Mining Listeria monocytogenes single nucleotide polymorphism sites to identify the major serotypes using allele-specific multiplex PCR

Abstract

Worldwide, Listeria monocytogenes is a common foodborne pathogen and serotyping is necessary for traceability and surveillance. Due to high accuracy and speed, PCR is commonly used for serotyping by targeting specific genes, such as lmo1118 and ORF2110 for 1/2c-3c and 4b-4d-4e, respectively. Single nucleotide polymorphisms (SNPs) are single base alterations at specific loci which are associated with various phenomena. In this study, a method was explored to mine specific SNPs from 253 L. monocytogenes genomes with known serotypes by writing Python programming language script. After blasting all the CDS, seventeen candidate genes with specific SNPs were obtained and these genes contained multiple types of SNPs, including lineages I, II, III, 1/2a-3a, 1/2b-3b-7, and 1/2c-3c specific SNPs. The sensitivity and specificity of these candidate SNP sites are higher than 85% in the genomes examined. Combining lineage I-specific, lineage II-specific, 1/2b-3b-7-specific, and 1/2c-3c-specific SNP sites together, using allele-specific multiplex PCR, we could serotype major L. monocytogenes serotypes. This method was used for 60 L. monocytogenes strains isolated from various food samples and the serotyping results were 100% identical to those of the currently accepted method with the reduced primers from ten to eight. Our results indicate that allele-specific multiplex PCR after mining specific SNPs from common genome database can be used for bacterial typing.

Keywords: Allele-specific PCR; Listeria monocytogenes; Mining; Serotype; Single nucleotide polymorphisms (SNPs).