Reemergence of Plague

There has been abnormal upsurge in cases of plague, caused by the bacterium Yersinia pestis, in the United States this year (CDC). As of April 1st of this year, there have been 11 reported cases and 4 confirmed fatalities in the USA as of August 27th, 2015 (AP). Many of the cases have been tied to people who have traveled to Yosemite National Park (CDC).

 Plague is epidemic in populations of wild rodentssuch as prairie dogs in many western states. Transmission to humans can occur through infected fleabites, direct contact with body fluids, and inhalation of droplets from infected individuals. After initial exposure, symptoms including fever, malaise, nausea, abdominal pain, “bubos” or lymph node swellings and even pneumonia can occur(CDC).

Mortality rate of untreated plague infected patients is between 66 to 93 percent. However, prompt treatment with appropriate antibiotics greatly reduces mortality of the infected. Misdiagnosis of Y. pestis is a common problem when using some automated bacterial identification systems (CDC). Fast and accurate identification in patients appears key for successful treatment and recovery of the disease.


Kwit et al. (2015). Human plague. Morbidity and Mortality Weekly Report, 64(33), 918-919.

Price, M. (2015). Utah man dies from plague in 4th fatal case in US this year. AP. Retrieved from

Hidden dangers during Pool Season

Summer is the season when many people from many different demographics head to their local public pools and water parks to beat the heat. People aren’t the only comers to these watery playgrounds. They bring their microbiome with them. This is why pools are often treated with chemicals like chlorine and bromine derivatives in order to guard against the spread of waterborne pathogens. One group of pathogens that is resistant to such commonly utilized disinfectants is Cryptosporidium

Cryptosporidium is a genus of eukaryotic, unicellular parasites that causes cryptosporidiosis, a gastrointestinal disorder with symptoms including diarrhea. Cryptosporidiosis can even be fatal in those that are immunocompromised. Cryptosporidium have the ability to form tiny, nearly invisible cysts (oocysts) that are difficult to detect and destroy with standard water surveillance and treatment methods (CDC).

Cryptosporidium’s biological characteristics make it a public health hazard. According to the CDC, outbreaks of Cryptosporidium are on the increase. Cryptosporidium is not tested for routinely in most diagnostic labs. The need for a sensitive, specific, and accurate detection method for Cryptosporidium seems apparent.


CDC. 2015.  Parasites-Cryptosporidium.  Centers For Disease Control & Prevention.

Crawford, Chris.  2015.  Cryptosporidiosis Outbreaks on the Rise, CDC Warns. American Academy of Family Physicians. 

Rettner, Rachael. 2015. 'Crypto' Parasite Outbreaks Increasing in Pools Across US. LiveScience. 



GENIUS Metagenomics' Illumina Webinar Now Online!

Our webinar featuring our BaseSpace App, GENIUS Metagenomics is now online!  You can watch it here.  We provide a demo of our app and answer some questions afterward.  Try out GENIUS Metagenomics for yourself!  It is FREE to try for a limited period.

If you have any questions about our BaseSpace App, please email us at  And if you want more info on our company and our software, including our standalone and BaseSpace versions, go here to contact us and/or schedule your own demo.

Press Release: CosmosID GENIUS Metagenomics Application Now Available in Illumina BaseSpace Apps

Rockville, Maryland, March 9, 2015—CosmosID® today announced it has added GENIUS® Metagenomics to BaseSpace® Apps, the Illumina applications store and informatics community dedicated to advancing genomic analysis.

Rapid and accurate identification of bacteria, including pathogens, is essential to disease control, prevention, and treatment, microbiome analysis, food safety, quality assurance, environmental monitoring, and health and wellness.

The GENIUS Metagenomics application employs CosmosID’s curated genome database and high performance algorithms to obtain, in just minutes, accurate and actionable bacterial identification at the species, subspecies, and/or strain level.

“As the NGS market continues to expand and replace culture methods with whole genome shotgun sequence analysis, the CosmosID GENIUS product will enable Illumina customers to obtain results superior in speed, accuracy and precision,” said Brian Nimmo, President and CEO of CosmosID.

GENIUS Metagenomics identifies the entire bacterial population in a shotgun metagenomic sample within minutes, including discriminating pathogens from closely related species. This is accomplished even when an organism is present at low concentration and without requiring prior knowledge of diversity, complexity, or community composition of the sample. In brief, GENIUS Metagenomics provides accurate bacterial identification.

BaseSpace users can upload sequencing reads directly from an Illumina sequencer, local storage, or the Sequence Read Archive to the BaseSpace cloud and analyze their metagenomic data using the GENIUS Metagenomics application. After the analysis is completed, a report containing accurate bacterial identification to strain as well as its relative abundance is provided. An interactive visual graph of the results is included. “This essentially revolutionizes the process of microbial identification,” according to Dr. Rita Colwell, Founder and Chairman of CosmosID.

Informatics solutions available through BaseSpace Apps allow customers to utilize the tools from a growing community of academic, commercial, and open source providers.

About CosmosID

CosmosID®, based in Rockville, Maryland, is a bioinformatics company focused on rapid identification of microorganisms for molecular diagnostics, public health, food safety, agriculture, and environmental applications. The CosmosID GENIUS solution uses proprietary sequence analysis algorithms to accurately profile all microorganisms in a metagenomic sample employing next-generation DNA sequencing reads. CosmosID was founded in 2008 by Dr. Rita Colwell, former director of the National Science Foundation and currently Distinguished University Professor at the University of Maryland and Johns Hopkins University. CosmosID employs a team of expert genomics scientists, bioinformaticians and software engineers to continuously improve the GENIUS solution with innovation and expertise. To learn more please visit