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Genotypic properties of collection plague microbes strains from the natural plague foci of Kazakhstan. ACTA BIOMEDICA SCIENTIFICA 2022. [DOI: 10.29413/abs.2022-7.6.11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
Background. Epidemiological and epizootological monitoring of natural plague foci requires an integrated approach to solving problems, taking into account the phenotypic and genetic variability of Y. pestis and zoning of natural plague foci. The introduction of a new molecular genetic methodology aimed at studying the genomic polymorphism of the plague pathogen provides reliable results for the differentiation of not only groups, but also individual strains.The aim. To determine the genotypes of the plague microbe from different autonomous foci of the Republic of Kazakhstan.Materials and methods. 105 strains of Y. pestis isolated from various natural plague foci of Kazakhstan in 1951–2015 were studied. The phenotypic properties of the strains were studied using standard microbiological methods. A polymerase chain reaction (PCR) was used to detect fragments of the cafl, pst and YPO2088 genes. Multilocus variable number tandem repeat (VNTR) analysis (MLVA) was performed for 25 VNTR loci.Results. The phenotypic properties of the strains were preliminarily studied and the strains of the plague microbe were tested for specificity using the Pest-Quest test system (Kazakhstan). The PCR study confirmed the species-specific affiliation of Y. pestis strains. A variety of strains with typical phenotypic characteristics was revealed. MLVA for 25 key loci (MLVA25) revealed that the studied strains of the plague microbe are phylogenetically closest to the Mediaevalis biovar representatives. A phylogenetic tree of the studied strains has been obtained. It was found that 9 genotypes circulate on the territory of Kazakhstan, and their distribution in certain natural plague foci was determined.Conclusions. The resulting clustering indicates the relationship between the strain groups obtained on the dendrogram by the MLVA25 method and the territories of certain natural plague foci.
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Suntsov VV. Host Aspect of Territorial Expansion of the Plague Microbe Yersinia pestis from the Populations of the Tarbagan Marmot (Marmota sibirica). BIOL BULL+ 2021. [DOI: 10.1134/s1062359021080288] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Soloveva IV, Novikova NA, Tochilina AG, Belova IV, Kashnikov AY, Sashina TA, Zhirnov VA, Molodtsova SB. The Probiotic Strain Lactobacillus fermentum 39: Biochemical Properties, Genomic Features, and Antiviral Activity. Microbiology (Reading) 2021. [DOI: 10.1134/s0026261721020132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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Barbieri R, Signoli M, Chevé D, Costedoat C, Tzortzis S, Aboudharam G, Raoult D, Drancourt M. Yersinia pestis: the Natural History of Plague. Clin Microbiol Rev 2020; 34:e00044-19. [PMID: 33298527 PMCID: PMC7920731 DOI: 10.1128/cmr.00044-19] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
The Gram-negative bacterium Yersinia pestis is responsible for deadly plague, a zoonotic disease established in stable foci in the Americas, Africa, and Eurasia. Its persistence in the environment relies on the subtle balance between Y. pestis-contaminated soils, burrowing and nonburrowing mammals exhibiting variable degrees of plague susceptibility, and their associated fleas. Transmission from one host to another relies mainly on infected flea bites, inducing typical painful, enlarged lymph nodes referred to as buboes, followed by septicemic dissemination of the pathogen. In contrast, droplet inhalation after close contact with infected mammals induces primary pneumonic plague. Finally, the rarely reported consumption of contaminated raw meat causes pharyngeal and gastrointestinal plague. Point-of-care diagnosis, early antibiotic treatment, and confinement measures contribute to outbreak control despite residual mortality. Mandatory primary prevention relies on the active surveillance of established plague foci and ectoparasite control. Plague is acknowledged to have infected human populations for at least 5,000 years in Eurasia. Y. pestis genomes recovered from affected archaeological sites have suggested clonal evolution from a common ancestor shared with the closely related enteric pathogen Yersinia pseudotuberculosis and have indicated that ymt gene acquisition during the Bronze Age conferred Y. pestis with ectoparasite transmissibility while maintaining its enteric transmissibility. Three historic pandemics, starting in 541 AD and continuing until today, have been described. At present, the third pandemic has become largely quiescent, with hundreds of human cases being reported mainly in a few impoverished African countries, where zoonotic plague is mostly transmitted to people by rodent-associated flea bites.
