and Clinical Center of Physical-Chemical Medicine, Moscow, Russia
| | - Andrey Letarov
- Research Center of Biotechnology of the Russian Academy of Sciences, Winogradsky Institute of Microbiology, Moscow, Russia
| | - Elena Ilina
- Federal Research and Clinical Center of Physical-Chemical Medicine, Moscow, Russia
| | - Egor Shitikov
- Federal Research and Clinical Center of Physical-Chemical Medicine, Moscow, Russia
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10
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Acosta F, Norman A, Sambrano D, Batista V, Mokrousov I, Shitikov E, Jurado J, Mayrena M, Luque O, Garay M, Solís L, Muñoz P, Folkvardsen DB, Lillebaek T, Pérez-Lago L, Goodridge A, García de Viedma D. Probable long-term prevalence for a predominant Mycobacterium tuberculosis clone of a Beijing genotype in Colon, Panama. Transbound Emerg Dis 2020; 68:2229-2238. [PMID: 33048439 DOI: 10.1111/tbed.13875] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Revised: 09/24/2020] [Accepted: 10/06/2020] [Indexed: 11/26/2022]
Abstract
Beijing genotype Mycobacterium tuberculosis strains associate with increased virulence, resistance and/or higher transmission rates. This study describes a specific Beijing strain predominantly identified in the Panamanian province of Colon with one of the highest incidences of tuberculosis in the country. Retrospective mycobacterial interspersed repetitive unit/variable number of tandem repeats analysis of 42 isolates collected between January and August 2018 allowed to identify a cluster (Beijing A) with 17 (40.5%) Beijing isolates. Subsequent prospective strain-specific PCR-based surveillance from September 2019 to March 2020 confirmed the predominance of the Beijing A strain (44.1%) in this province. Whole-genome sequencing revealed higher-than-expected diversity within the cluster, suggesting long-term prevalence of this strain and low number of cases caused by recent transmission. The Beijing A strain belongs to the Asian African 3 (Bmyc13, L2.2.5) branch of the modern Beijing sublineage, with their closest isolates corresponding to cases from Vietnam, probably introduced in Panama between 2000 and 2012.
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Affiliation(s)
- Fermin Acosta
- Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain.,Hospital General Universitario Gregorio Marañón, Madrid, Spain
| | - Anders Norman
- International Reference Laboratory of Mycobacteriology, Statens Serum Institut, Copenhagen, Denmark
| | - Dilcia Sambrano
- Unidad de Investigaciones de Biomarcadores de Tuberculosis, Centro de Biología Celular y Molecular de Enfermedades-Instituto de Investigaciones Científicas y Servicios de Alta Tecnología (INDICASAT-AIP), Ciudad del Saber, Panama, Panama
| | - Victoria Batista
- Unidad de Investigaciones de Biomarcadores de Tuberculosis, Centro de Biología Celular y Molecular de Enfermedades-Instituto de Investigaciones Científicas y Servicios de Alta Tecnología (INDICASAT-AIP), Ciudad del Saber, Panama, Panama
| | - Igor Mokrousov
- Laboratory of Molecular Epidemiology and Evolutionary Genetics, St. Petersburg Pasteur Institute, St. Petersburg, Russia
| | - Egor Shitikov
- Federal Research and Clinical Center of Physical-Chemical Medicine, Moscow, Russia
| | | | | | - Odemaris Luque
- Programa de Control de Tuberculosis, Ministerio de Salud, Colón, Panama
| | - Maybis Garay
- Unidad de Investigaciones de Biomarcadores de Tuberculosis, Centro de Biología Celular y Molecular de Enfermedades-Instituto de Investigaciones Científicas y Servicios de Alta Tecnología (INDICASAT-AIP), Ciudad del Saber, Panama, Panama
| | - Laura Solís
- Programa de Control de Tuberculosis, Ministerio de Salud, Colón, Panama
| | - Patricia Muñoz
- Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain.,Hospital General Universitario Gregorio Marañón, Madrid, Spain.,Centro de Investigación Biomédica en Red Enfermedades Respiratorias (CIBERES), Spain.,Departamento de Medicina, Universidad Complutense de Madrid, Madrid, Spain
| | - Dorte B Folkvardsen
- International Reference Laboratory of Mycobacteriology, Statens Serum Institut, Copenhagen, Denmark
| | - Troels Lillebaek
- International Reference Laboratory of Mycobacteriology, Statens Serum Institut, Copenhagen, Denmark.,Global Health Section, Department of Public Health, University of Copenhagen, Copenhagen, Denmark
| | - Laura Pérez-Lago
- Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain.,Hospital General Universitario Gregorio Marañón, Madrid, Spain
| | - Amador Goodridge
- Unidad de Investigaciones de Biomarcadores de Tuberculosis, Centro de Biología Celular y Molecular de Enfermedades-Instituto de Investigaciones Científicas y Servicios de Alta Tecnología (INDICASAT-AIP), Ciudad del Saber, Panama, Panama
| | - Darío García de Viedma
- Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain.,Hospital General Universitario Gregorio Marañón, Madrid, Spain.,Centro de Investigación Biomédica en Red Enfermedades Respiratorias (CIBERES), Spain
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11
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Bespyatykh J, Bespiatykh D, Malakhova M, Klimina K, Bespyatykh A, Varizhuk A, Tevyashova A, Nikolenko T, Pozmogova G, Ilina E, Shitikov E. Aureolic Acid Group of Agents as Potential Antituberculosis Drugs. Antibiotics (Basel) 2020; 9:E715. [PMID: 33086595 PMCID: PMC7650759 DOI: 10.3390/antibiotics9100715] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Revised: 10/15/2020] [Accepted: 10/16/2020] [Indexed: 11/16/2022] Open
Abstract
Mycobacterium tuberculosis is one of the most dangerous pathogens. Bacterial resistance to antituberculosis drugs grows each year, but searching for new drugs is a long process. Testing for available drugs to find active against mycobacteria may be a good alternative. In this work, antibiotics of the aureolic acid group were tested on a model organism Mycobacterium smegmatis. We presumed that antibiotics of this group may be potential G4 ligands. However, this was not confirmed in our analyses. We determined the antimicrobial activity of these drugs and revealed morphological changes in the cell structure upon treatment. Transcriptomic analysis documented increased expression of MSMEG_3743/soj and MSMEG_4228/ftsW, involved in cell division. Therefore, drugs may affect cell division, possibly disrupting the function of the Z-ring and the formation of a septum. Additionally, a decrease in the transcription level of several indispensable genes, such as nitrate reductase subunits (MSMEG_5137/narI and MSMEG_5139/narX) and MSMEG_3205/hisD was shown. We concluded that the mechanism of action of aureolic acid and its related compounds may be similar to that bedaquiline and disturb the NAD+/NADH balance in the cell. All of this allowed us to conclude that aureolic acid derivatives can be considered as potential antituberculosis drugs.
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Affiliation(s)
- Julia Bespyatykh
- Federal Research and Clinical Centre of Physical-Chemical Medicine, 119435 Moscow, Russia; (D.B.); (M.M.); (K.K.); (A.V.); (T.N.); (G.P.); (E.I.); (E.S.)
| | - Dmitry Bespiatykh
- Federal Research and Clinical Centre of Physical-Chemical Medicine, 119435 Moscow, Russia; (D.B.); (M.M.); (K.K.); (A.V.); (T.N.); (G.P.); (E.I.); (E.S.)
| | - Maja Malakhova
- Federal Research and Clinical Centre of Physical-Chemical Medicine, 119435 Moscow, Russia; (D.B.); (M.M.); (K.K.); (A.V.); (T.N.); (G.P.); (E.I.); (E.S.)
| | - Ksenia Klimina
- Federal Research and Clinical Centre of Physical-Chemical Medicine, 119435 Moscow, Russia; (D.B.); (M.M.); (K.K.); (A.V.); (T.N.); (G.P.); (E.I.); (E.S.)
