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To understand\n                      <jats:italic toggle=\"yes\">P. mirabilis<\/jats:italic>\n                      population genomics, we combined pangenome analysis,\n                      <jats:italic toggle=\"yes\">in silico<\/jats:italic>\n                      AMR prediction, and phenotypic antimicrobial susceptibility testing (AST) across 1,027\n                      <jats:italic toggle=\"yes\">P. mirabilis<\/jats:italic>\n                      genomes derived from human urine specimens. This revealed a mosaic pangenome driven by extensive accessory genome plasticity. Multilocus sequence typing (MLST) identified 213 MLSTs, with only 7% having \u226510 genomes, highlighting strain diversity. AMR gene profiles were largely lineage-specific, with 25% of genomes harboring resistances for &gt;6 antimicrobial subclasses. ST135 was identified as a highly MDR lineage, with 95% of genomes carrying \u226516 resistance genes. Mobile genetic element (MGE) analysis of 22 clinical isolates with complete, reference-level genomes revealed that Tn7 transposons, IS26-mediated genomic islands, and class 1 integrons act as vehicles for high AMR gene dissemination, including IS26-mediated gene stacking within a\n                      <jats:italic toggle=\"yes\">P. mirabilis<\/jats:italic>\n                      Genomic Resistance Island 1 (\n                      <jats:italic toggle=\"yes\">PmGRI1<\/jats:italic>\n                      ) in ST135 isolates. While the presence of genes like\n                      <jats:italic toggle=\"yes\">aph(3\u2032)-la<\/jats:italic>\n                      reliably predicted kanamycin resistance, discordance for antibiotics such as trimethoprim-sulfamethoxazole and chloramphenicol revealed that AMR gene stacking, regulatory context, and intrinsic mechanisms, like efflux pumps, modulate phenotypic outcomes. In summary, our study provides a comprehensive and phenotypic resolution of\n                      <jats:italic toggle=\"yes\">P. mirabilis<\/jats:italic>\n                      AMR, establishing that resistance architecture is lineage-structured, MGE-driven, and phenotypically non-deterministic. We emphasize the need to shift toward a standardized, genome-informed surveillance framework to translate into diagnostic and therapeutic strategies.\n                    <\/jats:p>\n                  <\/jats:sec>","DOI":"10.1128\/aac.01768-25","type":"journal-article","created":{"date-parts":[[2026,5,29]],"date-time":"2026-05-29T06:46:42Z","timestamp":1780037202000},"update-policy":"https:\/\/doi.org\/10.1128\/asmj-crossmark-policy-page","source":"Crossref","is-referenced-by-count":3,"title":["Pangenome analysis of\n                    <i>Proteus mirabilis<\/i>\n                    reveals lineage-specific antimicrobial resistance profiles and discordant genotype-phenotype correlations"],"prefix":"10.1128","volume":"70","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-1488-1569","authenticated-orcid":true,"given":"Namrata","family":"Deka","sequence":"first","affiliation":[{"name":"Department of Microbiology and Immunology, Jacobs School of Medicine and Biomedical 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