Volume: 2 Issue: 4
Year: 2025, Page: 163-169, Doi: https://doi.org/10.71325/ajjms.v2i4.2 5.64
Received: Oct. 17, 2025 Accepted: Dec. 4, 2025 Published: Dec. 31, 2025
Introduction: A common source of nosocomial infections, Klebsiella pneumoniae has a high morbidity and fatality rate, particularly in immunocompromised patients and infants. Public health is seriously threatened by its multidrug-resistant (MDR) strains. Despite therapy, the death rate from hospital-acquired pneumonia caused by K. pneumoniae is higher than 50%. The newly discovered species Klebsiella spallanzanii (Ko3 phylogroup) and K. oxytoca have recently become clinical concerns. Bacteriophage therapy is a promising alternative in light of the growing antibiotic resistance, however its effectiveness may be hampered by bacterial defence mechanisms. In order to improve phage therapy tactics, this work attempts to describe the defence mechanisms of K. spallanzanii. Methods: The three webservers PADLOC, CRISPRCasFinder, and DefenseFinder were used to analyse the defence mechanisms of Klebsiella spallanzanii, which was isolated from a Chinese patient suffering from urinary tract infections. DefenseFinder checks for a variety of defence mechanisms, CRISPRCasFinder finds CRISPR-Cas systems, and PADLOC finds prokaryotic antiviral defence systems. These methods were used to map and categorise the strain's defence mechanisms using genomic data. Results: Klebsiella spallanzanii has a strong anti-phage arsenal, as evidenced by the discovery of a CRISPR-Cas system and seven other defence mechanisms, including as restriction-modification, abortive infection, and toxin-antitoxin systems. Interpretation & conclusions: The discovery of seven additional defence systems, including CRISPR-Cas, indicates that K. spallanzanii has a variety of defence mechanisms against phage invasion, which may limit the effectiveness of bacteriophage therapy. These results demonstrate how intricate bacterial defences are, requiring specialised phage designs to avoid or interfere with these systems.
Keywords: <I>Klebsiella pneumoniae</I>, <I>K. oxytoca</I>, <I>Klebsiella spallanzanii</I>, Immunocompromised individuals, PADLOC webserver, CRISPRCasFinder
1. Frost LS, Leplae, R, Summers AO, Toussaint A. Mobile genetic elements: the agents of open source evolution. Nature Reviews Microbiology. 2005; 3 (9). Available from: https://doi.org/10.1038/nrmicro1235
2. Rocha EP, Bikard D. Microbial defenses against mobile genetic elements and viruses: Who defends whom from what?. PLOS Biology. 2022; 20 (1). Available from: https://doi.org/10.1371/journal.pbio.3001514
3. Mayo-Muñoz D, Pinilla-Redondo R, Birkholz N, Fineran PC. A host of armor: Prokaryotic immune strategies against mobile genetic elements. Cell Reports. 2023; 42 (7). Available from: https://doi.org/10.1016/j.celrep.2023.112672
4. Smith WPS, Wucher BR, Nadell CD, Foster KR. Bacterial defences: mechanisms, evolution and antimicrobial resistance. Nature Reviews Microbiology. 2023; 21 (8). Available from: https://doi.org/10.1038/s41579-023-00877-3
5. Bernheim A, Sorek R. The pan-immune system of bacteria: antiviral defence as a community resource. Nature Reviews Microbiology. 2020; 18 (2). Available from: https://doi.org/10.1038/s41579-019-0278-2
6. Kitts PA, Church DM, Thibaud-Nissen F, Choi J, Hem V, Sapojnikov V, et al. Assembly: a resource for assembled genomes at NCBI. Nucleic Acids Research. 2016; 44 (D1). Available from: https://doi.org/10.1093/nar/gkv1226
