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Khabibullina NF, Kutuzova DM, Burmistrova IA, Lyadova IV. The Biological and Clinical Aspects of a Latent Tuberculosis Infection. Trop Med Infect Dis 2022; 7:tropicalmed7030048. [PMID: 35324595 PMCID: PMC8955876 DOI: 10.3390/tropicalmed7030048] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Revised: 03/04/2022] [Accepted: 03/04/2022] [Indexed: 01/22/2023] Open
Abstract
Tuberculosis (TB), caused by bacilli from the Mycobacterium tuberculosis complex, remains a serious global public health problem, representing one of the main causes of death from infectious diseases. About one quarter of the world’s population is infected with Mtb and has a latent TB infection (LTBI). According to the World Health Organization (WHO), an LTBI is characterized by a lasting immune response to Mtb antigens without any TB symptoms. Current LTBI diagnoses and treatments are based on this simplified definition, although an LTBI involves a broad range of conditions, including when Mtb remains in the body in a persistent form and the immune response cannot be detected. The study of LTBIs has progressed in recent years; however, many biological and medical aspects of an LTBI are still under discussion. This review focuses on an LTBI as a broad spectrum of states, both of the human body, and of Mtb cells. The problems of phenotypic insusceptibility, diagnoses, chemoprophylaxis, and the necessity of treatment are discussed. We emphasize the complexity of an LTBI diagnosis and its treatment due to its ambiguous nature. We consider alternative ways of differentiating an LTBI from active TB, as well as predicting TB reactivation based on using mycobacterial “latency antigens” for interferon gamma release assay (IGRA) tests and the transcriptomic analysis of human blood cells.
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Žiemytė M, Carda-Diéguez M, Rodríguez-Díaz JC, Ventero MP, Mira A, Ferrer MD. Real-time monitoring of Pseudomonas aeruginosa biofilm growth dynamics and persister cells' eradication. Emerg Microbes Infect 2021; 10:2062-2075. [PMID: 34663186 PMCID: PMC8583918 DOI: 10.1080/22221751.2021.1994355] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Revised: 09/16/2021] [Accepted: 10/12/2021] [Indexed: 01/11/2023]
Abstract
Biofilm formation and the appearance of persister cells with low metabolic rates are key factors affecting conventional treatment failure and antibiotic resistance. Using impedance-based measurements, crystal violet staining and traditional culture we have studied the biofilm growth dynamics of 13 Pseudomonas aeruginosa strains under the effect of seven conventional antibiotics. Real-time growth quantifications revealed that the exposure of established P. aeruginosa biofilms to certain concentrations of ciprofloxacin, ceftazidime and tobramycin induced the emergence of persister cells, that showed different morphology and pigmentation, as well increased antibiotic resistance. Whole-genome sequencing of wildtype and persister cells identified several SNPs, a genomic inversion and a genomic duplication in one of the strains. However, these mutations were not uniquely associated with persisters, suggesting that the persistent phenotype may be related to metabolic and transcriptional changes. Given that mannitol has been proposed to activate bacterial metabolism, the synergistic combination of mannitol and ciprofloxacin was evaluated on clinical 48 h P. aeruginosa biofilms. When administered at doses ≥320 mg/L, mannitol was capable of preventing persister cell formation by efficiently activating dormant bacteria and making them susceptible to the antibiotic. These results were confirmed using viable colony counting. As the tested ciprofloxacin-mannitol combination appeared to fully eradicate mature biofilms, we conclude that impedance-based biofilm diagnostics, which permits antibiotic susceptibility testing and the identification of persister cells, is of great potential for the clinical practice and could aid in establishing treatment breakpoints for emerging biofilm-related infections.
