Periodic Genotype Shifts in Clinically Prevalent Mycoplasma pneumoniae Strains in Japan

Nationwide increases in <i>Mycoplasma pneumoniae</i> pneumonia cases in Japan were reported in 2011, 2012, 2015, and 2016. In this study, we isolated 554 <i>M. pneumoniae</i> strains in 4 areas in Japan (Kanagawa, Okayama, Osaka, and Saitama) between 2006 and 2019, and performed genotyping analysis. More than 80% of the strains isolated in 2011 and 2012 harbored type 1 <i>p1</i> adhesin gene; however, strains harboring type 2 or its variant <i>p1</i> gene increased in 2015 and 2016 and dominated after 2017. These findings suggested that a shift in the prevalent genotype of <i>M. pneumoniae</i> clinical strains occurred recently in Japan. More than 90% of the type 1 strains isolated after 2010 harbored macrolide-resistance mutations in their 23S rRNA gene, whereas most type 2 lineage strains had no such mutations. Consequently, the increase in type 2 lineage strains in Japan has reduced the macrolide resistance rate of clinical <i>M. pneumoniae</i> strains. During this analysis, we also identified <i>M. pneumoniae</i> strains carrying a novel variant type 1 <i>p1</i> gene, and we classified it as type 1b. We then sequenced the genomes of 81 selected <i>M. pneumoniae</i> strains that we collected between 1976 and 2017 in Japan, and compared them with 156 <i>M. pneumoniae</i> genomes deposited in public databases to provide insights into the interpretation of <i>M. pneumoniae</i> genotyping methods, including <i>p1</i> typing, multiple-locus variable-number tandem repeat analysis (MLVA), multi-locus sequence typing (MLST), and typing by 8 single-nucleotide polymorphism markers (SNP-8). As expected, <i>p1</i> typing, MLST, and SNP-8 results exhibited good correlation with whole-genome SNP analysis results in terms of phylogenetic relationships; however, MLVA typing results were less comparable to those of the other methods. MLVA may be useful for the discrimination of strains derived from a single outbreak within a limited area; however, is not reliable for classification of strains collected from distantly separated areas at different time points. This study showed the usefulness of genome-based comparison of <i>M. pneumoniae</i> for molecular epidemiology. Genome sequencing of more strains will improve our understanding of global propagation routes of this pathogen and evolutionary aspects of <i>M. pneumoniae</i> strains.