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Beck C, Krusche J, Elsherbini AMA, Du X, Peschel A. Phage susceptibility determinants of the opportunistic pathogen Staphylococcus epidermidis. Curr Opin Microbiol 2024; 78:102434. [PMID: 38364502 DOI: 10.1016/j.mib.2024.102434] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Revised: 01/16/2024] [Accepted: 01/18/2024] [Indexed: 02/18/2024]
Abstract
Staphylococcus epidermidis is a common member of the human skin and nose microbiomes and a frequent cause of invasive infections. Transducing phages accomplish the horizontal transfer of resistance and virulence genes by mispackaging of mobile-genetic elements, contributing to severe, therapy-refractory S. epidermidis infections. Lytic phages on the other hand can be interesting candidates for new anti-S. epidermidis phage therapies. Despite the importance of phages, we are only beginning to unravel S. epidermidis phage interactions. Recent studies shed new light on S. epidermidis phage diversity, host range, and receptor specificities. Modulation of cell wall teichoic acids, the major phage receptor structures, along with other phage defense mechanisms, are crucial determinants for S. epidermidis susceptibility to different phage groups.
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Affiliation(s)
- Christian Beck
- Cluster of Excellence "Controlling Microbes to Fight Infections (CMFI)", University of Tübingen, 72076 Tübingen, Germany; Interfaculty Institute of Microbiology and Infection Medicine Tübingen, Infection Biology, University of Tübingen, 72076 Tübingen, Germany; German Centre for Infection Research (DZIF), Partner Site Tübingen, 72076 Tübingen, Germany
| | - Janes Krusche
- Cluster of Excellence "Controlling Microbes to Fight Infections (CMFI)", University of Tübingen, 72076 Tübingen, Germany; Interfaculty Institute of Microbiology and Infection Medicine Tübingen, Infection Biology, University of Tübingen, 72076 Tübingen, Germany; German Centre for Infection Research (DZIF), Partner Site Tübingen, 72076 Tübingen, Germany
| | - Ahmed M A Elsherbini
- Cluster of Excellence "Controlling Microbes to Fight Infections (CMFI)", University of Tübingen, 72076 Tübingen, Germany; Interfaculty Institute of Microbiology and Infection Medicine Tübingen, Infection Biology, University of Tübingen, 72076 Tübingen, Germany; German Centre for Infection Research (DZIF), Partner Site Tübingen, 72076 Tübingen, Germany
| | - Xin Du
- Cluster of Excellence "Controlling Microbes to Fight Infections (CMFI)", University of Tübingen, 72076 Tübingen, Germany; Interfaculty Institute of Microbiology and Infection Medicine Tübingen, Infection Biology, University of Tübingen, 72076 Tübingen, Germany; German Centre for Infection Research (DZIF), Partner Site Tübingen, 72076 Tübingen, Germany
| | - Andreas Peschel
- Cluster of Excellence "Controlling Microbes to Fight Infections (CMFI)", University of Tübingen, 72076 Tübingen, Germany; Interfaculty Institute of Microbiology and Infection Medicine Tübingen, Infection Biology, University of Tübingen, 72076 Tübingen, Germany; German Centre for Infection Research (DZIF), Partner Site Tübingen, 72076 Tübingen, Germany.
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Hossain M, Aslan B, Hatoum-Aslan A. Tandem mobilization of anti-phage defenses alongside SCC mec cassettes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.17.533233. [PMID: 36993521 PMCID: PMC10055296 DOI: 10.1101/2023.03.17.533233] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
Bacterial viruses (phages) and the immune systems targeted against them significantly impact bacterial survival, evolution, and the emergence of pathogenic strains. While recent research has made spectacular strides towards discovering and validating new defenses in a few model organisms1-3, the inventory of immune systems in clinically-relevant bacteria remains underexplored, and little is known about the mechanisms by which these systems horizontally spread. Such pathways not only impact the evolutionary trajectory of bacterial pathogens, but also threaten to undermine the effectiveness of phage-based therapeutics. Here, we investigate the battery of defenses in staphylococci, opportunistic pathogens that constitute leading causes of antibiotic-resistant infections. We show that these organisms harbor a variety of anti-phage defenses encoded within/near the infamous SCC (staphylococcal cassette chromosome) mec cassettes, mobile genomic islands that confer methicillin resistance. Importantly, we demonstrate that SCCmec-encoded recombinases mobilize not only SCCmec, but also tandem cassettes enriched with diverse defenses. Further, we show that phage infection potentiates cassette mobilization. Taken together, our findings reveal that beyond spreading antibiotic resistance, SCCmec cassettes play a central role in disseminating anti-phage defenses. This work underscores the urgent need for developing adjunctive treatments that target this pathway to save the burgeoning phage therapeutics from suffering the same fate as conventional antibiotics.
