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Xu Q, Tang L, Liu W, Xu N, Hu Y, Zhang Y, Chen S. Phage protein Gp11 blocks Staphylococcus aureus cell division by inhibiting peptidoglycan biosynthesis. mBio 2024; 15:e0067924. [PMID: 38752726 PMCID: PMC11237401 DOI: 10.1128/mbio.00679-24] [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: 03/08/2024] [Accepted: 04/10/2024] [Indexed: 06/13/2024] Open
Abstract
Phages and bacteria have a long history of co-evolution. However, these dynamics of phage-host interactions are still largely unknown; identification of phage inhibitors that remodel host metabolism will provide valuable information for target development for antimicrobials. Here, we perform a comprehensive screen for early-gene products of ΦNM1 that inhibit cell growth in Staphylococcus aureus. A small membrane protein, Gp11, with inhibitory effects on S. aureus cell division was identified. A bacterial two-hybrid library containing 345 essential S. aureus genes was constructed to screen for targets of Gp11, and Gp11 was found to interact with MurG and DivIC. Defects in cell growth and division caused by Gp11 were dependent on MurG and DivIC, which was further confirmed using CRISPRi hypersensitivity assay. Gp11 interacts with MurG, the protein essential for cell wall formation, by inhibiting the production of lipid II to regulate peptidoglycan (PG) biosynthesis on the cell membrane. Gp11 also interacts with cell division protein DivIC, an essential part of the division machinery necessary for septal cell wall assembly, to disrupt the recruitment of division protein FtsW. Mutations in Gp11 result in loss of its ability to cause growth defects, whereas infection with phage in which the gp11 gene has been deleted showed a significant increase in lipid II production in S. aureus. Together, our findings reveal that a phage early-gene product interacts with essential host proteins to disrupt PG biosynthesis and block S. aureus cell division, suggesting a potential pathway for the development of therapeutic approaches to treat pathogenic bacterial infections. IMPORTANCE Understanding the interplay between phages and their hosts is important for the development of novel therapies against pathogenic bacteria. Although phages have been used to control methicillin-resistant Staphylococcus aureus infections, our knowledge related to the processes in the early stages of phage infection is still limited. Owing to the fact that most of the phage early proteins have been classified as hypothetical proteins with uncertain functions, we screened phage early-gene products that inhibit cell growth in S. aureus, and one protein, Gp11, selectively targets essential host genes to block the synthesis of the peptidoglycan component lipid II, ultimately leading to cell growth arrest in S. aureus. Our study provides a novel insight into the strategy by which Gp11 blocks essential host cellular metabolism to influence phage-host interaction. Importantly, dissecting the interactions between phages and host cells will contribute to the development of new and effective therapies to treat bacterial infections.
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Affiliation(s)
- Qi Xu
- CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Li Tang
- CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Weilin Liu
- CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, China
| | - Neng Xu
- CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, China
| | - Yangbo Hu
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, China
| | - Yong Zhang
- CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, China
| | - Shiyun Chen
- CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, China
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2
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Kengmo Tchoupa A, Elsherbini AMA, Camus J, Fu X, Hu X, Ghaneme O, Seibert L, Lebtig M, Böcker MA, Horlbeck A, Lambidis SP, Schittek B, Kretschmer D, Lämmerhofer M, Peschel A. Lipase-mediated detoxification of host-derived antimicrobial fatty acids by Staphylococcus aureus. Commun Biol 2024; 7:572. [PMID: 38750133 PMCID: PMC11096360 DOI: 10.1038/s42003-024-06278-3] [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: 10/30/2023] [Accepted: 05/02/2024] [Indexed: 05/18/2024] Open
Abstract
Long-chain fatty acids with antimicrobial properties are abundant on the skin and mucosal surfaces, where they are essential to restrict the proliferation of opportunistic pathogens such as Staphylococcus aureus. These antimicrobial fatty acids (AFAs) elicit bacterial adaptation strategies, which have yet to be fully elucidated. Characterizing the pervasive mechanisms used by S. aureus to resist AFAs could open new avenues to prevent pathogen colonization. Here, we identify the S. aureus lipase Lip2 as a novel resistance factor against AFAs. Lip2 detoxifies AFAs via esterification with cholesterol. This is reminiscent of the activity of the fatty acid-modifying enzyme (FAME), whose identity has remained elusive for over three decades. In vitro, Lip2-dependent AFA-detoxification was apparent during planktonic growth and biofilm formation. Our genomic analysis revealed that prophage-mediated inactivation of Lip2 was rare in blood, nose, and skin strains, suggesting a particularly important role of Lip2 for host - microbe interactions. In a mouse model of S. aureus skin colonization, bacteria were protected from sapienic acid (a human-specific AFA) in a cholesterol- and lipase-dependent manner. These results suggest Lip2 is the long-sought FAME that exquisitely manipulates environmental lipids to promote bacterial growth in otherwise inhospitable niches.
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Affiliation(s)
- Arnaud Kengmo Tchoupa
- Interfaculty Institute of Microbiology and Infection Medicine Tübingen, Infection Biology Section, University of Tübingen, Tübingen, Germany.
- Cluster of Excellence EXC 2124 Controlling Microbes to Fight Infections, University of Tübingen, Tübingen, Germany.
- German Center for Infection Research (DZIF), Partner Site Tübingen, Tübingen, Germany.
| | - Ahmed M A Elsherbini
- Interfaculty Institute of Microbiology and Infection Medicine Tübingen, Infection Biology Section, University of Tübingen, Tübingen, Germany
- Cluster of Excellence EXC 2124 Controlling Microbes to Fight Infections, University of Tübingen, Tübingen, Germany
- German Center for Infection Research (DZIF), Partner Site Tübingen, Tübingen, Germany
| | - Justine Camus
- Interfaculty Institute of Microbiology and Infection Medicine Tübingen, Infection Biology Section, University of Tübingen, Tübingen, Germany
- Cluster of Excellence EXC 2124 Controlling Microbes to Fight Infections, University of Tübingen, Tübingen, Germany
- German Center for Infection Research (DZIF), Partner Site Tübingen, Tübingen, Germany
| | - Xiaoqing Fu
- Institute of Pharmaceutical Sciences, University of Tübingen, Tübingen, Germany
| | - Xuanheng Hu
- Interfaculty Institute of Microbiology and Infection Medicine Tübingen, Infection Biology Section, University of Tübingen, Tübingen, Germany
- Cluster of Excellence EXC 2124 Controlling Microbes to Fight Infections, University of Tübingen, Tübingen, Germany
- German Center for Infection Research (DZIF), Partner Site Tübingen, Tübingen, Germany
| | - Oumayma Ghaneme
- Interfaculty Institute of Microbiology and Infection Medicine Tübingen, Infection Biology Section, University of Tübingen, Tübingen, Germany
- Cluster of Excellence EXC 2124 Controlling Microbes to Fight Infections, University of Tübingen, Tübingen, Germany
- German Center for Infection Research (DZIF), Partner Site Tübingen, Tübingen, Germany
| | - Lea Seibert
- Interfaculty Institute of Microbiology and Infection Medicine Tübingen, Infection Biology Section, University of Tübingen, Tübingen, Germany
- Cluster of Excellence EXC 2124 Controlling Microbes to Fight Infections, University of Tübingen, Tübingen, Germany
- German Center for Infection Research (DZIF), Partner Site Tübingen, Tübingen, Germany
| | - Marco Lebtig
- Interfaculty Institute of Microbiology and Infection Medicine Tübingen, Infection Biology Section, University of Tübingen, Tübingen, Germany
- Cluster of Excellence EXC 2124 Controlling Microbes to Fight Infections, University of Tübingen, Tübingen, Germany
- German Center for Infection Research (DZIF), Partner Site Tübingen, Tübingen, Germany
| | - Marieke A Böcker
- Interfaculty Institute of Microbiology and Infection Medicine Tübingen, Infection Biology Section, University of Tübingen, Tübingen, Germany
- Cluster of Excellence EXC 2124 Controlling Microbes to Fight Infections, University of Tübingen, Tübingen, Germany
- German Center for Infection Research (DZIF), Partner Site Tübingen, Tübingen, Germany
| | - Anima Horlbeck
- Interfaculty Institute of Microbiology and Infection Medicine Tübingen, Infection Biology Section, University of Tübingen, Tübingen, Germany
- Cluster of Excellence EXC 2124 Controlling Microbes to Fight Infections, University of Tübingen, Tübingen, Germany
- German Center for Infection Research (DZIF), Partner Site Tübingen, Tübingen, Germany
| | - Stilianos P Lambidis
- Interfaculty Institute of Microbiology and Infection Medicine Tübingen, Infection Biology Section, University of Tübingen, Tübingen, Germany
- Cluster of Excellence EXC 2124 Controlling Microbes to Fight Infections, University of Tübingen, Tübingen, Germany
- German Center for Infection Research (DZIF), Partner Site Tübingen, Tübingen, Germany
| | - Birgit Schittek
- Cluster of Excellence EXC 2124 Controlling Microbes to Fight Infections, University of Tübingen, Tübingen, Germany
- Dermatology Department, University Hospital Tübingen, Tübingen, Germany
| | - Dorothee Kretschmer
- Interfaculty Institute of Microbiology and Infection Medicine Tübingen, Infection Biology Section, University of Tübingen, Tübingen, Germany
- Cluster of Excellence EXC 2124 Controlling Microbes to Fight Infections, University of Tübingen, Tübingen, Germany
- German Center for Infection Research (DZIF), Partner Site Tübingen, Tübingen, Germany
| | - Michael Lämmerhofer
- Institute of Pharmaceutical Sciences, University of Tübingen, Tübingen, Germany
| | - Andreas Peschel
- Interfaculty Institute of Microbiology and Infection Medicine Tübingen, Infection Biology Section, University of Tübingen, Tübingen, Germany
- Cluster of Excellence EXC 2124 Controlling Microbes to Fight Infections, University of Tübingen, Tübingen, Germany
- German Center for Infection Research (DZIF), Partner Site Tübingen, Tübingen, Germany
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Ulrich RJ, Podkowik M, Tierce R, Irnov I, Putzel G, Samhadaneh N, Lacey KA, Boff D, Morales SM, Makita S, Karagounis TK, Zwack EE, Zhou C, Kim R, Drlica K, Pironti A, van Bakel H, Torres VJ, Shopsin B. Prophage-encoded methyltransferase drives adaptation of community-acquired methicillin-resistant Staphylococcus aureus. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.17.589803. [PMID: 38659881 PMCID: PMC11042277 DOI: 10.1101/2024.04.17.589803] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
We recently described the evolution of a community-acquired methicillin-resistant Staphylococcus aureus (CA-MRSA) USA300 variant responsible for an outbreak of skin and soft tissue infections. Acquisition of a mosaic version of the Φ11 prophage (mΦ11) that increases skin abscess size was an early step in CA-MRSA adaptation that primed the successful spread of the clone. The present report shows how prophage mΦ11 exerts its effect on virulence for skin infection without encoding a known toxin or fitness genes. Abscess size and skin inflammation were associated with DNA methylase activity of an mΦ11-encoded adenine methyltransferase (designated pamA). pamA increased expression of fibronectin-binding protein A (fnbA; FnBPA), and inactivation of fnbA eliminated the effect of pamA on abscess virulence without affecting strains lacking pamA. Thus, fnbA is a pamA-specific virulence factor. Mechanistically, pamA was shown to promote biofilm formation in vivo in skin abscesses, a phenotype linked to FnBPA's role in biofilm formation. Collectively, these data reveal a novel mechanism-epigenetic regulation of staphylococcal gene expression-by which phage can regulate virulence to drive adaptive leaps by S. aureus.
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Affiliation(s)
- Robert J. Ulrich
- Department of Medicine, NYU Grossman School of Medicine, New York, NY, USA
| | - Magdalena Podkowik
- Department of Medicine, NYU Grossman School of Medicine, New York, NY, USA
- Antimicrobial-Resistant Pathogens Program, NYU Grossman School of Medicine, New York, NY, USA
| | - Rebecca Tierce
- Division of Comparative Medicine, NYU Langone Health, New York, NY, USA
| | - Irnov Irnov
- Department of Microbiology, NYU Grossman School of Medicine, New York, NY, USA
| | - Gregory Putzel
- Antimicrobial-Resistant Pathogens Program, NYU Grossman School of Medicine, New York, NY, USA
- Department of Microbiology, NYU Grossman School of Medicine, New York, NY, USA
| | - Nora Samhadaneh
- Antimicrobial-Resistant Pathogens Program, NYU Grossman School of Medicine, New York, NY, USA
- Department of Microbiology, NYU Grossman School of Medicine, New York, NY, USA
| | - Keenan A. Lacey
- Department of Microbiology, NYU Grossman School of Medicine, New York, NY, USA
| | - Daiane Boff
- Department of Microbiology, NYU Grossman School of Medicine, New York, NY, USA
| | - Sabrina M. Morales
- Department of Medicine, NYU Grossman School of Medicine, New York, NY, USA
| | - Sohei Makita
- Department of Pathology, NYU Grossman School of Medicine, New York, NY, USA
| | - Theodora K. Karagounis
- Ronald O. Perelman Department of Dermatology, NYU Grossman School of Medicine, New York, NY, USA
| | - Erin E. Zwack
- Department of Microbiology, NYU Grossman School of Medicine, New York, NY, USA
| | - Chunyi Zhou
- Department of Microbiology, NYU Grossman School of Medicine, New York, NY, USA
| | - Randie Kim
- Ronald O. Perelman Department of Dermatology, NYU Grossman School of Medicine, New York, NY, USA
| | - Karl Drlica
- Department of Microbiology, Biochemistry & Molecular Genetics, New Jersey Medical School, Rutgers University, Newark, NJ, USA
- Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY, USA
| | - Alejandro Pironti
- Antimicrobial-Resistant Pathogens Program, NYU Grossman School of Medicine, New York, NY, USA
- Department of Microbiology, NYU Grossman School of Medicine, New York, NY, USA
| | - Harm van Bakel
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Icahn Genomics Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Victor J. Torres
- Antimicrobial-Resistant Pathogens Program, NYU Grossman School of Medicine, New York, NY, USA
- Department of Microbiology, NYU Grossman School of Medicine, New York, NY, USA
- Department of Host-Microbe Interactions, St. Jude Children’s Research Hospital, Memphis, TN, USA
| | - Bo Shopsin
- Department of Medicine, NYU Grossman School of Medicine, New York, NY, USA
- Antimicrobial-Resistant Pathogens Program, NYU Grossman School of Medicine, New York, NY, USA
- Department of Microbiology, NYU Grossman School of Medicine, New York, NY, USA
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4
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Turchi B, Campobasso C, Nardinocchi A, Wagemans J, Torracca B, Lood C, Di Giuseppe G, Nieri P, Bertelloni F, Turini L, Ruffo V, Lavigne R, Di Luca M. Isolation and characterization of novel Staphylococcus aureus bacteriophage Hesat from dairy origin. Appl Microbiol Biotechnol 2024; 108:299. [PMID: 38619619 PMCID: PMC11018700 DOI: 10.1007/s00253-024-13129-y] [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: 09/05/2023] [Revised: 03/05/2024] [Accepted: 03/27/2024] [Indexed: 04/16/2024]
Abstract
A novel temperate phage, named Hesat, was isolated by the incubation of a dairy strain of Staphylococcus aureus belonging to spa-type t127 with either bovine or ovine milk. Hesat represents a new species of temperate phage within the Phietavirus genus of the Azeredovirinae subfamily. Its genome has a length of 43,129 bp and a GC content of 35.11% and contains 75 predicted ORFs, some of which linked to virulence. This includes (i) a pathogenicity island (SaPln2), homologous to the type II toxin-antitoxin system PemK/MazF family toxin; (ii) a DUF3113 protein (gp30) that is putatively involved in the derepression of the global repressor Stl; and (iii) a cluster coding for a PVL. Genomic analysis of the host strain indicates Hesat is a resident prophage. Interestingly, its induction was obtained by exposing the bacterium to milk, while the conventional mitomycin C-based approach failed. The host range of phage Hesat appears to be broad, as it was able to lyse 24 out of 30 tested S. aureus isolates. Furthermore, when tested at high titer (108 PFU/ml), Hesat phage was also able to lyse a Staphylococcus muscae isolate, a coagulase-negative staphylococcal strain. KEY POINTS: • A new phage species was isolated from a Staphylococcus aureus bovine strain. • Pathogenicity island and PVL genes are encoded within phage genome. • The phage is active against most of S. aureus strains from both animal and human origins.