| | - Andrey Bespyatykh
- Institute of Fundamental Medicine and Biology, Kazan Federal University, 420008 Kazan, Russia;
| | - Anna Varizhuk
- Federal Research and Clinical Centre of Physical-Chemical Medicine, 119435 Moscow, Russia; (D.B.); (M.M.); (K.K.); (A.V.); (T.N.); (G.P.); (E.I.); (E.S.)
| | | | - Tatiana Nikolenko
- Federal Research and Clinical Centre of Physical-Chemical Medicine, 119435 Moscow, Russia; (D.B.); (M.M.); (K.K.); (A.V.); (T.N.); (G.P.); (E.I.); (E.S.)
- Moscow Institute of Physics and Technology, Dolgoprudny, 141700 Moscow, Russia
| | - Galina Pozmogova
- Federal Research and Clinical Centre of Physical-Chemical Medicine, 119435 Moscow, Russia; (D.B.); (M.M.); (K.K.); (A.V.); (T.N.); (G.P.); (E.I.); (E.S.)
| | - Elena Ilina
- Federal Research and Clinical Centre of Physical-Chemical Medicine, 119435 Moscow, Russia; (D.B.); (M.M.); (K.K.); (A.V.); (T.N.); (G.P.); (E.I.); (E.S.)
| | - Egor Shitikov
- Federal Research and Clinical Centre of Physical-Chemical Medicine, 119435 Moscow, Russia; (D.B.); (M.M.); (K.K.); (A.V.); (T.N.); (G.P.); (E.I.); (E.S.)
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12
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Bespyatykh J, Shitikov E, Bespiatykh D, Guliaev A, Klimina K, Veselovsky V, Arapidi G, Dogonadze M, Zhuravlev V, Ilina E, Govorun V. Metabolic Changes of Mycobacterium tuberculosis during the Anti-Tuberculosis Therapy. Pathogens 2020; 9:pathogens9020131. [PMID: 32085490 PMCID: PMC7168336 DOI: 10.3390/pathogens9020131] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Revised: 02/12/2020] [Accepted: 02/15/2020] [Indexed: 11/16/2022] Open
Abstract
Tuberculosis, caused by Mycobacterium tuberculosis complex bacteria, remains one of the most pressing health problems. Despite the general trend towards reduction of the disease incidence rate, the situation remains extremely tense due to the distribution of the resistant forms. Most often, these strains emerge through the intra-host microevolution of the pathogen during treatment failure. In the present study, the focus was on three serial clinical isolates of Mycobacterium tuberculosis Beijing B0/W148 cluster from one patient with pulmonary tuberculosis, to evaluate their changes in metabolism during anti-tuberculosis therapy. Using whole genome sequencing (WGS), 9 polymorphisms were determined, which occurred in a stepwise or transient manner during treatment and were linked to the resistance (GyrA D94A; inhA t-8a) or virulence. The effect of the inhA t-8a mutation was confirmed on both proteomic and transcriptomic levels. Additionally, the amount of RpsL protein, which is a target of anti-tuberculosis drugs, was reduced. At the systemic level, profound changes in metabolism, linked to the evolution of the pathogen in the host and the effects of therapy, were documented. An overabundance of the FAS-II system proteins (HtdX, HtdY) and expression changes in the virulence factors have been observed at the RNA and protein levels.
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Affiliation(s)
- Julia Bespyatykh
- Federal Research and Clinical Centre of Physical-Chemical Medicine, 119435 Moscow, Russia; (D.B.); (A.G.); (K.K.); (V.V.); (G.A.); (E.I.); (V.G.)
- Correspondence: (J.B.); (E.S.)
| | - Egor Shitikov
- Federal Research and Clinical Centre of Physical-Chemical Medicine, 119435 Moscow, Russia; (D.B.); (A.G.); (K.K.); (V.V.); (G.A.); (E.I.); (V.G.)