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Affiliation(s)
- R Barbieri
- Aix-Marseille University, IRD, MEPHI, IHU Méditerranée Infection, Marseille, France
- Aix-Marseille University, CNRS, EFS, ADES, Marseille, France
- Fondation Méditerranée Infection, Marseille, France
| | - M Signoli
- Aix-Marseille University, CNRS, EFS, ADES, Marseille, France
| | - D Chevé
- Aix-Marseille University, CNRS, EFS, ADES, Marseille, France
| | - C Costedoat
- Aix-Marseille University, CNRS, EFS, ADES, Marseille, France
| | - S Tzortzis
- Ministère de la Culture, Direction Régionale des Affaires Culturelles de Provence-Alpes-Côte d'Azur, Service Régional de l'Archéologie, Aix-en-Provence, France
| | - G Aboudharam
- Aix-Marseille University, IRD, MEPHI, IHU Méditerranée Infection, Marseille, France
- Aix-Marseille University, Faculty of Odontology, Marseille, France
| | - D Raoult
- Aix-Marseille University, IRD, MEPHI, IHU Méditerranée Infection, Marseille, France
- Fondation Méditerranée Infection, Marseille, France
| | - M Drancourt
- Aix-Marseille University, IRD, MEPHI, IHU Méditerranée Infection, Marseille, France
- Fondation Méditerranée Infection, Marseille, France
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Yersinia pestis Plasminogen Activator. Biomolecules 2020; 10:biom10111554. [PMID: 33202679 PMCID: PMC7696990 DOI: 10.3390/biom10111554] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Revised: 11/12/2020] [Accepted: 11/12/2020] [Indexed: 12/18/2022] Open
Abstract
The Gram-negative bacterium Yersinia pestis causes plague, a fatal flea-borne anthropozoonosis, which can progress to aerosol-transmitted pneumonia. Y. pestis overcomes the innate immunity of its host thanks to many pathogenicity factors, including plasminogen activator, Pla. This factor is a broad-spectrum outer membrane protease also acting as adhesin and invasin. Y. pestis uses Pla adhesion and proteolytic capacity to manipulate the fibrinolytic cascade and immune system to produce bacteremia necessary for pathogen transmission via fleabite or aerosols. Because of microevolution, Y. pestis invasiveness has increased significantly after a single amino-acid substitution (I259T) in Pla of one of the oldest Y. pestis phylogenetic groups. This mutation caused a better ability to activate plasminogen. In paradox with its fibrinolytic activity, Pla cleaves and inactivates the tissue factor pathway inhibitor (TFPI), a key inhibitor of the coagulation cascade. This function in the plague remains enigmatic. Pla (or pla) had been used as a specific marker of Y. pestis, but its solitary detection is no longer valid as this gene is present in other species of Enterobacteriaceae. Though recovering hosts generate anti-Pla antibodies, Pla is not a good subunit vaccine. However, its deletion increases the safety of attenuated Y. pestis strains, providing a means to generate a safe live plague vaccine.
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Kislichkina AA, Platonov ME, Vagaiskaya AS, Bogun AG, Dentovskaya SV, Anisimov AP. Rational Taxonomy of Yersinia pestis. MOLECULAR GENETICS, MICROBIOLOGY AND VIROLOGY 2019. [DOI: 10.3103/s0891416819020058] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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7
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Kislichkina AA, Bogun AG, Kadnikova LA, Maiskaya NV, Solomentsev VI, Sizova AA, Dentovskaya SV, Balakhonov SV, Anisimov AP. Six Whole-Genome Assemblies of Yersinia pestis subsp. microtus bv. ulegeica (Phylogroup 0.PE5) Strains Isolated from Mongolian Natural Plague Foci. GENOME ANNOUNCEMENTS 2018; 6:e00536-18. [PMID: 29930050 PMCID: PMC6013636 DOI: 10.1128/genomea.00536-18] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Accepted: 05/14/2018] [Indexed: 12/04/2022]
Abstract
Here, we report the draft genome sequences of six Yersinia pestis subsp. microtus bv. ulegeica strains isolated from the territory of Mongolia and representing the 0.PE5 phylogroup circulating in populations of voles and picas.