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Affiliation(s)
- Barbara Turchi
- Department of Veterinary Sciences, University of Pisa, Viale Delle Piagge 2, 56124, Pisa, Italy
| | - Claudia Campobasso
- Department of Biology, University of Pisa, Via San Zeno 37, 56127, Pisa, Italy
- Department of Biosystems, KU Leuven, Kasteelpark Arenberg 21, Box 2462, 3001, Louvain, Belgium
| | - Arianna Nardinocchi
- Department of Biology, University of Pisa, Via San Zeno 37, 56127, Pisa, Italy
| | - Jeroen Wagemans
- Department of Biosystems, KU Leuven, Kasteelpark Arenberg 21, Box 2462, 3001, Louvain, Belgium
| | - Beatrice Torracca
- Department of Veterinary Sciences, University of Pisa, Viale Delle Piagge 2, 56124, Pisa, Italy
| | - Cédric Lood
- Department of Biosystems, KU Leuven, Kasteelpark Arenberg 21, Box 2462, 3001, Louvain, Belgium
- Department of Microbial and Molecular Systems, Centre for Microbial and Plant Genetics, KU Leuven, Kasteelpark Arenberg 20, Box 2460, 3001, Leuven, Belgium
| | | | - Paola Nieri
- Department of Pharmacy, University of Pisa, Via Bonanno Pisano 6, 56126, Pisa, Italy
| | - Fabrizio Bertelloni
- Department of Veterinary Sciences, University of Pisa, Viale Delle Piagge 2, 56124, Pisa, Italy
| | - Luca Turini
- Department of Veterinary Sciences, University of Pisa, Viale Delle Piagge 2, 56124, Pisa, Italy
| | - Valeria Ruffo
- Department of Veterinary Sciences, University of Pisa, Viale Delle Piagge 2, 56124, Pisa, Italy
| | - Rob Lavigne
- Department of Biosystems, KU Leuven, Kasteelpark Arenberg 21, Box 2462, 3001, Louvain, Belgium
| | - Mariagrazia Di Luca
- Department of Biology, University of Pisa, Via San Zeno 37, 56127, Pisa, Italy.
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5
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Aviram N, Shilton AK, Lyn NG, Reis BS, Brivanlou A, Marraffini LA. The Cas10 nuclease activity relieves host dormancy to facilitate spacer acquisition and retention during type III-A CRISPR immunity. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.11.579731. [PMID: 38405743 PMCID: PMC10888962 DOI: 10.1101/2024.02.11.579731] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/27/2024]
Abstract
A hallmark of CRISPR immunity is the acquisition of short viral DNA sequences, known as spacers, that are transcribed into guide RNAs to recognize complementary sequences. The staphylococcal type III-A CRISPR-Cas system uses guide RNAs to locate viral transcripts and start a response that displays two mechanisms of immunity. When immunity is triggered by an early-expressed phage RNA, degradation of viral ssDNA can cure the host from infection. In contrast, when the RNA guide targets a late-expressed transcript, defense requires the activity of Csm6, a non-specific RNase. Here we show that Csm6 triggers a growth arrest of the host that provides immunity at the population level which hinders viral propagation to allow the replication of non-infected cells. We demonstrate that this mechanism leads to defense against not only the target phage but also other viruses present in the population that fail to replicate in the arrested cells. On the other hand, dormancy limits the acquisition and retention of spacers that trigger it. We found that the ssDNase activity of type III-A systems is required for the re-growth of a subset of the arrested cells, presumably through the degradation of the phage DNA, ending target transcription and inactivating the immune response. Altogether, our work reveals a built-in mechanism within type III-A CRISPR-Cas systems that allows the exit from dormancy needed for the subsistence of spacers that provide broad-spectrum immunity.
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Affiliation(s)
- Naama Aviram
- Laboratory of Bacteriology, the Rockefeller University, 1230 York Ave, New York, NY 10065, USA
| | - Amanda K Shilton
- Laboratory of Bacteriology, the Rockefeller University, 1230 York Ave, New York, NY 10065, USA
| | - Nia G Lyn
- Laboratory of Bacteriology, the Rockefeller University, 1230 York Ave, New York, NY 10065, USA
| | - Bernardo S Reis
- Laboratory of Mucosal Immunology, the Rockefeller University, 1230 York Ave, New York, NY 10065, USA
| | - Amir Brivanlou
- Laboratory of Bacteriology, the Rockefeller University, 1230 York Ave, New York, NY 10065, USA
| | - Luciano A Marraffini
- Laboratory of Bacteriology, the Rockefeller University, 1230 York Ave, New York, NY 10065, USA
- Howard Hughes Medical Institute, The Rockefeller University, 1230 York Ave, New York, NY 10065, USA
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6
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Chapman JE, George SE, Wolz C, Olson ME. Biofilms: A developmental niche for vancomycin-intermediate Staphylococcus aureus. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2024; 117:105545. [PMID: 38160879 DOI: 10.1016/j.meegid.2023.105545] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Revised: 12/14/2023] [Accepted: 12/26/2023] [Indexed: 01/03/2024]
Abstract
Staphylococcus aureus are gram-positive bacteria responsible for a wide array of diseases, ranging from skin and soft tissue infections to more chronic illnesses such as toxic shock syndrome, osteomyelitis, and endocarditis. Vancomycin is currently one of the most effective antibiotics available in treating patients infected with methicillin-resistant S. aureus (MRSA), however the emergence of vancomycin-resistant S. aureus (VRSA), and more commonly vancomycin-intermediate S. aureus (VISA), threaten the future efficacy of vancomycin. Intermediate resistance to vancomycin occurs due to mutations within the loci of Staphylococcal genes involved in cell wall formation such as rpoB, graS, and yycG. We hypothesized the VISA phenotype may also arise as a result of the natural stress occurring within S. aureus biofilms, and that this phenomenon is mediated by the RecA/SOS response. Wildtype and recA null mutant/lexAG94E strains of S. aureus biofilms were established in biofilm microtiter assays or planktonic cultures with or without the addition of sub-inhibitory concentrations of vancomycin (0.063 mg/l - 0.25 mg/L ciprofloxacin, 0.5 mg/l vancomycin). Efficiency of plating techniques were used to quantify the subpopulation of biofilm-derived S. aureus cells that developed vancomycin-intermediate resistance. The results indicated that a greater subpopulation of cells from wildtype biofilms (4.16 × 102 CFUs) emerged from intermediate-resistant concentrations of vancomycin (4 μg/ml) compared with the planktonic counterpart (1.53 × 101 CFUs). Wildtype biofilms (4.16 × 102 CFUs) also exhibited greater resistance to intermediate-resistant concentrations of vancomycin compared with strains deficient in the recA null mutant (8.15 × 101 CFUs) and lexA genes (8.00 × 101 CFUs). While the VISA phenotype would be an unintended consequence of genetic diversity and potentially gene transfer in the biofilm setting, it demonstrates that mutations occurring within biofilms allow for S. aureus to adapt to new environments, including the presence of widely used antibiotics.
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Affiliation(s)
- Jenelle E Chapman
- Department of Medical Microbiology, Immunology, and Cell Biology, Southern Illinois University School of Medicine, USA
| | - Shilpa E George
- Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen, Germany
| | - Christiane Wolz
- Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen, Germany
| | - Michael E Olson
- Department of Medical Microbiology, Immunology, and Cell Biology, Southern Illinois University School of Medicine, USA.
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7
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Wielscher M, Pfisterer K, Samardzic D, Balsini P, Bangert C, Jäger K, Buchberger M, Selitsch B, Pjevac P, Willinger B, Weninger W. The phageome in normal and inflamed human skin. SCIENCE ADVANCES 2023; 9:eadg4015. [PMID: 37774017 PMCID: PMC10541010 DOI: 10.1126/sciadv.adg4015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Accepted: 08/29/2023] [Indexed: 10/01/2023]
Abstract
Dysbiosis of skin microbiota drives the progression of atopic dermatitis (AD). The contribution of bacteriophages to bacterial community compositions in normal and inflamed skin is unknown. Using shotgun metagenomics from skin swabs of healthy individuals and patients with AD, we found 13,586 potential viral contiguous DNA sequences, which could be combined into 164 putative viral genomes including 133 putative phages. The Shannon diversity index for the viral metagenome-assembled genomes (vMAGs) did not correlate with AD. In total, we identified 28 vMAGs that differed significantly between normal and AD skin. Quantitative polymerase chain reaction validation of three complete vMAGs revealed their independence from host bacterium abundance. Our data indicate that normal and inflamed skin harbor distinct phageomes and suggest a causative relationship between changing viral and bacterial communities as a driver of skin pathology.
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Affiliation(s)
- M. Wielscher
- Department of Dermatology, Medical University of Vienna, Vienna, Austria
| | - K. Pfisterer
- Department of Dermatology, Medical University of Vienna, Vienna, Austria
| | - D. Samardzic
- Department of Dermatology, Medical University of Vienna, Vienna, Austria
| | - P. Balsini
- Department of Dermatology, Medical University of Vienna, Vienna, Austria
| | - C. Bangert
- Department of Dermatology, Medical University of Vienna, Vienna, Austria
| | - K. Jäger
- Department of Dermatology, Medical University of Vienna, Vienna, Austria
| | - M. Buchberger
- Department of Dermatology, Medical University of Vienna, Vienna, Austria
| | - B. Selitsch
- Department of Laboratory Medicine, Division of Clinical Microbiology, Medical University of Vienna, Vienna, Austria
| | - P. Pjevac
- University of Vienna, Centre for Microbiology and Environmental Systems Science, Division of Microbial Ecology, Vienna, Austria
- Joint Microbiome Facility of the Medical University of Vienna and the University of Vienna, Vienna, Austria
| | - B. Willinger
- Department of Laboratory Medicine, Division of Clinical Microbiology, Medical University of Vienna, Vienna, Austria
| | - W. Weninger
- Department of Dermatology, Medical University of Vienna, Vienna, Austria
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8
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Mikkelsen K, Bowring JZ, Ng YK, Svanberg Frisinger F, Maglegaard JK, Li Q, Sieber RN, Petersen A, Andersen PS, Rostøl JT, Høyland-Kroghsbo NM, Ingmer H. An Endogenous Staphylococcus aureus CRISPR-Cas System Limits Phage Proliferation and Is Efficiently Excised from the Genome as Part of the SCC mec Cassette. Microbiol Spectr 2023; 11:e0127723. [PMID: 37404143 PMCID: PMC10434264 DOI: 10.1128/spectrum.01277-23] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Accepted: 06/11/2023] [Indexed: 07/06/2023] Open
Abstract
CRISPR-Cas is an adaptive immune system that allows bacteria to inactivate mobile genetic elements. Approximately 50% of bacteria harbor CRISPR-Cas; however, in the human pathogen Staphylococcus aureus, CRISPR-Cas loci are less common and often studied in heterologous systems. We analyzed the prevalence of CRISPR-Cas in genomes of methicillin-resistant Staphylococcus aureus (MRSA) strains isolated in Denmark. Only 2.9% of the strains carried CRISPR-Cas systems, but for strains of sequence type ST630, over half were positive. All CRISPR-Cas loci were type III-A and located within the staphylococcal cassette chromosome mec (SCCmec) type V(5C2&5), conferring β-lactam resistance. Curiously, only 23 different CRISPR spacers were identified in 69 CRISPR-Cas positive strains, and almost identical SCCmec cassettes, CRISPR arrays, and cas genes are present in staphylococcal species other than S. aureus, suggesting that these were transferred horizontally. For the ST630 strain 110900, we demonstrate that the SCCmec cassette containing CRISPR-Cas is excised from the chromosome at high frequency. However, the cassette was not transferable under the conditions investigated. One of the CRISPR spacers targets a late gene in the lytic bacteriophage phiIPLA-RODI, and we show that the system protects against phage infection by reducing phage burst size. However, CRISPR-Cas can be overloaded or circumvented by CRISPR escape mutants. Our results imply that the endogenous type III-A CRISPR-Cas system in S. aureus is active against targeted phages, albeit with low efficacy. This suggests that native S. aureus CRISPR-Cas offers only partial immunity and in nature may work in tandem with other defense systems. IMPORTANCE CRISPR-Cas is an adaptive immune system protecting bacteria and archaea against mobile genetic elements such as phages. In strains of Staphylococcus aureus, CRISPR-Cas is rare, but when present, it is located within the SCCmec element, which encodes resistance to methicillin and other β-lactam antibiotics. We show that the element is excisable, suggesting that the CRISPR-Cas locus is transferable. In support of this, we found almost identical CRISPR-Cas-carrying SCCmec elements in different species of non-S. aureus staphylococci, indicating that the system is mobile but only rarely acquires new spacers in S. aureus. Additionally, we show that in its endogenous form, the S. aureus CRISPR-Cas is active but inefficient against lytic phages that can overload the system or form escape mutants. Thus, we propose that CRISPR-Cas in S. aureus offers only partial immunity in native systems and so may work with other defense systems to prevent phage-mediated killing.
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Affiliation(s)
- Kasper Mikkelsen
- Department of Veterinary and Animal Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Janine Zara Bowring
- Department of Veterinary and Animal Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Yong Kai Ng
- Department of Veterinary and Animal Sciences, University of Copenhagen, Copenhagen, Denmark
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark
| | | | | | - Qiuchun Li
- Jiangsu Key Lab of Zoonosis/Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, China
| | - Raphael N. Sieber
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - Andreas Petersen
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - Paal Skytt Andersen
- Department of Veterinary and Animal Sciences, University of Copenhagen, Copenhagen, Denmark
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - Jakob T. Rostøl
- Centre for Bacterial Resistance Biology, Imperial College London, London, United Kingdom
| | - Nina Molin Høyland-Kroghsbo
- Department of Veterinary and Animal Sciences, University of Copenhagen, Copenhagen, Denmark
- Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Hanne Ingmer
- Department of Veterinary and Animal Sciences, University of Copenhagen, Copenhagen, Denmark
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9
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Li Y, Zhu F, Manna AC, Chen L, Jiang J, Hong JI, Proctor RA, Bayer AS, Cheung AL, Xiong YQ. Gp05, a Prophage-Encoded Virulence Factor, Contributes to Persistent Methicillin-Resistant Staphylococcus aureus Endovascular Infection. Microbiol Spectr 2023; 11:e0060023. [PMID: 37358448 PMCID: PMC10434118 DOI: 10.1128/spectrum.00600-23] [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: 02/08/2023] [Accepted: 05/24/2023] [Indexed: 06/27/2023] Open
Abstract
Persistent methicillin-resistant Staphylococcus aureus (MRSA) endovascular infections represent a serious public health threat. We recently demonstrated that the presence of a novel prophage ϕSA169 was associated with vancomycin (VAN) treatment failure in experimental MRSA endocarditis. In this study, we assessed the role of a ϕSA169 gene, ϕ80α_gp05 (gp05), in VAN-persistent outcome using gp05 isogenic MRSA strain sets. Of note, Gp05 significantly influences the intersection of MRSA virulence factors, host immune responses, and antibiotic treatment efficacy, including the following: (i) activity of the significant energy-yielding metabolic pathway (e.g., tricarboxylic acid cycle); (ii) carotenoid pigment production; (iii) (p)ppGpp (guanosine tetra- and pentaphosphate) production, which activates the stringent response and subsequent downstream functional factors (e.g., phenol-soluble modulins and polymorphonuclear neutrophil bactericidal activity); and (iv) persistence to VAN treatment in an experimental infective endocarditis model. These data suggest that Gp05 is a significant virulence factor which contributes to the persistent outcomes in MRSA endovascular infection by multiple pathways. IMPORTANCE Persistent endovascular infections are often caused by MRSA strains that are susceptible to anti-MRSA antibiotics in vitro by CLSI breakpoints. Thus, the persistent outcome represents a unique variant of traditional antibiotic resistance mechanisms and a significant therapeutic challenge. Prophage, a critical mobile genetic element carried by most MRSA isolates, provides their bacterial host with metabolic advantages and resistance mechanisms. However, how prophage-encoded virulence factors interact with the host defense system and antibiotics, driving the persistent outcome, is not well known. In the current study, we demonstrated that a novel prophage gene, gp05, significantly impacts tricarboxylic acid cycle activity, stringent response, and pigmentation, as well as vancomycin treatment outcome in an experimental endocarditis model using isogenic gp05 overexpression and chromosomal deletion mutant MRSA strain sets. The findings significantly advance our understanding of the role of Gp05 in persistent MRSA endovascular infection and provide a potential target for development of novel drugs against these life-threatening infections.
