T1-10 NeoSeek Salmonella: A Rapid Salmonella Serotyping Platform via Next-Generation Sequencing

Monday, August 1, 2016: 11:15 AM
240 (America's Center - St. Louis)
Edan Hosking, Neogen Corporation, Lansing, MI
Barry Simpson, Neogen Corporation, Lansing, MI
Jaehyoung Kim, Neogen Corporation, Lansing, MI
Andy Benson, Metagenome Analytics, Lincoln, NE
Rohita Sinha, Metagenome Analytics, Lincoln, NE
Jean Guard, U.S. Department of Agriculture, Athens, GA
Eric Tovar, Neogen Corporation, Lansing, MI
Lisa Pinkava, Neogen Corporation, Lansing, MI
Mark Mozola, Neogen Corporation, Lansing, MI
Jennifer Rice, Neogen Corporation, Lansing, MI
Introduction: Antibody based serotyping is the most common form of sub-typing for Salmonella among diagnostic laboratories, public health entities and regulatory agencies.  This Next-Generation Sequencing-based service produces definitive, gene-driven serotypes for isolates in 72 hours while removing the subjective interpretation of traditional methods.  The method combines the throughput of NGS-based targeted amplicon sequencing with bioinformatics pipelines developed by MetaGenome Analytics.  Targets for the assay were developed in collaboration with Dr. Jean Guard (USDA-ARS).

Purpose: With 2,557 recognized serotypes, accurate Salmonella serotyping by traditional methods is complex, expensive, and time consuming.  Moreover, the availability of validated antisera can pose challenges.  To circumvent these issues, NeoSeek Salmonella was developed.  

Methods: NeoSeek Salmonella serotyping utilizes targeted amplicon sequencing of four distinct regions within the genome of Salmonella.  PCR products for these regions are generated and sequenced on a MiSeq instrument. Assembled sequences are compared to a curated database of Salmonella whole genome and individual target sequences from known serotypes.  Serotype assignment uses a sophisticated scoring matrix and built-in target redundancy for serotype determination.

Results: The targeted regions were examined in a single-blind, in silico study.  The markers and scoring algorithm yielded a precision of >0.93 (n=68 strains) with strains that included the CDC “Top 30” Salmonella, as well as over 70 of the most common serotypes.  The assay was subsequently validated with a panel of known serotypes (n=96 strains), yielding a precision of >0.95.  Additional in silico analysis of the NeoSeek Salmonella targets against our database estimated that it can accurately differentiate over 1,500 different Salmonella serotypes.

Significance: NeoSeek Salmonella accurately reports Salmonella serotypes for isolates based on targeted amplicon sequencing.  This genetics based platform does not rely on antisera to deliver accurate results.  The shorter time to result provides for faster response times and can lead to quicker interventions over current methods.