1
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Calabro C, Sadhu R, Xu Y, Aprea M, Guarino C, Cazer CL. Longitudinal antimicrobial susceptibility trends of canine Staphylococcus pseudintermedius. Prev Vet Med 2024; 226:106170. [PMID: 38493570 DOI: 10.1016/j.prevetmed.2024.106170] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Revised: 02/28/2024] [Accepted: 03/04/2024] [Indexed: 03/19/2024]
Abstract
Antimicrobial resistance within Staphylococcus pseudintermedius poses a significant risk for the treatment of canine pyoderma and as a reservoir for resistance and potential zoonoses, but few studies examine long-term temporal trends of resistance. This study assesses the antimicrobial resistance prevalence and minimum inhibitory concentration (MIC) trends in S. pseudintermedius (n=1804) isolated from canine skin samples at the Cornell University Animal Health Diagnostic Center (AHDC) between 2007 and 2020. Not susceptible (NS) prevalence, Cochran-Armitage tests, logrank tests, MIC50 and MIC90 quantiles, and survival analysis models were used to evaluate resistance prevalence and temporal trends to 23 antimicrobials. We use splines as predictors in accelerated failure time (AFT) models to model non-linear temporal trends in MICs. Multidrug resistance was common among isolates (47%), and isolates had moderate to high NS prevalence to the beta-lactams, chloramphenicol, the fluoroquinolones, gentamicin, the macrolides/lincosamides, the tetracyclines, and trimethoprim-sulfamethoxazole. However, low levels of NS to amikacin, rifampin, and vancomycin were observed. Around one third of isolates (38%) were found to be methicillin resistant S. pseudintermedius (MRSP), and these isolates had a higher prevalence of NS to all tested antimicrobials than methicillin susceptible isolates. Amongst the MRSP isolates, one phenotypically vancomycin resistant isolate (MIC >16 µg/mL) was identified, but genomic sequence data was unavailable. AFT models showed increasing MICs across time to the beta-lactams, chloramphenicol, the fluoroquinolones, gentamicin, and the macrolides/lincosamides, and decreasing temporal resistance (decreasing MICs) to doxycycline was observed amongst isolates. Notably, ATF modeling showed changes in MIC distributions that were not identified using Cochran-Armitage tests on prevalence, MIC quantiles, and logrank tests. Increasing resistance amongst these S. pseudintermedius isolates highlights the need for rational, empirical prescribing practices and increased antimicrobial resistance (AMR) surveillance to maintain the efficacy of current therapeutic agents. AFT models with non-linear predictors may be a useful, breakpoint-independent, surveillance tool alongside other modeling methods and antibiograms.
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Affiliation(s)
- Caroline Calabro
- Department of Public and Ecosystem Health, Cornell University College of Veterinary Medicine, Ithaca, NY, USA; Department of Clinical Sciences, Cornell University College of Veterinary Medicine, Ithaca, NY, USA
| | - Ritwik Sadhu
- Department of Statistics and Data Science, Cornell University, Ithaca, NY, USA
| | - Yuchen Xu
- Department of Statistics and Data Science, Cornell University, Ithaca, NY, USA
| | - Melissa Aprea
- Department of Population Medicine and Diagnostic Sciences, Cornell University College of Veterinary Medicine, Ithaca, NY, USA
| | - Cassandra Guarino
- Department of Population Medicine and Diagnostic Sciences, Cornell University College of Veterinary Medicine, Ithaca, NY, USA
| | - Casey L Cazer
- Department of Public and Ecosystem Health, Cornell University College of Veterinary Medicine, Ithaca, NY, USA; Department of Clinical Sciences, Cornell University College of Veterinary Medicine, Ithaca, NY, USA.
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2
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Beck C, Krusche J, Elsherbini AMA, Du X, Peschel A. Phage susceptibility determinants of the opportunistic pathogen Staphylococcus epidermidis. Curr Opin Microbiol 2024; 78:102434. [PMID: 38364502 DOI: 10.1016/j.mib.2024.102434] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Revised: 01/16/2024] [Accepted: 01/18/2024] [Indexed: 02/18/2024]
Abstract
Staphylococcus epidermidis is a common member of the human skin and nose microbiomes and a frequent cause of invasive infections. Transducing phages accomplish the horizontal transfer of resistance and virulence genes by mispackaging of mobile-genetic elements, contributing to severe, therapy-refractory S. epidermidis infections. Lytic phages on the other hand can be interesting candidates for new anti-S. epidermidis phage therapies. Despite the importance of phages, we are only beginning to unravel S. epidermidis phage interactions. Recent studies shed new light on S. epidermidis phage diversity, host range, and receptor specificities. Modulation of cell wall teichoic acids, the major phage receptor structures, along with other phage defense mechanisms, are crucial determinants for S. epidermidis susceptibility to different phage groups.
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Affiliation(s)
- Christian Beck
- Cluster of Excellence "Controlling Microbes to Fight Infections (CMFI)", University of Tübingen, 72076 Tübingen, Germany; Interfaculty Institute of Microbiology and Infection Medicine Tübingen, Infection Biology, University of Tübingen, 72076 Tübingen, Germany; German Centre for Infection Research (DZIF), Partner Site Tübingen, 72076 Tübingen, Germany
| | - Janes Krusche
- Cluster of Excellence "Controlling Microbes to Fight Infections (CMFI)", University of Tübingen, 72076 Tübingen, Germany; Interfaculty Institute of Microbiology and Infection Medicine Tübingen, Infection Biology, University of Tübingen, 72076 Tübingen, Germany; German Centre for Infection Research (DZIF), Partner Site Tübingen, 72076 Tübingen, Germany
| | - Ahmed M A Elsherbini
- Cluster of Excellence "Controlling Microbes to Fight Infections (CMFI)", University of Tübingen, 72076 Tübingen, Germany; Interfaculty Institute of Microbiology and Infection Medicine Tübingen, Infection Biology, University of Tübingen, 72076 Tübingen, Germany; German Centre for Infection Research (DZIF), Partner Site Tübingen, 72076 Tübingen, Germany
| | - Xin Du
- Cluster of Excellence "Controlling Microbes to Fight Infections (CMFI)", University of Tübingen, 72076 Tübingen, Germany; Interfaculty Institute of Microbiology and Infection Medicine Tübingen, Infection Biology, University of Tübingen, 72076 Tübingen, Germany; German Centre for Infection Research (DZIF), Partner Site Tübingen, 72076 Tübingen, Germany
| | - Andreas Peschel
- Cluster of Excellence "Controlling Microbes to Fight Infections (CMFI)", University of Tübingen, 72076 Tübingen, Germany; Interfaculty Institute of Microbiology and Infection Medicine Tübingen, Infection Biology, University of Tübingen, 72076 Tübingen, Germany; German Centre for Infection Research (DZIF), Partner Site Tübingen, 72076 Tübingen, Germany.
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3
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Chu Yuan Kee MJ, Chen J. Phage Transduction of Staphylococcus aureus. Methods Mol Biol 2024; 2738:263-275. [PMID: 37966605 DOI: 10.1007/978-1-0716-3549-0_17] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2023]
Abstract
Bacteriophage transduction is the major mechanism of horizontal gene transfer (HGT) among many bacteria. In Staphylococcus aureus, the phage-mediated acquisition of mobile genetic elements (MGEs) that encode virulence and antibiotic resistance genes largely contribute to its evolutionary adaptation and genetic plasticity. In molecular biology, generalized transduction is routinely used as a technique to manipulate and construct bacterial strains. Here, we describe optimized protocols for generalized transduction, applicable for the transfer of plasmid or chromosomal deoxyribonucleic acid (DNA) from donor to recipient S. aureus strains.
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Affiliation(s)
- Melissa-Jane Chu Yuan Kee
- Infectious Diseases Translational Research Programme, Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - John Chen
- Infectious Diseases Translational Research Programme, Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.
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4
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da Silva JD, Melo LDR, Santos SB, Kropinski AM, Xisto MF, Dias RS, da Silva Paes I, Vieira MS, Soares JJF, Porcellato D, da Silva Duarte V, de Paula SO. Genomic and proteomic characterization of vB_SauM-UFV_DC4, a novel Staphylococcus jumbo phage. Appl Microbiol Biotechnol 2023; 107:7231-7250. [PMID: 37741937 PMCID: PMC10638138 DOI: 10.1007/s00253-023-12743-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 04/03/2023] [Accepted: 08/21/2023] [Indexed: 09/25/2023]
Abstract
Staphylococcus aureus is one of the most relevant mastitis pathogens in dairy cattle, and the acquisition of antimicrobial resistance genes presents a significant health issue in both veterinary and human fields. Among the different strategies to tackle S. aureus infection in livestock, bacteriophages have been thoroughly investigated in the last decades; however, few specimens of the so-called jumbo phages capable of infecting S. aureus have been described. Herein, we report the biological, genomic, and structural proteomic features of the jumbo phage vB_SauM-UFV_DC4 (DC4). DC4 exhibited a remarkable killing activity against S. aureus isolated from the veterinary environment and stability at alkaline conditions (pH 4 to 12). The complete genome of DC4 is 263,185 bp (GC content: 25%), encodes 263 predicted CDSs (80% without an assigned function), 1 tRNA (Phe-tRNA), multisubunit RNA polymerase, and an RNA-dependent DNA polymerase. Moreover, comparative analysis revealed that DC4 can be considered a new viral species belonging to a new genus DC4 and showed a similar set of lytic proteins and depolymerase activity with closely related jumbo phages. The characterization of a new S. aureus jumbo phage increases our understanding of the diversity of this group and provides insights into the biotechnological potential of these viruses. KEY POINTS: • vB_SauM-UFV_DC4 is a new viral species belonging to a new genus within the class Caudoviricetes. • vB_SauM-UFV_DC4 carries a set of RNA polymerase subunits and an RNA-directed DNA polymerase. • vB_SauM-UFV_DC4 and closely related jumbo phages showed a similar set of lytic proteins.