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Affiliation(s)
- Yi Li
- The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, California, USA
| | - Fengli Zhu
- The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, California, USA
| | - Adhar C. Manna
- Department of Microbiology & Immunology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, USA
| | - Liang Chen
- Center for Discovery and Innovation, Nutley, New Jersey, USA
| | - Jason Jiang
- The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, California, USA
| | - Jong-In Hong
- Department of Chemistry, Seoul National University, Seoul, South Korea
| | - Richard A. Proctor
- Department of Medicine, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, USA
- Department of Medical Microbiology and Immunology, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, USA
| | - Arnold S. Bayer
- The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, California, USA
- David Geffen School of Medicine at UCLA, Los Angeles, California, USA
| | - Ambrose L. Cheung
- Department of Microbiology & Immunology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, USA
| | - Yan Q. Xiong
- The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, California, USA
- David Geffen School of Medicine at UCLA, Los Angeles, California, USA
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10
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Chee MSJ, Serrano E, Chiang YN, Harling-Lee J, Man R, Bacigalupe R, Fitzgerald JR, Penadés JR, Chen J. Dual pathogenicity island transfer by piggybacking lateral transduction. Cell 2023; 186:3414-3426.e16. [PMID: 37541198 DOI: 10.1016/j.cell.2023.07.001] [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: 08/11/2022] [Revised: 03/30/2023] [Accepted: 07/03/2023] [Indexed: 08/06/2023]
Abstract
Lateral transduction (LT) is the process by which temperate phages mobilize large sections of bacterial genomes. Despite its importance, LT has only been observed during prophage induction. Here, we report that superantigen-carrying staphylococcal pathogenicity islands (SaPIs) employ a related but more versatile and complex mechanism of gene transfer to drive chromosomal hypermobility while self-transferring with additional virulence genes from the host. We found that after phage infection or prophage induction, activated SaPIs form concatamers in the bacterial chromosome by switching between parallel genomic tracks in replication bubbles. This dynamic life cycle enables SaPIbov1 to piggyback its LT of staphylococcal pathogenicity island vSaα, which encodes an array of genes involved in host-pathogen interactions, allowing both islands to be mobilized intact and transferred in a single infective particle. Our findings highlight previously unknown roles of pathogenicity islands in bacterial virulence and show that their evolutionary impact extends beyond the genes they carry.
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Affiliation(s)
- Melissa Su Juan Chee
- Infectious Diseases Translational Research Programme and Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117545, Singapore
| | - Ester Serrano
- School of Infection and Immunity, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8TA, UK
| | - Yin Ning Chiang
- Infectious Diseases Translational Research Programme and Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117545, Singapore
| | - Joshua Harling-Lee
- The Roslin Institute, University of Edinburgh, Easter Bush Campus, Edinburgh EH259RG, UK
| | - Rebecca Man
- The Roslin Institute, University of Edinburgh, Easter Bush Campus, Edinburgh EH259RG, UK
| | - Rodrigo Bacigalupe
- The Roslin Institute, University of Edinburgh, Easter Bush Campus, Edinburgh EH259RG, UK
| | - J Ross Fitzgerald
- The Roslin Institute, University of Edinburgh, Easter Bush Campus, Edinburgh EH259RG, UK
| | - José R Penadés
- School of Infection and Immunity, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8TA, UK; Departamento de Ciencias Biomédicas, Universidad CEU Cardenal Herrera, 46113 Moncada, Spain; Centre for Bacterial Resistance Biology, Imperial College London, London SW7 2AZ, UK.
| | - John Chen
- Infectious Diseases Translational Research Programme and Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117545, Singapore.
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11
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Štrancar V, Marušić M, Tušar J, Praček N, Kolenc M, Šuster K, Horvat S, Janež N, Peterka M. Isolation and in vitro characterization of novel S. epidermidis phages for therapeutic applications. Front Cell Infect Microbiol 2023; 13:1169135. [PMID: 37293203 PMCID: PMC10244729 DOI: 10.3389/fcimb.2023.1169135] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2023] [Accepted: 05/08/2023] [Indexed: 06/10/2023] Open
Abstract
S. epidermidis is an important opportunistic pathogen causing chronic prosthetic joint infections associated with biofilm growth. Increased tolerance to antibiotic therapy often requires prolonged treatment or revision surgery. Phage therapy is currently used as compassionate use therapy and continues to be evaluated for its viability as adjunctive therapy to antibiotic treatment or as an alternative treatment for infections caused by S. epidermidis to prevent relapses. In the present study, we report the isolation and in vitro characterization of three novel lytic S. epidermidis phages. Their genome content analysis indicated the absence of antibiotic resistance genes and virulence factors. Detailed investigation of the phage preparation indicated the absence of any prophage-related contamination and demonstrated the importance of selecting appropriate hosts for phage development from the outset. The isolated phages infect a high proportion of clinically relevant S. epidermidis strains and several other coagulase-negative species growing both in planktonic culture and as a biofilm. Clinical strains differing in their biofilm phenotype and antibiotic resistance profile were selected to further identify possible mechanisms behind increased tolerance to isolated phages.
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Affiliation(s)
- Vida Štrancar
- Centre of Excellence for Biosensors, Instrumentation and Process Control, Ajdovščina, Slovenia
- Department of Animal Science, Biotechnical Faculty, University of Ljubljana, Domžale, Slovenia
| | - Monika Marušić
- Centre of Excellence for Biosensors, Instrumentation and Process Control, Ajdovščina, Slovenia
| | - Jasmina Tušar
- Centre of Excellence for Biosensors, Instrumentation and Process Control, Ajdovščina, Slovenia
| | - Neža Praček
- Centre of Excellence for Biosensors, Instrumentation and Process Control, Ajdovščina, Slovenia
| | - Marko Kolenc
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Katja Šuster
- Valdoltra Orthopaedic Hospital, Ankaran, Slovenia
| | - Simon Horvat
- Department of Animal Science, Biotechnical Faculty, University of Ljubljana, Domžale, Slovenia
| | - Nika Janež
- Centre of Excellence for Biosensors, Instrumentation and Process Control, Ajdovščina, Slovenia
| | - Matjaž Peterka
- Centre of Excellence for Biosensors, Instrumentation and Process Control, Ajdovščina, Slovenia
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12
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Staphylococcus aureus Prophage-Encoded Protein Causes Abortive Infection and Provides Population Immunity against Kayviruses. mBio 2023; 14:e0249022. [PMID: 36779718 PMCID: PMC10127798 DOI: 10.1128/mbio.02490-22] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/14/2023] Open
Abstract
Both temperate and obligately lytic phages have crucial roles in the biology of staphylococci. While superinfection exclusion among closely related temperate phages is a well-characterized phenomenon, the interactions between temperate and lytic phages in staphylococci are not understood. Here, we present a resistance mechanism toward lytic phages of the genus Kayvirus, mediated by the membrane-anchored protein designated PdpSau encoded by Staphylococcus aureus prophages, mostly of the Sa2 integrase type. The prophage accessory gene pdpSau is strongly linked to the lytic genes for holin and ami2-type amidase and typically replaces genes for the toxin Panton-Valentine leukocidin (PVL). The predicted PdpSau protein structure shows the presence of a membrane-binding α-helix in its N-terminal part and a cytoplasmic positively charged C terminus. We demonstrated that the mechanism of action of PdpSau does not prevent the infecting kayvirus from adsorbing onto the host cell and delivering its genome into the cell, but phage DNA replication is halted. Changes in the cell membrane polarity and permeability were observed from 10 min after the infection, which led to prophage-activated cell death. Furthermore, we describe a mechanism of overcoming this resistance in a host-range Kayvirus mutant, which was selected on an S. aureus strain harboring prophage 53 encoding PdpSau, and in which a chimeric gene product emerged via adaptive laboratory evolution. This first case of staphylococcal interfamily phage-phage competition is analogous to some other abortive infection defense systems and to systems based on membrane-destructive proteins. IMPORTANCE Prophages play an important role in virulence, pathogenesis, and host preference, as well as in horizontal gene transfer in staphylococci. In contrast, broad-host-range lytic staphylococcal kayviruses lyse most S. aureus strains, and scientists worldwide have come to believe that the use of such phages will be successful for treating and preventing bacterial diseases. The effectiveness of phage therapy is complicated by bacterial resistance, whose mechanisms related to therapeutic staphylococcal phages are not understood in detail. In this work, we describe a resistance mechanism targeting kayviruses that is encoded by a prophage. We conclude that the defense mechanism belongs to a broader group of abortive infections, which is characterized by suicidal behavior of infected cells that are unable to produce phage progeny, thus ensuring the survival of the host population. Since the majority of staphylococcal strains are lysogenic, our findings are relevant for the advancement of phage therapy.
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13
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Francis D, Bhairaddy A, Joy A, Hari GV, Francis A. Secretory proteins in the orchestration of microbial virulence: The curious case of Staphylococcus aureus. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2023; 133:271-350. [PMID: 36707204 DOI: 10.1016/bs.apcsb.2022.10.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Microbial virulence showcases an excellent model for adaptive changes that enable an organism to survive and proliferate in a hostile environment and exploit host resources to its own benefit. In Staphylococcus aureus, an opportunistic pathogen of the human host, known for the diversity of the disease conditions it inflicts and the rapid evolution of antibiotic resistance, virulence is a consequence of having a highly plastic genome that is amenable to quick reprogramming and the ability to express a diverse arsenal of virulence factors. Virulence factors that are secreted to the host milieu effectively manipulate the host conditions to favor bacterial survival and growth. They assist in colonization, nutrient acquisition, immune evasion, and systemic spread. The structural and functional characteristics of the secreted virulence proteins have been shaped to assist S. aureus in thriving and disseminating effectively within the host environment and exploiting the host resources to its best benefit. With the aim of highlighting the importance of secreted virulence proteins in bacterial virulence, the present chapter provides a comprehensive account of the role of the major secreted proteins of S. aureus in orchestrating its virulence in the human host.
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Affiliation(s)
- Dileep Francis
- Department of Life Sciences, Kristu Jayanti College, Autonomous, Bengaluru, Karnataka, India.
| | - Anusha Bhairaddy
- Department of Life Sciences, Kristu Jayanti College, Autonomous, Bengaluru, Karnataka, India
| | - Atheene Joy
- Department of Life Sciences, Kristu Jayanti College, Autonomous, Bengaluru, Karnataka, India
| | | | - Ashik Francis
- Rajiv Gandhi Centre for Biotechnology, Trivandrum, Kerala, India
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14
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Kim H, Kim ES, Cho JH, Song M, Cho JH, Kim S, Keum GB, Kwak J, Doo H, Pandey S, Park SH, Lee JH, Jung H, Hur TY, Kim JK, Oh KK, Kim HB, Lee JH. Exploring the Microbial Community and Functional Characteristics of the Livestock Feces Using the Whole Metagenome Shotgun Sequencing. J Microbiol Biotechnol 2023; 33:51-60. [PMID: 36517072 PMCID: PMC9896000 DOI: 10.4014/jmb.2209.09013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Revised: 11/17/2022] [Accepted: 12/06/2022] [Indexed: 12/23/2022]
Abstract
The foodborne illness is the important public health concerns, and the livestock feces are known to be one of the major reservoirs of foodborne pathogens. Also, it was reported that 45.5% of foodborne illness outbreaks have been associated with the animal products contaminated with the livestock feces. In addition, it has been known that the persistence of a pathogens depends on many potential virulent factors including the various virulent genes. Therefore, the first step to understanding the public health risk of livestock feces is to identify and describe microbial communities and potential virulent genes that contribute to bacterial pathogenicity. We used the whole metagenome shotgun sequencing to evaluate the prevalence of foodborne pathogens and to characterize the virulence associated genes in pig and chicken feces. Our data showed that the relative abundance of potential foodborne pathogens, such as Bacillus cereus was higher in chickens than pigs at the species level while the relative abundance of foodborne pathogens including Campylobacter coli was only detected in pigs. Also, the microbial functional characteristics of livestock feces revealed that the gene families related to "Biofilm formation and quorum sensing" were highly enriched in pigs than chicken. Moreover, the variety of gene families associated with "Resistance to antibiotics and toxic compounds" were detected in both animals. These results will help us to prepare the scientific action plans to improve awareness and understanding of the public health risks of livestock feces.
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Affiliation(s)
- Hyeri Kim
- Department of Animal Resources Science, Dankook University, Cheonan, Republic of Korea
| | - Eun Sol Kim
- Department of Animal Resources Science, Dankook University, Cheonan, Republic of Korea
| | - Jin Ho Cho
- Department of Animal Science, Chungbuk National University, Cheongju, Republic of Korea
| | - Minho Song
- Division of Animal and Dairy Science, Chungnam National University, Daejeon, Republic of Korea
| | - Jae Hyoung Cho
- Department of Animal Resources Science, Dankook University, Cheonan, Republic of Korea
| | - Sheena Kim
- Department of Animal Resources Science, Dankook University, Cheonan, Republic of Korea
| | - Gi Beom Keum
- Department of Animal Resources Science, Dankook University, Cheonan, Republic of Korea
| | - Jinok Kwak
- Department of Animal Resources Science, Dankook University, Cheonan, Republic of Korea
| | - Hyunok Doo
- Department of Animal Resources Science, Dankook University, Cheonan, Republic of Korea
| | - Sriniwas Pandey
- Department of Animal Resources Science, Dankook University, Cheonan, Republic of Korea
| | - Seung-Hwan Park
- Korean Collection for Type Cultures, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Jeongeup, Republic of Korea
| | - Ju Huck Lee
- Korean Collection for Type Cultures, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Jeongeup, Republic of Korea
| | - Hyunjung Jung
- Animal Nutrition & Physiology Division, National Institute of Animal Science, RDA, Wanju, Republic of Korea
| | - Tai Young Hur
- Animal Diseases & Health Division, National Institute of Animal Science, RDA, Wanju, Republic of Korea
| | - Jae-Kyung Kim
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup, Republic of Korea
| | - Kwang Kyo Oh
- Microbial Safety Division, National Institute of Agricultural Sciences, Rural Development Administration, Wanju, 55365, Republic of Korea
| | - Hyeun Bum Kim
- Department of Animal Resources Science, Dankook University, Cheonan, Republic of Korea,Corresponding authors H.B. Kim Phone: +82-41-550-3653 E-mail:
| | - Ju-Hoon Lee
- Department of Food Animal Biotechnology, Department of Agricultural Biotechnology, Center for Food and Bioconvergence, Seoul National University, Seoul 08826, Republic of Korea,J.H. Lee Phone: +82-2-880-4854 E-mail:
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15
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Genomic and Epidemiological Features of Two Dominant Methicillin-Susceptible Staphylococcus aureus Clones from a Neonatal Intensive Care Unit Surveillance Effort. mSphere 2022; 7:e0040922. [PMID: 36218345 PMCID: PMC9769867 DOI: 10.1128/msphere.00409-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
Methicillin-susceptible Staphylococcus aureus (MSSA) is a more prevalent neonatal intensive care unit (NICU) pathogen than methicillin-resistant S. aureus (MRSA). However, the introduction and spread of MSSA, the role of systematic decolonization, and optimal infection prevention and control strategies remain incompletely understood. We previously screened infants hospitalized in a university-affiliated level III to IV NICU twice monthly over 18 months for S. aureus colonization and identified several prevalent staphylococcal protein A (spa) types. Here, we performed whole-genome sequencing (WGS) and phylogenetic comparisons of 140 isolates from predominant spa types t279, t1451, and t571 to examine possible transmission routes and identify genomic and epidemiologic features associated with the spread of dominant clones. We identified two major MSSA clones: sequence type 398 (ST398), common in the local community, and ST1898, not previously encountered in the region. ST398 NICU isolates formed distinct clusters with closely related community isolates from previously published data sets, suggesting multiple sources of acquisition, such as family members or staff, including residents of the local community. In contrast, ST1898 isolates were nearly identical, pointing to clonal expansion within the NICU. Almost all ST1898 isolates harbored plasmids encoding mupirocin resistance (mupA), suggesting an association between the proliferation of this clone and decolonization efforts with mupirocin. Comparative genomics indicated genotype-specific pathways of introduction and spread of MSSA via community-associated (ST398) or health care-associated (ST1898) sources and the potential role of mupirocin resistance in dissemination of ST1898. Future surveillance efforts could benefit from routine genotyping to inform clone-specific infection prevention strategies. IMPORTANCE Methicillin-susceptible Staphylococcus aureus (MSSA) is a significant pathogen in neonates. However, surveillance efforts in neonatal intensive care units (NICUs) have focused primarily on methicillin-resistant S. aureus (MRSA), limiting our understanding of colonizing and infectious MSSA clones which are prevalent in the NICU. Here, we identify two dominant colonizing MSSA clones during an 18-month surveillance effort in a level III to IV NICU, ST398 and ST1898. Using genomic surveillance and phylogenetic analysis, coupled with epidemiological investigation, we found that these two sequence types had distinct modes of spread, namely the suggested exchange with community reservoirs for ST398 and the contribution of antibiotic resistance to dissemination of ST1898 in the health care setting. This study highlights the additional benefits of whole-genome surveillance for colonizing pathogens, beyond routine species identification and genotyping, to inform targeted infection prevention strategies.
