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Comparative Sequencing Study Sheds Light on Mycoplasma Pneumoniae Evolution

NEW YORK  (GenomeWeb) — Researchers at the University of Alabama, Birmingham have sequenced and compared 15 strains of the pathogen Mycoplasma pneumoniae to gain a better understanding of the physiology and pathogenicity of the bacterium. 

Their work, reported earlier this month in BMC Genomics, suggested, among other findings, that the bacterium's genome seems to be more stable than previously thought. 

M. pneumoniae is a common pathogen known to cause lower and upper respiratory tract infections in adults under 40 years of age. About 40 percent of all community-acquired pneumonia cases are caused by this pathogen, according to the authors of the study. 

Previously, there were only four complete genome sequences of M. pneumoniae isolates. Seeking to expand on this genetic knowledge, the UAB researchers used the Illumina MiSeq platform to perform complete next-generation sequencing on 15 strains of M. pneumoniae, including 11 clinical isolates and four reference ATCC strains collected over the past six decades from diverse localities. 

Based on observed P1 sequence polymorphisms, the 15 strains were divided into type 1 and type 2 subtypes. NGS sequencing reads were assembled de novo using ABySS v 1.3.7, a parallel assembler for short-read sequence data. Once the sequenced genomes were assembled and annotated, the strains were put through comparative analysis.

The researchers stated in the paper that learning more about the genetics of the different strains of M. pneumoniae and similar species could help lay the groundwork for the study of how highly specialized pathogens evolve. Expanding knowledge about these types of pathogens could also aid in better prevention and treatment options for diseases such as pneumonia.

Upon comparative analysis it became clear that there were about 1,500 SNP and indel variants existing between the type 1 and type 2 strains of the pathogen. Even so, the researchers found an overall high degree of sequence similarity among the strains with 99 percent sequence identity. Within each subtype group, the gene conservation was even stronger with less than 0.1 percent difference among strains of the same subtype. 

While the similarity between the strains was strong, there was also some notable variation — for instance, in the P1 and ORF6 genes, two adjacent genes associated with coding in the adhesin complex, which is necessary for successful colonization of the respiratory tract. These genes each have a long region of divergence between the type 1 and type 2 strains, while the rest of the protein sequence is almost completely identical. A few of the strains had variations in their codes for the CARDS toxin, an important factor that also contributes to M. pneumoniae's ability to colonize a niche in the host. Additionally, in all 15 genomes, the researchers identified multiple hsdS genes — the genes responsible for reading chemical markers that note inclusion of foreign DNA — with variable tandem repeat numbers, suggesting the importance of epigenetics in the bacterium. 

All of these observations seem to indicate that despite the strains' geographic separation, they may have only recently diverged. This goes against previous estimates based primarily on rRNA analysis that suggested a high mutation rate for mycoplasma species. The researchers concluded that further epigenetic studies of M. pneumoniae and related species might provide better insight into environmental effects on the pathogen's evolution.