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

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Authors
Lee, Joon Kee; Seong, Moon-Woo; Shin, Dongjin; Kim, Jong-Il; Han, Mi Seon; Yeon, Youbin; Cho, Sung Im; Park, Sung Sup; Choi, Eun Hwa
Issue Date
2019-11-29
Publisher
BMC
Citation
BMC Genomics, 20(1):910
Keywords
Mycoplasma pneumoniaeWhole genome analysisComparative genomics
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.
ISSN
1471-2164
Language
English
URI
https://doi.org/10.1186/s12864-019-6306-9

http://hdl.handle.net/10371/164757
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College of Medicine/School of Medicine (의과대학/대학원)Pediatrics (소아과학전공)Journal Papers (저널논문_소아과학전공)
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