USDA/FSIS/OPHS/Eastern Laboratory/Outbreaks Section
950 College Station Rd.
Athens, GA 30605
FSIS detection and characterization of STEC from raw beef products
In 1994 FSIS declared E. coli O157:H7 an adulterant in ground beef and began testing. In 2012, the adulterant STEC list expanded to include 6 additional serogroups (O26, O45, O103, O111, O121 and O145). FSIS’ definition of STECs requires them to not only possess Stx encoding genes but Eae encoding genes as well. In 2014 FSIS analyzed 19146 raw beef samples for E. coli O157:H7, and 4344 for non-O157 STEC. Of the samples analyzed 23 (0.12%) samples were positive for E. coli O157:H7 and 32 (0.74%) were positive for at least one STEC. In an effort to expand and refine its STEC testing program FSIS is collaborating with USDA-ARS researchers to identify non-top six STEC, and characterize these isolates based on virulence factors. In fiscal year 2015 FSIS began sequencing STEC isolates in real-time. The sequence data are shared not only with public health partners (CDC and FDA) but also publically via upload to the NCBI database. Limited metadata will be shared publically, and will not include information that can link sequences to an establishment. Since FSIS obtained its MiSeq instruments and began capability and capacity testing for whole genome sequencing, 30 STEC isolates have been sequenced. Their sequences were analyzed using CLC genomics and python scripts for stx and eae type and presence of virulence factors. Isolates contained a combination of stx type 1a and 2a, and 4 different eae alleles were detected in the subset (Beta 1, Epsilon 1, Gamma 1, and Gamma 2/Theta). The isolates were predominately stx type 1a, and eae type epsilon 1.