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Affiliation(s)
- Motaher Hossain
- University of Illinois at Urbana-Champaign, Department of Microbiology, Urbana, IL, USA
| | - Barbaros Aslan
- University of Illinois at Urbana-Champaign, Department of Microbiology, Urbana, IL, USA
| | - Asma Hatoum-Aslan
- University of Illinois at Urbana-Champaign, Department of Microbiology, Urbana, IL, USA
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3
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Tian F, Li J, Li L, Li F, Tong Y. Molecular dissection of the first Staphylococcus cohnii temperate phage IME1354_01. Virus Res 2022; 318:198812. [DOI: 10.1016/j.virusres.2022.198812] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Revised: 05/06/2022] [Accepted: 05/12/2022] [Indexed: 10/18/2022]
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Bari SMN, Chou-Zheng L, Howell O, Hossain M, Hill CM, Boyle TA, Cater K, Dandu VS, Thomas A, Aslan B, Hatoum-Aslan A. A unique mode of nucleic acid immunity performed by a multifunctional bacterial enzyme. Cell Host Microbe 2022; 30:570-582.e7. [PMID: 35421352 DOI: 10.1016/j.chom.2022.03.001] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Revised: 12/10/2021] [Accepted: 03/01/2022] [Indexed: 11/24/2022]
Abstract
The perpetual arms race between bacteria and their viruses (phages) has given rise to diverse immune systems, including restriction-modification and CRISPR-Cas, which sense and degrade phage-derived nucleic acids. These complex systems rely upon production and maintenance of multiple components to achieve antiphage defense. However, the prevalence and effectiveness of minimal, single-component systems that cleave DNA remain unknown. Here, we describe a unique mode of nucleic acid immunity mediated by a single enzyme with nuclease and helicase activities, herein referred to as Nhi (nuclease-helicase immunity). This enzyme provides robust protection against diverse staphylococcal phages and prevents phage DNA accumulation in cells stripped of all other known defenses. Our observations support a model in which Nhi targets and degrades phage-specific replication intermediates. Importantly, Nhi homologs are distributed in diverse bacteria and exhibit functional conservation, highlighting the versatility of such compact weapons as major players in antiphage defense.
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Affiliation(s)
- S M Nayeemul Bari
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, IL 61821, USA
| | - Lucy Chou-Zheng
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, IL 61821, USA
| | - Olivia Howell
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, IL 61821, USA
| | - Motaher Hossain
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, IL 61821, USA
| | - Courtney M Hill
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, IL 61821, USA
| | - Tori A Boyle
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, IL 61821, USA
| | - Katie Cater
- Department of Biological Sciences, University of Alabama, Tuscaloosa, AL 35487, USA
| | - Vidya Sree Dandu
- Department of Biological Sciences, University of Alabama, Tuscaloosa, AL 35487, USA
| | - Alexander Thomas
- Department of Biological Sciences, University of Alabama, Tuscaloosa, AL 35487, USA
| | - Barbaros Aslan
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, IL 61821, USA
| | - Asma Hatoum-Aslan
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, IL 61821, USA.
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Ramsey J, Rasche H, Maughmer C, Criscione A, Mijalis E, Liu M, Hu JC, Young R, Gill JJ. Galaxy and Apollo as a biologist-friendly interface for high-quality cooperative phage genome annotation. PLoS Comput Biol 2020; 16:e1008214. [PMID: 33137082 PMCID: PMC7660901 DOI: 10.1371/journal.pcbi.1008214] [Citation(s) in RCA: 85] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Revised: 11/12/2020] [Accepted: 08/02/2020] [Indexed: 01/21/2023] Open
Abstract
In the modern genomic era, scientists without extensive bioinformatic training need to apply high-power computational analyses to critical tasks like phage genome annotation. At the Center for Phage Technology (CPT), we developed a suite of phage-oriented tools housed in open, user-friendly web-based interfaces. A Galaxy platform conducts computationally intensive analyses and Apollo, a collaborative genome annotation editor, visualizes the results of these analyses. The collection includes open source applications such as the BLAST+ suite, InterProScan, and several gene callers, as well as unique tools developed at the CPT that allow maximum user flexibility. We describe in detail programs for finding Shine-Dalgarno sequences, resources used for confident identification of lysis genes such as spanins, and methods used for identifying interrupted genes that contain frameshifts or introns. At the CPT, genome annotation is separated into two robust segments that are facilitated through the automated execution of many tools chained together in an operation called a workflow. First, the structural annotation workflow results in gene and other feature calls. This is followed by a functional annotation workflow that combines sequence comparisons and conserved domain searching, which is contextualized to allow integrated evidence assessment in functional prediction. Finally, we describe a workflow used for comparative genomics. Using this multi-purpose platform enables researchers to easily and accurately annotate an entire phage genome. The portal can be accessed at https://cpt.tamu.edu/galaxy-pub with accompanying user training material.
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Affiliation(s)
- Jolene Ramsey
- Center for Phage Technology, Texas A&M University, College Station, Texas, United States of America
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas, United States of America
| | - Helena Rasche
- Center for Phage Technology, Texas A&M University, College Station, Texas, United States of America
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas, United States of America
| | - Cory Maughmer
- Center for Phage Technology, Texas A&M University, College Station, Texas, United States of America
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas, United States of America
| | - Anthony Criscione
- Center for Phage Technology, Texas A&M University, College Station, Texas, United States of America
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas, United States of America
| | - Eleni Mijalis
- Center for Phage Technology, Texas A&M University, College Station, Texas, United States of America
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas, United States of America
| | - Mei Liu
- Center for Phage Technology, Texas A&M University, College Station, Texas, United States of America
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas, United States of America
| | - James C. Hu
- Center for Phage Technology, Texas A&M University, College Station, Texas, United States of America
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas, United States of America
| | - Ry Young
- Center for Phage Technology, Texas A&M University, College Station, Texas, United States of America
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas, United States of America
| | - Jason J. Gill
- Center for Phage Technology, Texas A&M University, College Station, Texas, United States of America
- Department of Animal Science, Texas A&M University, College Station, Texas, United States of America
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