Comparative Genomic Analysis ofCampylobacter rectusand Closely Related Species

Abstract

ABSTRACTCampylobacter rectusis a gram-negative, anaerobic bacterium strongly associated with periodontitis. It also causes various extraoral infections and is linked to adverse pregnancy outcomes in humans and murine models.C. rectusand related oralCampylobactershave been termed “emergingCampylobacterspecies” because infections by these organisms are likely underreported. Previously, no comparative methods have been used to analyze more than singleC. rectusstrains and until recently, very fewC. rectusgenomes have been publicly available. More sequenced genomes and comparative analyses are needed to study the genomic features and pathogenicity of this species. We sequenced eight newC. rectusstrains and used comparative methods to identify regions of interest. An emphasis was put on the type III flagellar secretion system (T3SS), type IV secretion system (T4SS), and type VI secretion system (T6SS) because these protein complexes are important for pathogenesis in otherCampylobacterspecies. RAST, BV-BRC, and other bioinformatics tools were used to assemble, annotate, and compare these regions in the genomes. The pan-genome ofC. rectusconsists of 2670 genes with core and accessory genomes of 1429 and 1241 genes, respectively. All isolates analyzed in this study have T3SS and T6SS hallmark proteins, while five of the isolates are missing a T4SS system. Twenty-one prophage clusters were identified across the panel of isolates, including four that appear intact. Overall, significant genomic islands were found, suggesting regions in the genomes that underwent horizontal gene transfer. Additionally, the high frequency of CRISPR arrays and other repetitive elements has led to genome rearrangements across the strains, including in areas adjacent to secretion system gene clusters. This study describes the substantial diversity present amongC. rectusisolates and highlights tools/assays that have been developed to permit functional genomic studies. Additionally, we have expanded the studies onC. showaeT4SS since we have two newC. showaegenomes to report. We also demonstrate that unlikeC. rectus,C showaedoes not demonstrate evidence of intact T6SS except for the strain CAM. The only strain of sequencedC. massilensishas neither T4SS or T6SS.