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Affiliation(s)
- Jéssica Duarte da Silva
- Department of Microbiology, Federal University of Viçosa, Av. Peter Henry Rolfs, S/N, Campus Universitário, Viçosa, Minas Gerais, 36570-900, Brazil
| | - Luís D R Melo
- Centre of Biological Engineering - CEB, University of Minho, 4710-057, Braga, Portugal
- LABBELS - Associate Laboratory, Braga, Portugal
| | - Sílvio B Santos
- Centre of Biological Engineering - CEB, University of Minho, 4710-057, Braga, Portugal
- LABBELS - Associate Laboratory, Braga, Portugal
| | - Andrew M Kropinski
- Department of Pathobiology, University of Guelph, Guelph, ON, N1G 2W1, Canada
| | - Mariana Fonseca Xisto
- Department of General Biology, Federal University of Viçosa, Av. Peter Henry Rolfs, S/N, Campus Universitário, Viçosa, Minas Gerais, 36570-900, Brazil
| | - Roberto Sousa Dias
- Department of General Biology, Federal University of Viçosa, Av. Peter Henry Rolfs, S/N, Campus Universitário, Viçosa, Minas Gerais, 36570-900, Brazil
| | - Isabela da Silva Paes
- Department of General Biology, Federal University of Viçosa, Av. Peter Henry Rolfs, S/N, Campus Universitário, Viçosa, Minas Gerais, 36570-900, Brazil
| | - Marcella Silva Vieira
- Department of General Biology, Federal University of Viçosa, Av. Peter Henry Rolfs, S/N, Campus Universitário, Viçosa, Minas Gerais, 36570-900, Brazil
| | - José Júnior Ferreira Soares
- Department of General Biology, Federal University of Viçosa, Av. Peter Henry Rolfs, S/N, Campus Universitário, Viçosa, Minas Gerais, 36570-900, Brazil
| | - Davide Porcellato
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, P.O. Box 5003, 1432, Ås, Norway
| | - Vinícius da Silva Duarte
- Department of Microbiology, Federal University of Viçosa, Av. Peter Henry Rolfs, S/N, Campus Universitário, Viçosa, Minas Gerais, 36570-900, Brazil.
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, P.O. Box 5003, 1432, Ås, Norway.
| | - Sérgio Oliveira de Paula
- Department of General Biology, Federal University of Viçosa, Av. Peter Henry Rolfs, S/N, Campus Universitário, Viçosa, Minas Gerais, 36570-900, Brazil
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Kaneki M, Ohira C, Takahashi M, Iwashita N, Takagi Y, Nagane M, Uchiyama J, Fukuyama T. Therapeutic potential of ozone water treatment in alleviating atopic dermatitis symptoms in mouse models: Exploring its bactericidal and direct anti-inflammatory properties. Int Immunopharmacol 2023; 124:110920. [PMID: 37716162 DOI: 10.1016/j.intimp.2023.110920] [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: 06/09/2023] [Revised: 08/30/2023] [Accepted: 09/07/2023] [Indexed: 09/18/2023]
Abstract
Currently, ozone water is utilized for antibacterial and antiviral purposes without any reported safety concerns. Therefore, ozone water may have clinical applications in treating staphylococcal-specific cutaneous diseases, such as atopic dermatitis (AD) and pyoderma. This study aimed to verify the bactericidal effects of ozone water at different concentrations (3 and 11 mg/L) against staphylococcal species in vitro, as well as evaluate the anti-inflammatory effects of ozone water in a mouse model of AD and pyoderma. Initially, the bactericidal properties of several concentrations of ozone water were confirmed with Staphylococcus aureus and methicillin-resistant S. pseudintermedius. Both 3 and 11 mg/L of ozone water exhibited a significant bactericidal effect against staphylococci at less than 100 times dilution. We next examined the cellular cytotoxicity and cytokine production (Interleukin (IL)-6 and IL-8) induced by S. pseudintermedius pre-treated with ozone water, and our findings indicated that cytotoxicity and cytokine production induced by staphylococci were significantly inhibited after ozone water pre-treatment. In vivo experiments showed that ozone water-pre-treated S. pseudintermedius significantly inhibited the development of pyoderma in mice; however, limited effects were observed in a therapeutic setting. Interestingly, ozone water at concentrations of 3 and 11 mg/L exhibits dual bactericidal and anti-inflammatory effects in mice with AD. This observation was corroborated by the significant inhibition of cytokine production in interferon-γ/tumor necrosis factor-stimulated human epidermal keratinocyte cells exposed to ozone in vitro. These findings indicate that administering ozone can be a novel therapeutic approach for managing allergic skin diseases, such as AD.
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Affiliation(s)
- Mao Kaneki
- Laboratory of Veterinary Pharmacology, Azabu University, 1-17-71, Fuchinobe, Chuo-ku, Sagamihara-shi, Kanagawa, Japan
| | - Chiharu Ohira
- Laboratory of Veterinary Pharmacology, Azabu University, 1-17-71, Fuchinobe, Chuo-ku, Sagamihara-shi, Kanagawa, Japan
| | - Miyu Takahashi
- Laboratory of Veterinary Pharmacology, Azabu University, 1-17-71, Fuchinobe, Chuo-ku, Sagamihara-shi, Kanagawa, Japan
| | - Naoki Iwashita
- Laboratory of Veterinary Pharmacology, Azabu University, 1-17-71, Fuchinobe, Chuo-ku, Sagamihara-shi, Kanagawa, Japan; Bioalch Co. Ltd., 3-28 Honshuku-cho, Fuchu-shi, Tokyo, Japan
| | - Yoshiichi Takagi
- Laboratory of Veterinary Pharmacology, Azabu University, 1-17-71, Fuchinobe, Chuo-ku, Sagamihara-shi, Kanagawa, Japan; Japan SLC Inc, 85 Ohara-cho, Kita-ku, Hamamatsu-shi, Shizuoka, Japan
| | - Masaki Nagane
- Laboratory of Veterinary Pharmacology, Azabu University, 1-17-71, Fuchinobe, Chuo-ku, Sagamihara-shi, Kanagawa, Japan; Center for Human and Animal Symbiosis Science, Azabu University, Sagamihara, Kanagawa, Japan
| | - Jumpei Uchiyama
- Department of Bacteriology, Graduate School of Medicine Dentistry and Pharmaceutical Sciences, Okayama University, Japan
| | - Tomoki Fukuyama
- Laboratory of Veterinary Pharmacology, Azabu University, 1-17-71, Fuchinobe, Chuo-ku, Sagamihara-shi, Kanagawa, Japan; Center for Human and Animal Symbiosis Science, Azabu University, Sagamihara, Kanagawa, Japan.
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6
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Muselmani W, Kashif-Khan N, Bagnéris C, Santangelo R, Williams MA, Savva R. A Multimodal Approach towards Genomic Identification of Protein Inhibitors of Uracil-DNA Glycosylase. Viruses 2023; 15:1348. [PMID: 37376646 DOI: 10.3390/v15061348] [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: 04/14/2023] [Revised: 06/02/2023] [Accepted: 06/06/2023] [Indexed: 06/29/2023] Open
Abstract
DNA-mimicking proteins encoded by viruses can modulate processes such as innate cellular immunity. An example is Ung-family uracil-DNA glycosylase inhibition, which prevents Ung-mediated degradation via the stoichiometric protein blockade of the Ung DNA-binding cleft. This is significant where uracil-DNA is a key determinant in the replication and distribution of virus genomes. Unrelated protein folds support a common physicochemical spatial strategy for Ung inhibition, characterised by pronounced sequence plasticity within the diverse fold families. That, and the fact that relatively few template sequences are biochemically verified to encode Ung inhibitor proteins, presents a barrier to the straightforward identification of Ung inhibitors in genomic sequences. In this study, distant homologs of known Ung inhibitors were characterised via structural biology and structure prediction methods. A recombinant cellular survival assay and in vitro biochemical assay were used to screen distant variants and mutants to further explore tolerated sequence plasticity in motifs supporting Ung inhibition. The resulting validated sequence repertoire defines an expanded set of heuristic sequence and biophysical signatures shared by known Ung inhibitor proteins. A computational search of genome database sequences and the results of recombinant tests of selected output sequences obtained are presented here.
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Affiliation(s)
- Wael Muselmani
- Institute of Structural and Molecular Biology, Department of Biological Sciences, Birkbeck, University of London, Malet Street, London WC1E 7HX, UK
| | - Naail Kashif-Khan
- Institute of Structural and Molecular Biology, Department of Biological Sciences, Birkbeck, University of London, Malet Street, London WC1E 7HX, UK
| | - Claire Bagnéris
- Institute of Structural and Molecular Biology, Department of Biological Sciences, Birkbeck, University of London, Malet Street, London WC1E 7HX, UK
| | - Rosalia Santangelo
- Institute of Structural and Molecular Biology, Department of Biological Sciences, Birkbeck, University of London, Malet Street, London WC1E 7HX, UK
| | - Mark A Williams
- Institute of Structural and Molecular Biology, Department of Biological Sciences, Birkbeck, University of London, Malet Street, London WC1E 7HX, UK
| | - Renos Savva
- Institute of Structural and Molecular Biology, Department of Biological Sciences, Birkbeck, University of London, Malet Street, London WC1E 7HX, UK
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Michaelis C, Grohmann E. Horizontal Gene Transfer of Antibiotic Resistance Genes in Biofilms. Antibiotics (Basel) 2023; 12:antibiotics12020328. [PMID: 36830238 PMCID: PMC9952180 DOI: 10.3390/antibiotics12020328] [Citation(s) in RCA: 49] [Impact Index Per Article: 49.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Revised: 01/30/2023] [Accepted: 01/31/2023] [Indexed: 02/08/2023] Open
Abstract
Most bacteria attach to biotic or abiotic surfaces and are embedded in a complex matrix which is known as biofilm. Biofilm formation is especially worrisome in clinical settings as it hinders the treatment of infections with antibiotics due to the facilitated acquisition of antibiotic resistance genes (ARGs). Environmental settings are now considered as pivotal for driving biofilm formation, biofilm-mediated antibiotic resistance development and dissemination. Several studies have demonstrated that environmental biofilms can be hotspots for the dissemination of ARGs. These genes can be encoded on mobile genetic elements (MGEs) such as conjugative and mobilizable plasmids or integrative and conjugative elements (ICEs). ARGs can be rapidly transferred through horizontal gene transfer (HGT) which has been shown to occur more frequently in biofilms than in planktonic cultures. Biofilm models are promising tools to mimic natural biofilms to study the dissemination of ARGs via HGT. This review summarizes the state-of-the-art of biofilm studies and the techniques that visualize the three main HGT mechanisms in biofilms: transformation, transduction, and conjugation.