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16
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In Silico Genome-Scale Analysis of Molecular Mechanisms Contributing to the Development of a Persistent Infection with Methicillin-Resistant Staphylococcus aureus (MRSA) ST239. Int J Mol Sci 2022; 23:ijms232416086. [PMID: 36555727 PMCID: PMC9781258 DOI: 10.3390/ijms232416086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2022] [Revised: 12/05/2022] [Accepted: 12/11/2022] [Indexed: 12/23/2022] Open
Abstract
The increasing frequency of isolation of methicillin-resistant Staphylococcus aureus (MRSA) limits the chances for the effective antibacterial therapy of staphylococcal diseases and results in the development of persistent infection such as bacteremia and osteomyelitis. The aim of this study was to identify features of the MRSAST239 0943-1505-2016 (SA943) genome that contribute to the formation of both acute and chronic musculoskeletal infections. The analysis was performed using comparative genomics data of the dominant epidemic S. aureus lineages, namely ST1, ST8, ST30, ST36, and ST239. The SA943 genome encodes proteins that provide resistance to the host's immune system, suppress immunological memory, and form biofilms. The molecular mechanisms of adaptation responsible for the development of persistent infection were as follows: amino acid substitution in PBP2 and PBP2a, providing resistance to ceftaroline; loss of a large part of prophage DNA and restoration of the nucleotide sequence of beta-hemolysin, that greatly facilitates the escape of phagocytosed bacteria from the phagosome and formation of biofilms; dysfunction of the AgrA system due to the presence of psm-mec and several amino acid substitutions in the AgrC; partial deletion of the nucleotide sequence in genomic island vSAβ resulting in the loss of two proteases of Spl-operon; and deletion of SD repeats in the SdrE amino acid sequence.
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17
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Rohmer C, Dobritz R, Tuncbilek-Dere D, Lehmann E, Gerlach D, George SE, Bae T, Nieselt K, Wolz C. Influence of Staphylococcus aureus Strain Background on Sa3int Phage Life Cycle Switches. Viruses 2022; 14:2471. [PMID: 36366569 PMCID: PMC9694928 DOI: 10.3390/v14112471] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Accepted: 11/04/2022] [Indexed: 11/09/2022] Open
Abstract
Staphylococcus aureus asymptomatically colonizes the nasal cavity of mammals, but it is also a leading cause of life-threatening infections. Most human nasal isolates carry Sa3 phages, which integrate into the bacterial hlb gene encoding a sphingomyelinase. The virulence factor-encoding genes carried by the Sa3-phages are highly human-specific, and most animal strains are Sa3 negative. Thus, both insertion and excision of the prophage could potentially confer a fitness advantage to S. aureus. Here, we analyzed the phage life cycle of two Sa3 phages, Φ13 and ΦN315, in different phage-cured S. aureus strains. Based on phage transfer experiments, strains could be classified into low (8325-4, SH1000, and USA300c) and high (MW2c and Newman-c) transfer strains. High-transfer strains promoted the replication of phages, whereas phage adsorption, integration, excision, or recA transcription was not significantly different between strains. RNASeq analyses of replication-deficient lysogens revealed no strain-specific differences in the CI/Mor regulatory switch. However, lytic genes were significantly upregulated in the high transfer strain MW2c Φ13 compared to strain 8325-4 Φ13. By transcriptional start site prediction, new promoter regions within the lytic modules were identified, which are likely targeted by specific host factors. Such host-phage interaction probably accounts for the strain-specific differences in phage replication and transfer frequency. Thus, the genetic makeup of the host strains may determine the rate of phage mobilization, a feature that might impact the speed at which certain strains can achieve host adaptation.
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Affiliation(s)
- Carina Rohmer
- Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen, 72074 Tübingen, Germany
- Fraunhofer Institute for Interfacial Engineering and Biotechnology IGB, 70569 Stuttgart, Germany
| | - Ronja Dobritz
- Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen, 72074 Tübingen, Germany
| | - Dilek Tuncbilek-Dere
- Cluster of Excellence EXC 2124 “Controlling Microbes to Fight Infections”, University of Tübingen, 72074 Tübingen, Germany
- Institute for Bioinformatics and Medical Informatics, University of Tübingen, 72076 Tübingen, Germany
| | - Esther Lehmann
- Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen, 72074 Tübingen, Germany
| | - David Gerlach
- Department of Microbiology, University of Würzburg, 97074 Würzburg, Germany
| | - Shilpa Elizabeth George
- Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen, 72074 Tübingen, Germany
| | - Taeok Bae
- Department of Microbiology and Immunology, Indiana University School of Medicine-Northwest, Gary, IN 46408, USA
| | - Kay Nieselt
- Cluster of Excellence EXC 2124 “Controlling Microbes to Fight Infections”, University of Tübingen, 72074 Tübingen, Germany
- Institute for Bioinformatics and Medical Informatics, University of Tübingen, 72076 Tübingen, Germany
| | - Christiane Wolz
- Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen, 72074 Tübingen, Germany
- Cluster of Excellence EXC 2124 “Controlling Microbes to Fight Infections”, University of Tübingen, 72074 Tübingen, Germany
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18
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Leigh RJ, McKenna C, McWade R, Lynch B, Walsh F. Comparative genomics and pangenomics of vancomycin-resistant and susceptible Enterococcus faecium from Irish hospitals. J Med Microbiol 2022; 71. [DOI: 10.1099/jmm.0.001590] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Introduction.
Enterococcus faecium
has emerged as an important nosocomial pathogen, which is increasingly difficult to treat due to the genetic acquisition of vancomycin resistance. Ireland has a recalcitrant vancomycin-resistant bloodstream infection rate compared to other developed countries.
Hypothesis/Gap statement. Vancomycin resistance rates persist amongst
E. faecium
isolates from Irish hospitals. The evolutionary genomics governing these trends have not been fully elucidated.
Methodology. A set of 28 vancomycin-resistant isolates was sequenced to construct a dataset alongside 61 other publicly available Irish genomes. This dataset was extensively analysed using in silico methodologies (comparative genomics, pangenomics, phylogenetics, genotypics and comparative functional analyses) to uncover distinct evolutionary, coevolutionary and clinically relevant population trends.
Results. These results suggest that a stable (in terms of genome size, GC% and number of genes), yet genetically diverse population (in terms of gene content) of
E. faecium
persists in Ireland with acquired resistance arising via plasmid acquisition (vanA) or, to a lesser extent, chromosomal recombination (vanB). Population analysis revealed five clusters with one cluster partitioned into four clades which transcend isolation dates. Pangenomic and recombination analyses revealed an open (whole genome and chromosomal specific) pangenome illustrating a rampant evolutionary pattern. Comparative resistomics and virulomics uncovered distinct chromosomal and mobilomal propensity for multidrug resistance, widespread chromosomal point-mutation-mediated resistance and chromosomally harboured arsenals of virulence factors. Interestingly, a potential difference in biofilm formation strategies was highlighted by coevolutionary analysis, suggesting differential biofilm genotypes between vanA and vanB isolates.
Conclusions. These results highlight the evolutionary history of Irish
E. faecium
isolates and may provide insight into underlying infection dynamics in a clinical setting. Due to the apparent ease of vancomycin resistance acquisition over time, susceptible
E. faecium
should be concurrently reduced in Irish hospitals to mitigate potential resistant infections.
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Affiliation(s)
- Robert J. Leigh
- Department of Biology, Maynooth University, Mariavilla, Maynooth, Co. Kildare, Ireland
| | - Chloe McKenna
- Department of Biology, Maynooth University, Mariavilla, Maynooth, Co. Kildare, Ireland
| | - Robert McWade
- Department of Microbiology, Mater Misericordiae University Hospital, Eccles St., Dublin 7, D07 R2WY, Ireland
| | - Breda Lynch
- Department of Microbiology, Mater Misericordiae University Hospital, Eccles St., Dublin 7, D07 R2WY, Ireland
| | - Fiona Walsh
- Department of Biology, Maynooth University, Mariavilla, Maynooth, Co. Kildare, Ireland
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19
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Transcriptome Analyses of Prophage in Mediating Persistent Methicillin-Resistant Staphylococcus aureus Endovascular Infection. Genes (Basel) 2022; 13:genes13091527. [PMID: 36140695 PMCID: PMC9498598 DOI: 10.3390/genes13091527] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2022] [Revised: 08/23/2022] [Accepted: 08/23/2022] [Indexed: 12/24/2022] Open
Abstract
Persistent methicillin-resistant Staphylococcus aureus (MRSA) endovascular infections represent a significant subset of S. aureus infections and correlate with exceptionally high mortality. We have recently demonstrated that the lysogenization of prophage ϕSA169 from a clinical persistent MRSA bacteremia isolate (300-169) into a clinical resolving bacteremia MRSA isolate (301-188) resulted in the acquisition of well-defined in vitro and in vivo phenotypic and genotypic profiles related to persistent outcome. However, the underlying mechanism(s) of this impact is unknown. In the current study, we explored the genetic mechanism that may contribute to the ϕSA169-correlated persistence using RNA sequencing. Transcriptomic analyses revealed that the most significant impacts of ϕSA169 were: (i) the enhancement of fatty acid biosynthesis and purine and pyrimidine metabolic pathways; (ii) the repression of galactose metabolism and phosphotransferase system (PTS); and (iii) the down-regulation of the mutual prophage genes in both 300-169 and 301-188 strains. In addition, the influence of different genetic backgrounds between 300-169 and 301-188 might also be involved in the persistent outcome. These findings may provide targets for future studies on the persistence of MRSA.
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20
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Ribeiro HG, Nilsson A, Melo LDR, Oliveira A. Analysis of intact prophages in genomes of Paenibacillus larvae: An important pathogen for bees. Front Microbiol 2022; 13:903861. [PMID: 35923395 PMCID: PMC9341999 DOI: 10.3389/fmicb.2022.903861] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Accepted: 06/24/2022] [Indexed: 11/13/2022] Open
Abstract
Paenibacillus larvae is the etiological agent of American Foulbrood (AFB), a highly contagious and worldwide spread bacterial disease that affects honeybee brood. In this study, all complete P. larvae genomes available on the NCBI database were analyzed in order to detect presence of prophages using the PHASTER software. A total of 55 intact prophages were identified in 11 P. larvae genomes (5.0 ± 2.3 per genome) and were further investigated for the presence of genes encoding relevant traits related to P. larvae. A closer look at the prophage genomes revealed the presence of several putative genes such as metabolic and antimicrobial resistance genes, toxins or bacteriocins, potentially influencing host performance. Some of the coding DNA sequences (CDS) were present in all ERIC-genotypes, while others were only found in a specific genotype. While CDS encoding toxins and antitoxins such as HicB and MazE were found in prophages of all bacterial genotypes, others, from the same category, were provided by prophages particularly to ERIC I (enhancin-like toxin), ERIC II (antitoxin SocA) and ERIC V strains (subunit of Panton-Valentine leukocidin system (PVL) LukF-PV). This is the first in-depth analysis of P. larvae prophages. It provides better knowledge on their impact in the evolution of virulence and fitness of P. larvae, by discovering new features assigned by the viruses.
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Affiliation(s)
- Henrique G. Ribeiro
- LIBRO – Laboratório de Investigação em Biofilmes Rosário Oliveira, Centre of Biological Engineering, University of Minho, Braga, Portugal
- LABBELS – Associate Laboratory on Biotechnology and Bioengineering, and Electromechanical Systems, Centre of Biological Engineering, University of Minho, Braga, Portugal
| | - Anna Nilsson
- Department of Ecology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Luís D. R. Melo
- LIBRO – Laboratório de Investigação em Biofilmes Rosário Oliveira, Centre of Biological Engineering, University of Minho, Braga, Portugal
- LABBELS – Associate Laboratory on Biotechnology and Bioengineering, and Electromechanical Systems, Centre of Biological Engineering, University of Minho, Braga, Portugal
- *Correspondence: Luís D. R. Melo,
| | - Ana Oliveira
- LIBRO – Laboratório de Investigação em Biofilmes Rosário Oliveira, Centre of Biological Engineering, University of Minho, Braga, Portugal
- LABBELS – Associate Laboratory on Biotechnology and Bioengineering, and Electromechanical Systems, Centre of Biological Engineering, University of Minho, Braga, Portugal
- Ana Oliveira,
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21
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Wang M, Buist G, van Dijl JM. Staphylococcus aureus cell wall maintenance - the multifaceted roles of peptidoglycan hydrolases in bacterial growth, fitness, and virulence. FEMS Microbiol Rev 2022; 46:6604383. [PMID: 35675307 PMCID: PMC9616470 DOI: 10.1093/femsre/fuac025] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Revised: 04/22/2022] [Accepted: 05/25/2022] [Indexed: 01/07/2023] Open
Abstract
Staphylococcus aureus is an important human and livestock pathogen that is well-protected against environmental insults by a thick cell wall. Accordingly, the wall is a major target of present-day antimicrobial therapy. Unfortunately, S. aureus has mastered the art of antimicrobial resistance, as underscored by the global spread of methicillin-resistant S. aureus (MRSA). The major cell wall component is peptidoglycan. Importantly, the peptidoglycan network is not only vital for cell wall function, but it also represents a bacterial Achilles' heel. In particular, this network is continuously opened by no less than 18 different peptidoglycan hydrolases (PGHs) encoded by the S. aureus core genome, which facilitate bacterial growth and division. This focuses attention on the specific functions executed by these enzymes, their subcellular localization, their control at the transcriptional and post-transcriptional levels, their contributions to staphylococcal virulence and their overall importance in bacterial homeostasis. As highlighted in the present review, our understanding of the different aspects of PGH function in S. aureus has been substantially increased over recent years. This is important because it opens up new possibilities to exploit PGHs as innovative targets for next-generation antimicrobials, passive or active immunization strategies, or even to engineer them into effective antimicrobial agents.
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Affiliation(s)
- Min Wang
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Hanzeplein 1, PO Box 30001, 9700 RB Groningen, the Netherlands
| | | | - Jan Maarten van Dijl
- Corresponding author: Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Hanzeplein 1, P.O. box 30001, HPC EB80, 9700 RB Groningen, the Netherlands, Tel. +31-50-3615187; Fax. +31-50-3619105; E-mail:
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22
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Staphylococcus aureus Does Not Synthesize Arginine from Proline under Physiological Conditions. J Bacteriol 2022; 204:e0001822. [PMID: 35546540 DOI: 10.1128/jb.00018-22] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The Gram-positive pathogen Staphylococcus aureus is the only bacterium known to synthesize arginine from proline via the arginine-proline interconversion pathway despite having genes for the well-conserved glutamate pathway. Since the proline-arginine interconversion pathway is repressed by CcpA-mediated carbon catabolite repression (CCR), CCR has been attributed to the arginine auxotrophy of S. aureus. Using ribose as a secondary carbon source, here, we demonstrate that S. aureus arginine auxotrophy is not due to CCR but due to the inadequate concentration of proline degradation product. Proline is degraded by proline dehydrogenase (PutA) into pyrroline-5-carboxylate (P5C). Although the PutA expression was fully induced by ribose, the P5C concentration remained insufficient to support arginine synthesis because P5C was constantly consumed by the P5C reductase ProC. When the P5C concentration was artificially increased by either PutA overexpression or proC deletion, S. aureus could synthesize arginine from proline regardless of carbon source. In contrast, when the P5C concentration was reduced by overexpression of proC, it inhibited the growth of the ccpA deletion mutant without arginine. Intriguingly, the ectopic expression of the glutamate pathway enzymes converted S. aureus into arginine prototroph. In an animal experiment, the arginine-proline interconversion pathway was not required for the survival of S. aureus. Based on these results, we concluded that S. aureus does not synthesize arginine from proline under physiological conditions. We also propose that arginine auxotrophy of S. aureus is not due to the CcpA-mediated CCR but due to the inactivity of the conserved glutamate pathway. IMPORTANCE Staphylococcus aureus is a versatile Gram-positive human pathogen infecting various human organs. The bacterium's versatility is partly due to efficient metabolic regulation via the carbon catabolite repression system (CCR). S. aureus is known to interconvert proline and arginine, and CCR represses the synthesis of both amino acids. However, when CCR is released by a nonpreferred carbon source, S. aureus can synthesize proline but not arginine. In this study, we show that, in S. aureus, the intracellular concentration of pyrroline-5-carboxylate (P5C), the degradation product of proline and the substrate of proline synthesis, is too low to synthesize arginine from proline. These results call into question the notion that S. aureus synthesizes arginine from proline.
