Genomic surveillance enables suitability assessment of Salmonella gene targets used for culture-independent diagnostic testing

Abstract

Salmonella is a highly diverse genus consisting of over 2600 serovars responsible for high-burden food- and water-borne gastroenteritis worldwide. Sensitivity and specificity of PCR-based culture-independent diagnostic testing (CIDT) systems for Salmonella, which depend on a highly conserved gene target, can be affected by single nucleotide polymorphisms (SNPs), indels and genomic rearrangements within primer and probe sequences. This report demonstrates the value of prospectively collected genomic data for verifying CIDT targets. We utilised the genomes of 3165 Salmonella isolates prospectively collected and sequenced in Australia. The sequence of Salmonella CIDT PCR gene targets (ttrA, spaO and invA) were systematically interrogated to measure nucleotide dissimilarity. Analysis of 52 different serovars and 79 MLST types demonstrated dissimilarity within and between PCR gene targets ranging between 0 - 81.3 SNP/Kbp (0 and 141 SNPs). Lowest average dissimilarity was observed in the ttrA target gene used by the Roche LightMix at 2.0 SNP/Kbp [range 0 - 46.7]), however entropy across the gene demonstrates it may not be the most stable CIDT target. While debate continues over the benefits and pitfalls of replacing bacterial culture with molecular assays, the growing volumes of genomic surveillance data enable periodic regional reassessment and validation of CIDT targets against both prevalent and emerging serovars. If PCR systems are to become the primary screening and diagnostic tool for laboratory diagnosis of salmonellosis, ongoing monitoring of the genomic diversity in PCR target regions is warranted as is the potential inclusion of two Salmonella PCR targets into frontline diagnostic systems.