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Tuesday, 6 December 2016

Metagenomics can accelerate early detection of Food borne bacterial threats

Microbiologists use next-generation sequencing technology to identify a bacterial DNA fingerprint. (Credit: Centers for Disease Control and Prevention).

Metagenomics, a new field of study can accelerate the diagnosis of bacterial outbreaks where public health officials can identify potential bacteria in food borne disease in a single day. The methodology also able to answer about the co-infection with seconday microbes playing infective role.

Georgia Institute of Technology researchers along with U.S. Centers for Disease Control and Prevention (CDC) recently compared the new methodology against culture based technique from two different outbreaks of Salmonella. The metagenomics approach relies on DNA sequencing directly from the stool samples of the patients and analyzing them with Bioinformatics. This will not only pin point the bacterial culprit but also find out the secondary pathogen participating in co-infection.

The research was reported in the journal Applied and Environmental Microbiology on 23rd of November, 2016.

“When we receive the samples, we can move directly to characterizing them by sequencing the genomes of the microbes that are in the sample without waiting for conventional culturing techniques,” explained Kostas Konstantinidis, the Carlton Wilder Associate Professor in the Georgia Tech School of Civil and Environmental Engineering. “Using computational analysis, we can then say what the pathogen is and identify the variant, its virulence factors, even what antibiotic might be effective against it. That can usually be done in a single day.” (Quoted from Georgia Tech)

Conventional methods take 2-3days and problem lies when some bacteria do not grow on culture media. In metagenomics approach microbes are identified by sequencing all the DNA samples present in the sample and also specifies the relative abundance of such microorganisms with their virulence potential.

Researchers pointed out that in whole genome sequencing one has to make a pure culture to proceed forward for identification of the sick causing bacteria, but in metagenomics whole sample can be used for direct identification. Thus this method saves a lot of time with detailed diagnosis of thepatient.

Apart from benefits, the scientists also pointed out two challenges. First is the cost, where metagenomic study proved to be costlier than traditional methods, hence can be used when the situation seems to be complicated or urgent. Second challenge is it also sequence Human DNA where it covers about 99 percent of genomic data and this may be possible hindrance that accelerate the analysis.

Source: Georgia Tech


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