Whole genome sequencing for typing and characterisation of Listeria monocytogenes isolated in a rabbit meat processing plant

Abstract

Listeria monocytogenes is a food-borne pathogen able to survive and grow in different environments including food processing plants where it can persist for month or years. In the present study the discriminatory power of Whole Genome Sequencing (WGS)-based analysis (cgMLST) was compared to that of molecular typing methods on 34 L. monocytogenes isolates collected over one year in the same rabbit meat processing plant and belonging to three genotypes (ST14, ST121, ST224). Each genotype included isolates indistinguishable by standard molecular typing methods. The virulence potential of all isolates was assessed by Multi Virulence-Locus Sequence Typing (MVLST) and the investigation of a representative database of virulence determinant genes. The whole genome of each isolate was sequenced on a MiSeq platform. The cgMLST, MVLST, and in silico identification of virulence genes were performed using publicly available tools. Draft genomes included a number of contigs ranging from 13 to 28 and N50 ranging from 456298 to 580604. The coverage ranged from 41 to 187X. The cgMLST showed a significantly superior discriminatory power only in comparison to ribotyping, nevertheless it allows the detection of two singletons belonging to ST14 that were not observed by other molecular methods. All ST14 isolates belonged to VT107, which 7-loci concatenated sequence differs for only 4 nucleotides to VT1 (Epidemic clone III). Analysis of virulence genes showed the presence of a fulllength inlA version in all ST14 isolates and of a mutated version including a premature stop codon (PMSC) associated to attenuated virulence in all ST121 isolates.

Heterogeneity, Characteristics, and Public Health Implications of Listeria monocytogenes in Ready-to-Eat Foods and Pasteurized Milk in China

“…Interestingly, six (100%) ST9/CC9 and one (25%) ST5/CC5 isolates harbored PMSCs in the inlA gene, concurrent with previous studies reported in China (Chen et al, 2018a(Chen et al, , 2019a. Similarly, the PMSCs in the inlA gene were frequent in ST121/CC121 strains, which were predominant in foods and associated environments (Ciolacu et al, 2015;Palma et al, 2017;Rychli et al, 2017Rychli et al, , 2018. These data indicate that the ST9 and ST121 strains predominant in foods may acquire PMSCs in the inlA gene.…”

Occurrence, Antibiotic Resistance, and Population Diversity of Listeria monocytogenes Isolated From Fresh Aquatic Products in China

“…Interestingly, three fourths of isolates with PMSCs belonged to ST9 in this study. In contrast, none of the ST121 isolates was identified as PMSC, which was most identified as PMSCs in food and associated environments in the other countries ( Hein et al, 2011 ; Ciolacu et al, 2015 ; Palma et al, 2017 ). In recent years, LIPI-3 genes were identified as important virulence factors that acts to target the host gut microbiota, responsible for the majority of listeriosis outbreaks ( Cotter et al, 2008 ; Quereda et al, 2017 ), and human central nervous system (CNS) or MN listeriosis was mainly attributed to LIPI-4 ( Maury et al, 2016 ).…”

Dynamics of mobile genetic elements of Listeria monocytogenes persisting in ready-to-eat seafood processing plants in France

“…In the last decades, several studies aiming to determine the basis of persistence in RTE industry and to trace-back outbreaks-related L. monocytogenes strains have been performed based on conventional molecular typing [72][73][74][75]. However, the advantages provided by analyses of genome-scale data through comparative genomic approaches have been recently demonstrated in the context of L. monocytogenes strains persisting in FPEs [4,16,18,19,23,[76][77][78]. These studies also suggested differences in distribution and fitness of CCs in geographical regions and evolutionary niches.…”