Genomic sequencing gives insight into Shigella outbreaks

New study could have major impact on how disease outbreaks are managed.
By Amy Wallace  |  Dec. 23, 2016 at 1:13 PM
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SACRAMENTO, Dec. 23 (UPI) -- Researchers have sequenced and analyzed genomes from Shigella sonnei bacteria associated with major shigellosis outbreaks in California in 2014 and 2015.

Shigellosis causes abdominal pain, diarrhea and other gastrointestinal problems and results in roughly 500,000 infections, 6,000 hospitalizations and 70 deaths in the United States each year.

A team from UC Davis and the California Department of Public Health conducted the first major whole-genome study of S. sonnei strains in North America to gain insight into how the bacteria acquired virulence and antibiotic resistance, and to show the California strains' relationship to other strains throughout the world.

"If you have an outbreak and you want to know what is causing a particular problem, like antibiotic resistance, sequencing the genome can identify the genes involved," Jonathan Eisen, professor with appointments in the Department of Medical Microbiology and Immunology and the Department of Evolution and Ecology at UC Davis and collaborator on the study, said in a press release. "Eventually, we should be able to sequence whole genomes of bacteria to support patient care."

S. sonnei is responsible for most shigellosis outbreaks throughout the world. The team from the Microbial Diseases Laboratory at CDPH sequenced the genomes of 68 isolates, including samples from the California outbreaks and historical strains from California, Asia and elsewhere.

Researchers found two clusters in the outbreaks: one that struck San Diego and the San Joaquin Valley and another that struck the San Francisco Bay area. The San Diego/San Joaquin strain has been in California since 2008 but some of the isolates had been infected with a bacteriophage that carried a Shiga toxin, or STX, gene found in more virulent strains.

"Shigella sonnei bacteria normally cause a less severe disease and are not known to produce Shia toxin," Dr. James Watt, chief, Division of Communicable Disease Control at CDPH, said in a press release. "The toxin gene was most likely acquired by Shigella sonnei via genetic exchanges with E. coli and other Shigella species. Discovering a functional toxin gene was concerning in this large outbreak. Finding this gene raises concerns that illness due to Shigella sonnei could become more severe in the future."

The San Francisco strain did not contain STX but did have genes that gave it resistance to the fluoroquinolone class of antibiotics, which were similar to genes found in Southeast Asian strains.

"We know these movements of DNA can be important for the spread of antibiotic resistance, virulence and pathogenicity factors," Eisen said. "Having the genome data from outbreaks allows us to try to figure out what happened."

Researchers believe understanding genetic variants in pathogens can aid in antibiotic choices and improve hospital procedures.

The study was published in mSphere.

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