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Affiliation(s)
- Miglė Žiemytė
- Genomics & Health Department, FISABIO Foundation, Valencia, Spain
| | | | - Juan C. Rodríguez-Díaz
- Servicio de Microbiología, Hospital General Universitario de Alicante, ISABIAL, Alicante, Spain
| | - Maria P. Ventero
- Servicio de Microbiología, Hospital General Universitario de Alicante, ISABIAL, Alicante, Spain
| | - Alex Mira
- Genomics & Health Department, FISABIO Foundation, Valencia, Spain
- CIBER of Epidemiology and Public Health, Madrid, Spain
| | - María D. Ferrer
- Genomics & Health Department, FISABIO Foundation, Valencia, Spain
- CIBER of Epidemiology and Public Health, Madrid, Spain
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Santa Maria PL, Kaufman AC, Bacacao B, Thai A, Chen X, Xia A, Cao Z, Fouad A, Bekale LA. Topical Therapy Failure in Chronic Suppurative Otitis Media is Due to Persister Cells in Biofilms. Otol Neurotol 2021; 42:e1263-e1272. [PMID: 34149028 DOI: 10.1097/mao.0000000000003222] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
OBJECTIVE Chronic suppurative otitis media (CSOM) is characterized by a chronically draining middle ear. CSOM is typically treated with multiple courses of antibiotics or antiseptics which are successful in achieving quiescence; however, the disease is prone to relapse. Understanding why these treatment failures occur is essential. STUDY DESIGN The minimum inhibitory concentration (MIC), minimal biofilm eradication concentration, and the inhibitory zone were determined for ototopicals and ofloxacin for the laboratory strains and CSOM-derived isolates. The percentage of persister cells and bacterial biofilm formation were measured. Disease eradication was tested in a validated in-vivo model of CSOM after treatment with ofloxacin. SETTING Microbiology Laboratory. METHODS Basic science experiments were performed to measure the effectiveness of a number of compounds against CSOM bacteria in a number of distinct settings. RESULTS The minimal biofilm eradication concentration is higher than is physiologically achievable with commercial preparations, except for povo-iodine. Clincial isolates of CSOM have equivalent biofilm-forming ability but increased proportions of persister cells. Ofloxacin can convert to inactive disease temporarily but fails to eradicate disease in an in-vivo model. CONCLUSIONS Higher percentages of persister cells in clinical CSOM isolates are associated with resistance to ototopicals. Current ototopicals, except povo-iodine, have limited clinical effectiveness; however, it is unknown what the maximum achievable concentration is and there are ototoxicity concerns. Fluoroquinolones, while successful in producing inactive disease in the short term, have the potential to encourage antimicrobial resistance and disease recalcitrance and do not achieve a permanent remission. Given these limitations, clinicians should consider surgery earlier or use of clinically safe concentrations of povo-iodine earlier into the treatment algorithm.
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Affiliation(s)
- Peter L Santa Maria
- Department of Otolaryngology, Head and Neck Surgery, Stanford University, Stanford, California, USA
| | - Adam C Kaufman
- Department of Otolaryngology, Head and Neck Surgery, Stanford University, Stanford, California, USA
| | - Brian Bacacao
- Department of Otolaryngology, Head and Neck Surgery, Stanford University, Stanford, California, USA
| | - Anthony Thai
- Department of Otolaryngology, Head and Neck Surgery, Stanford University, Stanford, California, USA
| | - Xiaohua Chen
- Department of Otolaryngology, Head and Neck Surgery, Stanford University, Stanford, California, USA
- Department of Otolaryngology, Head and Neck Surgery, First Affiliated Hospital of Zhengzhou University, Henan, China
| | - Anping Xia
- Department of Otolaryngology, Head and Neck Surgery, Stanford University, Stanford, California, USA
| | - Zhixin Cao
- Department of Otolaryngology, Head and Neck Surgery, Stanford University, Stanford, California, USA
- Department of Pathology, Shandong Provincial Hospital Affiliated to Shandong University, Ji'nan, China
| | - Ayman Fouad
- Department of Otolaryngology, Head and Neck Surgery, Stanford University, Stanford, California, USA
- Department of Otolaryngology, Head and Neck Surgery, Tanta University, Tanta, Eqypt
| | - Laurent A Bekale
- Department of Otolaryngology, Head and Neck Surgery, Stanford University, Stanford, California, USA
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Likhoshvai VA, Khlebodarova TM. Evolution and extinction can occur rapidly: a modeling approach. PeerJ 2021; 9:e11130. [PMID: 33954033 PMCID: PMC8051336 DOI: 10.7717/peerj.11130] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Accepted: 02/27/2021] [Indexed: 11/25/2022] Open
Abstract