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8
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Uchiyama J, Takemura-Uchiyama I, Gotoh K, Kato SI, Sakaguchi Y, Murakami H, Fukuyama T, Kaneki M, Matsushita O, Matsuzaki S. Phylogenic analysis of new viral cluster of large phages with unusual DNA genomes containing uracil in place of thymine in gene-sharing network, using phages S6 and PBS1 and relevant uncultured phages derived from sewage metagenomics. Virus Res 2022; 319:198881. [PMID: 35934259 DOI: 10.1016/j.virusres.2022.198881] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Revised: 06/28/2022] [Accepted: 07/28/2022] [Indexed: 11/19/2022]
Abstract
Bacteriophages (phages) are the most diverse and abundant life-form on Earth. Jumbophages are phages with double-stranded DNA genomes longer than 200 kbp. Among these, some jumbophages with uracil in place of thymine as a nucleic acid base, which we have tentatively termed "dU jumbophages" in this study, have been reported. Because the dU jumbophages are considered to be a living fossil from the RNA world, the evolutionary traits of dU jumbophages are of interest. In this study, we examined the phylogeny of dU jumbophages. First, tBLASTx analysis of newly sequenced dU jumbophages such as Bacillus phage PBS1 and previously isolated Staphylococcus phage S6 showed similarity to the other dU jumbophages. Second, we detected the two partial genome sequences of uncultured phages possibly relevant to dU jumbophages, scaffold_002 and scaffold_007, from wastewater metagenomics. Third, according to the gene-sharing network analysis, the dU jumbophages, including phages PBS1 and S6, and uncultured phage scaffold_002 formed a cluster, which suggested a new viral subfamily/family. Finally, analyses of the phylogenetic relationship with other phages showed that the dU jumbophage cluster, which had two clades of phages infecting Gram-negative and Gram-positive bacteria, diverged from the single ancestral phage. These findings together with previous reports may imply that dU jumbophages evolved from the same origin before divergence of Gram-negative and Gram-positive bacteria.
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Affiliation(s)
- Jumpei Uchiyama
- Department of Bacteriology, Graduate School of Medicine Dentistry and Pharmaceutical Sciences, Okayama University, Okayama 700-8558, Japan.
| | - Iyo Takemura-Uchiyama
- Department of Bacteriology, Graduate School of Medicine Dentistry and Pharmaceutical Sciences, Okayama University, Okayama 700-8558, Japan
| | - Kazuyoshi Gotoh
- Department of Bacteriology, Graduate School of Medicine Dentistry and Pharmaceutical Sciences, Okayama University, Okayama 700-8558, Japan
| | - Shin-Ichiro Kato
- Research Institute of Molecular Genetics, Kochi University, Kochi 783-0093, Japan
| | - Yoshihiko Sakaguchi
- Department of Microbiology, Kitasato University School of Medicine, Kanagawa 252-0374, Japan
| | - Hironobu Murakami
- School of Veterinary Medicine, Azabu University, Kanagawa 252-5201, Japan
| | - Tomoki Fukuyama
- School of Veterinary Medicine, Azabu University, Kanagawa 252-5201, Japan
| | - Mao Kaneki
- School of Veterinary Medicine, Azabu University, Kanagawa 252-5201, Japan
| | - Osamu Matsushita
- Department of Bacteriology, Graduate School of Medicine Dentistry and Pharmaceutical Sciences, Okayama University, Okayama 700-8558, Japan
| | - Shigenobu Matsuzaki
- Department of Medical Laboratory Science, Faculty of Health Sciences, Kochi Gakuen University, Kochi 780-0955, Japan
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9
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Zhang B, Sun H, Zhao F, Wang Q, Pan Q, Tong Y, Ren H. Characterization and Genomic Analysis of a Novel Jumbo Bacteriophage vB_StaM_SA1 Infecting Staphylococcus aureus With Two Lysins. Front Microbiol 2022; 13:856473. [PMID: 35572667 PMCID: PMC9096886 DOI: 10.3389/fmicb.2022.856473] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Accepted: 04/04/2022] [Indexed: 11/30/2022] Open
Abstract
The development of new antimicrobial agents is critically needed due to the alarming increase in antibiotic resistance in bacterial pathogens. Phages have been widely considered as effective alternatives to antibiotics. A novel phage vB_StaM_SA1 (hereinafter as SA1) that can infect multiple Staphylococcus strains was isolated from untreated sewage of a pig farm, which belonged to Myoviridae family. At MOI of 0.1, the latent period of phage SA1 was 55 min, and the final titer reached about 109 PFU/mL. The genome of phage SA1 was 260,727 bp, indicating that it can be classified as a jumbo phage. The genome of SA1 had 258 ORFs and a serine tRNA, while only 53 ORFs were annotated with functions. Phage SA1 contained a group of core genes that was characterized by multiple RNA polymerase subunits and also found in phiKZ-related jumbo phages. The phylogenetic tree showed that phage SA1 was a phiKZ-related phage and was closer to jumbo phages compared with Staphylococcus phages with small genome. Three proteins (lys4, lys210, and lys211) were predicted to be associated with lysins, and two proteins with lytic function were verified by recombinant expression and bacterial survival test. Both lys210 and lys211 possessed efficient bactericidal ability, and lys210 could lyse all test strains. The results show that phage SA1 and lys210/lys211 could be potentially used as antibiotic agents to treat Staphylococcus infection.
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Affiliation(s)
- Bingyan Zhang
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, China.,College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
| | - Huzhi Sun
- Qingdao Phagepharm Bio-tech Co., Ltd., Qingdao, China
| | - Feiyang Zhao
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, China
| | - Qian Wang
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, China
| | - Qiang Pan
- Qingdao Phagepharm Bio-tech Co., Ltd., Qingdao, China
| | - Yigang Tong
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
| | - Huiying Ren
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, China
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10
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Hatoum-Aslan A. The phages of staphylococci: critical catalysts in health and disease. Trends Microbiol 2021; 29:1117-1129. [PMID: 34030968 PMCID: PMC8578144 DOI: 10.1016/j.tim.2021.04.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Revised: 04/26/2021] [Accepted: 04/28/2021] [Indexed: 01/21/2023]
Abstract
The phages that infect Staphylococcus species are dominant residents of the skin microbiome that play critical roles in health and disease. While temperate phages, which can integrate into the host genome, have the potential to promote staphylococcal pathogenesis, the strictly lytic variety are powerful antimicrobials that are being exploited for therapeutic applications. This article reviews recent insights into the diversity of staphylococcal phages and newly described mechanisms by which they influence host pathogenicity. The latest efforts to harness these viruses to eradicate staphylococcal infections are also highlighted. Decades of research has focused on the temperate phages of Staphylococcus aureus as model systems, thus underscoring the need to broaden basic research efforts to include diverse phages that infect other clinically relevant Staphylococcus species.
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Affiliation(s)
- Asma Hatoum-Aslan
- University of Illinois at Urbana-Champaign, Department of Microbiology, Urbana, IL, 61801, USA.
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11
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Göller PC, Elsener T, Lorgé D, Radulovic N, Bernardi V, Naumann A, Amri N, Khatchatourova E, Coutinho FH, Loessner MJ, Gómez-Sanz E. Multi-species host range of staphylococcal phages isolated from wastewater. Nat Commun 2021; 12:6965. [PMID: 34845206 PMCID: PMC8629997 DOI: 10.1038/s41467-021-27037-6] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Accepted: 10/21/2021] [Indexed: 12/19/2022] Open
Abstract
The host range of bacteriophages defines their impact on bacterial communities and genome diversity. Here, we characterize 94 novel staphylococcal phages from wastewater and establish their host range on a diversified panel of 117 staphylococci from 29 species. Using this high-resolution phage-bacteria interaction matrix, we unveil a multi-species host range as a dominant trait of the isolated staphylococcal phages. Phage genome sequencing shows this pattern to prevail irrespective of taxonomy. Network analysis between phage-infected bacteria reveals that hosts from multiple species, ecosystems, and drug-resistance phenotypes share numerous phages. Lastly, we show that phages throughout this network can package foreign genetic material enclosing an antibiotic resistance marker at various frequencies. Our findings indicate a weak host specialism of the tested phages, and therefore their potential to promote horizontal gene transfer in this environment.
