Genome Evolution to Penicillin Resistance in Serotype 3 Streptococcus pneumoniae by Capsular Switching

Abstract

Streptococcus pneumoniae isolates of serotype 3 were collected from cases of invasive pneumococcal disease (n = 124) throughout Japan between April 2010 and March 2013. A penicillin-resistant S. pneumoniae (PRSP) isolate from an adult patient, strain KK0981 of serotype 3, was identified among these strains. Whole-genome analysis characterized this PRSP as a recombinant strain derived from PRSP of serotype 23F with the cps locus (20.3 kb) replaced by that of a penicillin-susceptible strain of serotype 3.

Keywords: Streptococcus pneumoniae; capsular switching; gPRSP; serotype 3.

FIG 1

Circular representation of the genome of S. pneumoniae strain KK0981 (gPRSP/serotype 3, ST242) compared with the genomes of the KK0381 (gPISP/serotype 3, ST180) and KK1157 (gPRSP/serotype 23F, ST242) strains. KK0981 presented a chromosome 2,148,476 bp long, which contained 2164 coding sequences (CDSs), 12 rRNAs, and 58 tRNAs, showing an overall 39.6% GC content (accession number AP017971). Three contiguous sequences were obtained for KK0381, with a total length of 2,158,744 bp (i, 2,074,518 bp; ii, 43,298 bp; iii; 40,928 bp), and for KK1157, with a total length of 2,267,745 bp (i; 2,200,203 bp, ii, 36,583 bp, iii, 30,959 bp). The concentric circles represent the following information (from the outside in): circle 1, BLAST comparisons of the KK1157 draft genome against KK0981 (green); circle 2, BLAST comparisons of the KK0381 against KK0981 (blue); circle 3, annotated CDSs encoded on forward (green) and reverse (yellow) chromosomal strands, respectively; circle 4, distance from the putative origin of replication; circle 5, GC skew (black); circle 6, GC content (green/blue). Two arrows indicate the region with no homology between KK0981 and KK1157. The circular map was constructed using BRIG software and ArcWithColor software (12) with modification.

FIG 2

Comparison of the cps locus and its flanking region. Genomic organization of cps loci and their flanking regions in KK0381, KK0981, and KK1157 were aligned. OXC141 (NC_017592.1) and ATCC 700669 (NC_011900.1) were reference strains for the locus tag or gene names of type 3 and type 23F cps loci, respectively. Arrows represent CDSs and their functions in color: pbp2x (red), mraY (yellow), dexB (blue), transposase (gray), aliA (green), SPNOXC03640 (orange), pbp1a (pink), serotype 3 cps genes (cyan), serotype 23F cps genes (light green). Hatched arrows represent genotypic (g) resistant pbp genes. KK0981 of gPRSP of serotype 3 and ST242 was identified definitely as a transformant caused by recombination in regions from mraY to the SPOXC03640 gene of the serotype 3 pneumococcal strain of ST180 as a donor type and KK1157 of gPRSP of serotype 23F and ST242 derived from the Taiwan^23F-15 clone as a recipient type. The cyan or light green bar behind the CDSs represents the genetic background of KK0381 or KK1157, respectively, based upon SNV analysis. The alignment was generated with GenomeMatcher software (10); tnpIS630 is a pseudogene.