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Affiliation(s)
| | - Alexandr G Bogun
- State Research Center for Applied Microbiology and Biotechnology, Obolensk, Russia
| | - Lidiya A Kadnikova
- State Research Center for Applied Microbiology and Biotechnology, Obolensk, Russia
| | - Nadezhda V Maiskaya
- State Research Center for Applied Microbiology and Biotechnology, Obolensk, Russia
| | - Viktor I Solomentsev
- State Research Center for Applied Microbiology and Biotechnology, Obolensk, Russia
| | - Angelika A Sizova
- State Research Center for Applied Microbiology and Biotechnology, Obolensk, Russia
| | | | - Sergey V Balakhonov
- Irkutsk Antiplague Research Institute of Siberia and the Far East, Irkutsk, Russia
| | - Andrey P Anisimov
- State Research Center for Applied Microbiology and Biotechnology, Obolensk, Russia
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Shi L, Yang G, Zhang Z, Xia L, Liang Y, Tan H, He J, Xu J, Song Z, Li W, Wang P. Reemergence of human plague in Yunnan, China in 2016. PLoS One 2018; 13:e0198067. [PMID: 29897940 PMCID: PMC5999221 DOI: 10.1371/journal.pone.0198067] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2017] [Accepted: 04/11/2018] [Indexed: 01/15/2023] Open
Abstract
The third plague pandemic originated from Yunnan Province, China in the middle of the 19th century. The last human plague epidemic in Yunnan occurred from 1986-2005. On June 6, 2016, a case of human plague was reported in the Xishuangbanna Prefecture, Yunnan. The patient suffered from primary septicemic plague after exposure to a dead house rat (Rattus flavipectus), which has been identified as the main plague reservoir in the local epizootic area. Moreover, a retrospective investigation identified another bubonic plague case in this area. Based on these data, human plague reemerged after a silent period of ten years. In this study, three molecular typing methods, including a clustered regularly interspaced short palindromic repeats (CRISPR) analysis, different region analysis (DFR), and multiple-locus variable number of tandem repeats analysis (MLVA), were used to illustrate the molecular characteristics of Yersinia pestis (Y. pestis) strains isolated in Yunnan. The DFR profiles of the strains isolated in Yunnan in 2016 were the same as the strains that had previously been isolated in this Rattus flavipectus plague focus. The c3 spacer present in the previously isolated strains was absent in the spacer arrays of the Ypc CRISPR loci of the strains isolated in 2016. The MLVA analysis using MLVA (14+12) showed that the strains isolated from the human plague case and host animal plague infection in 2016 in Yunnan displayed different molecular patterns than the strains that had previously been isolated from Yunnan and adjacent provinces.
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Affiliation(s)
- Liyuan Shi
- Yunnan Institute for Endemic Disease Control and Prevention, Yunnan, China
- Yunnan Provincial Key Laboratory for Zoonosis Control and Prevention, Yunnan, China
| | - Guirong Yang
- Yunnan Institute for Endemic Disease Control and Prevention, Yunnan, China
- Yunnan Provincial Key Laboratory for Zoonosis Control and Prevention, Yunnan, China
| | - Zhikai Zhang
- National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease control and Prevention, Changping, Beijing, China
- State Key Laboratory of Infectious Disease Prevention and Control, Beijing, China
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Disease, Zhejiang, China
| | - Lianxu Xia
- National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease control and Prevention, Changping, Beijing, China
- State Key Laboratory of Infectious Disease Prevention and Control, Beijing, China
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Disease, Zhejiang, China
| | - Ying Liang
- National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease control and Prevention, Changping, Beijing, China
- State Key Laboratory of Infectious Disease Prevention and Control, Beijing, China
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Disease, Zhejiang, China
| | - Hongli Tan
- Yunnan Institute for Endemic Disease Control and Prevention, Yunnan, China
- Yunnan Provincial Key Laboratory for Zoonosis Control and Prevention, Yunnan, China
| | - Jinrong He
- National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease control and Prevention, Changping, Beijing, China
- State Key Laboratory of Infectious Disease Prevention and Control, Beijing, China
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Disease, Zhejiang, China
| | - Jianguo Xu
- National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease control and Prevention, Changping, Beijing, China
- State Key Laboratory of Infectious Disease Prevention and Control, Beijing, China
