SRA

Genomes of 16 Mycoplasma pneumoniae clinical isolates were sequenced and compared with 5 previously reported M. pneumoniae genome sequences of M129, M129-B7, FH, 309 and PO1 strains by comparative genomics approaches. Pangenomic analysis showed that 97% of pangenome sequence of 21 M. pneumoniae strains are shared by coregenome sequence of these strains, indicating highly closed pangenomic feature of this species, although there are deep genetic divergence between P1 ctyadhesin subtype 1 and 2 strain linages. From the comparison of coregenome sequences of 21 strains, we identified 1,370 single-nucleotide polymorphism (SNP) sites. Based on these SNPs, all of 21 strains were phylogenetically discriminated, demonstrating high discrimination power of whole-genome SNP analysis and its usability in M. pneumoniae strain classification. The results of whole-genome SNP analysis were largely consistent with MLVA typing, which is currently used as a standard classification method for M. pneumoniae strains. We also performed synonymous and nonsynonymous codon substitution rate (dN/dS) analysis using 21 M. pneumoniae genome sequences. Six ORFs, MPN049, MPN080, MPN278, MPN376, MPN496 and MPN571 were positively selected by this analysis. Five of these except for MPN278 were putative membrane-localized proteins and thought to be the candidates of proteins that undergo antigenic variation.