Accumulation of defense systems in phage-resistant strains of Pseudomonas aeruginosa

Prokaryotes encode multiple distinct anti-phage defense systems in their genomes. However, the impact of carrying a multitude of defense systems on phage resistance remains unclear, especially in a clinical context. Using a collection of antibiotic-resistant clinical strains of Pseudomonas aeruginosa and a broad panel of phages, we demonstrate that defense systems contribute substantially to defining phage host range and that overall phage resistance scales with the number of defense systems in the bacterial genome. We show that many individual defense systems are specific to phage genera, and that defense systems with complementary phage specificities co-occur in P. aeruginosa genomes likely to provide benefits in phage-diverse environments. Overall, we show that phage-resistant phenotypes of P. aeruginosa with at least 19 phage defense systems exist in the populations of clinical, antibiotic-resistant P. aeruginosa strains.

[1]  S. Brady,et al.  Bacterial cGAS senses a viral RNA to initiate immunity , 2023, bioRxiv.

[2]  M. Wiedmann,et al.  Restriction endonuclease cleavage of phage DNA enables resuscitation from Cas13-induced bacterial dormancy , 2023, Nature Microbiology.

[3]  Yina Gao,et al.  Molecular basis of RADAR anti-phage supramolecular assemblies , 2023, Cell.

[4]  J. Ren,et al.  Bacteriophages inhibit and evade cGAS-like immune function in bacteria , 2023, Cell.

[5]  R. Sorek,et al.  A conserved family of immune effectors cleaves cellular ATP upon viral infection , 2023, Cell.

[6]  Sam P. B. van Beljouw,et al.  RNA-targeting CRISPR–Cas systems , 2022, Nature reviews. Microbiology.

[7]  Gil Amitai,et al.  Discovery of phage determinants that confer sensitivity to bacterial immune systems , 2022, Cell.

[8]  Franklin L. Nobrega,et al.  Defence systems provide synergistic anti-phage activity in E. coli , 2022, bioRxiv.

[9]  Gil Amitai,et al.  Cryo-EM structure of the RADAR supramolecular anti-phage defense complex , 2022, Cell.

[10]  E. Koonin,et al.  Prokaryotic innate immunity through pattern recognition of conserved viral proteins , 2022, Science.

[11]  Kathryn M. Kauffman,et al.  Phage–host coevolution in natural populations , 2022, Nature Microbiology.

[12]  V. Rao,et al.  The complex roles of genomic DNA modifications of bacteriophage T4 in resistance to nuclease-based defense systems of E. coli , 2022, bioRxiv.

[13]  D. Feldman,et al.  Bacteriophage anti-defense genes that neutralize TIR and STING immune responses , 2022, bioRxiv.

[14]  T. Zhang,et al.  Direct activation of an innate immune system in bacteria by a viral capsid protein , 2022, bioRxiv.

[15]  M. Laub,et al.  Mapping the landscape of anti-phage defense mechanisms in the E. coli pangenome , 2022, bioRxiv.

[16]  Gil Amitai,et al.  An expanding arsenal of immune systems that protect bacteria from phages , 2022, bioRxiv.

[17]  R. Sorek,et al.  Phage anti-CBASS and anti-Pycsar nucleases subvert bacterial immunity , 2022, Nature.

[18]  M. Blokesch,et al.  Two defence systems eliminate plasmids from seventh pandemic Vibrio cholerae , 2022, Nature.

[19]  J. Bondy-Denomy,et al.  Bacteriophages antagonize cGAS-like immunity in bacteria , 2022, bioRxiv.

[20]  E. Rocha,et al.  Phages and their satellites encode hotspots of antiviral systems , 2022, Cell host & microbe.

[21]  P. C. Fineran,et al.  A mobile restriction–modification system provides phage defence and resolves an epigenetic conflict with an antagonistic endonuclease , 2022, Nucleic acids research.

[22]  R. Sorek,et al.  SnapShot: Bacterial immunity , 2022, Cell.

[23]  Kathryn M. Kauffman,et al.  Rapid evolutionary turnover of mobile genetic elements drives bacterial resistance to phages , 2021, Science.

[24]  Franklin L. Nobrega,et al.  Identification and classification of antiviral defence systems in bacteria and archaea with PADLOC reveals new system types , 2021, Nucleic acids research.

[25]  Stan J. J. Brouns,et al.  Mechanisms and clinical importance of bacteriophage resistance , 2021, FEMS microbiology reviews.

[26]  D. Fusco,et al.  Superinfection exclusion: A viral strategy with short-term benefits and long-term drawbacks , 2021, bioRxiv.

[27]  M. Touchon,et al.  Systematic and quantitative view of the antiviral arsenal of prokaryotes , 2021, Nature Communications.

[28]  Tom O. Delmont,et al.  VirSorter2: a multi-classifier, expert-guided approach to detect diverse DNA and RNA viruses , 2021, Microbiome.

[29]  S. Zhavoronok,et al.  Phage phiKZ—The First of Giants , 2021, Viruses.