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Disease, Zhejiang, China
| | - Zhizhong Song
- Yunnan Institute for Endemic Disease Control and Prevention, Yunnan, China
- Yunnan Provincial Key Laboratory for Zoonosis Control and Prevention, Yunnan, China
| | - Wei Li
- National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease control and Prevention, Changping, Beijing, China
- State Key Laboratory of Infectious Disease Prevention and Control, Beijing, China
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Disease, Zhejiang, China
| | - Peng Wang
- Yunnan Institute for Endemic Disease Control and Prevention, Yunnan, China
- Yunnan Provincial Key Laboratory for Zoonosis Control and Prevention, Yunnan, China
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Kislichkina AA, Solomentsev VI, Blagodatskikh SA, Kadnikova LA, Platonov ME, Maiskaya NV, Dubyanskiy VM, Bogun AG, Kulichenko AN, Anisimov AP. Three Genetically Different Lineages of Yersinia pestis subsp. Microtus bv. Caucasica (0.PE2) Strains Circulate among Common Voles in Natural Plague Foci in the Caucasus. MOLECULAR GENETICS, MICROBIOLOGY AND VIROLOGY 2018. [DOI: 10.3103/s0891416817040024] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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10
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Kutyrev VV, Eroshenko GA, Motin VL, Nosov NY, Krasnov JM, Kukleva LM, Nikiforov KA, Al’khova ZV, Oglodin EG, Guseva NP. Phylogeny and Classification of Yersinia pestis Through the Lens of Strains From the Plague Foci of Commonwealth of Independent States. Front Microbiol 2018; 9:1106. [PMID: 29887859 PMCID: PMC5980970 DOI: 10.3389/fmicb.2018.01106] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2018] [Accepted: 05/08/2018] [Indexed: 12/21/2022] Open
Abstract
The established phylogeny of the etiological agent of plague, Yersinia pestis, is not perfect, as it does not take into account the strains from numerous natural foci of Commonwealth of Independent States (CIS). We have carried out PCR and SNP typing of 359 strains and whole genome sequencing of 51 strains from these plague foci and determined the phylogenetic diversity of the strains circulating here. They belong to 0.ANT3, 0.ANT5, 2.ANT3, 4.ANT branches of antique biovar, 2.MED0, 2.MED1 branches of medieval biovar and to 0.PE2, 0.PE4a. 0.PE4h, 0.PE4t branches. Based on the studies of 178 strains from 23 plague foci of CIS countries, it was determined that the population structure of 2.MED strains is subdivided into Caucasian-Caspian and Central Asian-Chinese branches. In Central-Caucasian high-mountain plague foci in the Russian Federation (RF) the most deeply diverged branch of medieval biovar, 2.MED0, has been found. With the data obtained, the current population structure of Y. pestis species has been refined. New subspecies classification is developed, comprising seven subspecies: pestis, caucasica (0.PE2), angolica (0.PE3), central asiatica (0.PE4), tibetica (0.PE7), ulegeica (0.PE5), and qinghaica (0.PE10).
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Affiliation(s)
- Vladimir V. Kutyrev
- Russian Research Anti-Plague Institute “Microbe”, Federal Service for Surveillance in the Sphere of Consumers Rights Protection and Human Welfare, Saratov, Russia
| | - Galina A. Eroshenko
- Russian Research Anti-Plague Institute “Microbe”, Federal Service for Surveillance in the Sphere of Consumers Rights Protection and Human Welfare, Saratov, Russia
| | - Vladimir L. Motin
- Department of Pathology, University of Texas Medical Branch, Galveston, TX, United States
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, United States
| | - Nikita Y. Nosov
- Russian Research Anti-Plague Institute “Microbe”, Federal Service for Surveillance in the Sphere of Consumers Rights Protection and Human Welfare, Saratov, Russia
| | - Jaroslav M. Krasnov
- Russian Research Anti-Plague Institute “Microbe”, Federal Service for Surveillance in the Sphere of Consumers Rights Protection and Human Welfare, Saratov, Russia
| | - Lyubov M. Kukleva
- Russian Research Anti-Plague Institute “Microbe”, Federal Service for Surveillance in the Sphere of Consumers Rights Protection and Human Welfare, Saratov, Russia
| | - Konstantin A. Nikiforov
- Russian Research Anti-Plague Institute “Microbe”, Federal Service for Surveillance in the Sphere of Consumers Rights Protection and Human Welfare, Saratov, Russia
| | - Zhanna V. Al’khova
- Russian Research Anti-Plague Institute “Microbe”, Federal Service for Surveillance in the Sphere of Consumers Rights Protection and Human Welfare, Saratov, Russia
| | - Eugene G. Oglodin
- Russian Research Anti-Plague Institute “Microbe”, Federal Service for Surveillance in the Sphere of Consumers Rights Protection and Human Welfare, Saratov, Russia