Fossil record of Earth describing the last 500 million years is characterized by evolution discontinuity as well as recurring global extinctions of some species and their replacement by new types, the causes of which are still debate. We developed a model of evolutionary self-development of a large ecosystem. This model of biota evolution based on the universal laws of living systems functioning: reproduction, dependence of reproduction efficiency and mortality on biota density, mutational variability in the process of reproduction and selection of the most adapted individuals. We have shown that global extinctions and phases of rapid growth and biodiversity stasis can be a reflection of the emergence of bistability in a self-organizing system, which is the Earth’s biota. Bistability was found to be characteristic only for ecosystems with predominant sexual reproduction. The reason for the transition from one state to another is the selection of the most adapted individuals. That is, we explain the characteristics of the Earth’s fossil record during the last 500 million years by the internal laws of Earth’s ecosystem functioning, which appeared at a certain stage of evolution as a result of the emergence of life forms with an increased adaptive diversification associated with sexual dimorphism.
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Affiliation(s)
- Vitaly A Likhoshvai
- Department of Systems Biology, Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russian Federation
| | - Tamara M Khlebodarova
- Department of Systems Biology, Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russian Federation.,Kurchatov Genomics Center, Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russian Federation
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Affiliation(s)
- Yuriy L. Orlov
- The Digital Health Institute, I.M.Sechenov First Moscow State Medical University (Sechenov University), 119991 Moscow, Russia
- Novosibirsk State University, 630090 Novosibirsk, Russia
- Agrarian and Technological Institute, Peoples’ Friendship University of Russia (RUDN), 117198 Moscow, Russia
| | - Elvira R. Galieva
- Novosibirsk State University, 630090 Novosibirsk, Russia
- Agrarian and Technological Institute, Peoples’ Friendship University of Russia (RUDN), 117198 Moscow, Russia
| | - Tatiana V. Tatarinova
- La Verne University, La Verne, CA 91750 USA
- Department of Fundamental Biology and Biotechnology, Siberian Federal University, 660074 Krasnoyarsk, Russia
- Vavilov Instutute of General Genetics RAS, 119991 Moscow, Russia
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Khlebodarova TM, Likhoshvai VA. Causes of global extinctions in the history of life: facts and hypotheses. Vavilovskii Zhurnal Genet Selektsii 2020; 24:407-419. [PMID: 33659824 PMCID: PMC7716527 DOI: 10.18699/vj20.633] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Paleontologists define global extinctions on Earth as a loss of about three-quarters of plant and animal species over a relatively short period of time. At least five global extinctions are documented in the Phanerozoic fossil record (~500-million-year period): ~65, 200, 260, 380, and 440 million years ago. In addition, there is evidence of global extinctions in earlier periods of life on Earth - during the Late Cambrian (~500 million years ago) and Ediacaran periods (more than 540 million years ago). There is still no common opinion on the causes of their occurrence. The current study is a systematized review of the data on recorded extinctions of complex life forms on Earth from the moment of their occurrence during the Ediacaran period to the modern period. The review discusses possible causes for mass extinctions in the light of the influence of abiogenic factors, planetary or astronomical, and the consequences of their actions. We evaluate the pros and cons of the hypothesis on the presence of periodicity in the extinction of Phanerozoic marine biota. Strong evidence that allows us to hypothesize that additional mechanisms associated with various internal biotic factors are responsible for the emergence of extinctions in the evolution of complex life forms is discussed. Developing the idea of the internal causes of periodicity and discontinuity in evolution, we propose our own original hypothesis, according to which the bistability phenomenon underlies the complex dynamics of the biota development, which is manifested in the form of global extinctions. The bistability phenomenon arises only in ecosystems with predominant sexual reproduction. Our hypothesis suggests that even in the absence of global abiotic catastrophes, extinctions of biota would occur anyway. However, our hypothesis does not exclude the possibility that in different periods of the Earth's history the biota was subjected to powerful external influences that had a significant impact on its further development, which is reflected in the Earth's fossil record.
