1
|
Chen Q, Zhang F, Bai J, Che Q, Xiang L, Zhang Z, Wang Y, Sjöling Å, Martín-Rodríguez AJ, Zhu B, Fu L, Zhou Y. Bacteriophage-resistant carbapenem-resistant Klebsiella pneumoniae shows reduced antibiotic resistance and virulence. Int J Antimicrob Agents 2024; 64:107221. [PMID: 38810938 DOI: 10.1016/j.ijantimicag.2024.107221] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2023] [Revised: 04/21/2024] [Accepted: 05/20/2024] [Indexed: 05/31/2024]
Abstract
Phage therapy has shown great promise in the treatment of bacterial infections. However, the effectiveness of phage therapy is compromised by the inevitable emergence of phage-resistant strains. In this study, a phage-resistant carbapenem-resistant Klebsiella pneumoniae strain SWKP1711R, derived from parental carbapenem-resistant K. pneumoniae strain SWKP1711 was identified. The mechanism of bacteriophage resistance in SWKP1711R was investigated and the molecular determinants causing altered growth characteristics, antibiotic resistance, and virulence of SWKP1711R were tested. Compared to SWKP1711, SWKP1711R showed slower growth, smaller colonies, filamentous cells visible under the microscope, reduced production of capsular polysaccharide (CPS) and lipopolysaccharide, and reduced resistance to various antibiotics accompanied by reduced virulence. Adsorption experiments showed that phage vB_kpnM_17-11 lost the ability to adsorb onto SWKP1711R, and the adsorption receptor was identified to be bacterial surface polysaccharides. Genetic variation analysis revealed that, compared to the parental strain, SWKP1711R had only one thymine deletion at position 78 of the open reading frame of the lpcA gene, resulting in a frameshift mutation that caused alteration of the bacterial surface polysaccharide and inhibition of phage adsorption, ultimately leading to phage resistance. Transcriptome analysis and quantitative reverse transcriptase PCR revealed that genes encoding lipopolysaccharide synthesis, ompK35, blaTEM-1, and type II and Hha-TomB toxin-antitoxin systems, were all downregulated in SWKP1711R. Taken together, the evidence presented here indicates that the phenotypic alterations and phage resistance displayed by the mutant may be related to the frameshift mutation of lpcA and altered gene expression. While evolution of phage resistance remains an issue, our study suggests that the reduced antibiotic resistance and virulence of phage-resistant strain derivatives might be beneficial in alleviating the burden caused by multidrug-resistant bacteria.
Collapse
Affiliation(s)
- Qiao Chen
- Department of Pathogeic Biology, School of Basic Medical, Southwest Medical University, Luzhou, Sichuan, 646000, China
| | - Feiyang Zhang
- Department of Pathogeic Biology, School of Basic Medical, Southwest Medical University, Luzhou, Sichuan, 646000, China
| | - Jiawei Bai
- Department of Pathogeic Biology, School of Basic Medical, Southwest Medical University, Luzhou, Sichuan, 646000, China
| | - Qian Che
- Sichuan Center For Disease Control And Prevention, Chengdu, 610000, China
| | - Li Xiang
- Department of Pathogeic Biology, School of Basic Medical, Southwest Medical University, Luzhou, Sichuan, 646000, China
| | - Zhikun Zhang
- Department of Pathogeic Biology, School of Basic Medical, Southwest Medical University, Luzhou, Sichuan, 646000, China
| | - Ying Wang
- Department of Pathogeic Biology, School of Basic Medical, Southwest Medical University, Luzhou, Sichuan, 646000, China
| | - Åsa Sjöling
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, 17165, Stockholm, Sweden; Department of Chemistry and Molecular Biology, University of Gothenburg, 413 90 Gothenburg, Sweden
| | - Alberto J Martín-Rodríguez
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, 17165, Stockholm, Sweden; Department of Clinical Sciences, University of Las Palmas de Gran Canaria, 35016, Las Palmas de Gran Canaria, Spain
| | - Baoli Zhu
- Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Li Fu
- The Affiliated Hospital, Southwest Medical University, Luzhou, 646000, China.
