Twenty-eight divergent polysaccharide loci specifying within and amongst strain capsule diversity in three strains of Bacteroides fragilis

Comparison of the complete genome sequence of Bacteroides fragilis 638R originally isolated in the USA, was made with two previously sequenced strains isolated in the UK (NCTC 9343) and Japan (YCH46). The presence of 10 loci containing genes associated with polysaccharide biosynthesis, each including a putative Wzx flippase and Wzy polymerase, was confirmed in all three strains, despite a lack of cross-reactivity between NCTC 9343 and 638R surface polysaccharide-specific antibodies by immunolabelling and microscopy. Genomic comparisons revealed an exceptional level of polysaccharide biosynthesis locus diversity. Of the 10 divergent polysaccharide associated loci apparent in each strain, none are similar between NCTC9343 and 638R. YCH46 shares one locus with NCTC9343, confirmed by MAb labelling, and a second different locus with 638R, making a total of 28 divergent polysaccharide biosynthesis loci amongst the three strains. The lack of expression of the phase variable large capsule (LC) in strain 638R, observed in NCTC9343, is likely to be due to a point mutation that generates a stop codon within a putative initiating glycosyl transferase, necessary for the expression of the LC in NCTC9343. Other major sequence differences were observed to arise from different numbers and variety of inserted extra-chromosomal elements, in particular prophages. Extensive horizontal gene transfer has occurred within these strains despite the presence of a significant number of divergent DNA restriction and modification systems that act to prevent acquisition of foreign DNA. The level of amongst strain diversity in polysaccharide biosynthesis loci is unprecedented.