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Affiliation(s)
- T M Khlebodarova
- Institute of Cytology and Genetics of Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - V A Likhoshvai
- Institute of Cytology and Genetics of Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
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Olszak T, Danis-Wlodarczyk K, Arabski M, Gula G, Maciejewska B, Wasik S, Lood C, Higgins G, Harvey BJ, Lavigne R, Drulis-Kawa Z. Pseudomonas aeruginosa PA5oct Jumbo Phage Impacts Planktonic and Biofilm Population and Reduces Its Host Virulence. Viruses 2019; 11:E1089. [PMID: 31771160 PMCID: PMC6950013 DOI: 10.3390/v11121089] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Revised: 11/19/2019] [Accepted: 11/20/2019] [Indexed: 12/20/2022] Open
Abstract
The emergence of phage-resistant mutants is a key aspect of lytic phages-bacteria interaction and the main driver for the co-evolution between both organisms. Here, we analyze the impact of PA5oct jumbo phage treatment on planktonic/cell line associated and sessile P. aeruginosa population. Besides its broad-spectrum activity and efficient bacteria reduction in both airway surface liquid (ASL) model, and biofilm matrix degradation, PA5oct appears to persist in most of phage-resistant clones. Indeed, a high percentage of resistance (20/30 clones) to PA5oct is accompanied by the presence of phage DNA within bacterial culture. Moreover, the maintenance of this phage in the bacterial population correlates with reduced P. aeruginosa virulence, coupled with a sensitization to innate immune mechanisms, and a significantly reduced growth rate. We observed rather unusual consequences of PA5oct infection causing an increased inflammatory response of monocytes to P. aeruginosa. This phenomenon, combined with the loss or modification of the phage receptor, makes most of the phage-resistant clones significantly less pathogenic in in vivo model. These findings provide new insights into the general knowledge of giant phages biology and the impact of their application in phage therapy.
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Affiliation(s)
- Tomasz Olszak
- Department of Pathogen Biology and Immunology, Institute of Genetics and Microbiology, University of Wroclaw, 51-148 Wroclaw, Poland; (T.O.); (K.D.-W.); (G.G.); (B.M.)
| | - Katarzyna Danis-Wlodarczyk
- Department of Pathogen Biology and Immunology, Institute of Genetics and Microbiology, University of Wroclaw, 51-148 Wroclaw, Poland; (T.O.); (K.D.-W.); (G.G.); (B.M.)
- Laboratory of Gene Technology, KU Leuven, 3001 Heverlee, Belgium; (C.L.); (R.L.)
| | - Michal Arabski
- Department of Biochemistry and Genetics, Institute of Biology, The Jan Kochanowski University in Kielce, 25-406 Kielce, Poland;
| | - Grzegorz Gula
- Department of Pathogen Biology and Immunology, Institute of Genetics and Microbiology, University of Wroclaw, 51-148 Wroclaw, Poland; (T.O.); (K.D.-W.); (G.G.); (B.M.)
| | - Barbara Maciejewska
- Department of Pathogen Biology and Immunology, Institute of Genetics and Microbiology, University of Wroclaw, 51-148 Wroclaw, Poland; (T.O.); (K.D.-W.); (G.G.); (B.M.)
| | - Slawomir Wasik
- Department of Molecular Physics, Institute of Physics, The Jan Kochanowski University in Kielce, 25-406 Kielce, Poland;
| | - Cédric Lood
- Laboratory of Gene Technology, KU Leuven, 3001 Heverlee, Belgium; (C.L.); (R.L.)
