{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,1]],"date-time":"2026-10-01T18:02:10Z","timestamp":1790877730579,"version":"4.1.0"},"reference-count":43,"publisher":"Microbiology Society","issue":"10","license":[{"start":{"date-parts":[[2026,10,1]],"date-time":"2026-10-01T00:00:00Z","timestamp":1790812800000},"content-version":"unspecified","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Natural Science Foundation of Shanxi Province","award":["202403021221279"],"award-info":[{"award-number":["202403021221279"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2026,10,1]]},"abstract":"<jats:p>\n                    <jats:italic>Pseudomonas aeruginosa<\/jats:italic>\n                    is a major opportunistic pathogen with a remarkable capacity to develop resistance to multiple antibiotics. Although numerous resistance determinants have been characterized, broader genomic features associated with antibiotic resistance remain incompletely understood. In this study, more than 3\u2009million CDSs were extracted from 7,801\n                    <jats:italic>P<\/jats:italic>\n                    .\n                    <jats:italic>aeruginosa<\/jats:italic>\n                    genomes and clustered into a non-redundant CDS set comprising 87,744 centroid CDSs. Functional characterization of the CDSs was conducted using the Comprehensive Antibiotic Resistance Database, the Virulence Factor Database and KEGG annotations, and genome-wide enrichment analyses were performed to identify CDSs and functions associated with antibiotic resistance. Resistant strains generally carried more resistance- and virulence-associated CDSs than susceptible strains. Several CDSs encoding efflux pumps and antibiotic-modifying enzymes, e.g.\n                    <jats:italic>aad<\/jats:italic>\n                    genes,\n                    <jats:italic>tet(G<\/jats:italic>\n                    ) and\n                    <jats:italic>cmlA9<\/jats:italic>\n                    , were significantly enriched in resistant strains. Pathway enrichment analyses revealed antibiotic-specific functional signatures, including porphyrin metabolism, sulphur metabolism and folate-related pathways among aminoglycoside-resistant strains, and homologous recombination, DNA replication and mismatch repair pathways among levofloxacin-resistant strains. However, polysaccharide production was enriched among CDSs nominally significantly associated with susceptible strains. Random forest models demonstrated moderate to excellent predictive performance with external validation confirming robustness. Co-occurrence network analyses further identified associations among virulence genes, e.g. between lipopolysaccharide biosynthesis- and O-antigen-associated genes, as well as associations between resistance determinants and virulence-associated genes, such as\n                    <jats:italic>\u03b2<\/jats:italic>\n                    -lactam resistance and iron acquisition genes. These findings revealed antibiotic-specific gene and pathway signatures, enabled the prediction of antibiotic resistance using genomic features and revealed potential genomic linkages between canonical resistance determinants and other resistance-associated features.\n                  <\/jats:p>","DOI":"10.1099\/mgen.0.001854","type":"journal-article","created":{"date-parts":[[2026,10,1]],"date-time":"2026-10-01T17:24:01Z","timestamp":1790875441000},"source":"Crossref","is-referenced-by-count":0,"title":["Genomic signatures associated with antibiotic resistance and predictive modelling in Pseudomonas aeruginosa"],"prefix":"10.1099","volume":"12","author":[{"given":"Jianghong","family":"Cao","sequence":"first","affiliation":[{"name":"The Critical Care Medicine Department of Shanxi Provincial People\u2019s Hospital, Heping Branch, Taiyuan, 030001, PR China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Gangli","family":"Zhang","sequence":"additional","affiliation":[{"name":"The Neurosurgery Department of Shanxi Provincial People\u2019s Hospital, Taiyuan, 030001, PR China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Dongdong","family":"Xue","sequence":"additional","affiliation":[{"name":"The Critical Care Medicine Department of Shanxi Provincial People\u2019s Hospital, Heping Branch, Taiyuan, 030001, PR China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Dan","family":"Gao","sequence":"additional","affiliation":[{"name":"The Critical Care Medicine Department of Shanxi Provincial People\u2019s Hospital, Heping Branch, Taiyuan, 030001, PR China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xiaoyang","family":"Li","sequence":"additional","affiliation":[{"name":"The Critical Care Medicine Department of Shanxi Provincial People\u2019s Hospital, Heping Branch, Taiyuan, 030001, PR China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jinlin","family":"Guo","sequence":"additional","affiliation":[{"name":"The Pharmacy Department of Shanxi Provincial People\u2019s Hospital, Taiyuan, 030001, PR China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Peng","family":"Dai","sequence":"additional","affiliation":[{"name":"The Hepato-Pancreatic-Biliary Surgery Department of Shanxi Provincial People\u2019s Hospital, Taiyuan, 030001, PR 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