100K Pathogen Genome Project
Genomes for Public Health & Food Safety
Fri, 14 Apr 2017 15:07:01 +0000
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100K Pathogen Genome Project
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Multidrug-resistant abortive Campylobacter jejuni draft genome from Northern California
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Fri, 14 Apr 2017 15:06:42 +0000
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Weis, Allison M., Kristen A. Clothier, Bihua C. Huang, Nguyet Kong, and Bart C. Weimer. 2017. Multidrug-resistant abortive Campylobacter jejuni draft genome from Northern California. Genome Announcements 5(15):e 00171-17. (DOI:10.1128/genomeA.00171-17)
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Congratulations to Narine Arabyan on her newly published paper
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Mon, 11 Jul 2016 21:16:28 +0000
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Congratulations to Narine Arabyan on her recent paper published in Nature. The paper, Salmonella Degrades the Host Glycoalyx Leading to Altered Infection and Glycan Remodeling, can be read here.
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Coffee has a microbiome that alters flavor
/2016/03/coffee-has-a-microbiome-that-alters-flavor/
Tue, 29 Mar 2016 15:53:51 +0000
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contributed by Bart Weimer:
A fuel that keeps people and science moving is coffee. Humans have had a fascination with coffee for over 9000 years! We have long recognized that coffee flavor is extremely different among regions f the world, but also by brewing method. The exact same coffee variety can have different flavors depending on the soil, cultivation elevation, region of the world, roasting method, extraction temperature, and contact with metal during the brewing process. The popularity of coffee has boomed in recent years. Until recently, the microbiome of coffee was not widely characterized. Most knew that it was a fermentation process that altered the flavor, but a recent study by Ludlow et al. (2016) demonstrated that the flavor can be manipulated and tracked based on the fungal microbiome. This is a great step forward in the coffee world since the industry largely depends on the native biota to ferment the beans right after harvest. This could enable use of starter cultures to alter the microbiome so that it can direct the community diversity. Ludlow et al. demonstrated that the microbiome of coffee (oh and by the way, cocao) is directed by Saccharomyces cerevisiae – the common bread yeast!! They also demonstrated the the genomic variation was distinct between regions of the world and aligned with human migration around the world as we trekked out of Africa. Since coffee is native to Ethiopia they postulated that humans distributed coffee and variations in the microbiome around the world and that the microbiome adapted to the new locals. As a coffee snob, this work is fascinating because it starts to describe a microevolution for a commodity that humans have persisted with for thousands of years.
Ludlow, Catherine L., Gareth A. Cromie, Cecilia Garmendia-Torres, Amy Sirr, Michelle Hays, Colburn Field, Eric W. Jeffery, Justin C. Fay, Aimée M. Dudley. 2016. Independent Origins of Yeast Associated with Coffee and Cacao Fermentation. Current Biology ()
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100K Genome Project named in GenomeWeb Article
/2016/01/100k-genome-project-named-in-genomeweb-article/
Mon, 11 Jan 2016 14:54:51 +0000
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Outbreak Tracking, Infectious Disease Diagnostics Becoming Key Applications for NGS
Dec 28, 2015
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Monica Heger
Premium
NEW YORK (GenomeWeb) – In 2011, experts predicted that within five to 10 years, clinical microbiology labs would routinely sequence microbial genomes on a next-generation sequencing instrument, and that it would cost less than €100 ($109) to generate a complete bacterial genome.
Four years later, those predictions are starting to bear fruit.
“NGS is becoming more and more routine in clinical microbiology labs,” Ted Pak, a graduate student in Andrew Kasarkis’ lab at the Icahn School of Medicine at Mount Sinai, told GenomeWeb. His lab recently sequenced serial isolates of a patient with Stenotrophomonas maltophilia infection in order to determine whether the hospital’s recent uptick in infections was an outbreak or separate transmission events.
NGS offers a level of granularity that other technologies, like PCR or traditional strain typing methods like pulsed-field gel electrophoresis, do not. It is more comprehensive than PCR, able to analyze not just known genomic sites but the entire genome. And it has a much higher resolution than pulsed-field gel electrophoresis, which cannot say whether two hospital patients infected with the same bug acquired their infections separately, or whether their infections are related — a key difference that can impact measures the hospital takes to control the spread of infection.
In the US, there are a number of signs that point to the adoption of the technology within hospitals. The US Centers for Disease Control and Prevention, for example, has set aside $2.3 million in fiscal year 2016 to roll out NGS and bioinformatics technologies for the detection of infectious disease outbreaks in certain states.
The CDC has also been actively involved in a number of research projects. For instance, it collaborated with the Translational Genomics Research Institute to sequence multidrug resistant Klebsiella pneumoniae strains that produce carbapenemase enzyme, which confers resistance to the antibiotic carbapenem. These so-called KPC-producing organisms are fortunately still rare, although Brandi Limbago, deputy director of the CDC’s Division of Healthcare and Quality Promotion’s Clinical and Environmental Microbiology Branch, previously referred to them as “nightmare bacteria.” By focusing efforts to study the mechanism by which they’ve acquired drug resistance now, the hope is to stem the spread of these strains before they become problematic.
