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

Details

• Alternative Title:
  PLoS One
• Personal Author:
  Diaz, Maureen H. ; Desai, Heta P. ; Morrison, Shatavia S. ; Benitez, Alvaro J. ; Wolff, Bernard J. ; Caravas, Jason ; Read, Timothy D. ; Dean, Deborah ; Winchell, Jonas M.
• Description:
  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.
• Subjects:
  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

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• Source:
  PLoS One. 12(4).
• Pubmed ID:
  28410368
• Pubmed Central ID:
  PMC5391922
• Document Type:
  Journal Article
• Volume:
  12
• Issue:
  4
• Collection(s):
  CDC Public Access
• Main Document Checksum:
  urn:sha256:76a6bb9ef1f8490c7b81e2b8fca1e0aacbb065b6e301318bae2b692937589854
• Download URL:
  https://stacks.cdc.gov/view/cdc/45719/cdc_45719_DS1.pdf
• File Type:
  [PDF - 2.28 MB ]