[30]  J. Bondy-Denomy,et al.  Anti-CRISPRs go viral: the infection biology of CRISPR-Cas inhibitors. , 2020, Cell host & microbe.

[31]  N. Kyrpides,et al.  CheckV assesses the quality and completeness of metagenome-assembled viral genomes , 2020, Nature Biotechnology.

[32]  Thomas M. Keane,et al.  Twelve years of SAMtools and BCFtools , 2020, GigaScience.

[33]  P. C. Fineran,et al.  Conquering CRISPR: how phages overcome bacterial adaptive immunity. , 2020, Current opinion in biotechnology.

[34]  Stan J. J. Brouns,et al.  Extracting Transition Rates in Particle Tracking Using Analytical Diffusion Distribution Analysis. , 2020, Biophysical journal.

[35]  Jonathan L. Schmid-Burgk,et al.  Diverse enzymatic activities mediate antiviral immunity in prokaryotes , 2020, Science.

[36]  Agnieszka Onisko,et al.  PhageAI - Bacteriophage Life Cycle Recognition with Machine Learning and Natural Language Processing , 2020, bioRxiv.

[37]  R. Sorek,et al.  Abortive Infection: Bacterial Suicide as an Antiviral Immune Strategy. , 2020, Annual review of virology.

[38]  P. Turner,et al.  Pleiotropy complicates a trade-off between phage resistance and antibiotic resistance , 2020, Proceedings of the National Academy of Sciences.

[39]  Yanbin Yin,et al.  AcrFinder: genome mining anti-CRISPR operons in prokaryotes and their viruses , 2020, Nucleic Acids Res..

[40]  L. Marraffini,et al.  Faculty Opinions recommendation of HORMA Domain Proteins and a Trip13-like ATPase Regulate Bacterial cGAS-like Enzymes to Mediate Bacteriophage Immunity. , 2020, Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature.

[41]  P. C. Fineran,et al.  The arms race between bacteria and their phage foes , 2020, Nature.

[42]  Peter C. Fineran,et al.  A jumbo phage that forms a nucleus-like structure evades CRISPR–Cas DNA targeting but is vulnerable to type III RNA-based immunity , 2019, Nature Microbiology.

[43]  J. McInerney,et al.  Coinfinder: detecting significant associations and dissociations in pangenomes , 2019, bioRxiv.

[44]  Christophe Ambroise,et al.  PPanGGOLiN: Depicting microbial diversity via a partitioned pangenome graph , 2019, bioRxiv.

[45]  R. Sorek,et al.  The pan-immune system of bacteria: antiviral defence as a community resource , 2019, Nature Reviews Microbiology.

[46]  D. Agard,et al.  A bacteriophage nucleus-like compartment shields DNA from CRISPR nucleases , 2019, Nature.

[47]  Jennifer Lu,et al.  Improved metagenomic analysis with Kraken 2 , 2019, Genome Biology.

[48]  K. Whiteson,et al.  PQS Produced by the Pseudomonas aeruginosa Stress Response Repels Swarms Away from Bacteriophage and Antibiotics , 2019, Journal of bacteriology.

[49]  P. J. Kranzusch,et al.  Structure and mechanism of a cyclic trinucleotide-activated bacterial endonuclease mediating bacteriophage immunity , 2019, bioRxiv.

[50]  Evelien M. Adriaenssens,et al.  Taxonomic assignment of uncultivated prokaryotic virus genomes is enabled by gene-sharing networks , 2019, Nature Biotechnology.

[51]  Peter C. Fineran,et al.  Imprecise Spacer Acquisition Generates CRISPR-Cas Immune Diversity through Primed Adaptation. , 2019, Cell host & microbe.

[52]  P. J. Kranzusch,et al.  Bacterial cGAS-like enzymes synthesize diverse nucleotide signals , 2019, Nature.

[53]  S. Rice,et al.  Comparative genomics of clinical strains of Pseudomonas aeruginosa strains isolated from different geographic sites , 2018, Scientific Reports.

[54]  Stan J. J. Brouns,et al.  Targeting mechanisms of tailed bacteriophages , 2018, Nature Reviews Microbiology.

[55]  Evelien M. Adriaenssens,et al.  Evaluation of the genomic diversity of viruses infecting bacteria, archaea and eukaryotes using a common bioinformatic platform: steps towards a unified taxonomy , 2018, The Journal of general virology.

[56]  Rotem Sorek,et al.  Systematic discovery of antiphage defense systems in the microbial pangenome , 2018, Science.

[57]  E. Koonin,et al.  Evolutionary Genomics of Defense Systems in Archaea and Bacteria. , 2017, Annual review of microbiology.

[58]  D. Bikard,et al.  PhageTerm: a tool for fast and accurate determination of phage termini and packaging mechanism using next-generation sequencing data , 2017, Scientific Reports.

[59]  Heng Li,et al.  Minimap2: pairwise alignment for nucleotide sequences , 2017, Bioinform..