| | - Yingshun Zhou
- Department of Pathogeic Biology, School of Basic Medical, Southwest Medical University, Luzhou, Sichuan, 646000, China; Public Center of Experimental Technology of Pathogen Biology Technology Platform, Southwest Medical University, Luzhou, 646000, China.
| |
Collapse
|
2
|
Characteristics and Comparative Genomic Analysis of a Novel Virus, VarioGold, the First Bacteriophage of Variovorax. Int J Mol Sci 2022; 23:ijms232113539. [DOI: 10.3390/ijms232113539] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Revised: 10/29/2022] [Accepted: 10/31/2022] [Indexed: 11/10/2022] Open
Abstract
Variovorax represents a widespread and ecologically significant genus of soil bacteria. Despite the ecological importance of these bacteria, our knowledge about the viruses infecting Variovorax spp. is quite poor. This study describes the isolation and characterization of the mitomycin-induced phage, named VarioGold. To the best of our knowledge, VarioGold represents the first characterized virus for this genus. Comparative genomic analyses suggested that VarioGold is distinct from currently known bacteriophages at both the nucleotide and protein levels; thus, it could be considered a new virus genus. In addition, another 37 prophages were distinguished in silico within the complete genomic sequences of Variovorax spp. that are available in public databases. The similarity networking analysis highlighted their general high diversity, which, despite clustering with previously described phages, shows their unique genetic load. Therefore, the novelty of Variovorax phages warrants the great enrichment of databases, which could, in turn, improve bioinformatic strategies for finding (pro)phages.
Collapse
|
3
|
Maczuga NT, Tran ENH, Morona R. Topology of the Shigella flexneri Enterobacterial Common Antigen polymerase WzyE. MICROBIOLOGY (READING, ENGLAND) 2022; 168. [PMID: 35470793 DOI: 10.1099/mic.0.001183] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Enterobacteriales have evolved a specialized outer membrane polysaccharide [Enterobacterial Common Antigen (ECA)] which allows them to persist in various environmental niches. Biosynthesis of ECA initiates on the cytoplasmic leaflet of the inner membrane (IM) where glycosyltransferases assemble ECA repeat units (RUs). Complete RUs are then translocated across the IM and assembled into polymers by ECA-specific homologues of the Wzy-dependent pathway. Consisting of the membrane proteins Wzx, Wzy and Wzz, the Wzy-dependent pathway is the most common polysaccharide biosynthetic pathway in Gram-negative bacteria where it is most notably involved in LPS O antigen (Oag) biosynthesis. As such, the majority of research directed towards these proteins has been orientated towards Oag biosynthetic homologues with little directed towards ECA homologues. Belonging to the Shape, Elongation, Division and Sporulation (SEDS) protein family, Wzy proteins are polymerases, and are characterized as possessing little or no peptide homology among homologues as well as being polytopic membrane proteins with functionally relevant residues within periplasmic loops, as defined by C-terminal reporter fusion topology mapping. Here, we present the first the first major study into the ECA polymerase WzyE. Multiple sequence alignments and topology mapping showed that WzyE is unlike WzyB proteins involved with Oag biosynthesis WzyE displays high peptide conservation across Enterobacteriales. In silico structures and reporter mapping allowed us to identify possible functionally conserved residues with WzyESF's periplasmic loops, which we showed were crucial for its function. This work provides novel insight into Wzy proteins and suggests that WzyE is an optimal model to investigate Wzy proteins and the Wzy-dependent pathway.