- Correspondence: (J.B.); (E.S.)
| | - Dmitry Bespiatykh
- Federal Research and Clinical Centre of Physical-Chemical Medicine, 119435 Moscow, Russia; (D.B.); (A.G.); (K.K.); (V.V.); (G.A.); (E.I.); (V.G.)
| | - Andrei Guliaev
- Federal Research and Clinical Centre of Physical-Chemical Medicine, 119435 Moscow, Russia; (D.B.); (A.G.); (K.K.); (V.V.); (G.A.); (E.I.); (V.G.)
| | - Ksenia Klimina
- Federal Research and Clinical Centre of Physical-Chemical Medicine, 119435 Moscow, Russia; (D.B.); (A.G.); (K.K.); (V.V.); (G.A.); (E.I.); (V.G.)
| | - Vladimir Veselovsky
- Federal Research and Clinical Centre of Physical-Chemical Medicine, 119435 Moscow, Russia; (D.B.); (A.G.); (K.K.); (V.V.); (G.A.); (E.I.); (V.G.)
| | - Georgij Arapidi
- Federal Research and Clinical Centre of Physical-Chemical Medicine, 119435 Moscow, Russia; (D.B.); (A.G.); (K.K.); (V.V.); (G.A.); (E.I.); (V.G.)
- Moscow Institute of Physics and Technology (State University), 141701 Dolgoprudny, Russia
| | - Marine Dogonadze
- Research Institute of Phtisiopulmonology, 191036 St. Petersburg, Russia; (M.D.); (V.Z.)
| | - Viacheslav Zhuravlev
- Research Institute of Phtisiopulmonology, 191036 St. Petersburg, Russia; (M.D.); (V.Z.)
| | - Elena Ilina
- Federal Research and Clinical Centre of Physical-Chemical Medicine, 119435 Moscow, Russia; (D.B.); (A.G.); (K.K.); (V.V.); (G.A.); (E.I.); (V.G.)
| | - Vadim Govorun
- Federal Research and Clinical Centre of Physical-Chemical Medicine, 119435 Moscow, Russia; (D.B.); (A.G.); (K.K.); (V.V.); (G.A.); (E.I.); (V.G.)
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13
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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14
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Shitikov E, Guliaev A, Bespyatykh J, Malakhova M, Kolchenko S, Smirnov G, Merker M, Niemann S, Mokrousov I, Ilina E, Govorun V. The role of IS6110 in micro- and macroevolution of Mycobacterium tuberculosis lineage 2. Mol Phylogenet Evol 2019; 139:106559. [PMID: 31302224 DOI: 10.1016/j.ympev.2019.106559] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Revised: 05/16/2019] [Accepted: 07/10/2019] [Indexed: 11/29/2022]
Abstract
The insertion sequence 6110 (IS6110) is the most studied transposable element in the Mycobacterium tuberculosis complex species. The element plays a significant role in genome plasticity of this important human pathogen, but still many causes and consequences of its transposition have not been fully studied. Here, we analyzed insertion sites for 902 Mycobacterium tuberculosis lineage 2 strains using whole-genome sequencing data. In total, 17,972 insertions were found, corresponding to 827 independent positions in the genome of the reference strain H37Rv. To trace the history of IS6110 expansion since proto-Beijing strains up to modern sublineages, we looked at the distribution of IS6110 across the genome-wide SNP-based phylogenetic tree. This analysis demonstrated a stepwise transposition of IS6110 that occurs by «copy-and-paste» mechanism. Additionally, we detected evolutionary-scale and sublineage-specific integration sites, which can be used for typing and for understanding the reasons for the success of the lineage. A significant part of such insertions affected the genes that are essential for the pathogen. Finally, we identified and confirmed deletions that occurred between differently oriented elements, which is uncommon for this family of insertion elements and appears to be another mechanism of genome variability.
