Genomic Approach Identifies Food Pathogens

A collaborative team led by scientists at Cornell University (Ithaca, NY, USA) adopted a genomic approach to identifying food-borne pathogens. They sequenced the genome of 47 samples of the bacteria, 20 that had been collected from human sources during an outbreak, and 27 control samples collected from human, food, animal and environmental sources before the outbreak.

The team developed the single nucleotide polymorphism (SNP) test that is specific to the Salmonella enterica strain that had caused a previous outbreak. The sequencing was performed on the SOLiD systems (Life Technologies, Foster City, CA). Pulsed Field Gel Electrophoresis (PFGE) was also performed. Overall, 969 SNP positions were found among the 82 isolates analyzed.

Three SNPs were found to be completely specific for the isolates associated with the outbreak clade.

This study demonstrates that massively parallel sequencing can be used to assess the population structure of highly clonal, outbreak-associated pathogens at single base resolution. Martin Wiedmann, DVM, PhD, a professor at Cornell said, "The use of genome sequencing methods to investigate outbreaks of food-borne bacterial diseases is relatively new, and holds great promise as it can help to identify the temporal, geographical and evolutionary origin of an outbreak. In particular, full genome sequence data may help to identify small outbreaks that may not be easily detected with lower resolution subtyping approaches.” The study was published online on October 14, 2011, in the journal Applied and Environmental Microbiology.

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