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Affiliation(s)
- Pauline C. Göller
- grid.5801.c0000 0001 2156 2780Institute of Food, Nutrition and Health, ETH Zurich, 8092 Zurich, Switzerland
| | - Tabea Elsener
- grid.5801.c0000 0001 2156 2780Institute of Food, Nutrition and Health, ETH Zurich, 8092 Zurich, Switzerland
| | - Dominic Lorgé
- grid.5801.c0000 0001 2156 2780Institute of Food, Nutrition and Health, ETH Zurich, 8092 Zurich, Switzerland
| | - Natasa Radulovic
- grid.5801.c0000 0001 2156 2780Institute of Food, Nutrition and Health, ETH Zurich, 8092 Zurich, Switzerland
| | - Viona Bernardi
- grid.5801.c0000 0001 2156 2780Institute of Food, Nutrition and Health, ETH Zurich, 8092 Zurich, Switzerland
| | - Annika Naumann
- grid.5801.c0000 0001 2156 2780Institute of Food, Nutrition and Health, ETH Zurich, 8092 Zurich, Switzerland
| | - Nesrine Amri
- grid.5801.c0000 0001 2156 2780Institute of Food, Nutrition and Health, ETH Zurich, 8092 Zurich, Switzerland
| | - Ekaterina Khatchatourova
- grid.5801.c0000 0001 2156 2780Institute of Food, Nutrition and Health, ETH Zurich, 8092 Zurich, Switzerland
| | - Felipe Hernandes Coutinho
- grid.26811.3c0000 0001 0586 4893Departamento de Producción Vegetal y Microbiología, Universidad Miguel Hernández, San Juan de Alicante, Spain
| | - Martin J. Loessner
- grid.5801.c0000 0001 2156 2780Institute of Food, Nutrition and Health, ETH Zurich, 8092 Zurich, Switzerland
| | - Elena Gómez-Sanz
- Institute of Food, Nutrition and Health, ETH Zurich, 8092, Zurich, Switzerland. .,Área de Microbiología Molecular, Centro de Investigación Biomédica de La Rioja (CIBIR), Logroño, Spain.
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12
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Erickson S, Paulson J, Brown M, Hahn W, Gil J, Barron-Montenegro R, Moreno-Switt AI, Eisenberg M, Nguyen MM. Isolation and engineering of a Listeria grayi bacteriophage. Sci Rep 2021; 11:18947. [PMID: 34556683 PMCID: PMC8460666 DOI: 10.1038/s41598-021-98134-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Accepted: 09/03/2021] [Indexed: 01/02/2023] Open
Abstract
The lack of bacteriophages capable of infecting the Listeria species, Listeria grayi, is academically intriguing and presents an obstacle to the development of bacteriophage-based technologies for Listeria. We describe the isolation and engineering of a novel L. grayi bacteriophage, LPJP1, isolated from farm silage. With a genome over 200,000 base pairs, LPJP1 is the first and only reported jumbo bacteriophage infecting the Listeria genus. Similar to other Gram-positive jumbo phages, LPJP1 appeared to contain modified base pairs, which complicated initial attempts to obtain genomic sequence using standard methods. Following successful sequencing with a modified approach, a recombinant of LPJP1 encoding the NanoLuc luciferase was engineered using homologous recombination. This luciferase reporter bacteriophage successfully detected 100 stationary phase colony forming units of both subspecies of L. grayi in four hours. A single log phase colony forming unit was also sufficient for positive detection in the same time period. The recombinant demonstrated complete specificity for this particular Listeria species and did not infect 150 non-L. grayi Listeria strains nor any other bacterial genus. LPJP1 is believed to be the first reported lytic bacteriophage of L. grayi as well as the only jumbo bacteriophage to be successfully engineered into a luciferase reporter.
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Affiliation(s)
- Stephen Erickson
- Laboratory Corporation of America Holdings, New Brighton, MN, 55112, USA.
| | - John Paulson
- Laboratory Corporation of America Holdings, New Brighton, MN, 55112, USA
| | - Matthew Brown
- Laboratory Corporation of America Holdings, Burlington, NC, 27215, USA
| | - Wendy Hahn
- Laboratory Corporation of America Holdings, New Brighton, MN, 55112, USA
| | - Jose Gil
- Laboratory Corporation of America Holdings, Los Angeles, CA, 90062, USA
| | - Rocío Barron-Montenegro
- Escuela de Medicina Veterinaria, Facultad de Agronomía e Ingeniería Forestal, Facultad de Ciencias Biológicas, Facultad de Medicina, Pontificia Universidad Católica de Chile, Santiago, Chile.,Millennium Initiative for Collaborative Research on Bacteria Resistance (MICROB-R), Santiago, Chile
| | - Andrea I Moreno-Switt
- Escuela de Medicina Veterinaria, Facultad de Agronomía e Ingeniería Forestal, Facultad de Ciencias Biológicas, Facultad de Medicina, Pontificia Universidad Católica de Chile, Santiago, Chile.,Millennium Initiative for Collaborative Research on Bacteria Resistance (MICROB-R), Santiago, Chile
| | - Marcia Eisenberg
- Laboratory Corporation of America Holdings, Burlington, NC, 27215, USA
| | - Minh M Nguyen
- Laboratory Corporation of America Holdings, New Brighton, MN, 55112, USA
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13
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Comparative Genomics of Three Novel Jumbo Bacteriophages Infecting Staphylococcus aureus. J Virol 2021; 95:e0239120. [PMID: 34287047 DOI: 10.1128/jvi.02391-20] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
The majority of previously described Staphylococcus aureus bacteriophages belong to three major groups: P68-like podophages, Twort-like or K-like myophages, and a more diverse group of temperate siphophages. Here we present three novel S. aureus "jumbo" phages: MarsHill, Madawaska, and Machias. These phages were isolated from swine production environments in the United States and represent a novel clade of S. aureus myophage. The average genome size for these phages is ∼269 kb with each genome encoding ∼263 predicted protein-coding genes. Phage genome organization and content is similar to known jumbo phages of Bacillus, including AR9 and vB_BpuM-BpSp. All three phages possess genes encoding complete virion and non-virion RNA polymerases, multiple homing endonucleases, and a retron-like reverse transcriptase. Like AR9, all of these phages are presumed to have uracil-substituted DNA which interferes with DNA sequencing. These phages are also able to transduce host plasmids, which is significant as these phages were found circulating in swine production environments and can also infect human S. aureus isolates. Importance of work: This study describes the comparative genomics of three novel S. aureus jumbo phages: MarsHill, Madawaska, and Machias. These three S. aureus myophages represent an emerging class of S. aureus phage. These genomes contain abundant introns which show a pattern consistent with repeated acquisition rather than vertical inheritance, suggesting intron acquisition and loss is an active process in the evolution of these phages. These phages have presumably hypermodified DNA which inhibits sequencing by several different common platforms. Therefore, these phages also represent potential genomic diversity that has been missed due to the limitations of standard sequencing techniques. In particular, such hypermodified genomes may be missed by metagenomic studies due to their resistance to standard sequencing techniques. Phage MarsHill was found to be able to transduce host DNA at levels comparable to that found for other transducing S. aureus phages, making them a potential vector for horizontal gene transfer in the environment.
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14
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Viruses with U-DNA: New Avenues for Biotechnology. Viruses 2021; 13:v13050875. [PMID: 34068736 PMCID: PMC8150378 DOI: 10.3390/v13050875] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Revised: 05/05/2021] [Accepted: 05/06/2021] [Indexed: 02/07/2023] Open
Abstract
Deoxyuridine in DNA has recently been in the focus of research due to its intriguing roles in several physiological and pathophysiological situations. Although not an orthodox DNA base, uracil may appear in DNA via either cytosine deamination or thymine-replacing incorporations. Since these alterations may induce mutation or may perturb DNA–protein interactions, free living organisms from bacteria to human contain several pathways to counteract uracilation. These efficient and highly specific repair routes uracil-directed excision repair initiated by representative of uracil-DNA glycosylase families. Interestingly, some bacteriophages exist with thymine-lacking uracil-DNA genome. A detailed understanding of the strategy by which such phages can replicate in bacteria where an efficient repair pathway functions for uracil-excision from DNA is expected to reveal novel inhibitors that can also be used for biotechnological applications. Here, we also review the several potential biotechnological applications already implemented based on inhibitors of uracil-excision repair, such as Crispr-base-editing and detection of nascent uracil distribution pattern in complex genomes.
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15
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Langenfeld K, Chin K, Roy A, Wigginton K, Duhaime MB. Comparison of ultrafiltration and iron chloride flocculation in the preparation of aquatic viromes from contrasting sample types. PeerJ 2021; 9:e11111. [PMID: 33996275 PMCID: PMC8106395 DOI: 10.7717/peerj.11111] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Accepted: 02/23/2021] [Indexed: 12/24/2022] Open
Abstract
Viral metagenomes (viromes) are a valuable untargeted tool for studying viral diversity and the central roles viruses play in host disease, ecology, and evolution. Establishing effective methods to concentrate and purify viral genomes prior to sequencing is essential for high quality viromes. Using virus spike-and-recovery experiments, we stepwise compared two common approaches for virus concentration, ultrafiltration and iron chloride flocculation, across diverse matrices: wastewater influent, wastewater secondary effluent, river water, and seawater. Viral DNA was purified by removing cellular DNA via chloroform cell lysis, filtration, and enzymatic degradation of extra-viral DNA. We found that viral genomes were concentrated 1-2 orders of magnitude more with ultrafiltration than iron chloride flocculation for all matrices and resulted in higher quality DNA suitable for amplification-free and long-read sequencing. Given its widespread use and utility as an inexpensive field method for virome sampling, we nonetheless sought to optimize iron flocculation. We found viruses were best concentrated in seawater with five-fold higher iron concentrations than the standard used, inhibition of DNase activity reduced purification effectiveness, and five-fold more iron was needed to flocculate viruses from freshwater than seawater—critical knowledge for those seeking to apply this broadly used method to freshwater virome samples. Overall, our results demonstrated that ultrafiltration and purification performed better than iron chloride flocculation and purification in the tested matrices. Given that the method performance depended on the solids content and salinity of the samples, we suggest spike-and-recovery experiments be applied when concentrating and purifying sample types that diverge from those tested here.
