Whole-genome sequence analysis of Listeria innocua recovered from retail milk and dairy products in Egypt

Authors: RAMADAN, HAZEN - Mansoura University; AL-ASHMAWY, MAHA - Mansoura University; SOLIMAN, AHMED - Kafrelsheikh University; ELBEDIWI, MOHAMMED - Animal Health Research Institute; SABEQ, ISLAM - Benha University; YOUSEF, MONA - Mansoura University; ALGAMMAL, ABDELAZEEM - Suez Canal University; Hiott, Lari; Berrang, Mark; Frye, Jonathan; Jackson, Charlene

Submitted to: Frontiers in Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 4/14/2023
Publication Date: 5/10/2023
Citation: Ramadan, H., Al-Ashmawy, M., Soliman, A.M., Elbediwi, M., Sabeq, I., Yousef, M., Algammal, A., Hiott, L.M., Berrang, M.E., Frye, J.G., Jackson, C.R. 2023. Whole-genome sequence analysis of Listeria innocua recovered from retail milk and dairy products in Egypt. Frontiers in Genetics. https://doi.org/10.3389/fmicb.2023.1160244.
DOI: https://doi.org/10.3389/fmicb.2023.1160244

Interpretive Summary: Listeria innocua is considered to be a non-pathogenic species of Listeria. However, similarity of the L. innocua genome with the highly pathogenic Listeria monocytogenes and presence of these bacteria in the same environment may result in gene transfer between the two species. In this study, L. innocua isolated from milk and dairy products from Egypt were characterized to detect emergence of virulence genes and genetic components that enable L. innocua to survive, spread, and cause listeriosis. Results showed the presence of one antimicrobial resistance gene and thirteen virulence genes but no Listeria specific pathogenic genes. Isolates also contained a gene for heat resistance located on a plasmid. Although this plasmid has been linked to L. monocytogenes that was responsible for a serious outbreak, this is the first report of L. innocua containing the heat resistance gene on a plasmid. The common virulence and antimicrobial resistance genes as well as the heat resistance gene in L. innocua increases the possibility of the evolution of hypervirulent strains. This information is useful for the food industry as these strains could endanger processing and preservation protocols and pose health risks from dairy products from Egypt. Ongoing genomic research is needed to identify genetic changes for determining early preventive and control measures for Listeria species in food.

Technical Abstract: The high similarity of the Listeria innocua genome with Listeria monocytogenes and their presence in the same niche may facilitate gene transfer between them. A better understanding of the mechanisms responsible for bacterial virulence requires an in-depth knowledge of the genetic characteristics of these bacteria. In this context, draft whole genome sequences were completed on five L. innocua isolated from milk and dairy products from Egypt. The sequencing results revealed the presence of only one antimicrobial resistance gene, fosX, in the L. innocua isolates. The five isolates carried thirteen virulence genes involved in adhesion, invasion, surface protein anchoring, peptidoglycan degradation, intracellular survival, and heat stress but lacked the Listeria Pathogenicity Island 1 (LIPI-1) genes. Multi-locus sequence typing (MLST) assigned these five isolates into the same sequence type, ST-1085; however, the SNP-based phylogenetic analysis revealed no distinct trends when compared to both regional and global lineages of L. innocua. These isolates possessed ATP-dependent protease (clpL) gene, which mediates heat resistance, on a rep25 type plasmids. Although this plasmid has been linked to L. monocytogenes that was responsible for a serious outbreak, this is the first report of L. innocua containing a clpL-carrying plasmids. In addition to the common virulence and antimicrobial resistance genes, the first report of clpL-harboring plasmids in L. innocua, and various genetic mechanisms of virulence transfer among Listeria species and other genera, could raise the possibility of the evolution of hypervirulent strains. These strains could endanger processing and preservation protocols and pose unprecedented health risks from dairy products. Ongoing genomic research is necessary to identify these alarming genetic changes and consequently adopting early preventive and control measures.