Aggregatibacter actinomycetemcomitans evolves in vivo in patients with periodontal disease

2012-05-04Background: Periodontal pathogen Aggregatibacter actinomycetemcomitans exhibits marked variations in genomic content among strains. Such variations presumably arise from different evolution pathways of A. actinomycetemcomitans strains. However, it is not known whether genomic variation of A. actinomycetemcomitans may occur during short-term persistent infections in vivo. Hypothesis: A. actinomycetemcomitans may evolve in vivo in patients with periodontal disease. If true, the genomic variation may be related to the adaption mechanisms of the bacteria to the host. The information may provide insight to the mechanisms of persistent infection of A. actinomycetemcomitans in humans. Methods: Four pairs of A. actinomycetemcomitans strains (SCC393/A160, SCC1398/SCC4092, SCC2302/AAS4a, S23A/I23C) (henceforth referred to as "paired strains") recovered from four individuals respectively over a period of 0~10 years were subjected to (i) whole genome sequencing (WGS), (ii) phylogenetic analysis, (iii) comparative genomic hybridization (CGH) with an A. actinomycetemcomitans pan-genome microarray, and (iv) PCR analysis to confirm the mutations in selected genes between the paired strains. Results: Each paired strains were confirmed to derive from a recent ancestral strain by phylogenetic analysis of 150 core genes. Indications for short-term evolution were obtained from two sets of the paired strains. Two genes (encoding hypothetical proteins) in strain SCC2302 (the first strain) were not detected in strain AAS4a (isolated three years later). For the pair of S23A/I23C (isolated at the same time), S23A had ten genes that were not detected in I23C. These ten genes were found to be part of a 24.1 Kb plasmid in S23A. An intact serotype-specific gene cluster was found in serotype b antigen expressing S23A. In contrast, nontypeable I23C was found to have a 353-bp reversion in the gene cluster, which apparently has inactivated two ORFs of the cluster. Conclusion: A. actinomycetemcomitans genomes are largely stable during short-term persistent infections in humans, but may evolve via gene gains/losses or mutations