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Affiliation(s)
- Kathryn Langenfeld
- Department of Civil and Environmental Engineering, University of Michigan - Ann Arbor, Ann Arbor, MI, United States of America
| | - Kaitlyn Chin
- Department of Civil and Environmental Engineering, University of Michigan - Ann Arbor, Ann Arbor, MI, United States of America
| | - Ariel Roy
- Department of Civil and Environmental Engineering, University of Michigan - Ann Arbor, Ann Arbor, MI, United States of America
| | - Krista Wigginton
- Department of Civil and Environmental Engineering, University of Michigan - Ann Arbor, Ann Arbor, MI, United States of America
| | - Melissa B Duhaime
- Department of Ecology and Evolutionary Biology, University of Michigan - Ann Arbor, Ann Arbor, MI, United States of America
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16
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Lee Y, Son B, Cha Y, Ryu S. Characterization and Genomic Analysis of PALS2, a Novel Staphylococcus Jumbo Bacteriophage. Front Microbiol 2021; 12:622755. [PMID: 33763042 PMCID: PMC7982418 DOI: 10.3389/fmicb.2021.622755] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Accepted: 02/09/2021] [Indexed: 12/30/2022] Open
Abstract
Staphylococcus aureus is an important human pathogen that can be frequently encountered in clinical and food-processing surroundings. Among the various countermeasures, bacteriophages have been considered to be promising alternatives to antibiotics. In this study, the bacteriophage PALS2 was isolated from bird feces, and the genomic and biological characteristics of this phage were investigated. PALS2 was determined to belong to the Myoviridae family and exhibited extended host inhibition that persisted for up to 24 h with repeated bursts of 12 plaque-forming units/cell. The complete genome of PALS2 measured 268,746 base pairs (bp), indicating that PALS2 could be classified as a jumbo phage. The PALS2 genome contained 279 ORFs and 1 tRNA covering asparagine, and the majority of predicted PALS2 genes encoded hypothetical proteins. Additional genes involved in DNA replication and repair, nucleotide metabolism, and genes encoding multisubunit RNA polymerase were identified in the PALS2 genome, which is a common feature of typical jumbo phages. Comparative genomic analysis indicated that PALS2 is a phiKZ-related virus and is more similar to typical jumbo phages than to staphylococcal phages. Additionally, the effective antimicrobial activities of phage PALS2 suggest its possible use as a biocontrol agent in various clinical and food processing environments.
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Affiliation(s)
- Yoona Lee
- Department of Food and Animal Biotechnology, Seoul National University, Seoul, South Korea.,Department of Agricultural Biotechnology, Seoul National University, Seoul, South Korea
| | - Bokyung Son
- Department of Food and Animal Biotechnology, Seoul National University, Seoul, South Korea.,Department of Agricultural Biotechnology, Seoul National University, Seoul, South Korea
| | - Yoyeon Cha
- Department of Food and Animal Biotechnology, Seoul National University, Seoul, South Korea.,Department of Agricultural Biotechnology, Seoul National University, Seoul, South Korea
| | - Sangryeol Ryu
- Department of Food and Animal Biotechnology, Seoul National University, Seoul, South Korea.,Department of Agricultural Biotechnology, Seoul National University, Seoul, South Korea.,Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, South Korea.,Center for Food and Bioconvergence, Seoul National University, Seoul, South Korea
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17
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M. Iyer L, Anantharaman V, Krishnan A, Burroughs AM, Aravind L. Jumbo Phages: A Comparative Genomic Overview of Core Functions and Adaptions for Biological Conflicts. Viruses 2021; 13:v13010063. [PMID: 33466489 PMCID: PMC7824862 DOI: 10.3390/v13010063] [Citation(s) in RCA: 48] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Revised: 12/31/2020] [Accepted: 12/31/2020] [Indexed: 02/07/2023] Open
Abstract
Jumbo phages have attracted much attention by virtue of their extraordinary genome size and unusual aspects of biology. By performing a comparative genomics analysis of 224 jumbo phages, we suggest an objective inclusion criterion based on genome size distributions and present a synthetic overview of their manifold adaptations across major biological systems. By means of clustering and principal component analysis of the phyletic patterns of conserved genes, all known jumbo phages can be classified into three higher-order groups, which include both myoviral and siphoviral morphologies indicating multiple independent origins from smaller predecessors. Our study uncovers several under-appreciated or unreported aspects of the DNA replication, recombination, transcription and virion maturation systems. Leveraging sensitive sequence analysis methods, we identify novel protein-modifying enzymes that might help hijack the host-machinery. Focusing on host–virus conflicts, we detect strategies used to counter different wings of the bacterial immune system, such as cyclic nucleotide- and NAD+-dependent effector-activation, and prevention of superinfection during pseudolysogeny. We reconstruct the RNA-repair systems of jumbo phages that counter the consequences of RNA-targeting host effectors. These findings also suggest that several jumbo phage proteins provide a snapshot of the systems found in ancient replicons preceding the last universal ancestor of cellular life.
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Affiliation(s)
- Lakshminarayan M. Iyer
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA; (L.M.I.); (V.A.); (A.M.B.)
| | - Vivek Anantharaman
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA; (L.M.I.); (V.A.); (A.M.B.)
| | - Arunkumar Krishnan
- Department of Biological Sciences, Indian Institute of Science Education and Research (IISER) Berhampur, Odisha 760010, India;
| | - A. Maxwell Burroughs
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA; (L.M.I.); (V.A.); (A.M.B.)
| | - L. Aravind
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA; (L.M.I.); (V.A.); (A.M.B.)
- Correspondence:
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18
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Dragoš A, Priyadarshini B, Hasan Z, Strube ML, Kempen PJ, Maróti G, Kaspar C, Bose B, Burton BM, Bischofs IB, Kovács ÁT. Pervasive prophage recombination occurs during evolution of spore-forming Bacilli. ISME JOURNAL 2020; 15:1344-1358. [PMID: 33343000 DOI: 10.1038/s41396-020-00854-1] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Revised: 11/12/2020] [Accepted: 11/20/2020] [Indexed: 02/06/2023]
Abstract
Phages are the main source of within-species bacterial diversity and drivers of horizontal gene transfer, but we know little about the mechanisms that drive genetic diversity of these mobile genetic elements (MGEs). Recently, we showed that a sporulation selection regime promotes evolutionary changes within SPβ prophage of Bacillus subtilis, leading to direct antagonistic interactions within the population. Herein, we reveal that under a sporulation selection regime, SPβ recombines with low copy number phi3Ts phage DNA present within the B. subtilis population. Recombination results in a new prophage occupying a different integration site, as well as the spontaneous release of virulent phage hybrids. Analysis of Bacillus sp. strains suggests that SPβ and phi3T belong to a distinct cluster of unusually large phages inserted into sporulation-related genes that are equipped with a spore-related genetic arsenal. Comparison of Bacillus sp. genomes indicates that similar diversification of SPβ-like phages takes place in nature. Our work is a stepping stone toward empirical studies on phage evolution, and understanding the eco-evolutionary relationships between bacteria and their phages. By capturing the first steps of new phage evolution, we reveal striking relationship between survival strategy of bacteria and evolution of their phages.
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Affiliation(s)
- Anna Dragoš
- Bacterial Interactions and Evolution Group, Department of Biotechnology and Biomedicine, Technical University of Denmark, 2800, Kongens Lyngby, Denmark.
| | - B Priyadarshini
- Bacterial Interactions and Evolution Group, Department of Biotechnology and Biomedicine, Technical University of Denmark, 2800, Kongens Lyngby, Denmark
| | - Zahraa Hasan
- Bacterial Interactions and Evolution Group, Department of Biotechnology and Biomedicine, Technical University of Denmark, 2800, Kongens Lyngby, Denmark
| | - Mikael Lenz Strube
- Bacterial Ecophysiology and Biotechnology Group, Department of Biotechnology and Biomedicine, Technical University of Denmark, 2800, Kongens Lyngby, Denmark
| | - Paul J Kempen
- Department of Health Technology, Technical University of Denmark, 2800, Kongens Lyngby, Denmark
| | - Gergely Maróti
- Institute of Plant Biology, Biological Research Centre, Hungarian Academy of Sciences, Szeged, H-6701, Hungary
| | - Charlotte Kaspar
- BioQuant Center of the University of Heidelberg, 69120, Heidelberg, Germany.,Max-Planck-Institute for Terrestrial Microbiology, 35043, Marburg, Germany
| | | | - Briana M Burton
- Department of Bacteriology, University of Wisconsin, Madison, WI, 53706, USA
| | - Ilka B Bischofs
- BioQuant Center of the University of Heidelberg, 69120, Heidelberg, Germany.,Max-Planck-Institute for Terrestrial Microbiology, 35043, Marburg, Germany
| | - Ákos T Kovács
- Bacterial Interactions and Evolution Group, Department of Biotechnology and Biomedicine, Technical University of Denmark, 2800, Kongens Lyngby, Denmark.
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19
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Frosini SM, Bond R, McCarthy AJ, Feudi C, Schwarz S, Lindsay JA, Loeffler A. Genes on the Move: In Vitro Transduction of Antimicrobial Resistance Genes between Human and Canine Staphylococcal Pathogens. Microorganisms 2020; 8:E2031. [PMID: 33353175 PMCID: PMC7766859 DOI: 10.3390/microorganisms8122031] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Revised: 12/11/2020] [Accepted: 12/17/2020] [Indexed: 01/09/2023] Open
Abstract
Transmission of methicillin-resistant Staphylococcus aureus (MRSA) and methicillin-resistant Staphylococcus pseudintermedius (MRSP) between people and pets, and their co-carriage, are well-described. Potential exchange of antimicrobial resistance (AMR) genes amongst these staphylococci was investigated in vitro through endogenous bacteriophage-mediated transduction. Bacteriophages were UV-induced from seven donor isolates of canine (MRSP) and human (MRSA) origin, containing tet(M), tet(K), fusB or fusC, and lysates filtered. Twenty-seven tetracycline- and fusidic acid- (FA-) susceptible recipients were used in 122 donor-recipient combinations (22 tetracycline, 100 FA) across 415 assays (115 tetracycline, 300 FA). Bacteriophage lysates were incubated with recipients and presumed transductants quantified on antimicrobial-supplemented agar plates. Tetracycline resistance transduction from MRSP and MRSA to methicillin-susceptible S. pseudintermedius (MSSP) was confirmed by PCR in 15/115 assays. No FA-resistance transfer occurred, confirmed by negative fusB/fusC PCR, but colonies resulting from FA assays had high MICs (≥32 mg/L) and showed mutations in fusA, two at a novel position (F88L), nine at H457[Y/N/L]. Horizontal gene transfer of tetracycline-resistance confirms that resistance genes can be shared between coagulase-positive staphylococci from different hosts. Cross-species AMR transmission highlights the importance of good antimicrobial stewardship across humans and veterinary species to support One Health.
