Tracking path of virulent bacteria via the web

December 05, 2001

ITHACA, N.Y. -- Cornell University food science, engineering and computer science students have joined forces to develop a web-based software and a database to track and compare genetic footprints, or characteristics, of bacteria.

For scientists who track the spread and sources of virulent bacteria, the students' PathogenTracker software reduces from days and hours to minutes the time spent making tedious strain comparisons.

"Before PathogenTracker, in this laboratory we were using three different databases and two spreadsheets," says Martin Wiedmann, Cornell assistant professor of food science. The food scientists sought the help of the computer science and engineering students, he says, because, "we knew what we wanted but we didn't know how to put the idea together."

The new database is novel in that it allows easy comparisons of strain characteristics and visual images of molecular subtypes (DNA fingerprints). The tool thus allows researchers quickly to assemble strain subtype data from different laboratories in order to analyze outbreaks and epidemics of many different infectious diseases and to assess the biodiversity of bacteria in general.

Before PathogenTracker, scientists used off-the-shelf database programs to track food-borne pathogens. But in 1999 Wiedmann first used his then-primitive database to help limit the death toll from a listeriosis outbreak. Between October 1998 and February 1999, more than 100 people became ill and 21 people died around the country after eating hot dogs contaminated with a rare strain of Listeria monocytogenes -- the deadliest of all food-borne bacteria.

Wiedmann's work allowed the Centers for Disease Control (CDC) in Atlanta to determine the cause of the outbreak. Consequently, the contaminated hot dogs were immediately recalled in what was to become one of history's largest food recalls. That early version of PathogenTracker found that seven of the 15 samples had identical genetic fingerprints, meaning that the same strain had caused the illness in seven people. The CDC also had noticed a rise in the number of listeriosis cases, but until Wiedmann's fingerprints, they did not know the strain to look for.

One of the students who developed the new database in Wiedmann's laboratory, Michael Chung '02, began by assembling the pathogen characteristics that the database would need. This included ribotype, DNA sequence and phenotype characteristics. Last fall, Chung began working with a team of computer science students who programmed the software, set up the web server and developed the software's image-recognition capabilities.

By the end of fall 2000, the program was complete. But, says Chung, it could not be transferred onto multiple computers and it was difficult to add new features. Over the past year, Chung, Cornell graduate student Steven Cai, undergraduate student Mike Bohlander '03 and Qi Sun, of the Cornell Computational Biology Service Unit, have greatly improved the program so that it can now be installed on larger web servers and handle a larger load of data and queries.

Currently within the database there are thousands of digital fingerprints, or "isolates," of food-borne pathogens, spoilage organisms and other bacteria such as L. monocytogenes, Pseudomonas, Vibrio parahaemolyticus, Streptococcus and lactic acid bacteria. Thibet Rungrotkitiyot M.E.E. '98, M.E. (industrial) '99, M.E. (computer science) '01, whose experience writing the image-recognition software for the Cornell world champion robotic soccer (RoboCup) team, developed the image recognition software in PathogenTracker that allows the visual comparisons to be made between the genetic fingerprints of the different strains.
-end-
Programming for PathogenTracker was developed by Xiaozheng Zhong, '00, M.E. (computer science) '01; David Wang, '00, M.E. (computer science) '01; Joe Cheng-Yu Huang '00, M.E. (computer science) '01; Rungrotkitiyot, Jian-Ning Janet Cheng '01; and Ernie Ho, M.E. (computer science) '01. The development of the library and search engine was completed by Cai, Chung, Wiedmann and staff researcher Roger Jagoda. This project is supported by a special research grant from the U.S. Department of Agriculture and by Dairy Management Inc., by way of Kathryn Boor, Cornell associate professor of food science.

Cornell University

Related Bacteria Articles from Brightsurf:

Siblings can also differ from one another in bacteria
A research team from the University of Tübingen and the German Center for Infection Research (DZIF) is investigating how pathogens influence the immune response of their host with genetic variation.

How bacteria fertilize soya
Soya and clover have their very own fertiliser factories in their roots, where bacteria manufacture ammonium, which is crucial for plant growth.

Bacteria might help other bacteria to tolerate antibiotics better
A new paper by the Dynamical Systems Biology lab at UPF shows that the response by bacteria to antibiotics may depend on other species of bacteria they live with, in such a way that some bacteria may make others more tolerant to antibiotics.

Two-faced bacteria
The gut microbiome, which is a collection of numerous beneficial bacteria species, is key to our overall well-being and good health.

Microcensus in bacteria
Bacillus subtilis can determine proportions of different groups within a mixed population.

Right beneath the skin we all have the same bacteria
In the dermis skin layer, the same bacteria are found across age and gender.

Bacteria must be 'stressed out' to divide
Bacterial cell division is controlled by both enzymatic activity and mechanical forces, which work together to control its timing and location, a new study from EPFL finds.

How bees live with bacteria
More than 90 percent of all bee species are not organized in colonies, but fight their way through life alone.

The bacteria building your baby
Australian researchers have laid to rest a longstanding controversy: is the womb sterile?

Hopping bacteria
Scientists have long known that key models of bacterial movement in real-world conditions are flawed.

Read More: Bacteria News and Bacteria Current Events
Brightsurf.com is a participant in the Amazon Services LLC Associates Program, an affiliate advertising program designed to provide a means for sites to earn advertising fees by advertising and linking to Amazon.com.