7. Payne LJ, Meaden S, Mestre MR., Palmer C, Toro N, Fineran PC, et al. PADLOC: a web server for the identification of antiviral defence systems in microbial genomes. Nucleic Acids Research. 2022; 50 (W1). Available from: https://doi.org/10.1093/nar/gkac400
8. Couvin D, Bernheim A, Toffano-NiocheC, Touchon M, Michalik J, Néron B, et al CRISPRCasFinder, an update of CRISRFinder, includes a portable version, enhanced performance and integrates search for Cas proteins. Nucleic Acids Research. 2018; 46 (W1). Available from: https://doi.org/10.1093/nar/gky425
9. Tesson F, Hervé A, Mordret E, Touchon M, d'Humières C, Cury J, et al. Systematic and quantitative view of the antiviral arsenal of prokaryotes. Nature Communications. 2022; 13 (1). Available from: https://doi.org/10.1038/s41467-022-30269-9
10. Néron B, Denise R, Coluzzi C, Touchon, M, Rocha EPC, Abby SS, et al MacSyFinder v2: Improved modelling and search engine to identify molecular systems in genomes. Peer Community Journal. 2023; 3 Available from: https://doi.org/10.24072/pcjournal.250
11. Tesson F, Planel R, Egorov AA, Georjon H, Vaysset H, Brancotte, et al A Comprehensive Resource for Exploring Antiphage Defense: DefenseFinder Webservice,Wiki and Databases. Peer Community Journal. 2024; 4 Available from: https://doi.org/10.24072/pcjournal.470
12. Yang J, Long H, Hu Y, Feng Y, McNally A, Zong Z. <I>Klebsiella oxytoca</I> Complex: Update on Taxonomy, Antimicrobial Resistance, and Virulence. Clinical Microbiology Reviews. 2022; 35 (1). Available from: https://doi.org/10.1128/cmr.00006-21
13. Li HY, Kao CY, Lin WH, Zheng PX, Yan JJ, Wang MC, et al. Characterization of CRISPR-Cas Systems in Clinical <I>Klebsiella pneumoniae</I> Isolates Uncovers Its Potential Association With Antibiotic Susceptibility. Frontiers in Microbiology. 2018; 9 Available from: https://doi.org/10.3389/fmicb.2018.01595
14. Zhou Y, Tang Y, Fu P, Tian D, Yu L, Huang Y, et al The type I-E CRISPR-Cas system influences the acquisition of <I>blaKPC</I>-IncF plasmid in <I>Klebsiella pneumonia</I>. Emerging Microbes & Infections. 2020; 9 (1). Available from: https://doi.org/10.1080/22221751.2020.1763209
15. Ostria-Hernández ML, Sánchez-Vallejo CJ, Ibarra JA, Castro-Escarpulli G. Survey of clustered regularly interspaced short palindromic repeats and their associated Cas proteins (CRISPR/Cas) systems in multiple sequenced strains of Klebsiella pneumoniae. BMC Research Notes. 2015; 8 (1). Available from: https://doi.org/10.1186/s13104-015-1285-7
16. Marraffini LA. Impact of CRISPR Immunity on the Emergence of Bacterial Pathogens. Future Microbiology. 2010; 5 (5). Available from: https://doi.org/10.2217/fmb.10.38
17. Kadkhoda H, Gholizadeh P, Kafil HS, Ghotaslou R, Pirzadeh T, Rezaee MA, et al Role of CRISPR-Cas systems and anti-CRISPR proteins in bacterial antibiotic resistance. Heliyon. 2024; 10 (14). Available from: https://doi.org/10.1016/j.heliyon.2024.e34692
18. Agapov A, Baker KS, Bedekar P, Bhatia RP, Blower TR, Brockhurst MA, et al. Multi-layered genome defences in bacteria. Current Opinion in Microbiology. 2024; 78 Available from: https://doi.org/10.1016/j.mib.2024.102436
19. Gholizadeh O, Ghaleh HEG, Tat M, Ranjbar R, Dorostkar R. The potential use of bacteriophages as antibacterial agents against <I>Klebsiella pneumoniae</I>. Virology Journal. 2024; 21 (1). Available from: https://doi.org/10.1186/s12985-024-02450-7
© 2025 Published by Laxmi Memorial Education Trust. This is an open-access article under CC BY 4.0 license. (https://creativecommons.org/licenses/by/4.0/)
Ashraf A, Jeet A, Raju M, Prathiksha MA, Sudeepthi M, Kumar CS. In-Silico Systems Biology Analysis of the Klebsiella spallanzanii Defensome Against Bacteriophages. AJ J Med Sci 2025;2(4):163-169