Abstract
Nationwide increases in Mycoplasma pneumoniae pneumonia cases in Japan were reported in 2011, 2012, 2015, and 2016. In this study, we isolated 554 M. pneumoniae 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 p1 adhesin gene; however, strains harboring type 2 or its variant p1 gene increased in 2015 and 2016 and dominated after 2017. These findings suggested that a shift in the prevalent genotype of M. pneumoniae 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 M. pneumoniae strains. During this analysis, we also identified M. pneumoniae strains carrying a novel variant type 1 p1 gene, and we classified it as type 1b. We then sequenced the genomes of 81 selected M. pneumoniae strains that we collected between 1976 and 2017 in Japan, and compared them with 156 M. pneumoniae genomes deposited in public databases to provide insights into the interpretation of M. pneumoniae genotyping methods, including p1 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, p1 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 M. pneumoniae for molecular epidemiology. Genome sequencing of more strains will improve our understanding of global propagation routes of this pathogen and evolutionary aspects of M. pneumoniae strains.
Highlights
Mycoplasma pneumoniae is a major cause of communityacquired pneumonia worldwide, especially in children (Parrott et al, 2016; Waites et al, 2017)
A total of 554 M. pneumoniae isolates were collected in 4 areas in Japan between 2006 and 2019 in this study (Figure 1A); 231 were isolated in Kanagawa, 115 in Okayama, 33 in Osaka, and 175 in Saitama (Figures 1B–E)
The 33 isolates from Osaka (Figure 1D) were cultured from 65 throat swabs (50.8%), which all tested positive for M. pneumoniae DNA by loop-mediated isothermal amplification (LAMP)
Summary
Mycoplasma pneumoniae is a major cause of communityacquired pneumonia worldwide, especially in children (Parrott et al, 2016; Waites et al, 2017). Epidemiological studies have revealed that epidemic peaks occur every 3–7 years (Yamazaki and Kenri, 2016). Between 2010 and 2012, large epidemics have been reported globally, including in Asian and European countries (Chalker et al, 2011; Nir-Paz et al, 2012; Yamazaki and Kenri, 2016). As β-lactams are not effective, macrolides are used as first-line drugs for the clinical treatment of M. pneumoniae pneumonia (Yamazaki and Kenri, 2016). Since 2000, macrolide-resistant M. pneumoniae (MRMP) strains have spread widely, especially in East-Asian countries (Meyer Sauteur et al, 2016; Pereyre et al, 2016)
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