Interlaboratory evaluation of the FDA-ECID microarray for profiling Shiga toxin-producing Escherichia coli

Authors: PATEL, ISHA - Us Food & Drug Administration (FDA); GANGIREDLA, JAYANTHI - Food And Drug Administration(FDA); LACHER, DAVID - Food And Drug Administration(FDA); MAMMEL, MARK - Food And Drug Administration(FDA); Bagi, Lori; BARANZONI, GIAN MARCO - University Of Birmingham; Fratamico, Pina; ROBERTS, ELIZABETH - Pennsylvania State University; DEBROY, CHITRITA - Pennsylvania State University; LINDSEY, REBECCA - Centers For Disease Control And Prevention (CDC) - United States; STRIPLING, DEVON - Centers For Disease Control And Prevention (CDC) - United States; MARTIN, HALEY - Centers For Disease Control And Prevention (CDC) - United States; SMITH, PEYTON - Centers For Disease Control And Prevention (CDC) - United States; STROCKBINE, NANCY - Centers For Disease Control And Prevention (CDC) - United States; ELKINS, CHRISTOPHER - Centers For Disease Control And Prevention (CDC) - United States; SCHEUTZ, FLEMMING - World Health Organization (WHO) - Switzerland; FENG, PETER - Food And Drug Administration(FDA)

Submitted to: Journal of Food Protection
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 3/28/2018
Publication Date: 7/9/2018
Citation: Patel, I.R., Gangiredla, J., Lacher, D.W., Mammel, M.K., Bagi, L.K., Baranzoni, G., Fratamico, P.M., Roberts, E.L., Debroy, C., Lindsey, R.L., Stripling, D., Martin, H., Smith, P., Strockbine, N.A., Elkins, C.A., Scheutz, F., Feng, P.C. 2018. Interlaboratory evaluation of the FDA-ECID microarray for profiling Shiga toxin-producing Escherichia coli. Journal of Food Protection. 81:1275-1282.

Interpretive Summary: Shiga toxin-producing Escherichia coli (STEC) comprise a large, complex group of food-borne pathogens. Some STEC cause very serious illness, as well as death, while others cause milder illness. This difference is based on the presence of specific virulence genes (genes involved in the disease process) carried by different STEC strains. It is critical to be able to rapidly and accurately identify STEC that contaminate foods that are serious human pathogens. An inter-laboratory study was conducted to evaluate a method known as the Food and Drug Administration- E. coli Identification (FDA-ECID) microarray. This microarray allows characterization of E. coli strains to identify virulence, as well as the specific surface antigen genes, known as O-antigen and H-antigen genes that they carry. By testing a panel of 54 reference E. coli strains, previously characterized using other methods, the inter-laboratory study showed that the FDA-ECID micorarray was highly reproducible for molecular serotyping and for virulence gene detection and subtyping. In conclusion, the FDA-ECID microarray is a simple and fast alternative for potential use by regulatory, public health, and industry groups for characterization of STEC with a high degree of reproducibility for the selected traits examined.

Technical Abstract: The FDA-ECID microarray provides rapid molecular characterization of Escherichia coli. The effectiveness of FDA-ECID to characterize Shiga toxin-producing E. coli (STEC) was evaluated by three federal and one reference laboratory using a panel of 54 reference E. coli strains from the External Quality Assurance (EQA) program. Strains were tested by FDA-ECID for molecular serotyping (O and H antigens), Shiga toxin subtyping, and the presence of ehxA and eae genes for enterohemolysin and intimin, respectively. The FDA-ECID O typing was 96% reproducible among the four labs and 94% accurate compared to EQA. Discrepancies were due to the absence of O41 target loci on the array and to two pairs of O types with identical target sequences. H typing was 96% reproducible and 100% accurate, with discrepancies due to two strains from one laboratory that were identified as mixed by FDA-ECID. Stx1 subtyping was 100% reproducible and accurate, while Stx2 subtyping was 100% reproducible, but only 64% accurate. FDA-ECID identified most Stx2 subtypes but had difficulty distinguishing among stx2a, stx2c, and stx2d due to close similarities of these sequences. FDA-ECID was 100% effective in detecting ehxA and eae and also accurately subtyped the eae alleles. The interlaboratory study showed that FDA-ECID for STEC characterization was highly reproducible for molecular serotyping, stx and eae subtyping, and for ehxA detection. However, the array had some difficulty in discerning highly homologous O antigen genes as well as the stx2a, stx2c, and stx2d subtypes.