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23
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Basu S, Huynh L, Zhang S, Rabara R, Nguyen H, Velásquez Guzmán J, Hao G, Miles G, Shi Q, Stover E, Gupta G. Two Liberibacter Proteins Combine to Suppress Critical Innate Immune Defenses in Citrus. FRONTIERS IN PLANT SCIENCE 2022; 13:869178. [PMID: 35586217 PMCID: PMC9108871 DOI: 10.3389/fpls.2022.869178] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Accepted: 04/04/2022] [Indexed: 06/15/2023]
Abstract
We adopted a systems-based approach to determine the role of two Candidatus Liberibacter asiaticus (CLas) proteins, LasP 235 and Effector 3, in Huanglongbing (HLB) pathogenesis. While a published work suggests the involvement of these CLas proteins HLB pathogenesis, the exact structure-based mechanism of their action has not been elucidated. We conducted the following experiments to determine the structure-based mechanisms of action. First, we immunoprecipitated the interacting citrus protein partners of LasP 235 and Effector 3 from the healthy and CLas-infected Hamlin extracts and identified them by Liquid Chromatography with tandem mass spectrometry (LC-MS/MS). Second, we performed a split green fluorescent protein (GFP) assay in tobacco to validate that the interactions observed in vitro are also retained in planta. The notable in planta citrus targets of LasP 235 and Effector 3 include citrus innate immune proteins. Third, in vitro and in planta studies were performed to show that LasP 235 and Effector 3 interact with and inhibit the functions of multiple citrus proteins belonging to the innate immune pathways. These inhibitory interactions led to a high level of reactive oxygen species, blocking of bactericidal lipid transfer protein (LTP), and induction of premature programed cell death (PCD), all of which are beneficial to CLas lifecycle and HLB pathogenesis. Finally, we performed molecular dynamics simulations to visualize the interactions of LasP 235 and Effector 3, respectively, with LTP and Kunitz protease inhibitor. This led to the design of an LTP mimic, which sequestered and blocked LasP 235 and rescued the bactericidal activity of LTP thereby proving that LasP 235 , indeed, participates in HLB pathogenesis.
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Affiliation(s)
- Supratim Basu
- Biolab, New Mexico Consortium, Los Alamos, NM, United States
| | - Loan Huynh
- Biolab, New Mexico Consortium, Los Alamos, NM, United States
| | - Shujian Zhang
- Biolab, New Mexico Consortium, Los Alamos, NM, United States
| | - Roel Rabara
- Biolab, New Mexico Consortium, Los Alamos, NM, United States
| | - Hau Nguyen
- Biolab, New Mexico Consortium, Los Alamos, NM, United States
| | | | - Guixia Hao
- Horticulture and Breeding, U. S. Horticultural Research Laboratory, Fort Pierce, FL, United States
| | - Godfrey Miles
- Horticulture and Breeding, U. S. Horticultural Research Laboratory, Fort Pierce, FL, United States
| | - Qingchun Shi
- Horticulture and Breeding, U. S. Horticultural Research Laboratory, Fort Pierce, FL, United States
| | - Ed Stover
- Horticulture and Breeding, U. S. Horticultural Research Laboratory, Fort Pierce, FL, United States
| | - Goutam Gupta
- Biolab, New Mexico Consortium, Los Alamos, NM, United States
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24
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Abstract
Temperate phages (prophages) are ubiquitous in nature and persist as dormant components of host cells (lysogenic stage) before activating and lysing the host (lytic stage). Actively replicating prophages contribute to central community processes, such as enabling bacterial virulence, manipulating biogeochemical cycling, and driving microbial community diversification. Recent advances in sequencing technology have allowed for the identification and characterization of diverse phages, yet no approaches currently exist for identifying if a prophage has activated. Here, we present PropagAtE (Prophage Activity Estimator), an automated software tool for estimating if a prophage is in the lytic or lysogenic stage of infection. PropagAtE uses statistical analyses of prophage-to-host read coverage ratios to decipher actively replicating prophages, irrespective of whether prophages were induced or spontaneously activated. We demonstrate that PropagAtE is fast, accurate, and sensitive, regardless of sequencing depth. Application of PropagAtE to prophages from 348 complex metagenomes from human gut, murine gut, and soil environments identified distinct spatial and temporal prophage activation signatures, with the highest proportion of active prophages in murine gut samples. In infants treated with antibiotics or infants without treatment, we identified active prophage populations correlated with specific treatment groups. Within time series samples from the human gut, 11 prophage populations, some encoding the sulfur metabolism gene cysH or a rhuM-like virulence factor, were consistently present over time but not active. Overall, PropagAtE will facilitate accurate representations of viruses in microbiomes by associating prophages with their active roles in shaping microbial communities in nature. IMPORTANCE Viruses that infect bacteria are key components of microbiomes and ecosystems. They can kill and manipulate microorganisms, drive planetary-scale processes and biogeochemical cycling, and influence the structures of entire food networks. Prophages are viruses that can exist in a dormant state within the genome of their host (lysogenic stage) before activating in order to replicate and kill the host (lytic stage). Recent advances have allowed for the identification of diverse viruses in nature, but no approaches exist for characterizing prophages and their stages of infection (prophage activity). We develop and benchmark an automated approach, PropagAtE, to identify the stages of infection of prophages from genomic data. We provide evidence that active prophages vary in identity and abundance across multiple environments and scales. Our approach will enable accurate and unbiased analyses of viruses in microbiomes and ecosystems.
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25
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Maguin P, Varble A, Modell JW, Marraffini LA. Cleavage of viral DNA by restriction endonucleases stimulates the type II CRISPR-Cas immune response. Mol Cell 2022; 82:907-919.e7. [PMID: 35134339 PMCID: PMC8900293 DOI: 10.1016/j.molcel.2022.01.012] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Revised: 12/03/2021] [Accepted: 01/14/2022] [Indexed: 12/26/2022]
Abstract
Prokaryotic organisms have developed multiple defense systems against phages; however, little is known about whether and how these interact with each other. Here, we studied the connection between two of the most prominent prokaryotic immune systems: restriction-modification and CRISPR. While both systems employ enzymes that cleave a specific DNA sequence of the invader, CRISPR nucleases are programmed with phage-derived spacer sequences, which are integrated into the CRISPR locus upon infection. We found that restriction endonucleases provide a short-term defense, which is rapidly overcome through methylation of the phage genome. In a small fraction of the cells, however, restriction results in the acquisition of spacer sequences from the cleavage site, which mediates a robust type II-A CRISPR-Cas immune response against the methylated phage. This mechanism is reminiscent of eukaryotic immunity in which the innate response offers a first temporary line of defense and also activates a second and more robust adaptive response.
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Affiliation(s)
- Pascal Maguin
- Laboratory of Bacteriology, The Rockefeller University, 1230 York Ave, New York, NY 10065, USA
| | - Andrew Varble
- Laboratory of Bacteriology, The Rockefeller University, 1230 York Ave, New York, NY 10065, USA
| | - Joshua W. Modell
- Laboratory of Bacteriology, The Rockefeller University, 1230 York Ave, New York, NY 10065, USA.,Present address: Department of Molecular Biology & Genetics, Johns Hopkins University School of Medicine, 725 N. Wolfe St., PCTB 803, Baltimore, MD 21205, USA
| | - Luciano A. Marraffini
- Laboratory of Bacteriology, The Rockefeller University, 1230 York Ave, New York, NY 10065, USA.,Howard Hughes Medical Institute, The Rockefeller University, 1230 York Ave, New York, NY 10065, USA.,Correspondence to:
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26
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Wu S, Pang R, Huang J, Zhang F, Cai Z, Zhang J, Chen M, Xue L, Gu Q, Wang J, Ding Y, Wan Q, Wu Q. Evolutionary Divergence of the Novel Staphylococcal Species Staphylococcus argenteus. Front Microbiol 2021; 12:769642. [PMID: 34867903 PMCID: PMC8640356 DOI: 10.3389/fmicb.2021.769642] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Accepted: 10/25/2021] [Indexed: 11/17/2022] Open
Abstract
Currently, invasive infections caused by Staphylococcus argenteus, which is a recently named staphylococcal species, are increasingly reported worldwide. However, only a few genomic studies of S. argenteus have offered comprehensive information regarding its genetic diversity, epidemiological characteristics, antimicrobial resistance genes (ARGs), virulence genes and other profiles. Here, we describe a comparative genomic analysis by population structure, pangenome, panmobilome, region-specific accessory genes confer an adaptive advantage in 153 S. argenteus strains which comprised 24 strains sequenced in this study and 129 strains whose genome sequences were available from GenBank. As a result, the population of S. argenteus comprised seven genetically distinct clades, including two major clades (C1 and C2), with distinct isolation source patterns. Pangenome analysis revealed that S. argenteus has an open pangenome composed of 7,319 genes and a core genome composed of 1,508 genes. We further determined the distributions of 75 virulence factors (VFs) and 30 known ARGs and identified at least four types of plasmids and 93 complete or partial putative prophages. It indicate that S. argenteus may show a similar level of pathogenicity to that of S. aureus. This study also provides insights into the evolutionary divergence of this pathogen, indicating that the geographical distribution was a potential driving force behind the evolutionary divergence of S. argenteus. The preferential horizontal acquisition of particular elements, such as staphylococcal cassette chromosome mec elements and plasmids, was observed in specific regions, revealing potential gene exchange between S. argenteus strains and local S. aureus strains. Moreover, multiple specific genes related to environmental adaptation were identified in strains isolated from East Asia. However, these findings may help promote our understanding of the evolutionary divergence of this bacterium at a high genetic resolution by providing insights into the epidemiology of S. argenteus and may help combat its spread.
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Affiliation(s)
- Shi Wu
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Rui Pang
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Jiahui Huang
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Feng Zhang
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Zhihe Cai
- Guangdong Huankai Microbial Science and Technology Co. Ltd., Guangzhou, China
| | - Jumei Zhang
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Moutong Chen
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Liang Xue
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Qihui Gu
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Juan Wang
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Yu Ding
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Qiang Wan
- Guangdong Huankai Microbial Science and Technology Co. Ltd., Guangzhou, China
| | - Qingping Wu
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
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27
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Makky S, Dawoud A, Safwat A, Abdelsattar AS, Rezk N, El-Shibiny A. The bacteriophage decides own tracks: When they are with or against the bacteria. CURRENT RESEARCH IN MICROBIAL SCIENCES 2021; 2:100050. [PMID: 34841341 PMCID: PMC8610337 DOI: 10.1016/j.crmicr.2021.100050] [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: 03/17/2021] [Revised: 07/09/2021] [Accepted: 07/20/2021] [Indexed: 11/18/2022] Open
Abstract
Bacteriophages, bacteria-infecting viruses, are considered by many researchers a promising solution for antimicrobial resistance. On the other hand, some phages have shown contribution to bacterial resistance phenomenon by transducing antimicrobial resistance genes to their bacterial hosts. Contradictory consequences of infections are correlated to different phage lifecycles. Out of four known lifecycles, lysogenic and lytic pathways have been riddles since the uncontrolled conversion between them could negatively affect the intended use of phages. However, phages still can be engineered for applications against bacterial and viral infections to ensure high efficiency. This review highlights two main aspects: (1) the different lifecycles as well as the different factors that affect lytic-lysogenic switch are discussed, including the intracellular and molecular factors control this decision. In addition, different models which describe the effect of phages on the ecosystem are compared, besides the approaches to study the switch. (2) An overview on the contribution of the phage in the evolution of the bacteria, instead of eating them, as a consequence of different mode of actions. As well, how phage display has helped in restricting phage cheating and how it could open new gates for immunization and pandemics control will be tacked.
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Affiliation(s)
- Salsabil Makky
- Center for Microbiology and Phage Therapy, Zewail City of Science and Technology, October Gardens, 6th of October City, Giza, 12578, Egypt
| | - Alyaa Dawoud
- Center for Microbiology and Phage Therapy, Zewail City of Science and Technology, October Gardens, 6th of October City, Giza, 12578, Egypt
- Faculty of Pharmacy and Biotechnology, German University in Cairo, New Cairo, 16482, Egypt
| | - Anan Safwat
- Center for Microbiology and Phage Therapy, Zewail City of Science and Technology, October Gardens, 6th of October City, Giza, 12578, Egypt
| | - Abdallah S. Abdelsattar
- Center for Microbiology and Phage Therapy, Zewail City of Science and Technology, October Gardens, 6th of October City, Giza, 12578, Egypt
- Center for X-Ray and Determination of Structure of Matter, Zewail City of Science and Technology, October Gardens, 6th of October, Giza, 12578, Egypt
| | - Nouran Rezk
- Center for Microbiology and Phage Therapy, Zewail City of Science and Technology, October Gardens, 6th of October City, Giza, 12578, Egypt
| | - Ayman El-Shibiny
- Center for Microbiology and Phage Therapy, Zewail City of Science and Technology, October Gardens, 6th of October City, Giza, 12578, Egypt
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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: 43] [Impact Index Per Article: 14.3] [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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Dynamics of Antibacterial Drone Establishment in Staphylococcus aureus: Unexpected Effects of Antibiotic Resistance Genes. mBio 2021; 12:e0208321. [PMID: 34781740 PMCID: PMC8593670 DOI: 10.1128/mbio.02083-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
The antibacterial drone (ABD) system is based on repurposing the phage-inducible staphylococcal pathogenicity islands (SaPIs) for use as antibacterial agents that are indifferent to antibiotic resistance. The ABDs were constructed by inserting tetM for tetracycline resistance (Tcr) selection, replacing the SaPI virulence genes with bactericidal or bacteriostatic genes such as CRISPR/cas9/agrA, whose expression kills by double-strand cleavage of agrA, or CRISPR/dcas9/agrP2P3, whose expression blocks the target organism's virulence. ABD DNA is packaged in phage-like particles that attack their staphylococcal targets in vivo as well as in vitro. We determine ABD titers by transfer frequency, enumerate surviving cells as a function of multiplicity, and analyze the fate of ABD DNA with green fluorescent protein. An initial study revealed surprisingly that many more cells were killed by the ABD than were measured by transduction. Our study of this phenomenon has revealed several important features of the ABD system: (i) a significant number of entering ABD DNA molecules do not go on to establish stable transductants (i.e., are abortive); (ii) ABD cargo genes are expressed immediately following entry, even by the abortive ABDs; (iii) immediate plating on Tc-containing agar seriously underestimates particle numbers, partly owing to Tc inhibition of protein synthesis; (iv) replacement of tetM with cadA (conferring resistance to CdCl2) provides more accurate particle enumeration; (v) ABDs expressing CRISPR/cas9/agrA kill ∼99.99% of infected cells and provide the most accurate measurement of particle numbers as well as proof of principle for the system; and (vi) surprisingly, TetM interferes with stable establishment of ABD DNA independently of Tcr. IMPORTANCE For a particulate therapeutic agent, such as the ABD, accurate enumeration of particles is critical to enable evaluation of preparative procedures and calculation of therapeutic dosages. It is equally important that a selective marker used for these two purposes be biologically inert. We have long used tetM for these purposes but show here that tetM not only underestimates particle titers, by over 20-fold in some experiments, but also seriously impedes stable establishment of the therapeutic particle DNA. Given that tetM is a very convenient and widely used selective marker, publication of these findings is of considerable importance to the microbiological community as well as an interesting illustration of the unpredictable biological effects of genes taken out of their native context.