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Affiliation(s)
- Sian Marie Frosini
- Department of Clinical Science and Services, Royal Veterinary College, Hawkshead Lane, North Mymms, Hatfield, Hertfordshire AL9 7TA, UK; (R.B.); (A.L.)
| | - Ross Bond
- Department of Clinical Science and Services, Royal Veterinary College, Hawkshead Lane, North Mymms, Hatfield, Hertfordshire AL9 7TA, UK; (R.B.); (A.L.)
| | - Alex J. McCarthy
- MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London SW7 2AZ, UK;
| | - Claudia Feudi
- Centre for Infection Medicine, Department of Veterinary Medicine, Institute of Microbiology and Epizootics, Freie Universität Berlin, 14195 Berlin, Germany; (C.F.); (S.S.)
| | - Stefan Schwarz
- Centre for Infection Medicine, Department of Veterinary Medicine, Institute of Microbiology and Epizootics, Freie Universität Berlin, 14195 Berlin, Germany; (C.F.); (S.S.)
| | - Jodi A. Lindsay
- Institute of Infection and Immunity, St George’s, University of London, Cranmer Terrace, London SW17 0RE, UK;
| | - Anette Loeffler
- Department of Clinical Science and Services, Royal Veterinary College, Hawkshead Lane, North Mymms, Hatfield, Hertfordshire AL9 7TA, UK; (R.B.); (A.L.)
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20
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Nasukawa T, Sugimoto R, Uchiyama J, Takemura-Uchiyama I, Murakami H, Fukuda K, Matsuzaki S, Sakaguchi M. Purification of membrane vesicles from Gram-positive bacteria using flow cytometry, after iodixanol density-gradient ultracentrifugation. Res Microbiol 2020; 172:103792. [PMID: 33220407 DOI: 10.1016/j.resmic.2020.11.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2020] [Revised: 11/06/2020] [Accepted: 11/06/2020] [Indexed: 11/20/2022]
Abstract
Membrane vesicles (MVs) play biologically important roles in Gram-positive bacteria, and purification is essential for their study. Although high-performance flow cytometry has the capability to quantify and isolate specific small particles, it has not been examined for MV isolation. In this study, we used high-performance flow cytometry to analyze MV from Gram-positive bacteria, Staphylococcus aureus and Bacillus subtilis, prepared by iodixanol density-gradient ultracentrifugation. Analysis of the quality of MV samples before and after sorting showed that the flow cytometric sorting provided higher purity and uniformity compared to gradient isolation alone. The MV purification method using flow cytometry should prove useful for applications requiring a very high purity of MV samples such as proteomic, metagenomic or lipidomic studies.
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Affiliation(s)
| | - Ryosuke Sugimoto
- School of Veterinary Medicine, Azabu University, Kanagawa, Japan
| | - Jumpei Uchiyama
- School of Veterinary Medicine, Azabu University, Kanagawa, Japan.
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21
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Multisubunit RNA Polymerases of Jumbo Bacteriophages. Viruses 2020; 12:v12101064. [PMID: 32977622 PMCID: PMC7598289 DOI: 10.3390/v12101064] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2020] [Revised: 09/17/2020] [Accepted: 09/21/2020] [Indexed: 02/08/2023] Open
Abstract
Prokaryotic viruses with DNA genome longer than 200 kb are collectively referred to as “jumbo phages”. Some representatives of this phylogenetically diverse group encode two DNA-dependent RNA polymerases (RNAPs)—a virion RNAP and a non-virion RNAP. In contrast to most other phage-encoded RNAPs, the jumbo phage RNAPs are multisubunit enzymes related to RNAPs of cellular organisms. Unlike all previously characterized multisubunit enzymes, jumbo phage RNAPs lack the universally conserved alpha subunits required for enzyme assembly. The mechanism of promoter recognition is also different from those used by cellular enzymes. For example, the AR9 phage non-virion RNAP requires uracils in its promoter and is able to initiate promoter-specific transcription from single-stranded DNA. Jumbo phages encoding multisubunit RNAPs likely have a common ancestor allowing making them a separate subgroup within the very diverse group of jumbo phages. In this review, we describe transcriptional strategies used by RNAP-encoding jumbo phages and describe the properties of characterized jumbo phage RNAPs.
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22
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Savva R. The Essential Co-Option of Uracil-DNA Glycosylases by Herpesviruses Invites Novel Antiviral Design. Microorganisms 2020; 8:microorganisms8030461. [PMID: 32214054 PMCID: PMC7143999 DOI: 10.3390/microorganisms8030461] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Revised: 03/20/2020] [Accepted: 03/21/2020] [Indexed: 01/10/2023] Open
Abstract
Vast evolutionary distances separate the known herpesviruses, adapted to colonise specialised cells in predominantly vertebrate hosts. Nevertheless, the distinct herpesvirus families share recognisably related genomic attributes. The taxonomic Family Herpesviridae includes many important human and animal pathogens. Successful antiviral drugs targeting Herpesviridae are available, but the need for reduced toxicity and improved efficacy in critical healthcare interventions invites novel solutions: immunocompromised patients presenting particular challenges. A conserved enzyme required for viral fitness is Ung, a uracil-DNA glycosylase, which is encoded ubiquitously in Herpesviridae genomes and also host cells. Research investigating Ung in Herpesviridae dynamics has uncovered an unexpected combination of viral co-option of host Ung, along with remarkable Subfamily-specific exaptation of the virus-encoded Ung. These enzymes apparently play essential roles, both in the maintenance of viral latency and during initiation of lytic replication. The ubiquitously conserved Ung active site has previously been explored as a therapeutic target. However, exquisite selectivity and better drug-like characteristics might instead be obtained via targeting structural variations within another motif of catalytic importance in Ung. The motif structure is unique within each Subfamily and essential for viral survival. This unique signature in highly conserved Ung constitutes an attractive exploratory target for the development of novel beneficial therapeutics.
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Affiliation(s)
- Renos Savva
- Institute of Structural and Molecular Biology, Department of Biological Sciences, Birkbeck, University of London, Malet Street, London WC1E 7HX, UK
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23
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Ingmer H, Gerlach D, Wolz C. Temperate Phages of Staphylococcus aureus. Microbiol Spectr 2019; 7:10.1128/microbiolspec.gpp3-0058-2018. [PMID: 31562736 PMCID: PMC10921950 DOI: 10.1128/microbiolspec.gpp3-0058-2018] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Indexed: 12/22/2022] Open
Abstract
Most Staphylococcus aureus isolates carry multiple bacteriophages in their genome, which provide the pathogen with traits important for niche adaptation. Such temperate S. aureus phages often encode a variety of accessory factors that influence virulence, immune evasion and host preference of the bacterial lysogen. Moreover, transducing phages are primary vehicles for horizontal gene transfer. Wall teichoic acid (WTA) acts as a common phage receptor for staphylococcal phages and structural variations of WTA govern phage-host specificity thereby shaping gene transfer across clonal lineages and even species. Thus, bacteriophages are central for the success of S. aureus as a human pathogen.
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Affiliation(s)
- Hanne Ingmer
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - David Gerlach
- Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen, Tübingen, Germany
| | - Christiane Wolz
- Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen, Tübingen, Germany
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24
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Targeting uracil-DNA glycosylases for therapeutic outcomes using insights from virus evolution. Future Med Chem 2019; 11:1323-1344. [PMID: 31161802 DOI: 10.4155/fmc-2018-0319] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Ung-type uracil-DNA glycosylases are frontline defenders of DNA sequence fidelity in bacteria, plants and animals; Ungs also directly assist both innate and humoral immunity. Critically important in viral pathogenesis, whether acting for or against viral DNA persistence, Ungs also have therapeutic relevance to cancer, microbial and parasitic diseases. Ung catalytic specificity is uniquely conserved, yet selective antiviral drugging of the Ung catalytic pocket is tractable. However, more promising precision therapy approaches present themselves via insights from viral strategies, including sequestration or adaptation of Ung for noncanonical roles. A universal Ung inhibition mechanism, converged upon by unrelated viruses, could also inform design of compounds to inhibit specific distinct Ungs. Extrapolating current developments, the character of such novel chemical entities is proposed.
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25
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Bari SMN, Walker FC, Cater K, Aslan B, Hatoum-Aslan A. Strategies for Editing Virulent Staphylococcal Phages Using CRISPR-Cas10. ACS Synth Biol 2017; 6:2316-2325. [PMID: 28885820 DOI: 10.1021/acssynbio.7b00240] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Staphylococci are prevalent skin-dwelling bacteria that are also leading causes of antibiotic-resistant infections. Viruses that infect and lyse these organisms (virulent staphylococcal phages) can be used as alternatives to conventional antibiotics and represent promising tools to eliminate or manipulate specific species in the microbiome. However, since over half their genes have unknown functions, virulent staphylococcal phages carry inherent risk to cause unknown downstream side effects. Further, their swift and destructive reproductive cycle make them intractable by current genetic engineering techniques. CRISPR-Cas10 is an elaborate prokaryotic immune system that employs small RNAs and a multisubunit protein complex to detect and destroy phages and other foreign nucleic acids. Some staphylococci naturally possess CRISPR-Cas10 systems, thus providing an attractive tool already installed in the host chromosome to harness for phage genome engineering. However, the efficiency of CRISPR-Cas10 immunity against virulent staphylococcal phages and corresponding utility as a tool to facilitate their genome editing has not been explored. Here, we show that the CRISPR-Cas10 system native to Staphylococcus epidermidis exhibits robust immunity against diverse virulent staphylococcal phages. On the basis of this activity, a general two-step approach was developed to edit these phages that relies upon homologous recombination machinery encoded in the host. Variations of this approach to edit toxic phage genes and access phages that infect CRISPR-less staphylococci are also presented. This versatile set of genetic tools enables the systematic study of phage genes of unknown functions and the design of genetically defined phage-based antimicrobials that can eliminate or manipulate specific Staphylococcus species.
