{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,12]],"date-time":"2026-02-12T07:16:52Z","timestamp":1770880612066,"version":"3.50.1"},"reference-count":66,"publisher":"Frontiers Media SA","license":[{"start":{"date-parts":[[2026,2,12]],"date-time":"2026-02-12T00:00:00Z","timestamp":1770854400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["frontiersin.org"],"crossmark-restriction":true},"short-container-title":["Front. Immunol."],"abstract":"<jats:sec>\n                    <jats:title>Introduction<\/jats:title>\n                    <jats:p>\n                      <jats:italic>Providencia<\/jats:italic>\n                      species are emerging opportunistic pathogens associated with multidrug-resistant infections, yet their molecular defense mechanisms against phage or mobile genetic elements remain poorly characterized.\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Methods<\/jats:title>\n                    <jats:p>\n                      We present a comprehensive pan-genomic analysis of antiviral defense systems across 73 complete genomes (or chromosomes) of\n                      <jats:italic>Providencia stuartii<\/jats:italic>\n                      (n = 31) and\n                      <jats:italic>Providencia rettgeri<\/jats:italic>\n                      (n = 42), using DefenseFinder and CRISPRCasFinder. We further expanded analysis of contig\/scaffold assemblies to confirm conservation of core defense profiles across assembly types. BacMGEnet was employed to derive spacer-MGE interaction networks. Phylogenetic reconstruction and gene gain and loss modeling were performed to assess evolutionary patterns. To validate functionality, we experimentally tested the anti-phage activity of Gabija and Septu in heterologous\n                      <jats:italic>E. coli<\/jats:italic>\n                      assays, including point mutation analysis of conserved residues.\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>\n                      We reveal a diverse and complex defense repertoire dominated by restriction-modification systems and CRISPR-Cas Class 1 Type I-F, with significant contributions from toxin-antitoxin, GAPS2, PsyrTA, and Mokosh systems. Notably, defense genes are non-randomly distributed, often clustering into genomic islands suggestive of horizontal acquisition. Expanded analysis confirms conservation of core defense profiles across assembly types, supporting the utility of lower-quality data when complete genomes are scarce. Comparative analysis uncovers species-specific differences, with\n                      <jats:italic>P. rettgeri<\/jats:italic>\n                      harboring a higher abundance of non-CRISPR systems. BacMGEnet-derived spacer-MGE interaction networks further highlight species-specific dynamics, dense, hub-driven networks in\n                      <jats:italic>P. stuartii<\/jats:italic>\n                      versus sparser networks in\n                      <jats:italic>P. rettgeri<\/jats:italic>\n                      . Correlation analysis indicates potential associations between specific defense systems and virulence or antibiotic resistance genes. Phylogenetic reconstruction and gene gain and loss modeling further highlight dynamic evolutionary patterns. Both Gabija and Septu systems conferred robust, phage-specific protection; point mutations in conserved residues (GajA E465K and PtuB H53K) abolished defense.\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Discussion<\/jats:title>\n                    <jats:p>\n                      Our findings unveil a multi-layered, modular immune architecture in Providencia, providing crucial insights into its genome plasticity, phage resistance, and adaptation in clinical environments. This work establishes a foundation for understanding the role of defense systems in the evolution and pathogenicity of the\n                      <jats:italic>Providencia<\/jats:italic>\n                      genus.\n                    <\/jats:p>\n                  <\/jats:sec>","DOI":"10.3389\/fimmu.2026.1755933","type":"journal-article","created":{"date-parts":[[2026,2,12]],"date-time":"2026-02-12T06:51:03Z","timestamp":1770879063000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":0,"title":["Characterization and diversity of defense systems in Providencia pathogen"],"prefix":"10.3389","volume":"17","author":[{"given":"Xiaoyan","family":"Li","sequence":"first","affiliation":[{"name":"Department of Clinical Laboratory, Heping Branch, Shanxi Provincial People\u2019s Hospital","place":["Taiyuan, China"]},{"name":"Department of Blood Transfusion, Shanxi Provincial People\u2019s Hospital","place":["Taiyuan, 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Ultrasound, Beijing Chest Hospital, Capital Medical University & Beijing Tuberculosis and Thoracic Tumor Research Institute","place":["Beijing, China"]}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"1965","published-online":{"date-parts":[[2026,2,12]]},"reference":[{"key":"B1","doi-asserted-by":"publisher","DOI":"10.1038\/s41591-025-03629-3","article-title":"Changing climate and socioeconomic factors contribute to global antimicrobial resistance","volume":"31","author":"Li","year":"2025","journal-title":"Nat Med"},{"key":"B2","doi-asserted-by":"publisher","DOI":"10.1093\/cid\/ciae403","article-title":"Infectious diseases society of america 2024 guidance on the treatment of antimicrobial-resistant gram-negative infections","author":"Tamma","year":"2024","journal-title":"Clin Infect Dis"},{"key":"B3","doi-asserted-by":"publisher","first-page":"ciae403","DOI":"10.1016\/S0140-6736(24)02081-6","article-title":"Multidrug-resistant Gram-negative bacterial 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