Introduction: Proteus mirabilis is a Gram-negative bacterium recognized for its unique swarming motility, urease activity, and propensity to cause urinary tract infections. Early proteomic analysis on four strains indicated that, unlike other Gram-negative bacteria, P. mirabilis may not exhibit significant variation in gene content. However, there has not been a focused analysis of large numbers of P. mirabilis genomes from various sources. Our objective was to perform the first large scale genomic analysis of P. mirabilis to understand how bacterial diversity may impact if an isolate is recovered from a urinary or non urinary source. Methods: We performed comprehensive genomic analysis on 2,060 Proteus genomes. We sequenced the genomes of 893 clinical isolates from three large US academic medical centers, and also included 1,006 genomes from NCBI Assembly and 161 genomes assembled from Illumina reads previously uploaded to NCBI SRA. We used average nucleotide identity to delineate species and subspecies, core genome phylogenetic analysis to identify clusters of highly related P. mirabilis genomes, and pan-genome annotation to identify genes of interest not present in the model P. mirabilis strain HI4320. Results: Proteus is composed of 10 named species and 5 uncharacterized genomospecies. P. mirabilis can be subdivided into three subspecies; subspecies 1 represented 96.7% (1,822/1,883) of all genomes. The P. mirabilis pan-genome includes 15,399 genes outside of HI4320, and 34.3% (5,282/15,399) of these genes have no annotation. Subspecies 1 is composed of several highly related clonal groups. Prophages and genetic elements encoding putatively extracellular-facing proteins are associated with clonal groups. Uncharacterized outside of P. mirabilis HI4320 genes with homology to known virulence-associated operons can be identified within the pan-genome. Conclusions: Similar to other Gram-negative bacteria, P. mirabilis has a mosaic genome with a linkage between phylogenetic position and accessory genome content. Beyond what is represented in the model strain HI4320, P. mirabilis encodes a variety of genes that may impact host-microbe dynamics. The diverse, whole-genome characterized strain bank from this work can be used in conjunction with reverse genetic and infection models to better understand the impact of accessory genome content on bacterial physiology. SOURCE OF Funding: RFP received project support from Academy of Clinical Laboratory Physicians and Scientists Young Investigator Grant Program, and salary support from American Urologic Association Research Scholar Program.