Collapse
Affiliation(s)
- Nicholas T Maczuga
- Department of Molecular and Biomedical Sciences, Research Centre for Infectious Diseases, School of Biological Sciences, The University of Adelaide, Adelaide, SA, Australia
| | - Elizabeth N H Tran
- Department of Molecular and Biomedical Sciences, Research Centre for Infectious Diseases, School of Biological Sciences, The University of Adelaide, Adelaide, SA, Australia
| | - Renato Morona
- Department of Molecular and Biomedical Sciences, Research Centre for Infectious Diseases, School of Biological Sciences, The University of Adelaide, Adelaide, SA, Australia
| |
Collapse
|
4
|
Isaev AB, Musharova OS, Severinov KV. Microbial Arsenal of Antiviral Defenses. Part II. BIOCHEMISTRY (MOSCOW) 2021; 86:449-470. [PMID: 33941066 DOI: 10.1134/s0006297921040064] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Bacteriophages or phages are viruses that infect bacterial cells (for the scope of this review we will also consider viruses that infect Archaea). The constant threat of phage infection is a major force that shapes evolution of microbial genomes. To withstand infection, bacteria had evolved numerous strategies to avoid recognition by phages or to directly interfere with phage propagation inside the cell. Classical molecular biology and genetic engineering had been deeply intertwined with the study of phages and host defenses. Nowadays, owing to the rise of phage therapy, broad application of CRISPR-Cas technologies, and development of bioinformatics approaches that facilitate discovery of new systems, phage biology experiences a revival. This review describes variety of strategies employed by microbes to counter phage infection. In the first part defense associated with cell surface, roles of small molecules, and innate immunity systems relying on DNA modification were discussed. The second part focuses on adaptive immunity systems, abortive infection mechanisms, defenses associated with mobile genetic elements, and novel systems discovered in recent years through metagenomic mining.
Collapse
Affiliation(s)
- Artem B Isaev
- Skolkovo Institute of Science and Technology, Skolkovo, Moscow, 143028, Russia.
| | - Olga S Musharova
- Skolkovo Institute of Science and Technology, Skolkovo, Moscow, 143028, Russia. .,Institute of Molecular Genetics, Moscow, 119334, Russia
| | - Konstantin V Severinov
- Skolkovo Institute of Science and Technology, Skolkovo, Moscow, 143028, Russia. .,Waksman Institute of Microbiology, Piscataway, NJ 08854, USA
| |
Collapse
|
5
|
Balabanova L, Shkryl Y, Slepchenko L, Cheraneva D, Podvolotskaya A, Bakunina I, Nedashkovskaya O, Son O, Tekutyeva L. Genomic Features of a Food-Derived Pseudomonas aeruginosa Strain PAEM and Biofilm-Associated Gene Expression under a Marine Bacterial α-Galactosidase. Int J Mol Sci 2020; 21:ijms21207666. [PMID: 33081309 PMCID: PMC7593944 DOI: 10.3390/ijms21207666] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Revised: 10/09/2020] [Accepted: 10/14/2020] [Indexed: 12/15/2022] Open
Abstract
The biofilm-producing strains of P. aeruginosa colonize various surfaces, including food products and industry equipment that can cause serious human and animal health problems. The biofilms enable microorganisms to evolve the resistance to antibiotics and disinfectants. Analysis of the P. aeruginosa strain (serotype O6, sequence type 2502), isolated from an environment of meat processing (PAEM) during a ready-to-cook product storage (−20 °C), showed both the mosaic similarity and differences between free-living and clinical strains by their coding DNA sequences. Therefore, a cold shock protein (CspA) has been suggested for consideration of the evolution probability of the cold-adapted P. aeruginosa strains. In addition, the study of the action of cold-active enzymes from marine bacteria against the food-derived pathogen could contribute to the methods for controlling P. aeruginosa biofilms. The genes responsible for bacterial biofilm regulation are predominantly controlled by quorum sensing, and they directly or indirectly participate in the synthesis of extracellular polysaccharides, which are the main element of the intercellular matrix. The levels of expression for 14 biofilm-associated genes of the food-derived P. aeruginosa strain PAEM in the presence of different concentrations of the glycoside hydrolase of family 36, α-galactosidase α-PsGal, from the marine bacterium Pseudoalteromonas sp. KMM 701 were determined. The real-time PCR data clustered these genes into five groups according to the pattern of positive or negative regulation of their expression in response to the action of α-galactosidase. The results revealed a dose-dependent mechanism of the enzymatic effect on the PAEM biofilm synthesis and dispersal genes.