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Genomic Investigation of Methicillin-Resistant Staphylococcus aureus ST113 Strains Isolated from Tertiary Care Hospitals in Pakistan. Antibiotics (Basel) 2021; 10:antibiotics10091121. [PMID: 34572703 PMCID: PMC8465543 DOI: 10.3390/antibiotics10091121] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Revised: 09/12/2021] [Accepted: 09/14/2021] [Indexed: 11/16/2022] Open
Abstract
Methicillin-resistant Staphylococcus aureus (MRSA) is a multi-drug resistant and opportunistic pathogen. The emergence of new clones of MRSA in both healthcare settings and the community warrants serious attention and epidemiological surveillance. However, epidemiological data of MRSA isolates from Pakistan are limited. We performed a whole-genome-based comparative analysis of two (P10 and R46) MRSA strains isolated from two provinces of Pakistan to understand the genetic diversity, sequence type (ST), and distribution of virulence and antibiotic-resistance genes. The strains belong to ST113 and harbor the SCCmec type IV encoding mecA gene. Both the strains contain two plasmids, and three and two complete prophage sequences are present in P10 and R46, respectively. The specific antibiotic resistance determinants in P10 include two aminoglycoside-resistance genes, aph(3’)-IIIa and aad(6), a streptothrin-resistance gene sat-4, a tetracycline-resistance gene tet(K), a mupirocin-resistance gene mupA, a point mutation in fusA conferring resistance to fusidic acid, and in strain R46 a specific plasmid associated gene ant(4’)-Ib. The strains harbor many virulence factors common to MRSA. However, no Panton-Valentine leucocidin (lukF-PV/lukS-PV) or toxic shock syndrome toxin (tsst) genes were detected in any of the genomes. The phylogenetic relationship of P10 and R46 with other prevailing MRSA strains suggests that ST113 strains are closely related to ST8 strains and ST113 strains are a single-locus variant of ST8. These findings provide important information concerning the emerging MRSA clone ST113 in Pakistan and the sequenced strains can be used as reference strains for the comparative genomic analysis of other MRSA strains in Pakistan and ST113 strains globally.
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31
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IL-17C and IL-17RE Promote Wound Closure in a Staphylococcus aureus-Based Murine Wound Infection Model. Microorganisms 2021; 9:microorganisms9091821. [PMID: 34576717 PMCID: PMC8469012 DOI: 10.3390/microorganisms9091821] [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: 06/15/2021] [Revised: 08/06/2021] [Accepted: 08/13/2021] [Indexed: 11/17/2022] Open
Abstract
The epithelial cytokine interleukin-17C (IL-17C) mediates inflammation through the interleukin 17 receptor E (IL-17RE). Prior studies showed a detrimental role of IL-17C in the pathogenesis of immune-mediated skin diseases (e.g., psoriasis). Here, we examined the role of IL-17C/IL-17RE in wound closure in a Staphylococcus aureus wound infection model. We demonstrate that wound closure is significantly delayed in IL-17RE (Il-17re−/−)- and 17C (Il-17c−/−)-deficient mice. There was no significant difference between WT, Il-17re−/−, and Il-17c−/− mice in the absence of infection. Deficiency for IL-17RE and IL-17C did not significantly affect the elimination of bacteria. IL-17C expression was increased in the epidermis of human S. aureus-infected skin. Our results indicate that the IL-17C/IL-17RE axis contributes to the closure of infected wounds but does not contribute to the elimination of S. aureus.
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32
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Potential for Phages in the Treatment of Bacterial Sexually Transmitted Infections. Antibiotics (Basel) 2021; 10:antibiotics10091030. [PMID: 34572612 PMCID: PMC8466579 DOI: 10.3390/antibiotics10091030] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Revised: 08/19/2021] [Accepted: 08/20/2021] [Indexed: 12/30/2022] Open
Abstract
Bacterial sexually transmitted infections (BSTIs) are becoming increasingly significant with the approach of a post-antibiotic era. While treatment options dwindle, the transmission of many notable BSTIs, including Neisseria gonorrhoeae, Chlamydia trachomatis, and Treponema pallidum, continues to increase. Bacteriophage therapy has been utilized in Poland, Russia and Georgia in the treatment of bacterial illnesses, but not in the treatment of bacterial sexually transmitted infections. With the ever-increasing likelihood of antibiotic resistance prevailing and the continuous transmission of BSTIs, alternative treatments must be explored. This paper discusses the potentiality and practicality of phage therapy to treat BSTIs, including Neisseria gonorrhoeae, Chlamydia trachomatis, Treponema pallidum, Streptococcus agalactiae, Haemophilus ducreyi, Calymmatobacterium granulomatis, Mycoplasma genitalium, Ureaplasma parvum, Ureaplasma urealyticum, Shigella flexneri and Shigella sonnei. The challenges associated with the potential for phage in treatments vary for each bacterial sexually transmitted infection. Phage availability, bacterial structure and bacterial growth may impact the potential success of future phage treatments. Additional research is needed before BSTIs can be successfully clinically treated with phage therapy or phage-derived enzymes.
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33
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Higgins KV, Woodie LN, Hallowell H, Greene MW, Schwartz EH. Integrative Longitudinal Analysis of Metabolic Phenotype and Microbiota Changes During the Development of Obesity. Front Cell Infect Microbiol 2021; 11:671926. [PMID: 34414128 PMCID: PMC8370388 DOI: 10.3389/fcimb.2021.671926] [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: 02/24/2021] [Accepted: 06/15/2021] [Indexed: 01/04/2023] Open
Abstract
Obesity has increased at an alarming rate over the past two decades in the United States. In addition to increased body mass, obesity is often accompanied by comorbidities such as Type II Diabetes Mellitus and metabolic dysfunction-associated fatty liver disease, with serious impacts on public health. Our understanding of the role the intestinal microbiota in obesity has rapidly advanced in recent years, especially with respect to the bacterial constituents. However, we know little of when changes in these microbial populations occur as obesity develops. Further, we know little about how other domains of the microbiota, namely bacteriophage populations, are affected during the progression of obesity. Our goal in this study was to monitor changes in the intestinal microbiome and metabolic phenotype following western diet feeding. We accomplished this by collecting metabolic data and fecal samples for shotgun metagenomic sequencing in a mouse model of diet-induced obesity. We found that after two weeks of consuming a western diet (WD), the animals weighed significantly more and were less metabolically stable than their chow fed counterparts. The western diet induced rapid changes in the intestinal microbiome with the most pronounced dissimilarity at 12 weeks. Our study highlights the dynamic nature of microbiota composition following WD feeding and puts these events in the context of the metabolic status of the mammalian host.
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Affiliation(s)
- Keah V Higgins
- Department of Biological Sciences Auburn University, Auburn, AL, United States
| | - Lauren N Woodie
- Department of Nutrition, Dietetics and Hospitality Management, Auburn University, Auburn, AL, United States
| | - Haley Hallowell
- Department of Biological Sciences Auburn University, Auburn, AL, United States
| | - Michael W Greene
- Department of Nutrition, Dietetics and Hospitality Management, Auburn University, Auburn, AL, United States
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34
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Cornuault JK, Moineau S. Induction and Elimination of Prophages Using CRISPR Interference. CRISPR J 2021; 4:549-557. [PMID: 34406037 DOI: 10.1089/crispr.2021.0026] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Prophages are widely spread among bacterial genomes, and they can have positive or negative effects on their hosts. A key aspect in the study of prophages is the discovery of their induction signals. Prophage induction can occur by inactivating a phage transcriptional repressor, which is responsible for maintaining the lysogenic state. This repressor can be inactivated through the bacterial SOS response. However, the induction signals for numerous prophages do not involve the SOS system, and therefore significant efforts are needed to identify these conditions. Similarly, curing bacterial strains of inducible prophages is a tedious process, requiring the screening of several colonies. Here, we investigated whether transcriptional silencing of a prophage repressor using CRISPR interference (CRISPRi) would lead to prophage induction. Using Escherichia coli phages λ and P2 as models, we demonstrated the efficiency of CRISPRi for prophage induction and for curing lysogenic strains of their prophages.
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Affiliation(s)
- Jeffrey K Cornuault
- Département de Biochimie, de Mmicrobiologie, et de Bio-informatique, Faculté des sciences et de Génie, Université Laval, Québec City, Canada; Université Laval, Québec City, Canada.,Groupe de Recherche en Écologie Buccale, Faculté de Médecine Dentaire, Université Laval, Québec City, Canada; and Université Laval, Québec City, Canada
| | - Sylvain Moineau
- Département de Biochimie, de Mmicrobiologie, et de Bio-informatique, Faculté des sciences et de Génie, Université Laval, Québec City, Canada; Université Laval, Québec City, Canada.,Groupe de Recherche en Écologie Buccale, Faculté de Médecine Dentaire, Université Laval, Québec City, Canada; and Université Laval, Québec City, Canada.,Félix d'Hérelle Reference Center for Bacterial Viruses, Université Laval, Québec City, Canada
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35
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Distribution of Antimicrobial Resistance and Virulence Genes within the Prophage-Associated Regions in Nosocomial Pathogens. mSphere 2021; 6:e0045221. [PMID: 34232073 PMCID: PMC8386436 DOI: 10.1128/msphere.00452-21] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Prophages are often involved in host survival strategies and contribute toward increasing the genetic diversity of the host genome. Prophages also drive horizontal propagation of various genes as vehicles. However, there are few retrospective studies contributing to the propagation of antimicrobial resistance (AMR) and virulence factor (VF) genes by prophage. We extracted the complete genome sequences of seven pathogens, including ESKAPE bacteria and Escherichia coli from a public database, and examined the distribution of both the AMR and VF genes in prophage-like regions. We found that the ratios of AMR and VF genes greatly varied among the seven species. More than 70% of Enterobacter cloacae strains had VF genes, but only 1.2% of Klebsiella pneumoniae strains had VF genes from prophages. AMR and VF genes are unlikely to exist together in the same prophage region except in E. coli and Staphylococcus aureus, and the distribution patterns of prophage types containing AMR genes are distinct from those of VF gene-carrying prophage types. AMR genes in the prophage were located near transposase and/or integrase. The prophage containing class 1 integrase possessed a significantly greater number of AMR genes than did prophages with no class 1 integrase. The results of this study present a comprehensive picture of AMR and VF genes present within, or close to, prophage-like elements and different prophage patterns between AMR- or VF-encoding prophage-like elements. IMPORTANCE Although we believe phages play an important role in horizontal gene transfer in exchanging genetic material, we do not know the distribution of the antimicrobial resistance (AMR) and/or virulence factor (VF) genes in prophages. We collected different prophage elements from the complete genome sequences of seven species—Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, Enterobacter cloacae, and Escherichia coli—and characterized the distribution of antimicrobial resistance and virulence genes located in the prophage region. While virulence genes in prophage were species specific, antimicrobial resistance genes in prophages were highly conserved in various species. An integron structure was detected within specific prophage regions such as P1-like prophage element. Maximum of 10 antimicrobial resistance genes were found in a single prophage region, suggesting that prophages act as a reservoir for antimicrobial resistance genes. The results of this study show the different characteristic structures between AMR- or VF-encoding prophages.
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36
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Sieber RN, Urth TR, Petersen A, Møller CH, Price LB, Skov RL, Larsen AR, Stegger M, Larsen J. Phage-Mediated Immune Evasion and Transmission of Livestock-Associated Methicillin-Resistant Staphylococcus aureus in Humans. Emerg Infect Dis 2021; 26. [PMID: 33079052 PMCID: PMC7588543 DOI: 10.3201/eid2611.201442] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
These bacteria are capable of adapting to humans, leading to increased spread into the community and healthcare settings. Livestock-associated methicillin-resistant Staphylococcus aureus (LA-MRSA) can acquire phage-encoded immune modulators, such as the immune evasion cluster (IEC), which protects bacteria from components of the human innate immune system, and the enzyme TarP, which protects against antibody-mediated immune recognition. We used whole-genome sequencing and epidemiologic investigations to study the effects of IEC- and tarP-harboring phages on household transmission of LA-MRSA in North Denmark Region during 2004–2011. We reviewed information about all patients throughout Denmark who experienced LA-MRSA infection during 2007–2018 to determine whether IEC is associated with increased spread into the general population. Horizontal acquisition of IEC in the human host was associated with increased household transmission of LA-MRSA and spillover into the community and healthcare settings, whereas we found no evidence to suggest that IEC-positive LA-MRSA isolates have become self-sustainable in the general population. By contrast, TarP did not seem to influence household transmission of LA-MRSA.
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37
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Fuchs S, Kucklick M, Lehmann E, Beckmann A, Wilkens M, Kolte B, Mustafayeva A, Ludwig T, Diwo M, Wissing J, Jänsch L, Ahrens CH, Ignatova Z, Engelmann S. Towards the characterization of the hidden world of small proteins in Staphylococcus aureus, a proteogenomics approach. PLoS Genet 2021; 17:e1009585. [PMID: 34061833 PMCID: PMC8195425 DOI: 10.1371/journal.pgen.1009585] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Revised: 06/11/2021] [Accepted: 05/07/2021] [Indexed: 01/08/2023] Open
Abstract
Small proteins play essential roles in bacterial physiology and virulence, however, automated algorithms for genome annotation are often not yet able to accurately predict the corresponding genes. The accuracy and reliability of genome annotations, particularly for small open reading frames (sORFs), can be significantly improved by integrating protein evidence from experimental approaches. Here we present a highly optimized and flexible bioinformatics workflow for bacterial proteogenomics covering all steps from (i) generation of protein databases, (ii) database searches and (iii) peptide-to-genome mapping to (iv) visualization of results. We used the workflow to identify high quality peptide spectrum matches (PSMs) for small proteins (≤ 100 aa, SP100) in Staphylococcus aureus Newman. Protein extracts from S. aureus were subjected to different experimental workflows for protein digestion and prefractionation and measured with highly sensitive mass spectrometers. In total, 175 proteins with up to 100 aa (SP100) were identified. Out of these 24 (ranging from 9 to 99 aa) were novel and not contained in the used genome annotation.144 SP100 are highly conserved and were found in at least 50% of the publicly available S. aureus genomes, while 127 are additionally conserved in other staphylococci. Almost half of the identified SP100 were basic, suggesting a role in binding to more acidic molecules such as nucleic acids or phospholipids.
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Affiliation(s)
- Stephan Fuchs
- Robert Koch Institute, Methodenentwicklung und Forschungsinfrastruktur (MF), Berlin, Germany
| | - Martin Kucklick
- University of Technical Sciences Braunschweig, Institute for Microbiology, Braunschweig, Germany
- Helmholtz Center for Infection Research GmbH, Microbial Proteomics, Braunschweig, Germany
| | - Erik Lehmann
- University of Technical Sciences Braunschweig, Institute for Microbiology, Braunschweig, Germany
- Helmholtz Center for Infection Research GmbH, Microbial Proteomics, Braunschweig, Germany
| | - Alexander Beckmann
- University of Technical Sciences Braunschweig, Institute for Microbiology, Braunschweig, Germany
- Helmholtz Center for Infection Research GmbH, Microbial Proteomics, Braunschweig, Germany
| | - Maya Wilkens
- Robert Koch Institute, Methodenentwicklung und Forschungsinfrastruktur (MF), Berlin, Germany
- University of Technical Sciences Braunschweig, Institute for Microbiology, Braunschweig, Germany
- Helmholtz Center for Infection Research GmbH, Microbial Proteomics, Braunschweig, Germany
| | - Baban Kolte
- University of Hamburg, Institute of Biochemistry and Molecular Biology, Hamburg, Germany
| | - Ayten Mustafayeva
- University of Technical Sciences Braunschweig, Institute for Microbiology, Braunschweig, Germany
- Helmholtz Center for Infection Research GmbH, Microbial Proteomics, Braunschweig, Germany
| | - Tobias Ludwig
- University of Technical Sciences Braunschweig, Institute for Microbiology, Braunschweig, Germany
- Helmholtz Center for Infection Research GmbH, Microbial Proteomics, Braunschweig, Germany
| | - Maurice Diwo
- University of Technical Sciences Braunschweig, Institute for Microbiology, Braunschweig, Germany
- Helmholtz Center for Infection Research GmbH, Microbial Proteomics, Braunschweig, Germany
| | - Josef Wissing
- Helmholtz Center for Infection Research GmbH, Cellular Proteomics, Braunschweig, Germany
| | - Lothar Jänsch
- Helmholtz Center for Infection Research GmbH, Cellular Proteomics, Braunschweig, Germany
| | - Christian H Ahrens
- Agroscope, Research Group Molecular Diagnostics, Genomics and Bioinformatics & SIB Swiss Institute of Bioinformatics, Basel, Switzerland
| | - Zoya Ignatova
- University of Hamburg, Institute of Biochemistry and Molecular Biology, Hamburg, Germany
| | - Susanne Engelmann
- University of Technical Sciences Braunschweig, Institute for Microbiology, Braunschweig, Germany
- Helmholtz Center for Infection Research GmbH, Microbial Proteomics, Braunschweig, Germany
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38
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Cieślik M, Bagińska N, Jończyk-Matysiak E, Węgrzyn A, Węgrzyn G, Górski A. Temperate Bacteriophages-The Powerful Indirect Modulators of Eukaryotic Cells and Immune Functions. Viruses 2021; 13:v13061013. [PMID: 34071422 PMCID: PMC8228536 DOI: 10.3390/v13061013] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Revised: 05/22/2021] [Accepted: 05/27/2021] [Indexed: 12/11/2022] Open
Abstract
Bacteriophages are natural biological entities that limit the growth and amplification of bacteria. They are important stimulators of evolutionary variability in bacteria, and currently are considered a weapon against antibiotic resistance of bacteria. Nevertheless, apart from their antibacterial activity, phages may act as modulators of mammalian immune responses. In this paper, we focus on temperate phages able to execute the lysogenic development, which may shape animal or human immune response by influencing various processes, including phagocytosis of bacterial invaders and immune modulation of mammalian host cells.