[60]  Xiaofei Jiang,et al.  Anti-Restriction Protein, KlcAHS, Promotes Dissemination of Carbapenem Resistance , 2017, Front. Cell. Infect. Microbiol..

[61]  Markus Göker,et al.  VICTOR: genome-based phylogeny and classification of prokaryotic viruses , 2017, bioRxiv.

[62]  D. Agard,et al.  Assembly of a nucleus-like structure during viral replication in bacteria , 2017, Science.

[63]  Ryan R. Wick,et al.  Unicycler: Resolving bacterial genome assemblies from short and long sequencing reads , 2016, bioRxiv.

[64]  B. Bassler,et al.  Quorum sensing controls the Pseudomonas aeruginosa CRISPR-Cas adaptive immune system , 2016, Proceedings of the National Academy of Sciences.

[65]  Chris M. Brown,et al.  Interference-driven spacer acquisition is dominant over naive and primed adaptation in a native CRISPR–Cas system , 2016, Nature Communications.

[66]  Kira S. Makarova,et al.  Diverse evolutionary roots and mechanistic variations of the CRISPR-Cas systems , 2016, Science.

[67]  Chris M. Brown,et al.  CRISPRDetect: A flexible algorithm to define CRISPR arrays , 2016, BMC Genomics.

[68]  Evgeny M. Zdobnov,et al.  BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs , 2015, Bioinform..

[69]  Justin Zobel,et al.  Bandage: interactive visualization of de novo genome assemblies , 2015, bioRxiv.

[70]  Brian D. Ondov,et al.  The Harvest suite for rapid core-genome alignment and visualization of thousands of intraspecific microbial genomes , 2014, Genome Biology.

[71]  Torsten Seemann,et al.  Prokka: rapid prokaryotic genome annotation , 2014, Bioinform..

[72]  Jos Boekhorst,et al.  Degenerate target sites mediate rapid primed CRISPR adaptation , 2014, Proceedings of the National Academy of Sciences.

[73]  S. Moineau,et al.  CRISPR-Cas and restriction–modification systems are compatible and increase phage resistance , 2013, Nature Communications.

[74]  Robert D. Finn,et al.  HMMER web server: interactive sequence similarity searching , 2011, Nucleic Acids Res..

[75]  G. O’Toole,et al.  Prevalence, conservation and functional analysis of Yersinia and Escherichia CRISPR regions in clinical Pseudomonas aeruginosa isolates , 2011, Microbiology.

[76]  S. Abedon.  Lysis from without , 2011, Bacteriophage.

[77]  Martin C. J. Maiden,et al.  BIGSdb: Scalable analysis of bacterial genome variation at the population level , 2010, BMC Bioinformatics.

[78]  Sylvain Moineau,et al.  Bacteriophage resistance mechanisms , 2010, Nature Reviews Microbiology.

[79]  Miriam L. Land,et al.  Trace: Tennessee Research and Creative Exchange Prodigal: Prokaryotic Gene Recognition and Translation Initiation Site Identification Recommended Citation Prodigal: Prokaryotic Gene Recognition and Translation Initiation Site Identification , 2022 .

[80]  John H. White,et al.  The structure of the KlcA and ArdB proteins reveals a novel fold and antirestriction activity against Type I DNA restriction systems in vivo but not in vitro , 2009, Nucleic acids research.

[81]  Gonçalo R. Abecasis,et al.  The Sequence Alignment/Map format and SAMtools , 2009, Bioinform..

[82]  John H. White,et al.  Extensive DNA mimicry by the ArdA anti-restriction protein and its role in the spread of antibiotic resistance , 2009, Nucleic acids research.

[83]  Rick L. Stevens,et al.  The RAST Server: Rapid Annotations using Subsystems Technology , 2008, BMC Genomics.

[84]  R. Barrangou,et al.  CRISPR Provides Acquired Resistance Against Viruses in Prokaryotes , 2007, Science.

[85]  H. Schweizer,et al.  A 10-min method for preparation of highly electrocompetent Pseudomonas aeruginosa cells: application for DNA fragment transfer between chromosomes and plasmid transformation. , 2006, Journal of microbiological methods.

[86]  Johannes Söding,et al.  The HHpred interactive server for protein homology detection and structure prediction , 2005, Nucleic Acids Res..

[87]  T. Bickle,et al.  Restricting restriction , 2003, Molecular microbiology.

[88]  P. Shannon,et al.  Cytoscape: a software environment for integrated models of biomolecular interaction networks. , 2003, Genome research.

[89]  Thomas L. Madden,et al.  Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. , 1997, Nucleic acids research.

[90]  E. Myers,et al.  Basic local alignment search tool. , 1990, Journal of molecular biology.

[91]  W. Arber,et al.  Host specificity of DNA produced by Escherichia coli. II. Control over acceptance of DNA from infecting phage lambda. , 1962, Journal of molecular biology.

[92]  H. Schweizer,et al.  Escherichia-Pseudomonas shuttle vectors derived from pUC18/19. , 1991, Gene.