Open AccessEpidemiological analysis of pneumococcal strains isolated at Yangon Children’s Hospital in Myanmar via whole-genome sequencing-based methods
Author(s) -
M. Yamaguchi,
Hpoo Pwint Myo Win,
Kõtarõ Higashi,
M. Ono,
Yujiro Hirose,
Daisuke Motooka,
Daisuke Okuzaki,
Moe Moe Aye,
Moh Moh Htun,
Hlaing Myat Thu,
Shigetada Kawabata
Publication year - 2021
Publication title -
microbial genomics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 2.476
H-Index - 28
ISSN - 2057-5858
DOI - 10.1099/mgen.0.000523
Subject(s) - biology , multilocus sequence typing , serotype , streptococcus pneumoniae , molecular epidemiology , microbiology and biotechnology , penicillin , whole genome sequencing , typing , antibiotic resistance , virology , genome , genotype , genetics , gene , antibiotics
Streptococcus pneumoniae causes over one million deaths from lower respiratory infections per annum worldwide. Although mortality is very high in Southeast Asian countries, molecular epidemiological information remains unavailable for some countries. In this study, we report, for the first time, the whole-genome sequences and genetic profiles of pneumococcal strains isolated in Myanmar. We isolated 60 streptococcal strains from 300 children with acute respiratory infection at Yangon Children's Hospital in Myanmar. We obtained whole-genome sequences and identified the species, serotypes, sequence types, antimicrobial resistance (AMR) profiles, virulence factor profiles and pangenome structure using sequencing-based analysis. Average nucleotide identity analysis indicated that 58 strains were S. pneumoniae and the other 2 strains were Streptococcus mitis . The major serotype was 19F (11 strains), followed by 6E (6B genetic variant; 7 strains) and 15 other serotypes; 5 untypable strains were also detected. Multilocus sequence typing analysis revealed 39 different sequence types, including 11 novel ones. In addition, genetic profiling indicated that AMR genes and mutations spread among pneumococcal strains in Myanmar. A minimum inhibitory concentration assay indicated that several pneumococcal strains had acquired azithromycin and tetracycline resistance, whereas no strains were found to be resistant against levofloxacin and high-dose penicillin G. Phylogenetic and pangenome analysis showed various pneumococcal lineages and that the pneumococcal strains contain a rich and mobile gene pool, providing them with the ability to adapt to selective pressures. This molecular epidemiological information can help in tracking global infection and supporting AMR control in addition to public health interventions in Myanmar.