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Affiliation(s)
- S. M. Nayeemul Bari
- Department of Biological
Sciences, University of Alabama, Tuscaloosa, Alabama 35487, United States
| | - Forrest C. Walker
- Department of Biological
Sciences, University of Alabama, Tuscaloosa, Alabama 35487, United States
| | - Katie Cater
- Department of Biological
Sciences, University of Alabama, Tuscaloosa, Alabama 35487, United States
| | - Barbaros Aslan
- Department of Biological
Sciences, University of Alabama, Tuscaloosa, Alabama 35487, United States
| | - Asma Hatoum-Aslan
- Department of Biological
Sciences, University of Alabama, Tuscaloosa, Alabama 35487, United States
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26
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Abstract
Staphylococcus aureus is a serious human pathogen with remarkable adaptive powers. Antibiotic-resistant clones rapidly emerge mainly by acquisition of antibiotic-resistance genes from other S. aureus strains or even from other genera. Transfer is mediated by a diverse complement of mobile genetic elements and occurs primarily by conjugation or bacteriophage transduction, with the latter traditionally being perceived as the primary route. Recent work on conjugation and transduction suggests that transfer by these mechanisms may be more extensive than previously thought, in terms of the range of plasmids that can be transferred by conjugation and the efficiency with which transduction occurs. Here, we review the main routes of antibiotic resistance gene transfer in S. aureus in the context of its biology as a human commensal and a life-threatening pathogen.
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Affiliation(s)
- Jakob Haaber
- Department of Veterinary and Animal Sciences, Faculty of Health & Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - José R Penadés
- Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | - Hanne Ingmer
- Department of Veterinary and Animal Sciences, Faculty of Health & Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
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27
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Cafini F, Thi Le Thuy N, Román F, Prieto J, Dubrac S, Msadek T, Morikawa K. Methodology for the Study of Horizontal Gene Transfer in Staphylococcus aureus. J Vis Exp 2017. [PMID: 28362383 DOI: 10.3791/55087] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
One important feature of the major opportunistic human pathogen Staphylococcus aureus is its extraordinary ability to rapidly acquire resistance to antibiotics. Genomic studies reveal that S. aureus carries many virulence and resistance genes located in mobile genetic elements, suggesting that horizontal gene transfer (HGT) plays a critical role in S. aureus evolution. However, a full and detailed description of the methodology used to study HGT in S. aureus is still lacking, especially regarding natural transformation, which has been recently reported in this bacterium. This work describes three protocols that are useful for the in vitro investigation of HGT in S. aureus: conjugation, phage transduction, and natural transformation. To this aim, the cfr gene (chloramphenicol/florfenicol resistance), which confers the Phenicols, Lincosamides, Oxazolidinones, Pleuromutilins, and Streptogramin A (PhLOPSA)-resistance phenotype, was used. Understanding the mechanisms through which S. aureus transfers genetic materials to other strains is essential to comprehending the rapid acquisition of resistance and helps to clarify the modes of dissemination reported in surveillance programs or to further predict the spreading mode in the future.
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Affiliation(s)
- Fabio Cafini
- Division of Biomedical Science, Faculty of Medicine, University of Tsukuba; Department of Basic Biomedical Science, Universidad Europea de Madrid;
| | - Nguyen Thi Le Thuy
- Human Biology Program, School of Integrative and Global Majors, University of Tsukuba
| | - Federico Román
- Laboratory of Nosocomial Infections, Department of Bacteriology, Centro Nacional de MicrobiologÍa, Instituto de Salud Carlos III
| | - José Prieto
- Division of Microbiology, Department of Medicine, School of Medicine, Universidad Complutense
| | - Sarah Dubrac
- Biology of Gram-Positive Pathogens, Department of Microbiology, Institut Pasteur, Paris, France; ERL3526, CNRS, Paris, France
| | - Tarek Msadek
- Biology of Gram-Positive Pathogens, Department of Microbiology, Institut Pasteur, Paris, France; ERL3526, CNRS, Paris, France
| | - Kazuya Morikawa
- Division of Biomedical Science, Faculty of Medicine, University of Tsukuba
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28
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Huang H, Zheng X, Chen Y, Liu H, Wan R, Su Y. Alkaline fermentation of waste sludge causes a significant reduction of antibiotic resistance genes in anaerobic reactors. THE SCIENCE OF THE TOTAL ENVIRONMENT 2017; 580:380-387. [PMID: 28011019 DOI: 10.1016/j.scitotenv.2016.11.186] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2016] [Revised: 11/22/2016] [Accepted: 11/25/2016] [Indexed: 06/06/2023]
Abstract
Alkaline fermentation has been reported to be an effective method to recover valuable products from waste sludge. However, to date, the potential effect of alkaline pH on the fate of antibiotic resistance genes (ARGs) during anaerobic fermentation of sludge has never been documented. In this study, the target ARGs in sludge was observed to be removed effectively and stably when sludge was anaerobically fermented at pH10. Compared with the control (without pH adjustment), the abundances of target ARGs at pH10 were reduced by 0.87 (sulI), 1.36 (sulII), 0.42 (tet(O)), 1.11 (tet(Q)), 0.79 (tet(C)) and 1.04 (tet(X)) log units. Further investigations revealed that alkaline fermentation shifted the community structures of potential ARGs hosts. Moreover, alkaline fermentation remarkably decreased the quantities and the ARGs-possessing ability of genetic vectors (plasmid DNA, extracellular DNA and phage DNA), which might limit the transfer of ARGs via conjugation, transformation and transduction. These results suggest that the shifted compositions of gene hosts and restricted gene transfer potential might be the critical reasons for the attenuation of ARGs at pH10.
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Affiliation(s)
- Haining Huang
- State Key Laboratory of Pollution Control and Resource Reuse, School of Environmental Science and Engineering, Tongji University, 1239 Siping Road, Shanghai 200092, China
| | - Xiong Zheng
- State Key Laboratory of Pollution Control and Resource Reuse, School of Environmental Science and Engineering, Tongji University, 1239 Siping Road, Shanghai 200092, China
| | - Yinguang Chen
- State Key Laboratory of Pollution Control and Resource Reuse, School of Environmental Science and Engineering, Tongji University, 1239 Siping Road, Shanghai 200092, China.
| | - Hui Liu
- State Key Laboratory of Pollution Control and Resource Reuse, School of Environmental Science and Engineering, Tongji University, 1239 Siping Road, Shanghai 200092, China
| | - Rui Wan
- State Key Laboratory of Pollution Control and Resource Reuse, School of Environmental Science and Engineering, Tongji University, 1239 Siping Road, Shanghai 200092, China
| | - Yinglong Su
- State Key Laboratory of Pollution Control and Resource Reuse, School of Environmental Science and Engineering, Tongji University, 1239 Siping Road, Shanghai 200092, China
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29
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Kerepesi C, Szabó JE, Papp-Kádár V, Dobay O, Szabó D, Grolmusz V, Vértessy BG. Life without dUTPase. Front Microbiol 2016; 7:1768. [PMID: 27933035 PMCID: PMC5122711 DOI: 10.3389/fmicb.2016.01768] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2016] [Accepted: 10/21/2016] [Indexed: 11/22/2022] Open
Abstract
Fine-tuned regulation of the cellular nucleotide pools is indispensable for faithful replication of Deoxyribonucleic Acid (DNA). The genetic information is also safeguarded by DNA damage recognition and repair processes. Uracil is one of the most frequently occurring erroneous bases in DNA; it can arise from cytosine deamination or thymine-replacing incorporation. Two enzyme activities are primarily involved in keeping DNA uracil-free: dUTPase (dUTP pyrophosphatase) activity that prevent thymine-replacing incorporation and uracil-DNA glycosylase activity that excise uracil from DNA and initiate uracil-excision repair. Both dUTPase and the most efficient uracil-DNA glycosylase (UNG) is thought to be ubiquitous in free-living organisms. In the present work, we have systematically investigated the genotype of deposited fully sequenced bacterial and Archaeal genomes. We have performed bioinformatic searches in these genomes using the already well described dUTPase and UNG gene sequences. For dUTPases, we have included the trimeric all-beta and the dimeric all-alpha families and also, the bifunctional dCTP (deoxycytidine triphosphate) deaminase-dUTPase sequences. Surprisingly, we have found that in contrast to the generally held opinion, a wide number of bacterial and Archaeal species lack all of the previously described dUTPase gene(s). The dut– genotype is present in diverse bacterial phyla indicating that loss of this (or these) gene(s) has occurred multiple times during evolution. We discuss potential survival strategies in lack of dUTPases, such as simultaneous lack or inhibition of UNG and possession of exogenous or alternate metabolic enzymes involved in uracil-DNA metabolism. The potential that genes previously not associated with dUTPase activity may still encode enzymes capable of hydrolyzing dUTP is also discussed. Our data indicate that several unicellular microorganisms may efficiently cope with a dut– genotype lacking all of the previously described dUTPase genes, and potentially leading to an unusual uracil-enrichment in their genomic DNA.