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Affiliation(s)
- Martyna Cieślik
- Bacteriophage Laboratory, Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, 53-114 Wrocław, Poland; (M.C.); (N.B.); (E.J.-M.)
| | - Natalia Bagińska
- Bacteriophage Laboratory, Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, 53-114 Wrocław, Poland; (M.C.); (N.B.); (E.J.-M.)
| | - Ewa Jończyk-Matysiak
- Bacteriophage Laboratory, Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, 53-114 Wrocław, Poland; (M.C.); (N.B.); (E.J.-M.)
| | - Alicja Węgrzyn
- Laboratory of Phage Therapy, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Kładki 24, 80-822 Gdańsk, Poland;
| | - Grzegorz Węgrzyn
- Department of Molecular Biology, University of Gdańsk, Wita Stwosza 59, 80-308 Gdańsk, Poland;
| | - Andrzej Górski
- Bacteriophage Laboratory, Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, 53-114 Wrocław, Poland; (M.C.); (N.B.); (E.J.-M.)
- Phage Therapy Unit, Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, 53-114 Wrocław, Poland
- Infant Jesus Hospital, The Medical University of Warsaw, 02-006 Warsaw, Poland
- Correspondence:
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39
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Staphylococcus epidermidis Phages Transduce Antimicrobial Resistance Plasmids and Mobilize Chromosomal Islands. mSphere 2021; 6:6/3/e00223-21. [PMID: 33980677 PMCID: PMC8125051 DOI: 10.1128/msphere.00223-21] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Multidrug-resistant strains of S. epidermidis emerge in both nosocomial and livestock environments as the most important pathogens among coagulase-negative staphylococcal species. The study of transduction by phages is essential to understanding how virulence and antimicrobial resistance genes spread in originally commensal bacterial populations. Staphylococcus epidermidis is a leading opportunistic pathogen causing nosocomial infections that is notable for its ability to form a biofilm and for its high rates of antibiotic resistance. It serves as a reservoir of multiple antimicrobial resistance genes that spread among the staphylococcal population by horizontal gene transfer such as transduction. While phage-mediated transduction is well studied in Staphylococcus aureus, S. epidermidis transducing phages have not been described in detail yet. Here, we report the characteristics of four phages, 27, 48, 456, and 459, previously used for S. epidermidis phage typing, and the newly isolated phage E72, from a clinical S. epidermidis strain. The phages, classified in the family Siphoviridae and genus Phietavirus, exhibited an S. epidermidis-specific host range, and together they infected 49% of the 35 strains tested. A whole-genome comparison revealed evolutionary relatedness to transducing S. aureus phietaviruses. In accordance with this, all the tested phages were capable of transduction with high frequencies up to 10−4 among S. epidermidis strains from different clonal complexes. Plasmids with sizes from 4 to 19 kb encoding resistance to streptomycin, tetracycline, and chloramphenicol were transferred. We provide here the first evidence of a phage-inducible chromosomal island transfer in S. epidermidis. Similarly to S. aureus pathogenicity islands, the transfer was accompanied by phage capsid remodeling; however, the interfering protein encoded by the island was distinct. Our findings underline the role of S. epidermidis temperate phages in the evolution of S. epidermidis strains by horizontal gene transfer, which can also be utilized for S. epidermidis genetic studies. IMPORTANCE Multidrug-resistant strains of S. epidermidis emerge in both nosocomial and livestock environments as the most important pathogens among coagulase-negative staphylococcal species. The study of transduction by phages is essential to understanding how virulence and antimicrobial resistance genes spread in originally commensal bacterial populations. In this work, we provide a detailed description of transducing S. epidermidis phages. The high transduction frequencies of antimicrobial resistance plasmids and the first evidence of chromosomal island transfer emphasize the decisive role of S. epidermidis phages in attaining a higher pathogenic potential of host strains. To date, such importance has been attributed only to S. aureus phages, not to those of coagulase-negative staphylococci. This study also proved that the described transducing bacteriophages represent valuable genetic modification tools in S. epidermidis strains where other methods for gene transfer fail.
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Abril AG, Carrera M, Böhme K, Barros-Velázquez J, Cañas B, Rama JLR, Villa TG, Calo-Mata P. Proteomic Characterization of Bacteriophage Peptides from the Mastitis Producer Staphylococcus aureus by LC-ESI-MS/MS and the Bacteriophage Phylogenomic Analysis. Foods 2021; 10:799. [PMID: 33917943 PMCID: PMC8068337 DOI: 10.3390/foods10040799] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 03/28/2021] [Accepted: 04/06/2021] [Indexed: 01/21/2023] Open
Abstract
The present work describes LC-ESI-MS/MS MS (liquid chromatography-electrospray ionization-tandem mass spectrometry) analyses of tryptic digestion peptides from phages that infect mastitis-causing Staphylococcus aureus isolated from dairy products. A total of 1933 nonredundant peptides belonging to 1282 proteins were identified and analyzed. Among them, 79 staphylococcal peptides from phages were confirmed. These peptides belong to proteins such as phage repressors, structural phage proteins, uncharacterized phage proteins and complement inhibitors. Moreover, eighteen of the phage origin peptides found were specific to S. aureus strains. These diagnostic peptides could be useful for the identification and characterization of S. aureus strains that cause mastitis. Furthermore, a study of bacteriophage phylogeny and the relationship among the identified phage peptides and the bacteria they infect was also performed. The results show the specific peptides that are present in closely related phages and the existing links between bacteriophage phylogeny and the respective Staphylococcus spp. infected.
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Affiliation(s)
- Ana G. Abril
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Santiago de Compostela, 15898 Santiago de Compostela, Spain; (A.G.A.); (J.-L.R.R.); (T.G.V.)
| | - Mónica Carrera
- Department of Food Technology, Spanish National Research Council, Marine Research Institute, 36208 Vigo, Spain
| | - Karola Böhme
- Agroalimentary Technological Center of Lugo, 27002 Lugo, Spain;
| | - Jorge Barros-Velázquez
- Department of Analytical Chemistry, Nutrition and Food Science, School of Veterinary Sciences, University of Santiago de Compostela, 27002 Lugo, Spain;
| | - Benito Cañas
- Department of Analytical Chemistry, Complutense University of Madrid, 28040 Madrid, Spain;
| | - José-Luis R. Rama
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Santiago de Compostela, 15898 Santiago de Compostela, Spain; (A.G.A.); (J.-L.R.R.); (T.G.V.)
| | - Tomás G. Villa
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Santiago de Compostela, 15898 Santiago de Compostela, Spain; (A.G.A.); (J.-L.R.R.); (T.G.V.)
| | - Pilar Calo-Mata
- Department of Analytical Chemistry, Nutrition and Food Science, School of Veterinary Sciences, University of Santiago de Compostela, 27002 Lugo, Spain;
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Type III-A CRISPR immunity promotes mutagenesis of staphylococci. Nature 2021; 592:611-615. [PMID: 33828299 DOI: 10.1038/s41586-021-03440-3] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Accepted: 03/10/2021] [Indexed: 12/26/2022]
Abstract
Horizontal gene transfer and mutation are the two major drivers of microbial evolution that enable bacteria to adapt to fluctuating environmental stressors1. Clustered, regularly interspaced, short palindromic repeats (CRISPR) systems use RNA-guided nucleases to direct sequence-specific destruction of the genomes of mobile genetic elements that mediate horizontal gene transfer, such as conjugative plasmids2 and bacteriophages3, thus limiting the extent to which bacteria can evolve by this mechanism. A subset of CRISPR systems also exhibit non-specific degradation of DNA4,5; however, whether and how this feature affects the host has not yet been examined. Here we show that the non-specific DNase activity of the staphylococcal type III-A CRISPR-Cas system increases mutations in the host and accelerates the generation of antibiotic resistance in Staphylococcus aureus and Staphylococcus epidermidis. These mutations require the induction of the SOS response to DNA damage and display a distinct pattern. Our results demonstrate that by differentially affecting both mechanisms that generate genetic diversity, type III-A CRISPR systems can modulate the evolution of the bacterial host.
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Yang B, Chen C, Sun Y, Cao L, Zhang D, Sun W, Zhang L, Wang G, Shan X, Kang Y, Qian A. Comparative genomic analysis of different virulence strains reveals reasons for the increased virulence of Aeromonas veronii. JOURNAL OF FISH DISEASES 2021; 44:11-24. [PMID: 33137224 DOI: 10.1111/jfd.13262] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2020] [Revised: 08/17/2020] [Accepted: 08/19/2020] [Indexed: 06/11/2023]
Abstract
Aeromonas veronii is an important zoonotic and aquatic agent. More and more cases have shown that it has caused huge economic losses in the aquaculture industry in addition to threatening human health. But the reasons for the increasing virulence of A. veronii are still unclear. In order to further understand the reasons for the increased virulence of A. veronii, we conducted a comparative analysis of the genomes of A. veronii with different virulence. The analysis revealed that there are multiple virulence factors, such as those related to fimbriae, flagella, toxins, iron ion uptake systems and type II, type III and type VI secretion systems in the virulent strain TH0426 genome. And comparative analysis showed that there were two complete type III secretion systems (API1 and API2), of which the API2 and iron ion transport system were unique to the TH0426 strain. In addition, TH0426 strain also has unique functional gene clusters, which may play important roles in terms of resisting infection, adapting to different environments and genetic evolution. These particular virulence factors and gene clusters may be the important reasons for the increased virulence. These insights will provide a reference for the study of the pathogenesis of A. veronii.
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Affiliation(s)
- Bintong Yang
- College of Animal Science and Technology, Jilin Provincial Engineering Research Center of Animal Probiotics, Key Lab of Animal Production, Product Quality and Security, Joint Laboratory of Modern Agricultural Technology International Cooperation, Ministry of Education, Jilin Agricultural University, Changchun, China
- College of Life Science, Changchun Sci-Tech University, Changchun, China
| | - Chong Chen
- College of Animal Science and Technology, Jilin Provincial Engineering Research Center of Animal Probiotics, Key Lab of Animal Production, Product Quality and Security, Joint Laboratory of Modern Agricultural Technology International Cooperation, Ministry of Education, Jilin Agricultural University, Changchun, China
| | - Yufeng Sun
- College of Animal Science and Technology, Jilin Provincial Engineering Research Center of Animal Probiotics, Key Lab of Animal Production, Product Quality and Security, Joint Laboratory of Modern Agricultural Technology International Cooperation, Ministry of Education, Jilin Agricultural University, Changchun, China
| | - Linan Cao
- College of Animal Science and Technology, Jilin Provincial Engineering Research Center of Animal Probiotics, Key Lab of Animal Production, Product Quality and Security, Joint Laboratory of Modern Agricultural Technology International Cooperation, Ministry of Education, Jilin Agricultural University, Changchun, China
| | - Dongxing Zhang
- College of Animal Science and Technology, Jilin Provincial Engineering Research Center of Animal Probiotics, Key Lab of Animal Production, Product Quality and Security, Joint Laboratory of Modern Agricultural Technology International Cooperation, Ministry of Education, Jilin Agricultural University, Changchun, China
| | - Wuwen Sun
- College of Animal Science and Technology, Jilin Provincial Engineering Research Center of Animal Probiotics, Key Lab of Animal Production, Product Quality and Security, Joint Laboratory of Modern Agricultural Technology International Cooperation, Ministry of Education, Jilin Agricultural University, Changchun, China
| | - Lei Zhang
- College of Animal Science and Technology, Jilin Provincial Engineering Research Center of Animal Probiotics, Key Lab of Animal Production, Product Quality and Security, Joint Laboratory of Modern Agricultural Technology International Cooperation, Ministry of Education, Jilin Agricultural University, Changchun, China
| | - Guiqin Wang
- College of Animal Science and Technology, Jilin Provincial Engineering Research Center of Animal Probiotics, Key Lab of Animal Production, Product Quality and Security, Joint Laboratory of Modern Agricultural Technology International Cooperation, Ministry of Education, Jilin Agricultural University, Changchun, China
| | - Xiaofeng Shan
- College of Animal Science and Technology, Jilin Provincial Engineering Research Center of Animal Probiotics, Key Lab of Animal Production, Product Quality and Security, Joint Laboratory of Modern Agricultural Technology International Cooperation, Ministry of Education, Jilin Agricultural University, Changchun, China
| | - Yuanhuan Kang
- College of Animal Science and Technology, Jilin Provincial Engineering Research Center of Animal Probiotics, Key Lab of Animal Production, Product Quality and Security, Joint Laboratory of Modern Agricultural Technology International Cooperation, Ministry of Education, Jilin Agricultural University, Changchun, China
| | - Aidong Qian
- College of Animal Science and Technology, Jilin Provincial Engineering Research Center of Animal Probiotics, Key Lab of Animal Production, Product Quality and Security, Joint Laboratory of Modern Agricultural Technology International Cooperation, Ministry of Education, Jilin Agricultural University, Changchun, China
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Jian Y, Zhao L, Zhao N, Lv HY, Liu Y, He L, Liu Q, Li M. Increasing prevalence of hypervirulent ST5 methicillin susceptible Staphylococcus aureus subtype poses a serious clinical threat. Emerg Microbes Infect 2020; 10:109-122. [PMID: 33355507 PMCID: PMC7832517 DOI: 10.1080/22221751.2020.1868950] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022]
Abstract
Staphylococcus aureus (S. aureus) is a clinical pathogen of great significance causing metastatic or complicated infections. ST5 clonotype isolates have dominated S. aureus infections for more than 10 years in Shanghai, China, and the proportion of methicillin-susceptible S. aureus (MSSA) has remarkably increased in the past decades. By whole-genome sequencing (WGS) 121 ST5 clonotype S. aureus isolates using next-generation sequencing (NGS) platforms and characterizing the evolutionary dynamics of ST5 linages, we found that MSSA evolved independently, making it a subtype differed from other MRSA clones. Drug resistance gene analysis by using the NGS data demonstrated that ST5 clonotype MRSA might be more tolerant under the threat of antimicrobials, which was confirmed in further in vitro susceptibility tests. However, MSSA subtype isolates exhibited relatively high virulence upon the analysis of virulence factors. Furthermore, MSSA subtype isolates displayed higher hemolysis capacity and higher ability to adhere to epithelial cells including A549 human alveolar epithelial cells and HaCaT human skin keratinocytes, caused more severe infections in murine abscess model. With its high virulence and enhanced magnitude in the past decades, the ST5 MSSA subtype poses a serious clinical threat hence more attention should be paid to the prevention and control.
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Affiliation(s)
- Ying Jian
- Department of Laboratory Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, People's Republic of China
| | - Lin Zhao
- Department of Laboratory Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, People's Republic of China
| | - Na Zhao
- Department of Laboratory Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, People's Republic of China
| | - Hui-Ying Lv
- Department of Laboratory Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, People's Republic of China
| | - Yao Liu
- Department of Laboratory Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, People's Republic of China
| | - Lei He
- Department of Laboratory Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, People's Republic of China
| | - Qian Liu
- Department of Laboratory Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, People's Republic of China
| | - Min Li
- Department of Laboratory Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, People's Republic of China
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Staphylococcus aureus secretes immunomodulatory RNA and DNA via membrane vesicles. Sci Rep 2020; 10:18293. [PMID: 33106559 PMCID: PMC7589478 DOI: 10.1038/s41598-020-75108-3] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Accepted: 10/07/2020] [Indexed: 02/07/2023] Open
Abstract
Bacterial-derived RNA and DNA can function as ligands for intracellular receptor activation and induce downstream signaling to modulate the host response to bacterial infection. The mechanisms underlying the secretion of immunomodulatory RNA and DNA by pathogens such as Staphylococcus aureus and their delivery to intracellular host cell receptors are not well understood. Recently, extracellular membrane vesicle (MV) production has been proposed as a general secretion mechanism that could facilitate the delivery of functional bacterial nucleic acids into host cells. S. aureus produce membrane-bound, spherical, nano-sized, MVs packaged with a select array of bioactive macromolecules and they have been shown to play important roles in bacterial virulence and in immune modulation through the transmission of biologic signals to host cells. Here we show that S. aureus secretes RNA and DNA molecules that are mostly protected from degradation by their association with MVs. Importantly, we demonstrate that MVs can be delivered into cultured macrophage cells and subsequently stimulate a potent IFN-β response in recipient cells via activation of endosomal Toll-like receptors. These findings advance our understanding of the mechanisms by which bacterial nucleic acids traffic extracellularly to trigger the modulation of host immune responses.
