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Author Notes:

E-mail: zdx2@cdc.gov

Conceptualization: MHD SSM JMW. Data curation: HPD SSM JC. Formal analysis: HPD SSM JC. Funding acquisition: TDR DD JMW. Investigation: MHD HPD SSM AJB BJW JC. Methodology: MHD HPD SSM AJB BJW JC JMW. Project administration: MHD JMW. Software: HPD SSM JC. Supervision: MHD JMW. Validation: MHD HPD SSM. Visualization: MHD HPD SSM. Writing – original draft: MHD HPD SSM JMW. Writing – review & editing: MHD HPD SSM TDR DD JMW.

The authors have declared that no competing interests exist.

We thank Benjamin Metcalf, Reagan Kelly, and Yuan Li for helpful advice with bioinformatic analysis.

The findings and conclusions in this report are those of the authors and do not necessarily represent the official position of the Centers for Disease Control and Prevention.

Subjects:

Research Funding:

National Institutes of Health R01 AI098843-01 to Deborah Dean

This study was supported, in part, by funds made available through the Office of Advanced Molecular Detection (CDC) and Public Health Service grant from the National Institutes of Health R01 AI098843-01 (to DD and TDR).

Keywords:

  • Bacterial Typing Techniques
  • Bayes Theorem
  • Cluster Analysis
  • Computational Biology
  • Genetic Variation
  • Genome, Bacterial
  • High-Throughput Nucleotide Sequencing
  • Mycoplasma pneumoniae
  • Phylogeny
  • Polymorphism, Single Nucleotide
  • Sequence Analysis, DNA

Comprehensive bioinformatics analysis of Mycoplasma pneumoniae genomes to investigate underlying population structure and type-specific determinants

Tools:

Journal Title:

PLoS ONE

Volume:

Volume 12, Number 4

Publisher:

, Pages e0174701-e0174701

Type of Work:

Article | Final Publisher PDF

Abstract:

Mycoplasma pneumoniae is a significant cause of respiratory illness worldwide. Despite a minimal and highly conserved genome, genetic diversity within the species may impact disease. We performed whole genome sequencing (WGS) analysis of 107 M. pneumoniae isolates, including 67 newly sequenced using the Pacific BioSciences RS II and/or Illumina MiSeq sequencing platforms. Comparative genomic analysis of 107 genomes revealed >3,000 single nucleotide polymorphisms (SNPs) in total, including 520 type-specific SNPs. Population structure analysis supported the existence of six distinct subgroups, three within each type. We developed a predictive model to classify an isolate based on whole genome SNPs called against the reference genome into the identified subtypes, obviating the need for genome assembly. This study is the most comprehensive WGS analysis for M. pneumoniae to date, underscoring the power of combining complementary sequencing technologies to overcome difficult-to-sequence regions and highlighting potential differential genomic signatures in M. pneumoniae.

Copyright information:

This is an Open Access work distributed under the terms of the Creative Commons Universal : Public Domain Dedication License (http://creativecommons.org/publicdomain/zero/1.0/).

Creative Commons License

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