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Affiliation(s)
- Csaba Kerepesi
- PIT Bioinformatics Group, Institute of Mathematics, Eötvös Loránd University Budapest, Hungary
| | - Judit E Szabó
- Department of Applied Biotechnology and Food Sciences, Budapest University of Technology and EconomicsBudapest, Hungary; Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of SciencesBudapest, Hungary
| | - Veronika Papp-Kádár
- Department of Applied Biotechnology and Food Sciences, Budapest University of Technology and EconomicsBudapest, Hungary; Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of SciencesBudapest, Hungary
| | - Orsolya Dobay
- Institute of Medical Microbiology, Semmelweis University Budapest, Hungary
| | - Dóra Szabó
- Institute of Medical Microbiology, Semmelweis University Budapest, Hungary
| | - Vince Grolmusz
- PIT Bioinformatics Group, Institute of Mathematics, Eötvös Loránd UniversityBudapest, Hungary; Uratim Ltd.,Budapest, Hungary
| | - Beáta G Vértessy
- Department of Applied Biotechnology and Food Sciences, Budapest University of Technology and EconomicsBudapest, Hungary; Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of SciencesBudapest, Hungary
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30
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Mašlaňová I, Stříbná S, Doškař J, Pantůček R. Efficient plasmid transduction toStaphylococcus aureusstrains insensitive to the lytic action of transducing phage. FEMS Microbiol Lett 2016; 363:fnw211. [DOI: 10.1093/femsle/fnw211] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/26/2016] [Indexed: 11/15/2022] Open
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31
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Lavysh D, Sokolova M, Minakhin L, Yakunina M, Artamonova T, Kozyavkin S, Makarova KS, Koonin EV, Severinov K. The genome of AR9, a giant transducing Bacillus phage encoding two multisubunit RNA polymerases. Virology 2016; 495:185-96. [PMID: 27236306 DOI: 10.1016/j.virol.2016.04.030] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2016] [Revised: 04/27/2016] [Accepted: 04/29/2016] [Indexed: 11/17/2022]
Abstract
Bacteriophage AR9 and its close relative PBS1 have been extensively used to construct early Bacillus subtilis genetic maps. Here, we present the 251,042bp AR9 genome, a linear, terminally redundant double-stranded DNA containing deoxyuridine instead of thymine. Multiple AR9 genes are interrupted by non-coding sequences or sequences encoding putative endonucleases. We show that these sequences are group I and group II self-splicing introns. Eight AR9 proteins are homologous to fragments of bacterial RNA polymerase (RNAP) subunits β/β'. These proteins comprise two sets of paralogs of RNAP largest subunits, with each paralog encoded by two disjoint phage genes. Thus, AR9 is a phiKZ-related giant phage that relies on two multisubunit viral RNAPs to transcribe its genome independently of host transcription apparatus. Purification of one of PBS1/AR9 RNAPs has been reported previously, which makes AR9 a promising object for further studies of RNAP evolution, assembly and mechanism.
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Affiliation(s)
- Daria Lavysh
- Institute of Molecular Genetics and Gene Biology, Russian Academy of Sciences, Moscow, Russia.
| | - Maria Sokolova
- Peter the Great St. Petersburg Polytechnic University, St. Petersburg, Russia; Skolkovo Institute of Science and Technology, Skolkovo, Russia.
| | - Leonid Minakhin
- Waksman Institute, Rutgers, the State University of New Jersey, Piscataway, NJ, USA.
| | - Maria Yakunina
- Peter the Great St. Petersburg Polytechnic University, St. Petersburg, Russia.
| | - Tatjana Artamonova
- Peter the Great St. Petersburg Polytechnic University, St. Petersburg, Russia.
| | | | - Kira S Makarova
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA.
| | - Eugene V Koonin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA.
| | - Konstantin Severinov
- Institute of Molecular Genetics and Gene Biology, Russian Academy of Sciences, Moscow, Russia; Peter the Great St. Petersburg Polytechnic University, St. Petersburg, Russia; Skolkovo Institute of Science and Technology, Skolkovo, Russia; Waksman Institute, Rutgers, the State University of New Jersey, Piscataway, NJ, USA.
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32
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Cell wall-affecting antibiotics modulate natural transformation in SigH-expressing Staphylococcus aureus. J Antibiot (Tokyo) 2015; 69:464-6. [DOI: 10.1038/ja.2015.132] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2015] [Revised: 11/05/2015] [Accepted: 11/10/2015] [Indexed: 11/09/2022]
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33
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Méric G, Miragaia M, de Been M, Yahara K, Pascoe B, Mageiros L, Mikhail J, Harris LG, Wilkinson TS, Rolo J, Lamble S, Bray JE, Jolley KA, Hanage WP, Bowden R, Maiden MCJ, Mack D, de Lencastre H, Feil EJ, Corander J, Sheppard SK. Ecological Overlap and Horizontal Gene Transfer in Staphylococcus aureus and Staphylococcus epidermidis. Genome Biol Evol 2015; 7:1313-28. [PMID: 25888688 PMCID: PMC4453061 DOI: 10.1093/gbe/evv066] [Citation(s) in RCA: 95] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The opportunistic pathogens Staphylococcus aureus and Staphylococcus epidermidis represent major causes of severe nosocomial infection, and are associated with high levels of mortality and morbidity worldwide. These species are both common commensals on the human skin and in the nasal pharynx, but are genetically distinct, differing at 24% average nucleotide divergence in 1,478 core genes. To better understand the genome dynamics of these ecologically similar staphylococcal species, we carried out a comparative analysis of 324 S. aureus and S. epidermidis genomes, including 83 novel S. epidermidis sequences. A reference pan-genome approach and whole genome multilocus-sequence typing revealed that around half of the genome was shared between the species. Based on a BratNextGen analysis, homologous recombination was found to have impacted on 40% of the core genes in S. epidermidis, but on only 24% of the core genes in S. aureus. Homologous recombination between the species is rare, with a maximum of nine gene alleles shared between any two S. epidermidis and S. aureus isolates. In contrast, there was considerable interspecies admixture of mobile elements, in particular genes associated with the SaPIn1 pathogenicity island, metal detoxification, and the methicillin-resistance island SCCmec. Our data and analysis provide a context for considering the nature of recombinational boundaries between S. aureus and S. epidermidis and, the selective forces that influence realized recombination between these species.
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Affiliation(s)
- Guillaume Méric
- College of Medicine, Institute of Life Science, Swansea University, United Kingdom
| | - Maria Miragaia
- Laboratory of Molecular Genetics, Instituto de Tecnologia Química e Biológica António Xavier (ITQB), Universidade Nova de Lisboa, Oeiras, Portugal Laboratory of Bacterial Evolution and Molecular Epidemiology, Instituto de Tecnologia Química e Biológica António Xavier (ITQB), Universidade Nova de Lisboa, Oeiras, Portugal
| | - Mark de Been
- Department of Medical Microbiology, University Medical Center Utrecht, The Netherlands
| | - Koji Yahara
- College of Medicine, Institute of Life Science, Swansea University, United Kingdom The Biostatistics Center, Kurume University, Fukuoka, Japan
| | - Ben Pascoe
- College of Medicine, Institute of Life Science, Swansea University, United Kingdom MRC CLIMB Consortium, Institute of Life Science, Swansea University, United Kingdom
| | - Leonardos Mageiros
- College of Medicine, Institute of Life Science, Swansea University, United Kingdom
| | - Jane Mikhail
- College of Medicine, Institute of Life Science, Swansea University, United Kingdom
| | - Llinos G Harris
- College of Medicine, Institute of Life Science, Swansea University, United Kingdom
| | - Thomas S Wilkinson
- College of Medicine, Institute of Life Science, Swansea University, United Kingdom
| | - Joana Rolo
- Laboratory of Molecular Genetics, Instituto de Tecnologia Química e Biológica António Xavier (ITQB), Universidade Nova de Lisboa, Oeiras, Portugal Laboratory of Bacterial Evolution and Molecular Epidemiology, Instituto de Tecnologia Química e Biológica António Xavier (ITQB), Universidade Nova de Lisboa, Oeiras, Portugal
| | - Sarah Lamble
- Wellcome Trust Centre for Human Genetics, University of Oxford, United Kingdom
| | - James E Bray
- Department of Zoology, University of Oxford, United Kingdom
| | - Keith A Jolley
- Department of Zoology, University of Oxford, United Kingdom
| | - William P Hanage
- Center for Communicable Disease Dynamics, Harvard School of Public Health
| | - Rory Bowden
- Wellcome Trust Centre for Human Genetics, University of Oxford, United Kingdom
| | | | - Dietrich Mack
- College of Medicine, Institute of Life Science, Swansea University, United Kingdom College of Medicine, Institute of Life Science, Swansea University, United Kingdom
| | - Hermínia de Lencastre
- Laboratory of Molecular Genetics, Instituto de Tecnologia Química e Biológica António Xavier (ITQB), Universidade Nova de Lisboa, Oeiras, Portugal College of Medicine, Institute of Life Science, Swansea University, United Kingdom
| | - Edward J Feil
- College of Medicine, Institute of Life Science, Swansea University, United Kingdom
| | - Jukka Corander
- College of Medicine, Institute of Life Science, Swansea University, United Kingdom
| | - Samuel K Sheppard
- College of Medicine, Institute of Life Science, Swansea University, United Kingdom MRC CLIMB Consortium, Institute of Life Science, Swansea University, United Kingdom
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34
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Touchon M, Bobay LM, Rocha EPC. The chromosomal accommodation and domestication of mobile genetic elements. Curr Opin Microbiol 2014; 22:22-9. [DOI: 10.1016/j.mib.2014.09.010] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2014] [Accepted: 09/17/2014] [Indexed: 11/17/2022]
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35
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Intra- and inter-generic transfer of pathogenicity island-encoded virulence genes by cos phages. ISME JOURNAL 2014; 9:1260-3. [PMID: 25314321 DOI: 10.1038/ismej.2014.187] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2014] [Revised: 07/22/2014] [Accepted: 08/04/2014] [Indexed: 11/08/2022]
Abstract
Bacteriophage-mediated horizontal gene transfer is one of the primary driving forces of bacterial evolution. The pac-type phages are generally thought to facilitate most of the phage-mediated gene transfer between closely related bacteria, including that of mobile genetic elements-encoded virulence genes. In this study, we report that staphylococcal cos-type phages transferred the Staphylococcus aureus pathogenicity island SaPIbov5 to non-aureus staphylococcal species and also to different genera. Our results describe the first intra- and intergeneric transfer of a pathogenicity island by a cos phage, and highlight a gene transfer mechanism that may have important implications for pathogen evolution.
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