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Sanchez-Herrero JF, Bernabeu M, Prieto A, Hüttener M, Juárez A. Gene Duplications in the Genomes of Staphylococci and Enterococci. Front Mol Biosci 2020; 7:160. [PMID: 32850954 PMCID: PMC7396535 DOI: 10.3389/fmolb.2020.00160] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Accepted: 06/24/2020] [Indexed: 12/28/2022] Open
Abstract
Gene duplications are a feature of bacterial genomes. In the present work we analyze the extent of gene duplications in the genomes of three microorganisms that belong to the Firmicutes phylum and that are etiologic agents of several nosocomial infections: Staphylococcus aureus, Enterococcus faecium, and Enterococcus faecalis. In all three groups, there is an irregular distribution of duplications in the genomes of the strains analyzed. Whereas in some of the strains duplications are scarce, hundreds of duplications are present in others. In all three species, mobile DNA accounts for a large percentage of the duplicated genes: phage DNA in S. aureus, and plasmid DNA in the enterococci. Duplicates also include core genes. In all three species, a reduced group of genes is duplicated in all strains analyzed. Duplication of the deoC and rpmG genes is a hallmark of S. aureus genomes. Duplication of the gene encoding the PTS IIB subunit is detected in all enterococci genomes. In E. faecalis it is remarkable that the genomes of some strains encode duplicates of the prgB and prgU genes. They belong to the prgABCU cluster, which responds to the presence of the peptide pheromone cCF10 by expressing the surface adhesins PrgA, PrgB, and PrgC.
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Affiliation(s)
- José Francisco Sanchez-Herrero
- Department of Genetics, Microbiology and Statistics, University of Barcelona, Barcelona, Spain.,Biodiversity Research Institute (IRBio), University of Barcelona, Barcelona, Spain.,High Content Genomics and Bioinformatics Unit, Germans Trias i Pujol Research Institute (IGTP), Campus Can Ruti, Badalona, Spain
| | - Manuel Bernabeu
- Department of Genetics, Microbiology and Statistics, University of Barcelona, Barcelona, Spain
| | - Alejandro Prieto
- Department of Genetics, Microbiology and Statistics, University of Barcelona, Barcelona, Spain
| | - Mário Hüttener
- Department of Genetics, Microbiology and Statistics, University of Barcelona, Barcelona, Spain
| | - Antonio Juárez
- Department of Genetics, Microbiology and Statistics, University of Barcelona, Barcelona, Spain.,Institute for Bioengineering of Catalonia, The Barcelona Institute of Science and Technology, Barcelona, Spain
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Revealing 29 sets of independently modulated genes in Staphylococcus aureus, their regulators, and role in key physiological response. Proc Natl Acad Sci U S A 2020; 117:17228-17239. [PMID: 32616573 PMCID: PMC7382225 DOI: 10.1073/pnas.2008413117] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Staphylococcus aureus infections impose an immense burden on the healthcare system. To establish a successful infection in a hostile host environment, S. aureus must coordinate its gene expression to respond to a wide array of challenges. This balancing act is largely orchestrated by the transcriptional regulatory network. Here, we present a model of 29 independently modulated sets of genes that form the basis for a segment of the transcriptional regulatory network in clinical USA300 strains of S. aureus. Using this model, we demonstrate the concerted role of various cellular systems (e.g., metabolism, virulence, and stress response) underlying key physiological responses, including response during blood infection. The ability of Staphylococcus aureus to infect many different tissue sites is enabled, in part, by its transcriptional regulatory network (TRN) that coordinates its gene expression to respond to different environments. We elucidated the organization and activity of this TRN by applying independent component analysis to a compendium of 108 RNA-sequencing expression profiles from two S. aureus clinical strains (TCH1516 and LAC). ICA decomposed the S. aureus transcriptome into 29 independently modulated sets of genes (i-modulons) that revealed: 1) High confidence associations between 21 i-modulons and known regulators; 2) an association between an i-modulon and σS, whose regulatory role was previously undefined; 3) the regulatory organization of 65 virulence factors in the form of three i-modulons associated with AgrR, SaeR, and Vim-3; 4) the roles of three key transcription factors (CodY, Fur, and CcpA) in coordinating the metabolic and regulatory networks; and 5) a low-dimensional representation, involving the function of few transcription factors of changes in gene expression between two laboratory media (RPMI, cation adjust Mueller Hinton broth) and two physiological media (blood and serum). This representation of the TRN covers 842 genes representing 76% of the variance in gene expression that provides a quantitative reconstruction of transcriptional modules in S. aureus, and a platform enabling its full elucidation.
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Li L, Wang G, Li Y, Francois P, Bayer AS, Chen L, Seidl K, Cheung A, Xiong YQ. Impact of the Novel Prophage ϕSA169 on Persistent Methicillin-Resistant Staphylococcus aureus Endovascular Infection. mSystems 2020; 5:e00178-20. [PMID: 32606024 PMCID: PMC7329321 DOI: 10.1128/msystems.00178-20] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Accepted: 06/16/2020] [Indexed: 12/26/2022] Open
Abstract
Persistent methicillin-resistant Staphylococcus aureus (MRSA) endovascular infections are life-threatening syndromes with few therapeutic options. The potential impact of bacteriophages on the persistent outcome has not been well studied. In this study, we investigated the role of a novel prophage (ϕSA169) in MRSA persistence by using a lysogen-free clinically resolving bacteremia (RB) isolate and comparing it to a derivative which was obtained by infecting the RB strain with ϕSA169, which has been lysogenized in a clinical persistent MRSA bacteremia (PB) isolate. Similar to the PB isolate, the ϕSA169-lysogenized RB strain exhibited well-defined in vitro and in vivo phenotypic and genotypic signatures related to the persistent outcome, including earlier activation of global regulators (i.e., sigB, sarA, agr RNAIII, and sae); higher expression of a critical purine biosynthesis gene, purF; and higher growth rates accompanied by lower ATP levels and vancomycin (VAN) susceptibility and stronger δ-hemolysin and biofilm formation versus its isogenic parental RB isolate. Notably, the contribution of ϕSA169 in persistent outcome with VAN treatment was confirmed in an experimental infective endocarditis model. Taken together, these results indicate the critical role of the prophage ϕSA169 in persistent MRSA endovascular infections. Further studies are needed to identify the mechanisms of ϕSA169 in mediating the persistence, as well as establishing the scope of impact, of this prophage in other PB strains.IMPORTANCE Bacteriophages are viruses that invade the bacterial host, disrupt bacterial metabolism, and cause the bacterium to lyse. Because of its remarkable antibacterial activity and unique advantages over antibiotics, for instance, bacteriophage is specific for one species of bacteria and resistance to phage is less common than resistance to antibiotics. Indeed, bacteriophage therapy for treating infections due to multidrug-resistant pathogens in humans has become a research hot spot. However, it is also worth considering that bacteriophages are transferable and could cotransfer host chromosomal genes, e.g., virulence and antimicrobial resistance genes, while lysogenizing and integrating into the bacterial chromosome (prophage), thus playing a role in bacterial evolution and virulence. In the current study, we identified a novel prophage, ϕSA169, from a clinical persistent MRSA bacteremia isolate, and we determined that ϕSA169 mediated well-defined in vitro and in vivo phenotypic and genotypic signatures related to the persistent outcome, which may represent a unique and important persistent mechanism(s).
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Affiliation(s)
- Liang Li
- The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, California, USA
| | - Genzhu Wang
- The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, California, USA
| | - Yi Li
- The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, California, USA
| | | | - Arnold S Bayer
- The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, California, USA
- David Geffen School of Medicine at UCLA, Los Angeles, California, USA
- Department of Medicine, Division of Infectious Diseases, Harbor-UCLA Medical Center, Torrance, California, USA
| | - Liang Chen
- Center for Discovery and Innovation, Nutley, New Jersey, USA
| | - Kati Seidl
- University Hospital of Zurich, Zurich, Switzerland
| | | | - Yan Q Xiong
- The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, California, USA
- David Geffen School of Medicine at UCLA, Los Angeles, California, USA
- Department of Medicine, Division of Infectious Diseases, Harbor-UCLA Medical Center, Torrance, California, USA
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Badawy S, Pajunen MI, Haiko J, Baka ZAM, Abou-Dobara MI, El-Sayed AKA, Skurnik M. Identification and Functional Analysis of Temperate Siphoviridae Bacteriophages of Acinetobacter baumannii. Viruses 2020; 12:v12060604. [PMID: 32486497 PMCID: PMC7354433 DOI: 10.3390/v12060604] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Revised: 05/25/2020] [Accepted: 05/29/2020] [Indexed: 02/07/2023] Open
Abstract
Acinetobacter baumannii is an opportunistic pathogen that presents a serious clinical challenge due to its increasing resistance to all available antibiotics. Phage therapy has been introduced recently to treat antibiotic-incurable A. baumannii infections. In search for new A. baumannii specific bacteriophages, 20 clinical A. baumannii strains were used in two pools in an attempt to enrich phages from sewage. The enrichment resulted in induction of resident prophage(s) and three temperate bacteriophages, named vB_AbaS_fEg-Aba01, vB_AbaS_fLi-Aba02 and vB_AbaS_fLi-Aba03, all able to infect only one strain (#6597) of the 20 clinical strains, were isolated. Morphological characteristics obtained by transmission electron microscopy together with the genomic information revealed that the phages belong to the family Siphoviridae. The ca. 35 kb genomic sequences of the phages were >99% identical to each other. The linear ds DNA genomes of the phages contained 10 nt cohesive end termini, 52–54 predicted genes, an attP site and one tRNA gene each. A database search revealed an >99% identical prophage in the genome of A. baumannii strain AbPK1 (acc. no. CP024576.1). Over 99% identical prophages were also identified from two of the original 20 clinical strains (#5707 and #5920) and both were shown to be spontaneously inducible, thus very likely being the origins of the isolated phages. The phage vB_AbaS_fEg-Aba01 was also able to lysogenize the susceptible strain #6597 demonstrating that it was fully functional. The phages showed a very narrow host range infecting only two A. baumannii strains. In conclusion, we have isolated and characterized three novel temperate Siphoviridae phages that infect A.baumannii.
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Affiliation(s)
- Shimaa Badawy
- Department of Bacteriology and Immunology, Medicum, Human Microbiome Research Program, Faculty of Medicine, University of Helsinki, 00014 UH Helsinki, Finland; (S.B.); (M.I.P.)
- Department of Botany and Microbiology, Faculty of Science, Damietta University, 34511 New Damietta, Egypt; (Z.A.M.B.); (M.I.A.-D.); (A.K.A.E.-S.)
| | - Maria I. Pajunen
- Department of Bacteriology and Immunology, Medicum, Human Microbiome Research Program, Faculty of Medicine, University of Helsinki, 00014 UH Helsinki, Finland; (S.B.); (M.I.P.)
| | - Johanna Haiko
- Division of Clinical Microbiology, Helsinki University Hospital, HUSLAB, 00290 Helsinki, Finland;
| | - Zakaria A. M. Baka
- Department of Botany and Microbiology, Faculty of Science, Damietta University, 34511 New Damietta, Egypt; (Z.A.M.B.); (M.I.A.-D.); (A.K.A.E.-S.)
| | - Mohamed I. Abou-Dobara
- Department of Botany and Microbiology, Faculty of Science, Damietta University, 34511 New Damietta, Egypt; (Z.A.M.B.); (M.I.A.-D.); (A.K.A.E.-S.)
| | - Ahmed K. A. El-Sayed
- Department of Botany and Microbiology, Faculty of Science, Damietta University, 34511 New Damietta, Egypt; (Z.A.M.B.); (M.I.A.-D.); (A.K.A.E.-S.)
| | - Mikael Skurnik
- Department of Bacteriology and Immunology, Medicum, Human Microbiome Research Program, Faculty of Medicine, University of Helsinki, 00014 UH Helsinki, Finland; (S.B.); (M.I.P.)
- Division of Clinical Microbiology, Helsinki University Hospital, HUSLAB, 00290 Helsinki, Finland;
- Correspondence: ; Tel.: +358-2941-26464
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Jiang W, Oikonomou P, Tavazoie S. Comprehensive Genome-wide Perturbations via CRISPR Adaptation Reveal Complex Genetics of Antibiotic Sensitivity. Cell 2020; 180:1002-1017.e31. [PMID: 32109417 PMCID: PMC7169367 DOI: 10.1016/j.cell.2020.02.007] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Revised: 12/04/2019] [Accepted: 02/04/2020] [Indexed: 12/19/2022]
Abstract
Genome-wide CRISPR screens enable systematic interrogation of gene function. However, guide RNA libraries are costly to synthesize, and their limited diversity compromises the sensitivity of CRISPR screens. Using the Streptococcus pyogenes CRISPR-Cas adaptation machinery, we developed CRISPR adaptation-mediated library manufacturing (CALM), which turns bacterial cells into "factories" for generating hundreds of thousands of crRNAs covering 95% of all targetable genomic sites. With an average gene targeted by more than 100 distinct crRNAs, these highly comprehensive CRISPRi libraries produced varying degrees of transcriptional repression critical for uncovering novel antibiotic resistance determinants. Furthermore, by iterating CRISPR adaptation, we rapidly generated dual-crRNA libraries representing more than 100,000 dual-gene perturbations. The polarized nature of spacer adaptation revealed the historical contingency in the stepwise acquisition of genetic perturbations leading to increasing antibiotic resistance. CALM circumvents the expense, labor, and time required for synthesis and cloning of gRNAs, allowing generation of CRISPRi libraries in wild-type bacteria refractory to routine genetic manipulation.
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Affiliation(s)
- Wenyan Jiang
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA; Department of Systems Biology, Columbia University, New York, NY 10032, USA; Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA
| | - Panos Oikonomou
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA; Department of Systems Biology, Columbia University, New York, NY 10032, USA; Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA
| | - Saeed Tavazoie
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA; Department of Systems Biology, Columbia University, New York, NY 10032, USA; Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA.
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Calvo-Villamañán A, Bernheim A, Bikard D. Methods for the Analysis and Characterization of Defense Mechanisms Against Horizontal Gene Transfer: CRISPR Systems. Methods Mol Biol 2020; 2075:235-249. [PMID: 31584167 DOI: 10.1007/978-1-4939-9877-7_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: 06/10/2023]
Abstract
CRISPR-Cas systems provide RNA-guided adaptive immunity to the majority of archaea and many bacteria. They are able to capture pieces of invading genetic elements in the form of novel spacers in an array of repeats. These elements can then be used as a memory to destroy incoming DNA through the action of RNA-guided nucleases. This chapter describes general procedures to determine the ability of CRISPR-Cas systems to capture novel sequences and to use them to block phages and horizontal gene transfer. All protocols are performed in Staphylococcus aureus using Type II-A CRISPR-Cas systems. Nonetheless, the protocols provided can be adapted to work with other bacteria and other types of CRISPR-Cas systems.
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Affiliation(s)
- Alicia Calvo-Villamañán
- Synthetic Biology Group, Microbiology Department, Institut Pasteur, Paris, France
- École Doctorale FIRE-Programme Bettencourt, Centre de Recherches Interdisciplinaires, Paris, France
| | - Aude Bernheim
- Synthetic Biology Group, Microbiology Department, Institut Pasteur, Paris, France
- École Doctorale FIRE-Programme Bettencourt, Centre de Recherches Interdisciplinaires, Paris, France
- Microbial Evolutionary Genomics, Department of Genomes and Genetics, Institut Pasteur, Paris, France
- AgroParisTech, Paris, France
| | - David Bikard
- Synthetic Biology Group, Microbiology Department, Institut Pasteur, Paris, France.
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