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Sequencing Study Reveals Invasive Bacteria Epidemic Patterns

NEW YORK (GenomeWeb News) – In a paper scheduled to appear online this week in the Proceedings of the National Academy of Sciences, an international research team reported that they have sequenced and compared the genomes of nearly 100 group A Streptococcus strains — bacteria that can cause a severe form of necrotizing fasciitis, also known as flesh-eating disease — identifying features in the genomes that are linked to specific epidemics and patient phenotypes.

The researchers used an Illumina Genome Analyzer in a short-read approach to sequence 87 serotype M3 group A Streptococcus genomes from isolates collected over about 15 years during three consecutive epidemics in Ontario, Canada. They then compared the genomes with existing sequence data on another eight M3 isolates, analyzed SNP patterns using Sequenom's MassArray in more than 300 isolates, and compared expression patterns in a subset of the bacteria.

Information in the genomes is helping them define mutation rates between epidemics, find new genotypes, and determine relationships between bacterial genotypes and patient phenotypes, senior author James Musser, a pathology and infectious disease researcher and physician at Houston's Methodist Hospital Research Institute, told GenomeWeb Daily News.

"With this type of unique molecular portrait of the bacterial pathogen, we can more effectively develop drugs to prevent the spread of epidemics and construct novel diagnostic and treatment strategies," Musser said in a statement.

Although group A Streptococcus is usually susceptible to antibiotics, it can cause epidemics, which tend to occur periodically every four to seven years. Bacteria within this group are implicated in more than 10,000 serious, invasive infections in the US annually, the researchers noted, and cause hundreds of millions of infections around the world. Most of these infections are acquired within the community, Musser noted.

For the current study, researchers studied 344 group A Streptococcus belonging to the M3 serotype. The isolates had been collected in Ontario between early 1992 and late 2007 as part of a prospective, population-based study.

Using the Genome Analyzer, the team sequenced the 1.9 million base genomes of 87 of these isolates, which they subsequently compared with eight other isolates sequenced previously using a comparative microarray hybridization approach.

When they compared these M3 genomes with that of a reference strain called MGAS315, the researchers pinpointed 4,269 SNPs at 801 loci.

Even so, there were relatively few differences between each of the 95 invasive M3 strains tested: on average, just 49 SNPs and 11 small insertions and deletions differed from one strain to the next.

Still, while that genetic diversity is actually fairly low, some of these small genetic changes seem to dictate the type of infection a patient experiences. For instance, Musser said, the team identified a SNP in a strain from the second epidemic that seems to prevent that strain from causing the most severe form of necrotizing fasciitis.

And despite the limited genetic changes found in sequence data, the researchers found relatively widespread transcriptional changes when they compared the transcriptomes of four strains. Some of these expression changes also seem to relate to different clinical phenotypes, Musser noted.

"Until now, it has been a mystery why sometimes we see two opposing types of infection in patients who appear to have the same strain of flesh-eating bacteria," co-author Donald Low, chief microbiologist at Mount Sinai Hospital in Toronto and medical director of the Ontario Agency for Health Protection and Promotion's Public Health Laboratories, said in a statement. "Now, we understand in part why this happens."

In addition, the team's population structure analyses of the 95 sequenced strains (and later of all 344 of the strains from Ontario), suggest that, rather than re-emerging time after time, strains from each epidemic are genetically different from one another.

Musser said the team is currently doing a much larger study involving roughly a thousand strains collected in other parts of Canada and the US in collaboration with researchers from Europe and the UK.