| | - Natalia P. Guseva
- Russian Research Anti-Plague Institute “Microbe”, Federal Service for Surveillance in the Sphere of Consumers Rights Protection and Human Welfare, Saratov, Russia
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Kislichkina AA, Kadnikova LA, Platonov ME, Maiskaya NV, Kolombet LV, Solomentsev VI, Bogun AG, Anisimov AP. Differentiation of Yersinia pseudotuberculosis, Yersinia pestis subsp. pestis and subsp. microti strains and other representatives of Yersinia pseudotuberculosis complex. MOLECULAR GENETICS, MICROBIOLOGY AND VIROLOGY 2017. [DOI: 10.3103/s0891416817020070] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
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12
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Kislichkina AA, Bogun AG, Kadnikova LA, Maiskaya NV, Solomentsev VI, Platonov ME, Dentovskaya SV, Anisimov AP. Eight Whole-Genome Assemblies of Yersinia pestis subsp. microtus bv. caucasica Isolated from the Common Vole ( Microtus arvalis) Plague Focus in Dagestan, Russia. GENOME ANNOUNCEMENTS 2017; 5:e00847-17. [PMID: 28839028 PMCID: PMC5571414 DOI: 10.1128/genomea.00847-17] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 07/07/2017] [Accepted: 07/12/2017] [Indexed: 11/20/2022]
Abstract
We here report the draft genome sequences of 8 Yersinia pestis subsp. microtus bv. caucasica strains isolated from the East Caucasian (previous name, Dagestan) mountain focus (no. 39), representing the most ancient branch of the 0.PE2 phylogroup circulating in populations of common voles (Microtus arvalis).
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Affiliation(s)
| | - Aleksandr G Bogun
- State Research Center for Applied Microbiology and Biotechnology, Obolensk, Russia
| | - Lidiya A Kadnikova
- State Research Center for Applied Microbiology and Biotechnology, Obolensk, Russia
| | - Nadezhda V Maiskaya
- State Research Center for Applied Microbiology and Biotechnology, Obolensk, Russia
| | - Viktor I Solomentsev
- State Research Center for Applied Microbiology and Biotechnology, Obolensk, Russia
| | - Mikhail E Platonov
- State Research Center for Applied Microbiology and Biotechnology, Obolensk, Russia
| | | | - Andrey P Anisimov
- State Research Center for Applied Microbiology and Biotechnology, Obolensk, Russia
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Kopylov PK, Platonov ME, Ablamunits VG, Kombarova TI, Ivanov SA, Kadnikova LA, Somov AN, Dentovskaya SV, Uversky VN, Anisimov AP. Yersinia pestis Caf1 Protein: Effect of Sequence Polymorphism on Intrinsic Disorder Propensity, Serological Cross-Reactivity and Cross-Protectivity of Isoforms. PLoS One 2016; 11:e0162308. [PMID: 27606595 PMCID: PMC5015843 DOI: 10.1371/journal.pone.0162308] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2016] [Accepted: 08/19/2016] [Indexed: 12/11/2022] Open
Abstract
Yersinia pestis Caf1 is a multifunctional protein responsible for antiphagocytic activity and is a key protective antigen. It is generally conserved between globally distributed Y. pestis strains, but Y. pestis subsp. microtus biovar caucasica strains circulating within populations of common voles in Georgia and Armenia were reported to carry a single substitution of alanine to serine. We investigated polymorphism of the Caf1 sequences among other Y. pestis subsp. microtus strains, which have a limited virulence in guinea pigs and in humans. Sequencing of caf1 genes from 119 Y. pestis strains belonging to different biovars within subsp. microtus showed that the Caf1 proteins exist in three isoforms, the global type Caf1NT1 (Ala48 Phe117), type Caf1NT2 (Ser48 Phe117) found in Transcaucasian-highland and Pre-Araks natural plague foci #4-7, and a novel Caf1NT3 type (Ala48 Val117) endemic in Dagestan-highland natural plague focus #39. Both minor types are the progenies of the global isoform. In this report, Caf1 polymorphism was analyzed by comparing predicted intrinsic disorder propensities and potential protein-protein interactivities of the three Caf1 isoforms. The analysis revealed that these properties of Caf1 protein are minimally affected by its polymorphism. All protein isoforms could be equally detected by an immunochromatography test for plague at the lowest protein concentration tested (1.0 ng/mL), which is the detection limit. When compared to the classic Caf1NT1 isoform, the endemic Caf1NT2 or Caf1NT3 had lower immunoreactivity in ELISA and lower indices of self- and cross-protection. Despite a visible reduction in cross-protection between all Caf1 isoforms, our data suggest that polymorphism in the caf1 gene may not allow the carriers of Caf1NT2 or Caf1NT3 variants escaping from the Caf1NT1-mediated immunity to plague in the case of a low-dose flea-borne infection.