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Affiliation(s)
- 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
| | - Julia Bespyatykh
- Federal Research and Clinical Centre of Physical-Chemical Medicine, Moscow, Russian Federation
| | - Maja Malakhova
- Federal Research and Clinical Centre of Physical-Chemical Medicine, Moscow, Russian Federation
| | - Sergey Kolchenko
- Federal Research and Clinical Centre of Physical-Chemical Medicine, Moscow, Russian Federation
| | - Georgy Smirnov
- Federal Research and Clinical Centre of Physical-Chemical Medicine, Moscow, Russian Federation
| | - Matthias Merker
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Leibniz Lung Center, Borstel, Germany; German Center for Infection Research, Partner Site Hamburg-Lübeck-Borstel-Riems, Germany
| | - Stefan Niemann
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Leibniz Lung Center, Borstel, Germany; German Center for Infection Research, Partner Site Hamburg-Lübeck-Borstel-Riems, Germany
| | - 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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15
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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] [What about the content of this article? (0)] [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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16
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Mokrousov I, Shitikov E, Skiba Y, Kolchenko S, Chernyaeva E, Vyazovaya A. Emerging peak on the phylogeographic landscape of Mycobacterium tuberculosis in West Asia: Definitely smoke, likely fire. Mol Phylogenet Evol 2017; 116:202-212. [DOI: 10.1016/j.ympev.2017.09.002] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2017] [Revised: 08/31/2017] [Accepted: 09/05/2017] [Indexed: 12/16/2022]
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17
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Ischenko D, Alexeev D, Shitikov E, Kanygina A, Malakhova M, Kostryukova E, Larin A, Kovalchuk S, Pobeguts O, Butenko I, Anikanov N, Altukhov I, Ilina E, Govorun V. Large scale analysis of amino acid substitutions in bacterial proteomics. BMC Bioinformatics 2016; 17:450. [PMID: 27821049 PMCID: PMC5100282 DOI: 10.1186/s12859-016-1301-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2016] [Accepted: 10/21/2016] [Indexed: 11/17/2022] Open
Abstract
BACKGROUND Proteomics of bacterial pathogens is a developing field exploring microbial physiology, gene expression and the complex interactions between bacteria and their hosts. One of the complications in proteomic approach is micro- and macro-heterogeneity of bacterial species, which makes it impossible to build a comprehensive database of bacterial genomes for identification, while most of the existing algorithms rely largely on genomic data. RESULTS Here we present a large scale study of identification of single amino acid polymorphisms between bacterial strains. An ad hoc method was developed based on MS/MS spectra comparison without the support of a genomic database. Whole-genome sequencing was used to validate the accuracy of polymorphism detection. Several approaches presented earlier to the proteomics community as useful for polymorphism detection were tested on isolates of Helicobacter pylori, Neisseria gonorrhoeae and Escherichia coli. CONCLUSION The developed method represents a perspective approach in the field of bacterial proteomics allowing to identify hundreds of peptides with novel SAPs from a single proteome.
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Affiliation(s)
- Dmitry Ischenko
- Research Institute of Physical Chemical Medicine, Malaya Pirogovskaya, 1a, Moscow, 119435, Russian Federation.
- Moscow Institute of Physics and Technology, Institutskiy pereulok, 9, Dolgoprudny, 141700, Russian Federation.
