Updated Algorithm for the Enhanced Detection, Isolation, and Identification of Shiga Toxin-Producing Escherichia coli, NYSDOH, 2011-2020

Abstract

Purpose: Shiga toxin-producing Escherichia coli (STEC) are an important cause of enteric infections and isolation is critical for outbreak investigations. A shift from enzyme immunoassays to more sensitive, culture independent molecular methods at submitting laboratories has resulted in an increase in specimen submissions to public health laboratories. The Wadsworth Center (WC) saw a 172% increase in the number of STEC specimens received in 2019-2020 compared to 2011-2012. During the last decade, WC has updated testing algorithms to improve efficiency and optimize recovery of STEC isolates for surveillance and outbreak detection. Methods & Materials: WC utilizes an initial molecular screen to detect the presence of Shiga toxin genes (stx) and O157 DNA by real-time PCR. PCR positive samples are cultured to isolate the STEC organism. Real-time PCR is used to identify serogroups O26, O103, O111, O45, O121, and O145. Individual colonies and/or pools of colonies are screened for stx and immunomagnetic bead separation is performed as needed for serogroups identified by PCR. PCR positive isolates are confirmed as E. coli biochemically and sent for whole genome sequencing analysis. Results: From 2011-2020, 3,637 primary specimens were received at WC and 2,815 were positive by PCR. STEC was isolated from 63% (2,282/3,637) of these. Furthermore, 23% (822/3,637) of specimens were determined to be stx DNA negative. The most frequently isolated serogroup was O103, representing 20% (447/2,282) of total STEC isolated from primary specimens. Serogroup O157 was identified most frequently when isolates and primary specimens were assessed together. Our results indicate real-time PCR cycle threshold values (CT) are inversely related to isolate recovery from primary specimens. Isolate yield decreases with CT values >25 and is further reduced with CT's >30. CT values >30 may indicate that the organism is not viable or is not present in sufficient quantities for culture recovery. Conclusion: Isolation and characterization of STEC is essential for public health surveillance to monitor foodborne infections and outbreaks. The WC has determined that establishing a CT cutoff helps predict isolation of organism. The implementation of this updated algorithm that utilizes a CT cutoff allows for the most streamlined and efficient recovery of STEC.