The CDC is also involved with a large-scale project to sequence the genomes of 100,000 foodborne pathogens. The University of California, Davis is spearheading the 100K Genomes Project in order to build up a public database of genomes to help identify genes associated with antibiotic resistance, persistence, and pathogenesis, as well as genes that provide information about the strain’s location, serotype, and its associated host.
The National Institutes of Health is also playing a significant role. Its interest in using the technology to sequence pathogens responsible for infections and hospital outbreaks was piqued in 2012, when NIH researchers used NGS to figure out how 18 patients at the NIH Clinical Center became infected with drug-resistant K. pneumoniae.
Comparing the genomes from all 18 patients helped determine a likely transmission route in which the first patient transmitted the bacteria to other patients on two different occasions. The sequencing results were even able to determine that transmission occurred from two different parts of her body.
Now, NIH researchers are testing whole-genome and amplicon sequencing-based protocols to diagnose microbial infections. Initially, they plan to test the methods on discarded portions of 250 samples that have received standard testing in the clinical microbiology lab in order to evaluate the utility of NGS for infectious disease diagnostics in the context of a routine hospital clinical microbiology lab, Karen Frank, chief of the microbiology service at the NIH Clinical Center, told GenomeWeb.
“Initial results are very promising,” she said in an email, and the team has now progressed to testing primary specimens. Nonetheless, she said, there are still a number of challenges for integrating NGS into clinical microbiology labs, including the “expertise required for data analysis and interpretation, the absence of commercially available push-button diagnostic systems, and regulatory issues relating to validation, quality control, reporting to the medical record, and genetic privacy.”
Modern microbiology
Across the Atlantic, researchers and public health officials in the UK are taking a systematic approach to moving NGS into clinical microbiology labs. For the last several years, members of the UK Clinical Research Collaboration have been sequencing pathogen genomes to build up genomic databases of various bugs. Recently, a group led by the University of Cambridge published a database of over 1,000 methicillin-resistant Staphylococcus aureusgenomes. The genomes came from 46 laboratories that had submitted clinical isolates to the British Society for Antimicrobial Chemotherapy. The database can now be used as a resource for future surveillance and outbreak investigations of MRSA, the authors wrote.
Aside from MRSA, the research team is building up databases of other pathogens, including vancomycin-resistant Streptococci, Sharon Peacock, a clinical microbiology professor at the University of Cambridge, previously told GenomeWeb.
Other researchers within the Modernising Medical Microbiology group at the University of Oxford are working on developing an NGS-based test for Mycobacterium tuberculosis. The group published a validation of the test in The Lancet this month, demonstrating that it was accurate, faster than traditional testing methods, and would cost about 7 percent less than current diagnostic tests.
Public Health England is now conducting a feasibility study on 2,000 samples to see if the test can be implemented in routine diagnostics, and the Modernising Medical Microbiology team is working on developing NGS-based tests for Escherichia coli and S. aureus.
Real-time tracking
Last summer, researchers put NGS technology to the ultimate test, deploying it in the midst of an ongoing outbreak of a rapidly spreading pathogen in mostly rural areas of Western Africa without major medical laboratory infrastructure.
In the midst of the Ebola outbreak, researchers with the Liberian Institute for Biomedical Research and the US Army Medical Research of Infectious Diseases (USAMRIID) set up a genome sequencing laboratory to help manage outbreaks of the virus.
Earlier this month, the team published whole-genome sequencing results of 140 Ebola isolates collected during the second wave of the outbreak in Liberia. The data indicated that most Liberian infections came from an isolate from Sierra Leone. The researchers also noted that the results suggested the second wave of the outbreak may have been different from the first wave, which began in March 2014, but fizzled out much more quickly than the second wave that began in May 2014.
Understanding the origin of an outbreak and how it spreads is important for figuring out how to manage and stem transmission, and could help better manage future outbreaks.
Some groups are pushing to implement newer nanopore sequencing technology that could generate whole-genome sequence data faster and in the field. Two groups from Europe and the US took the USB stick-sized MinIon from Oxford Nanopore Technologies to Guinea and Liberia to sequence Ebola isolates. Joshua Quick, a graduate student in Nick Loman’s lab at the University of Birmingham, set up three MinIon devices, a PCR machine, and four laptops at a Guinean hospital with no lab equipment aside from a refrigerator, freezer, and a back-up generator. Quick was able to generate Ebola sequence data from samples shipped in from sites just a few hours north of the hospital, and analyzed over a dozen samples in a couple of weeks.
Challenges
Despite the progress made this year, a number of challenges remain. First, although the MinIon is especially promising for tracking outbreaks in resource-poor areas in real time, the technology is still new and needs further validation before it can be routinely used.
