Uncharacterized and lineage-specific accessory genes within the Proteus mirabilis pan-genome landscape

作者：Robert Potter, Kailun Zhang, Ben Reimler, Jamie Marino, Carol E. Muenks, Kelly Alvarado, Meghan A. Wallace, Lars F. Westblade, Erin McElvania, Melanie L. Yarbrough, David A. Hunstad, Gautam Dantas, Carey‐Ann D. Burnham · 发表于：mSystems · 年份：2023 · DOI：10.1128/msystems.00159-23 · 被引用次数：9 · 研究领域：Genomics and Phylogenetic Studies、Photosynthetic Processes and Mechanisms、Plant-Microbe Interactions and Immunity

ABSTRACT Proteus mirabilis is a Gram-negative bacterium recognized for its unique swarming motility and urease activity. A previous proteomic report on four strains hypothesized that, unlike other Gram-negative bacteria, P. mirabilis may not exhibit significant intraspecies variation in gene content. However, there has not been a comprehensive analysis of large numbers of P. mirabilis genomes from various sources to support or refute this hypothesis. We performed comparative genomic analysis on 2,060 Proteus genomes. We sequenced the genomes of 893 isolates recovered from clinical specimens from three large US academic medical centers, combined with 1,006 genomes from NCBI Assembly and 161 genomes assembled from Illumina reads in the public domain. We used average nucleotide identity (ANI) 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. Within our cohort, 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 putative assigned function. Subspecies 1 is composed of several highly related clonal groups. Prophages and gene clusters encoding...