| | - Dmitry Alexeev
- Research Institute of Physical Chemical Medicine, Malaya Pirogovskaya, 1a, Moscow, 119435, Russian Federation
- Moscow Institute of Physics and Technology, Institutskiy pereulok, 9, Dolgoprudny, 141700, Russian Federation
| | - Egor Shitikov
- Research Institute of Physical Chemical Medicine, Malaya Pirogovskaya, 1a, Moscow, 119435, Russian Federation
| | - Alexandra Kanygina
- Research Institute of Physical Chemical Medicine, Malaya Pirogovskaya, 1a, Moscow, 119435, Russian Federation
- Moscow Institute of Physics and Technology, Institutskiy pereulok, 9, Dolgoprudny, 141700, Russian Federation
| | - Maja Malakhova
- Research Institute of Physical Chemical Medicine, Malaya Pirogovskaya, 1a, Moscow, 119435, Russian Federation
| | - Elena Kostryukova
- Research Institute of Physical Chemical Medicine, Malaya Pirogovskaya, 1a, Moscow, 119435, Russian Federation
| | - Andrey Larin
- Research Institute of Physical Chemical Medicine, Malaya Pirogovskaya, 1a, Moscow, 119435, Russian Federation
| | - Sergey Kovalchuk
- Research Institute of Physical Chemical Medicine, Malaya Pirogovskaya, 1a, Moscow, 119435, Russian Federation
| | - Olga Pobeguts
- Research Institute of Physical Chemical Medicine, Malaya Pirogovskaya, 1a, Moscow, 119435, Russian Federation
| | - Ivan Butenko
- Research Institute of Physical Chemical Medicine, Malaya Pirogovskaya, 1a, Moscow, 119435, Russian Federation
| | - Nikolay Anikanov
- Research Institute of Physical Chemical Medicine, Malaya Pirogovskaya, 1a, Moscow, 119435, Russian Federation
| | - Ilya Altukhov
- Research Institute of Physical Chemical Medicine, Malaya Pirogovskaya, 1a, Moscow, 119435, Russian Federation
- Moscow Institute of Physics and Technology, Institutskiy pereulok, 9, Dolgoprudny, 141700, Russian Federation
| | - Elena Ilina
- Research Institute of Physical Chemical Medicine, Malaya Pirogovskaya, 1a, Moscow, 119435, Russian Federation
| | - Vadim Govorun
- Research Institute of Physical Chemical Medicine, Malaya Pirogovskaya, 1a, Moscow, 119435, Russian Federation
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Bespyatykh J, Shitikov E, Butenko I, Altukhov I, Alexeev D, Mokrousov I, Dogonadze M, Zhuravlev V, Yablonsky P, Ilina E, Govorun V. Proteome analysis of the Mycobacterium tuberculosis Beijing B0/W148 cluster. Sci Rep 2016; 6:28985. [PMID: 27356881 PMCID: PMC4928086 DOI: 10.1038/srep28985] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2016] [Accepted: 06/13/2016] [Indexed: 12/18/2022] Open
Abstract
Beijing B0/W148, a "successful" clone of Mycobacterium tuberculosis, is widespread in the Russian Federation and some countries of the former Soviet Union. Here, we used label-free gel-LC-MS/MS shotgun proteomics to discover features of Beijing B0/W148 strains that could explain their success. Qualitative and quantitative proteome analyses of Beijing B0/W148 strains allowed us to identify 1,868 proteins, including 266 that were differentially abundant compared with the control strain H37Rv. To predict the biological effects of the observed differences in protein abundances, we performed Gene Ontology analysis together with analysis of protein-DNA interactions using a gene regulatory network. Our results demonstrate that Beijing B0/W148 strains have increased levels of enzymes responsible for long-chain fatty acid biosynthesis, along with a coincident decrease in the abundance of proteins responsible for their degradation. Together with high levels of HsaA (Rv3570c) protein, involved in steroid degradation, these findings provide a possible explanation for the increased transmissibility of Beijing B0/W148 strains and their survival in host macrophages. Among other, we confirmed a very low level of the SseA (Rv3283) protein in Beijing B0/W148 characteristic for all «modern» Beijing strains, which could lead to increased DNA oxidative damage, accumulation of mutations, and potentially facilitate the development of drug resistance.
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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
| | - Ivan Butenko
- Federal Research and Clinical Centre of Physical-Chemical Medicine, Moscow, Russian Federation
| | - Ilya Altukhov
- Federal Research and Clinical Centre of Physical-Chemical Medicine, Moscow, Russian Federation
- Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Dmitry Alexeev
- Federal Research and Clinical Centre of Physical-Chemical Medicine, Moscow, Russian Federation
- Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Igor Mokrousov
- St. Petersburg Pasteur Institute, St. Petersburg, Russian Federation
| | - Marine Dogonadze
- Research Institute of Phtisiopulmonology, St. Petersburg, Russian Federation
| | | | - Peter Yablonsky
- Research Institute of Phtisiopulmonology, 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
- Moscow Institute of Physics and Technology, Dolgoprudny, Russia
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