Perhaps a more crucial hurdle will be to ensure that the vast amounts of pathogen sequence data are publicly available, according to Andrew Kasarskis, co-director of the Icahn Institute for Genomics and Multiscale Biology at Mount Sinai Hospital. His team is now sequencing clinical isolates of Clostridium difficile infections in attempt to develop a workflow for tracking infection in the hospital.
One problem with clinical data is that it is proprietary and often contains sensitive patient information, he said. But, if the hospitals and research groups work in isolation, the real insights into how pathogens spread and get transmitted, what types of antibiotic resistance elements are becoming more common, and detecting the start of an outbreak early will not be possible, he said.
For instance, if a patient with carbapenem-resistant Enterobacteriaceae was previously hospitalized in one state, but then a patient a different state becomes sick with the same strain, “you can say you’ve imported the bug from here to there,” he said. “But if those groups keep their data siloed, you wouldn’t know.”
Aside from data sharing, another challenge will be managing the sheer amount of data that is produced. Hospitals and clinical microbiology labs will “have to get used to the generation, storage, and interpretation of all that data,” Kasarskis said. “It’s not simple.”
These challenges are starting to be overcome though, Kasarskis said, as more and more clinical microbiology labs start testing NGS protocols. He predicted that such testing will be done both in large centralized laboratories as well as in hospitals.
Pak added that although PCR is a promising technology for rapid diagnostics, it “won’t give you as much information as sequencing.”
Click here for GenomeWeb
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UC Davis 100k Genome Project co-PI in Genome Canada’s $10 mil. grant
/2015/07/uc-davis-100k-genome-project-part-of-genome-canadas-10-mil-grant/
Tue, 28 Jul 2015 17:58:24 +0000
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Researchers from McGill and Laval universities will receive close to $10 million over the next four years for work that is designed to both identify and find natural solutions for the reducing the growth of the salmonella strains that cause human disease.
This is one of two Quebec-based research projects that will receive funding from Genome Canada and Génome Québec under the program Genomics and Feeding the Future.”
To read the full article, click here.
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FDA Demo Days Announced
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Thu, 18 Jun 2015 19:31:06 +0000
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The FDA Demo Days for the first ever Food Safety Challenge have been announced. Join us via live webcast on July 7, 2015 to see finalist UC Davis’ team presentation. The starting time is 12:00 pm, Eastern Daylight Time (EDT) Please notice the link below to sign in, (meeting ID: 278 279 836, meeting password: 07072015). Also, for anyone in the DC area who would like to go to demo days, it is now open to the public, you can register by clicking on the eventbrite link.
Live Webcast information
Eventbite public registration
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UC Davis/Mars Inc. FDA Food Safety Challenge Finalist News Articles
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Thu, 14 May 2015 21:04:26 +0000
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FDA Announcement
Food Safety News Article
Daily Democrat Article
The Packer Article
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UC Davis/Mars Inc. team advances to finals of FDA Food Safety Challenge
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Wed, 13 May 2015 21:12:29 +0000
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May 12th, 2015 @ 4:17 pm by Andy Fell
A team from the UC Davis School of Veterinary Medicine and scientists from Mars, Inc. has been selected as a finalist for the Food and Drug Administration Food Safety Challenge competition. UC Davis and four other finalists will travel to Washington D.C. this summer to participate in a technology “demo day” where the final winner will be selected.
The finalists were selected for potential breakthrough ideas on how to find disease-causing organisms in food – especially Salmonella in fresh, minimally processed produce. The FDA is also looking for solutions that can test for other microbial pathogens in other foods.
Food poisoning affects one in six Americans every year, according to the FDA. Salmonella alone causes over a million illnesses, thousands of hospitalizations and some 450 deaths a year. Yet identifying a small amount of harmful bacteria on produce, among many more that are harmless or even potentialy beneficial, is difficult.
Team members are: from the School of Veterinary Medicine, Professor Bart Weimer, graduate student Azarene Foutouhi and postdoc Dylan Storey; and Bob Baker and Peter Markwell, both senior scientists at Mars, Inc.
The UC Davis-Mars Inc. team entry features patented “high throughput captured concentration” technology invented by Weimer and further demonstrated through a research partnership with Mars Inc. for use in many foods. The test uses fluidized bed technology and beads that grab the bacteria from the food, and can recognize, detect and verify bacteria in less than four hours without the need for growing the microbes. This will provide the food industry with a test that reduces the time from about one week to less than one day.
“Our technology is sensitive, fast and accurate and allows us to test large sample volumes, which is needed by large food processing operations and has been lacking in the past,” said Weimer. “It doesn’t require the growing of bacteria which is time consuming.”
This first-ever FDA Food Safety Challenge was developed under the America Competes Reauthorization Act of 2010, which grants all federal agencies broad authority to conduct prize competitions to spur innovation, solve tough problems, and advance their core missions. A panel of food safety and pathogen detection experts from the FDA, the Centers for Disease Control and Prevention, and the U.S. Department of Agriculture judged the submissions, determined finalists, and will select a winner. The UC Davis-Mars Inc. team was awarded $20,000 from a total prize pool of $500,000, with the remaining pot to be distributed to the winner.
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