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Affiliation(s)
- Pavel Kh. Kopylov
- State Research Center for Applied Microbiology and Biotechnology, Obolensk, Moscow Region, Russia
| | - Mikhail E. Platonov
- State Research Center for Applied Microbiology and Biotechnology, Obolensk, Moscow Region, Russia
| | | | - Tat’yana I. Kombarova
- State Research Center for Applied Microbiology and Biotechnology, Obolensk, Moscow Region, Russia
| | - Sergey A. Ivanov
- State Research Center for Applied Microbiology and Biotechnology, Obolensk, Moscow Region, Russia
| | - Lidiya A. Kadnikova
- State Research Center for Applied Microbiology and Biotechnology, Obolensk, Moscow Region, Russia
| | - Aleksey N. Somov
- State Research Center for Applied Microbiology and Biotechnology, Obolensk, Moscow Region, Russia
| | - Svetlana V. Dentovskaya
- State Research Center for Applied Microbiology and Biotechnology, Obolensk, Moscow Region, Russia
| | - Vladimir N. Uversky
- Department of Molecular Medicine and Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, Florida, United States of America
- Laboratory of New Methods in Biology, Institute for Biological Instrumentation, Russian Academy of Sciences, Pushchino, Moscow Region, Russia
| | - Andrey P. Anisimov
- State Research Center for Applied Microbiology and Biotechnology, Obolensk, Moscow Region, Russia
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Shaban H, Na I, Kislichkina AA, Dentovskaya SV, Anisimov AP, Uversky VN. Effect of natural polymorphism on structure and function of the Yersinia pestis outer membrane porin F (OmpF protein): a computational study. J Biomol Struct Dyn 2016; 35:2588-2603. [PMID: 27593697 DOI: 10.1080/07391102.2016.1224734] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
The Yersinia pestis outer membrane porin F (OmpF) is a transmembrane protein located in the outer membrane of this Gram-negative bacterium which is the causative agent of plague, where it plays a significant role in controlling the selective permeability of the membrane. The amino acid sequences of OmpF proteins from 48 Y. pestis strains representing all currently available phylogenetic groups of this Gram-negative bacterium were recently deduced. Comparison of these amino acid sequences revealed that the OmpF can be present in four isoforms, the pestis-pestis type, and the pestis-microtus types I, II, and III. OmpF of the most recent pestis-pestis type has an alanine residue at the position 148, where all the pestis-microtus types have threonine there (T148A polymorphism). The variability of different pestis-microtus types is caused by an additional polymorphism at the 193rd position, where the OmpFs of the pestis-microtus type II and type III have isoleucine-glycine (IG+193) or isoleucine-glycine-isoleucine-glycine (IGIG+193) insertions, respectively (IG+193 and IGIG+193 polymorphism). To investigate potential effects of these sequence polymorphisms on the structural properties of the OmpF protein, we conducted multi-level computational analysis of its isoforms. Analysis of the I-TASSER-generated 3D-models revealed that the Yersinia OmpF is very similar to other non-specific enterobacterial porins. The T148A polymorphism affected a loop located in the external vestibule of the OmpF channel, whereas IG+193 and IGIG+193 polymorphisms affected one of its β-strands. Our analysis also suggested that polymorphism has moderate effect on the predicted local intrinsic disorder predisposition of OmpF, but might have some functional implementations.
