Molecular basis for avirulence of spontaneous variants of Porphyromonas gingivalis: Genomic analysis of strains W50, BE1 and BR1

Abstract The periodontal pathogen Porphyromonas gingivalis is genetically heterogeneous. However, the spontaneous generation of phenotypically different sub‐strains has also been reported. McKee et al. (1988) cultured P. gingivalis W50 in a chemostat during investigations into the growth and properties of this bacterium. Cell viability on blood agar plates revealed two types of non‐pigmenting variants, W50 beige (BE1), and W50 brown (BR1), in samples grown in a high‐hemin medium after day 7, and the population of these variants increased to approximately 25% of the total counts by day 21. W50, BE1 and BR1 had phenotypic alterations in pigmentation, reduced protease activity and haemagglutination and susceptibility to complement killing. Furthermore, the variants exhibited significant attenuation in a mouse model of virulence. Other investigators showed that in BE1, the predominant extracellular Arg‐gingipain was RgpB, and no reaction with an A‐lipopolysaccharide‐specific MAb 1B5 (Collinson et al., 1998; Slaney et al., 2006). In order to determine the genetic basis for these phenotypic properties, we performed hybrid DNA sequence long reads using Oxford Nanopore and the short paired‐end DNA sequence reads of Illumina HiSeq platforms to generate closed circular genomes of the parent and variants. Comparative analysis indicated loss of intact kgp in the 20 kb region of the hagA‐kgp locus in the two variants BE1 and BR1. Deletions in hagA led to smaller open reading frames in the variants, and BR1 had incurred a major chromosomal DNA inversion. Additional minor changes to the genomes of both variants were also observed. Given the importance of Kgp and HagA to protease activity and haemagglutination, respectively, in this bacterium, genomic changes at this locus may account for most of the phenotypic alterations of the variants. The homologous and repetitive nature of hagA and kgp and the features at the inverted junctions are indicative of specific and stable homologous recombination events, which may underlie the genetic heterogeneity of this species.