- Laboratory of Computational Systems Biology, KU Leuven, 3000 Leuven, Belgium
| | - Gerard Higgins
- National Children Research Centre, Our Lady’s Children’s Hospital, Crumlin, 12 Dublin, Ireland;
- Department of Molecular Medicine, Royal College of Surgeons in Ireland, Education and Research Centre, Beaumont Hospital, 9 Dublin, Ireland;
| | - Brian J. Harvey
- Department of Molecular Medicine, Royal College of Surgeons in Ireland, Education and Research Centre, Beaumont Hospital, 9 Dublin, Ireland;
| | - Rob Lavigne
- Laboratory of Gene Technology, KU Leuven, 3001 Heverlee, Belgium; (C.L.); (R.L.)
| | - Zuzanna Drulis-Kawa
- Department of Pathogen Biology and Immunology, Institute of Genetics and Microbiology, University of Wroclaw, 51-148 Wroclaw, Poland; (T.O.); (K.D.-W.); (G.G.); (B.M.)
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Behera S, Pattnaik S. Persister cell development among Enterobacteriaceae, Pseudomonadaceae, Mycobacteriaceae and Staphylococcaceae biotypes: A review. BIOCATALYSIS AND AGRICULTURAL BIOTECHNOLOGY 2019. [DOI: 10.1016/j.bcab.2019.101401] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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9
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Khlebodarova TM, Likhoshvai VA. Molecular Mechanisms of Non-Inherited Antibiotic Tolerance in Bacteria and Archaea. Mol Biol 2019. [DOI: 10.1134/s0026893319040058] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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10
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Does the Semiconservative Nature of DNA Replication Facilitate Coherent Phenotypic Diversity? J Bacteriol 2019; 201:JB.00119-19. [PMID: 30936370 DOI: 10.1128/jb.00119-19] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
It has been clear for over sixty years that the principal method whereby cells replicate and segregate their DNA is semiconservative. It is much less clear why it should be like this rather than, say, conservative. Recently, evidence has accumulated that supports the hypothesis that one of the functions of the cell cycle is to generate phenotypically different daughter cells, even in nondifferentiating bacteria such as Escherichia coli Evidence has also accumulated that the bacterial phenotype is determined by the functioning of extended assemblies of macromolecules termed hyperstructures. One class of these hyperstructures is attached dynamically to a DNA strand by the coupling of transcription and translation. Previously, we proposed in the strand segregation model that one set of hyperstructures accompanies one parental strand into one daughter cell while another set of hyperstructures accompanies the other parental strand into the other daughter cell. This epigenetic mechanism results in daughter cells having different phenotypes. Here, I propose that one of the reasons why semiconservative replication has been selected is because it allows the generation of a population containing cells with very different growth rates even in steady-state conditions.
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Orlov YL, Kochetov AV, Li G, Kolchanov NA. Genomics research at Bioinformatics of Genome Regulation and Structure\ Systems Biology (BGRS\SB) conferences in Novosibirsk. BMC Genomics 2019; 20:322. [PMID: 32039700 PMCID: PMC7227187 DOI: 10.1186/s12864-019-5707-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Affiliation(s)
- Yuriy L Orlov
- Institute of Cytology and Genetics SB RAS, 630090, Novosibirsk, Russia. .,Novosibirsk State University, 630090, Novosibirsk, Russia. .,A.O.Kovalevsky Institute of Marine Biological Research of RAS, 119334, Moscow, Russia.
| | - Alex V Kochetov
- Institute of Cytology and Genetics SB RAS, 630090, Novosibirsk, Russia
| | - Guoliang Li
- College of Informatics, Huazhong Agricultural University, Wuhan, 430070, China
| | - Nikolay A Kolchanov
- Institute of Cytology and Genetics SB RAS, 630090, Novosibirsk, Russia.,Novosibirsk State University, 630090, Novosibirsk, Russia
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