Collapse
Affiliation(s)
- Larissa Balabanova
- Laboratory of Marine Biochemistry, G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch, the Russian Academy of Sciences, 690022 Vladivostok, Russia; (L.S.); (D.C.); (I.B.); (O.N.)
- Basic Department of Bioeconomy and Food Security, School of Economics and Management, Far Eastern Federal University, 690090 Vladivostok, Russia; (A.P.); (O.S.); (L.T.)
- Correspondence: (L.B.); (Y.S.)
| | - Yuri Shkryl
- Federal Scientific Center of the East Asia Terrestrial Biodiversity, Far Eastern Branch, the Russian Academy of Sciences, 690022 Vladivostok, Russia
- Correspondence: (L.B.); (Y.S.)
| | - Lubov Slepchenko
- Laboratory of Marine Biochemistry, G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch, the Russian Academy of Sciences, 690022 Vladivostok, Russia; (L.S.); (D.C.); (I.B.); (O.N.)
- Basic Department of Bioeconomy and Food Security, School of Economics and Management, Far Eastern Federal University, 690090 Vladivostok, Russia; (A.P.); (O.S.); (L.T.)
| | - Daria Cheraneva
- Laboratory of Marine Biochemistry, G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch, the Russian Academy of Sciences, 690022 Vladivostok, Russia; (L.S.); (D.C.); (I.B.); (O.N.)
| | - Anna Podvolotskaya
- Basic Department of Bioeconomy and Food Security, School of Economics and Management, Far Eastern Federal University, 690090 Vladivostok, Russia; (A.P.); (O.S.); (L.T.)
| | - Irina Bakunina
- Laboratory of Marine Biochemistry, G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch, the Russian Academy of Sciences, 690022 Vladivostok, Russia; (L.S.); (D.C.); (I.B.); (O.N.)
| | - Olga Nedashkovskaya
- Laboratory of Marine Biochemistry, G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch, the Russian Academy of Sciences, 690022 Vladivostok, Russia; (L.S.); (D.C.); (I.B.); (O.N.)
| | - Oksana Son
- Basic Department of Bioeconomy and Food Security, School of Economics and Management, Far Eastern Federal University, 690090 Vladivostok, Russia; (A.P.); (O.S.); (L.T.)
| | - Liudmila Tekutyeva
- Basic Department of Bioeconomy and Food Security, School of Economics and Management, Far Eastern Federal University, 690090 Vladivostok, Russia; (A.P.); (O.S.); (L.T.)
| |
Collapse
|
6
|
Islam ST, Vergara Alvarez I, Saïdi F, Guiseppi A, Vinogradov E, Sharma G, Espinosa L, Morrone C, Brasseur G, Guillemot JF, Benarouche A, Bridot JL, Ravicoularamin G, Cagna A, Gauthier C, Singer M, Fierobe HP, Mignot T, Mauriello EMF. Modulation of bacterial multicellularity via spatio-specific polysaccharide secretion. PLoS Biol 2020; 18:e3000728. [PMID: 32516311 PMCID: PMC7310880 DOI: 10.1371/journal.pbio.3000728] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Revised: 06/23/2020] [Accepted: 05/21/2020] [Indexed: 11/21/2022] Open
Abstract
The development of multicellularity is a key evolutionary transition allowing for differentiation of physiological functions across a cell population that confers survival benefits; among unicellular bacteria, this can lead to complex developmental behaviors and the formation of higher-order community structures. Herein, we demonstrate that in the social δ-proteobacterium Myxococcus xanthus, the secretion of a novel biosurfactant polysaccharide (BPS) is spatially modulated within communities, mediating swarm migration as well as the formation of multicellular swarm biofilms and fruiting bodies. BPS is a type IV pilus (T4P)-inhibited acidic polymer built of randomly acetylated β-linked tetrasaccharide repeats. Both BPS and exopolysaccharide (EPS) are produced by dedicated Wzx/Wzy-dependent polysaccharide-assembly pathways distinct from that responsible for spore-coat assembly. While EPS is preferentially produced at the lower-density swarm periphery, BPS production is favored in the higher-density swarm interior; this is consistent with the former being known to stimulate T4P retraction needed for community expansion and a function for the latter in promoting initial cell dispersal. Together, these data reveal the central role of secreted polysaccharides in the intricate behaviors coordinating bacterial multicellularity. A study of the social bacterium Myxococcus xanthus reveals that the bacteria preferentially secrete specific polysaccharides within distinct zones of a swarm to facilitate spreading across a surface.
