An Endogenous Staphylococcus aureus CRISPR-Cas System Limits Phage Proliferation and Is Efficiently Excised from the Genome as Part of the SCCmec Cassette
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 t...
| Main Authors: | , , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
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American Society for Microbiology
2023-08-01
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| Series: | Microbiology Spectrum |
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| Online Access: | https://journals.asm.org/doi/10.1128/spectrum.01277-23 |
| _version_ | 1828717657829933056 |
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| author | Kasper Mikkelsen Janine Zara Bowring Yong Kai Ng Frida Svanberg Frisinger Julie Kjærsgaard Maglegaard Qiuchun Li Raphael N. Sieber Andreas Petersen Paal Skytt Andersen Jakob T. Rostøl Nina Molin Høyland-Kroghsbo Hanne Ingmer |
| author_facet | Kasper Mikkelsen Janine Zara Bowring Yong Kai Ng Frida Svanberg Frisinger Julie Kjærsgaard Maglegaard Qiuchun Li Raphael N. Sieber Andreas Petersen Paal Skytt Andersen Jakob T. Rostøl Nina Molin Høyland-Kroghsbo Hanne Ingmer |
| author_sort | Kasper Mikkelsen |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-03-12T14:30:35Z |
| format | Article |
| id | doaj.art-af56ee53f3ed4788bccc52594ef15625 |
| institution | Directory Open Access Journal |
| issn | 2165-0497 |
| language | English |
| last_indexed | 2024-03-12T14:30:35Z |
| publishDate | 2023-08-01 |
| publisher | American Society for Microbiology |
| record_format | Article |
| series | Microbiology Spectrum |
| spelling | doaj.art-af56ee53f3ed4788bccc52594ef156252023-08-17T13:04:15ZengAmerican Society for MicrobiologyMicrobiology Spectrum2165-04972023-08-0111410.1128/spectrum.01277-23An Endogenous Staphylococcus aureus CRISPR-Cas System Limits Phage Proliferation and Is Efficiently Excised from the Genome as Part of the SCCmec CassetteKasper Mikkelsen0Janine Zara Bowring1Yong Kai Ng2Frida Svanberg Frisinger3Julie Kjærsgaard Maglegaard4Qiuchun Li5Raphael N. Sieber6Andreas Petersen7Paal Skytt Andersen8Jakob T. Rostøl9Nina Molin Høyland-Kroghsbo10Hanne Ingmer11Department of Veterinary and Animal Sciences, University of Copenhagen, Copenhagen, DenmarkDepartment of Veterinary and Animal Sciences, University of Copenhagen, Copenhagen, DenmarkDepartment of Veterinary and Animal Sciences, University of Copenhagen, Copenhagen, DenmarkDepartment of Veterinary and Animal Sciences, University of Copenhagen, Copenhagen, DenmarkDepartment of Veterinary and Animal Sciences, University of Copenhagen, Copenhagen, DenmarkJiangsu Key Lab of Zoonosis/Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, ChinaDepartment of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, DenmarkDepartment of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, DenmarkDepartment of Veterinary and Animal Sciences, University of Copenhagen, Copenhagen, DenmarkCentre for Bacterial Resistance Biology, Imperial College London, London, United KingdomDepartment of Veterinary and Animal Sciences, University of Copenhagen, Copenhagen, DenmarkDepartment of Veterinary and Animal Sciences, University of Copenhagen, Copenhagen, DenmarkABSTRACT 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.https://journals.asm.org/doi/10.1128/spectrum.01277-23CRISPR-Cas type III-AStaphylococcus aureusMRSASCCmec type V(5C2&5)bacteriophageCRISPR-Cas |
| spellingShingle | Kasper Mikkelsen Janine Zara Bowring Yong Kai Ng Frida Svanberg Frisinger Julie Kjærsgaard Maglegaard Qiuchun Li Raphael N. Sieber Andreas Petersen Paal Skytt Andersen Jakob T. Rostøl Nina Molin Høyland-Kroghsbo Hanne Ingmer An Endogenous Staphylococcus aureus CRISPR-Cas System Limits Phage Proliferation and Is Efficiently Excised from the Genome as Part of the SCCmec Cassette Microbiology Spectrum CRISPR-Cas type III-A Staphylococcus aureus MRSA SCCmec type V(5C2&5) bacteriophage CRISPR-Cas |
| title | An Endogenous Staphylococcus aureus CRISPR-Cas System Limits Phage Proliferation and Is Efficiently Excised from the Genome as Part of the SCCmec Cassette |
| title_full | An Endogenous Staphylococcus aureus CRISPR-Cas System Limits Phage Proliferation and Is Efficiently Excised from the Genome as Part of the SCCmec Cassette |
| title_fullStr | An Endogenous Staphylococcus aureus CRISPR-Cas System Limits Phage Proliferation and Is Efficiently Excised from the Genome as Part of the SCCmec Cassette |
| title_full_unstemmed | An Endogenous Staphylococcus aureus CRISPR-Cas System Limits Phage Proliferation and Is Efficiently Excised from the Genome as Part of the SCCmec Cassette |
| title_short | An Endogenous Staphylococcus aureus CRISPR-Cas System Limits Phage Proliferation and Is Efficiently Excised from the Genome as Part of the SCCmec Cassette |
| title_sort | endogenous staphylococcus aureus crispr cas system limits phage proliferation and is efficiently excised from the genome as part of the sccmec cassette |
| topic | CRISPR-Cas type III-A Staphylococcus aureus MRSA SCCmec type V(5C2&5) bacteriophage CRISPR-Cas |
| url | https://journals.asm.org/doi/10.1128/spectrum.01277-23 |
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