Comparative genomics of Mycoplasma pneumoniae isolated from children with pneumonia: South Korea, 2010–2016

• Main Authors: Joon Kee Lee, Moon-Woo Seong, Dongjin Shin, Jong-Il Kim, Mi Seon Han, Youbin Yeon, Sung Im Cho, Sung Sup Park, Eun Hwa Choi
• Format: Article
• Language: English
• Published: BMC 2019-11-01
• Series: BMC Genomics
• Subjects: Mycoplasma pneumoniae; Whole genome analysis; Comparative genomics
• Online Access: https://doi.org/10.1186/s12864-019-6306-9

Abstract Background Mycoplasma pneumoniae is a common cause of respiratory tract infections in children and adults. This study applied high-throughput whole genome sequencing (WGS) technologies to analyze the genomes of 30 M. pneumoniae strains isolated from children with pneumonia in South Korea during the two epidemics from 2010 to 2016 in comparison with a global collection of 48 M. pneumoniae strains which includes seven countries ranging from 1944 to 2017. Results The 30 Korean strains had approximately 40% GC content and ranged from 815,686 to 818,669 base pairs, coding for a total of 809 to 828 genes. Overall, BRIG revealed 99% to > 99% similarity among strains. The genomic similarity dropped to approximately 95% in the P1 type 2 strains when aligned to the reference M129 genome, which corresponded to the region of the p1 gene. MAUVE detected four subtype-specific insertions (three in P1 type 1 and one in P1 type 2), of which were all hypothetical proteins except one tRNA insertion in all P1 type 1 strains. The phylogenetic associations of 30 strains were generally consistent with the multilocus sequence typing results. The phylogenetic tree constructed with 78 genomes including 30 genomes from Korea formed two clusters and further divided into two sub-clusters. eBURST analysis revealed two clonal complexes according to P1 typing results showing higher diversity among P1 type 2 strains. Conclusions The comparative whole genome approach was able to define high genetic identity, unique structural diversity, and phylogenetic associations among the 78 M. pneumoniae strains isolated worldwide.