Makarova, K. S., Wolf, Y. I., Snir, S. & Koonin, E. V. Defense islands in bacterial and archaeal genomes and prediction of novel defense systems. J. Bacteriol. 193, 6039–6056 (2011).
Article PubMed PubMed Central Google Scholar
Vassallo, C. N., Doering, C. R., Littlehale, M. L., Teodoro, G. I. C. & Laub, M. T. A functional selection reveals previously undetected anti-phage defence systems in the E. coli pangenome. Nat. Microbiol. 7, 1568–1579 (2022).
Article PubMed PubMed Central Google Scholar
Doron, S. et al. Systematic discovery of anti-phage defense systems in the microbial pan-genome. Science 359, eaar4120 (2018).
Article PubMed PubMed Central Google Scholar
Gao, L. et al. Diverse enzymatic activities mediate antiviral immunity in prokaryotes. Science 369, 1077–1084 (2020).
Article PubMed PubMed Central Google Scholar
Elmahdi, S., DaSilva, L. V. & Parveen, S. Antibiotic resistance of Vibrio parahaemolyticus and Vibrio vulnificus in various countries: a review. Food Microbiol. 57, 128–134 (2016).
Lei, T. et al. Prevalence, virulence, antimicrobial resistance, and molecular characterization of fluoroquinolone resistance of Vibrio parahaemolyticus from different types of food samples in China. Int. J. Food Microbiol. 317, 108461 (2020).
Li, L. et al. Comparative genomic analysis of clinical and environmental strains provides insight into the pathogenicity and evolution of Vibrio parahaemolyticus. BMC Genomics 15, 1135 (2014).
Article PubMed PubMed Central Google Scholar
Paudyal, N. et al. A meta-analysis of major foodborne pathogens in chinese food commodities between 2006 and 2016. Foodborne Pathog. Dis. 15, 187–197 (2018).
Johnson, M. C. et al. Core defense hotspots within Pseudomonas aeruginosa are a consistent and rich source of anti-phage defense systems. Nucleic Acids Res. 51, 4995–5005 (2023).
Article PubMed PubMed Central Google Scholar
Holmes, A. J. et al. The gene cassette metagenome is a basic resource for bacterial genome evolution. Environ. Microbiol. 5, 383–394 (2003).
Boucher, Y., Labbate, M., Koenig, J. E. & Stokes, H. W. Integrons: mobilizable platforms that promote genetic diversity in bacteria. Trends Microbiol. 15, 301–309 (2007).
Richard, E., Darracq, B., Loot, C. & Mazel, D. Unbridled integrons: a matter of host factors. Cells 11, 925 (2022).
Article PubMed PubMed Central Google Scholar
Bouvier, M., Demarre, G. & Mazel, D. Integron cassette insertion: a recombination process involving a folded single strand substrate. EMBO J. 24, 4356–4367 (2005).
Article PubMed PubMed Central Google Scholar
Nivina, A., Escudero, J. A., Vit, C., Mazel, D. & Loot, C. Efficiency of integron cassette insertion in correct orientation is ensured by the interplay of the three unpaired features of attC recombination sites. Nucleic Acids Res. 44, 7792–7803 (2016).
Article PubMed PubMed Central Google Scholar
Bouvier, M., Ducos-Galand, M., Loot, C., Bikard, D. & Mazel, D. Structural features of single-stranded integron cassette attC sites and their role in strand selection. PLoS Genet. 5, e1000632 (2009).
Article PubMed PubMed Central Google Scholar
Mazel, D. Integrons: agents of bacterial evolution. Nat. Rev. Microbiol. 4, 608–620 (2006).
Ghaly, T. M. et al. Discovery of integrons in Archaea: platforms for cross-domain gene transfer. Sci. Adv. 8, eabq6376 (2022).
Article PubMed PubMed Central Google Scholar
Rowe-Magnus, D. A., Guerout, A.-M., Biskri, L., Bouige, P. & Mazel, D. Comparative analysis of superintegrons: engineering extensive genetic diversity in the Vibrionaceae. Genome Res. 13, 428–442 (2003).
Article PubMed PubMed Central Google Scholar
Heidelberg, J. F. et al. DNA sequence of both chromosomes of the cholera pathogen Vibrio cholerae. Nature 406, 477–483 (2000).
Article PubMed PubMed Central Google Scholar
Makino, K. et al. Genome sequence of Vibrio parahaemolyticus: a pathogenic mechanism distinct from that of V cholerae. Lancet 361, 743–749 (2003).
Kinch, L. N. et al. Insights into virulence: structure classification of the Vibrio parahaemolyticus RIMD mobilome. mSystems 8, e0079623 (2023).
Oliveira, P. H., Touchon, M. & Rocha, E. P. C. The interplay of restriction-modification systems with mobile genetic elements and their prokaryotic hosts. Nucleic Acids Res. 42, 10618–10631 (2014).
Article PubMed PubMed Central Google Scholar
Buongermino Pereira, M. et al. A comprehensive survey of integron-associated genes present in metagenomes. BMC Genomics 21, 495 (2020).
Article PubMed PubMed Central Google Scholar
Ghaly, T. M. et al. Functional enrichment of integrons: facilitators of antimicrobial resistance and niche adaptation. iScience 26, 108301 (2023).
Article PubMed PubMed Central Google Scholar
Ghaly, T. M. et al. The natural history of integrons. Microorganisms 9, 2212 (2021).
Article PubMed PubMed Central Google Scholar
Tesson, F. et al. Systematic and quantitative view of the antiviral arsenal of prokaryotes. Nat. Commun. 13, 2561 (2022).
Article PubMed PubMed Central Google Scholar
Steinegger, M. & Söding, J. MMseqs2 enables sensitive protein sequence searching for the analysis of massive data sets. Nat. Biotechnol. 35, 1026–1028 (2017).
Mahata, T. et al. Gamma-Mobile-Trio systems are mobile elements rich in bacterial defensive and offensive tools. Nat. Microbiol. 9, 3268–3283 (2024).
Loot, C. et al. Differences in integron cassette excision dynamics shape a trade-off between evolvability and genetic capacitance. mBio 8, e02296-16 (2017).
Article PubMed PubMed Central Google Scholar
Néron, B. et al. IntegronFinder 2.0: identification and analysis of integrons across bacteria, with a focus on antibiotic resistance in Klebsiella. Microorganisms 10, 700 (2022).
Article PubMed PubMed Central Google Scholar
Li, Y. et al. Prophage encoding toxin/antitoxin system PfiT/PfiA inhibits Pf4 production in Pseudomonas aeruginosa. Microb. Biotechnol. 13, 1132–1144 (2020).
Article PubMed PubMed Central Google Scholar
Owen, S. V. et al. Prophages encode phage-defense systems with cognate self-immunity. Cell Host Microbe 29, 1620–1633 (2021).
Article PubMed PubMed Central Google Scholar
Mazel, D., Dychinco, B., Webb, V. A. & Davies, J. A distinctive class of integron in the Vibrio cholerae genome. Science 280, 605–608 (1998).
Maffei, E. et al. Systematic exploration of Escherichia coli phage–host interactions with the BASEL phage collection.
Comments (0)