Genome Analysis of Anti-Phage Defense Systems and Defense Islands in : Preservation and Variability

Overview

Journal Viruses

Publisher MDPI

Specialty Microbiology

Date 2025 Jan 8

PMID 39772210

Authors

Ghadeer Jdeed

Vera V Morozova

Nina V Tikunova

Affiliations

Soon will be listed here.

Abstract

Anti-phage defense systems are widespread in bacteria due to the latter continuous adaptation to infection by bacteriophages (phages). has a high degree of intrinsic antibiotic resistance, which makes phage therapy relevant for the treatment of infections caused by this species. Studying the array of anti-phage defense systems that could be found in helps in better adapting the phages to the systems present in the pathogenic bacteria. Pangenome analysis of the available strains with complete genomes that were downloaded from GenBank, including five local genomes, indicated a wide set of 72 defense systems and subsystems that varied between the strains. Seven of these systems were present in more than 20% of the studied genomes and the proteins encoded by the systems were variable in most of the cases. A total of 27 defense islands were revealed where defense systems were found; however, more than 60% of the instances of systems were found in four defense islands. Several elements linked to the transfer of these systems were found. No obvious associations between the pattern of distribution of the anti-phage defense systems of and the phylogenetic features or the isolation site were found.

References

Mikheenko A, Prjibelski A, Saveliev V, Antipov D, Gurevich A . Versatile genome assembly evaluation with QUAST-LG. Bioinformatics. 2018; 34(13):i142-i150. PMC: 6022658. DOI: 10.1093/bioinformatics/bty266. View

Morozova V, Yakubovskij V, Baykov I, Kozlova Y, Tikunov A, Babkin I . StenM_174: A Novel Podophage That Infects a Wide Range of spp. and Suggests a New Subfamily in the Family . Viruses. 2024; 16(1). PMC: 10820202. DOI: 10.3390/v16010018. View

Page A, Cummins C, Hunt M, Wong V, Reuter S, Holden M . Roary: rapid large-scale prokaryote pan genome analysis. Bioinformatics. 2015; 31(22):3691-3. PMC: 4817141. DOI: 10.1093/bioinformatics/btv421. View

Panahi B, Dehganzad B, Nami Y . CRISPR-Cas systems feature and targeting phages diversity in strains. Front Microbiol. 2023; 14:1281307. PMC: 10731254. DOI: 10.3389/fmicb.2023.1281307. View

Doron S, Melamed S, Ofir G, Leavitt A, Lopatina A, Keren M . Systematic discovery of antiphage defense systems in the microbial pangenome. Science. 2018; 359(6379). PMC: 6387622. DOI: 10.1126/science.aar4120. View

Johnson M, Laderman E, Huiting E, Zhang C, Davidson A, Bondy-Denomy J . Core defense hotspots within Pseudomonas aeruginosa are a consistent and rich source of anti-phage defense systems. Nucleic Acids Res. 2023; 51(10):4995-5005. PMC: 10250203. DOI: 10.1093/nar/gkad317. View

Bankevich A, Nurk S, Antipov D, Gurevich A, Dvorkin M, Kulikov A . SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol. 2012; 19(5):455-77. PMC: 3342519. DOI: 10.1089/cmb.2012.0021. View

Gerner-Smidt P, Bruun B, Arpi M, Schmidt J . Diversity of nosocomial Xanthomonas maltophilia (Stenotrophomonas maltophilia) as determined by ribotyping. Eur J Clin Microbiol Infect Dis. 1995; 14(2):137-40. DOI: 10.1007/BF02111874. View

Brooke J . Stenotrophomonas maltophilia: an emerging global opportunistic pathogen. Clin Microbiol Rev. 2012; 25(1):2-41. PMC: 3255966. DOI: 10.1128/CMR.00019-11. View

10.

Ochoa-Sanchez L, Vinuesa P . Evolutionary Genetic Analysis Uncovers Multiple Species with Distinct Habitat Preferences and Antibiotic Resistance Phenotypes in the Complex. Front Microbiol. 2017; 8:1548. PMC: 5562727. DOI: 10.3389/fmicb.2017.01548. View

11.

Romero-Calle D, Benevides R, Goes-Neto A, Billington C . Bacteriophages as Alternatives to Antibiotics in Clinical Care. Antibiotics (Basel). 2019; 8(3). PMC: 6784059. DOI: 10.3390/antibiotics8030138. View

12.

Fluit A, Bayjanov J, Aguilar M, Canton R, Elborn S, Tunney M . Taxonomic position, antibiotic resistance and virulence factor production by Stenotrophomonas isolates from patients with cystic fibrosis and other chronic respiratory infections. BMC Microbiol. 2022; 22(1):129. PMC: 9097388. DOI: 10.1186/s12866-022-02466-5. View

13.

Palleroni N, BRADBURY J . Stenotrophomonas, a new bacterial genus for Xanthomonas maltophilia (Hugh 1980) Swings et al. 1983. Int J Syst Bacteriol. 1993; 43(3):606-9. DOI: 10.1099/00207713-43-3-606. View

14.

Grant J, Enns E, Marinier E, Mandal A, Herman E, Chen C . Proksee: in-depth characterization and visualization of bacterial genomes. Nucleic Acids Res. 2023; 51(W1):W484-W492. PMC: 10320063. DOI: 10.1093/nar/gkad326. View

15.

Murtazalieva K, Mu A, Petrovskaya A, Finn R . The growing repertoire of phage anti-defence systems. Trends Microbiol. 2024; 32(12):1212-1228. DOI: 10.1016/j.tim.2024.05.005. View

16.

Brooke J . New strategies against Stenotrophomonas maltophilia: a serious worldwide intrinsically drug-resistant opportunistic pathogen. Expert Rev Anti Infect Ther. 2013; 12(1):1-4. DOI: 10.1586/14787210.2014.864553. View

17.

Madeira F, Pearce M, Tivey A, Basutkar P, Lee J, Edbali O . Search and sequence analysis tools services from EMBL-EBI in 2022. Nucleic Acids Res. 2022; 50(W1):W276-W279. PMC: 9252731. DOI: 10.1093/nar/gkac240. View

18.

Bolger A, Lohse M, Usadel B . Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics. 2014; 30(15):2114-20. PMC: 4103590. DOI: 10.1093/bioinformatics/btu170. View

19.

Jdeed G, Morozova V, Kozlova Y, Tikunov A, Ushakova T, Bardasheva A . StM171, a Bacteriophage That Affects Sensitivity to Antibiotics in Host Bacteria and Their Biofilm Formation. Viruses. 2023; 15(12). PMC: 10747581. DOI: 10.3390/v15122455. View

20.

Van den Mooter M, Swings J . Numerical analysis of 295 phenotypic features of 266 Xanthomonas strains and related strains and an improved taxonomy of the genus. Int J Syst Bacteriol. 1990; 40(4):348-69. DOI: 10.1099/00207713-40-4-348. View