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Affiliation(s)
- Hiba Shaban
- a Department of Molecular Medicine, Morsani College of Medicine , University of South Florida , Tampa 33612 , FL , USA
| | - Insing Na
- a Department of Molecular Medicine, Morsani College of Medicine , University of South Florida , Tampa 33612 , FL , USA
| | - Angelina A Kislichkina
- b State Research Center for Applied Microbiology and Biotechnology , Obolensk 142279 , Moscow Region , Russia
| | - Svetlana V Dentovskaya
- b State Research Center for Applied Microbiology and Biotechnology , Obolensk 142279 , Moscow Region , Russia
| | - Andrey P Anisimov
- b State Research Center for Applied Microbiology and Biotechnology , Obolensk 142279 , Moscow Region , Russia
| | - Vladimir N Uversky
- a Department of Molecular Medicine, Morsani College of Medicine , University of South Florida , Tampa 33612 , FL , USA.,c USF Health Byrd Alzheimer's Research Institute , Morsani College of Medicine, University of South Florida , Tampa 33612 , FL , USA.,d Laboratory of Structural Dynamics, Stability and Folding of Proteins , Institute of Cytology, Russian Academy of Sciences , St. Petersburg 194064 , Russia
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15
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Kislichkina AA, Bogun AG, Kadnikova LA, Maiskaya NV, Platonov ME, Anisimov NV, Galkina EV, Dentovskaya SV, Anisimov AP. Nineteen Whole-Genome Assemblies of Yersinia pestis subsp. microtus, Including Representatives of Biovars caucasica, talassica, hissarica, altaica, xilingolensis, and ulegeica. GENOME ANNOUNCEMENTS 2015; 3:e01342-15. [PMID: 26634751 PMCID: PMC4669392 DOI: 10.1128/genomea.01342-15] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 09/29/2015] [Accepted: 10/16/2015] [Indexed: 11/20/2022]
Abstract
The etiologic agent of plague, Yersinia pestis, includes two subspecies, of which Y. pestis subsp. microtus contains the strains that cause only occasional diseases in humans that are not accompanied by human-to-human transmission. Here, we report the draft genome sequences of 19 Y. pestis strains (across 6 biovars of Y. pestis subsp. microtus).
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Affiliation(s)
| | - Aleksandr G Bogun
- State Research Center for Applied Microbiology and Biotechnology, Obolensk, Russia
| | - Lidiya A Kadnikova
- State Research Center for Applied Microbiology and Biotechnology, Obolensk, Russia
| | - Nadezhda V Maiskaya
- State Research Center for Applied Microbiology and Biotechnology, Obolensk, Russia
| | - Mikhail E Platonov
- State Research Center for Applied Microbiology and Biotechnology, Obolensk, Russia
| | - Nikolai V Anisimov
- State Research Center for Applied Microbiology and Biotechnology, Obolensk, Russia
| | - Elena V Galkina
- State Research Center for Applied Microbiology and Biotechnology, Obolensk, Russia
| | | | - Andrey P Anisimov
- State Research Center for Applied Microbiology and Biotechnology, Obolensk, Russia
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16
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Vogler AJ, Keim P, Wagner DM. A review of methods for subtyping Yersinia pestis: From phenotypes to whole genome sequencing. INFECTION GENETICS AND EVOLUTION 2015; 37:21-36. [PMID: 26518910 DOI: 10.1016/j.meegid.2015.10.024] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2015] [Revised: 10/23/2015] [Accepted: 10/24/2015] [Indexed: 12/28/2022]
Abstract
Numerous subtyping methods have been applied to Yersinia pestis with varying success. Here, we review the various subtyping methods that have been applied to Y. pestis and their capacity for answering questions regarding the population genetics, phylogeography, and molecular epidemiology of this important human pathogen. Methods are evaluated in terms of expense, difficulty, transferability among laboratories, discriminatory power, usefulness for different study questions, and current applicability in light of the advent of whole genome sequencing.
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Affiliation(s)
- Amy J Vogler
- Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, AZ 86011-4073, USA.
| | - Paul Keim
- Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, AZ 86011-4073, USA; Translational Genomics Research Institute North, Flagstaff, AZ 86001, USA.
| | - David M Wagner
- Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, AZ 86011-4073, USA.
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17
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Evseeva VV, Platonov ME, Kopylov PK, Dentovskaya SV, Anisimov AP. PLASMINOGEN ACTIVATOR OF YERSINIA PESTIS. ACTA ACUST UNITED AC 2015. [DOI: 10.15789/2220-7619-2015-1-27-36] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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18
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Platonov ME, Evseeva VV, Efremenko DV, Afanas’ev MV, Verzhutski DB, Kuznetsova IV, Shestopalov MY, Dentovskaya SV, Kulichenko AN, Balakhonov SV, Anisimov AP. Intraspecies classification of rhamnose-positive Yersinia pestis strains from natural plague foci of Mongolia. MOLECULAR GENETICS MICROBIOLOGY AND VIROLOGY 2015. [DOI: 10.3103/s0891416815010073] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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