Collapse
Affiliation(s)
- Salim T. Islam
- Armand Frappier Health & Biotechnology Research Centre, Institut National de la Recherche Scientifique, Université du Québec, Institut Pasteur International Network, Laval, Québec, Canada
- PROTEO, the Quebec Network for Research on Protein Function, Engineering, and Applications, Université Laval, Québec, Québec, Canada
- Laboratoire de Chimie Bactérienne, CNRS–Université Aix-Marseille UMR, Institut de Microbiologie de la Méditerranée, Marseille, France
- * E-mail: (STI); (EMFM)
| | - Israel Vergara Alvarez
- Laboratoire de Chimie Bactérienne, CNRS–Université Aix-Marseille UMR, Institut de Microbiologie de la Méditerranée, Marseille, France
| | - Fares Saïdi
- Armand Frappier Health & Biotechnology Research Centre, Institut National de la Recherche Scientifique, Université du Québec, Institut Pasteur International Network, Laval, Québec, Canada
- PROTEO, the Quebec Network for Research on Protein Function, Engineering, and Applications, Université Laval, Québec, Québec, Canada
- Laboratoire de Chimie Bactérienne, CNRS–Université Aix-Marseille UMR, Institut de Microbiologie de la Méditerranée, Marseille, France
| | - Annick Guiseppi
- Laboratoire de Chimie Bactérienne, CNRS–Université Aix-Marseille UMR, Institut de Microbiologie de la Méditerranée, Marseille, France
| | - Evgeny Vinogradov
- Human Health Therapeutics Portfolio, National Research Council of Canada, Ottawa, Ontario, Canada
| | - Gaurav Sharma
- Department of Microbiology and Molecular Genetics, University of California–Davis, Davis, California, United States of America
- Institute of Bioinformatics and Applied Biotechnology, Electronic City, Bengaluru, Karnataka, India
| | - Leon Espinosa
- Laboratoire de Chimie Bactérienne, CNRS–Université Aix-Marseille UMR, Institut de Microbiologie de la Méditerranée, Marseille, France
| | - Castrese Morrone
- Laboratoire de Chimie Bactérienne, CNRS–Université Aix-Marseille UMR, Institut de Microbiologie de la Méditerranée, Marseille, France
| | - Gael Brasseur
- Laboratoire de Chimie Bactérienne, CNRS–Université Aix-Marseille UMR, Institut de Microbiologie de la Méditerranée, Marseille, France
| | | | | | | | - Gokulakrishnan Ravicoularamin
- Armand Frappier Health & Biotechnology Research Centre, Institut National de la Recherche Scientifique, Université du Québec, Institut Pasteur International Network, Laval, Québec, Canada
| | - Alain Cagna
- Teclis Scientific, Civrieux d’Azergue, France
| | - Charles Gauthier
- Armand Frappier Health & Biotechnology Research Centre, Institut National de la Recherche Scientifique, Université du Québec, Institut Pasteur International Network, Laval, Québec, Canada
| | - Mitchell Singer
- Department of Microbiology and Molecular Genetics, University of California–Davis, Davis, California, United States of America
| | - Henri-Pierre Fierobe
- Laboratoire de Chimie Bactérienne, CNRS–Université Aix-Marseille UMR, Institut de Microbiologie de la Méditerranée, Marseille, France
| | - Tâm Mignot
- Laboratoire de Chimie Bactérienne, CNRS–Université Aix-Marseille UMR, Institut de Microbiologie de la Méditerranée, Marseille, France
| | - Emilia M. F. Mauriello
- Laboratoire de Chimie Bactérienne, CNRS–Université Aix-Marseille UMR, Institut de Microbiologie de la Méditerranée, Marseille, France
- * E-mail: (STI); (EMFM)
| |
Collapse
|