Whole-genome sequencing-based characterization of 100 Listeria monocytogenes isolates collected from food processing environments over a four-year period

Authors: HURLEY, DANIEL - University College Dublin; LUQUE-SASTRE, LAURA - University Of Dublin; Parker, Craig; Huynh, Steven; ESHWAR, ATHMANYA - University Of Zurich; NGUYEN, SCOTT - University College Dublin; ANDREWS, NICHOLAS - University College Dublin; MOURA, ALEXANDRA - Institut Pasteur - France; FOX, EDWARD - Commonwealth Scientific And Industrial Research Organisation (CSIRO); JORDAN, KIERAN - Teagasc (AGRICULTURE AND FOOD DEVELOPMENT AUTHORITY); LEHNER, ANGELIKA - University Of Zurich; STEPHAN, ROGER - University Of Zurich; FANNING, SÉAMUS - University College Dublin

Submitted to: mSphere
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 7/12/2019
Publication Date: 8/7/2019
Citation: Hurley, D., Luque-Sastre, L., Parker, C., Huynh, S., Eshwar, A.K., Nguyen, S.V., Andrews, N., Moura, A., Fox, E.M., Jordan, K., Lehner, A., Stephan, R., Fanning, S. 2019. Whole-genome sequencing-based characterization of 100 Listeria monocytogenes isolates collected from food processing environments over a four-year period. mSphere. 4(4):e00252-19. https://doi.org/10.1128/mSphere.00252-19.
DOI: https://doi.org/10.1128/mSphere.00252-19

Interpretive Summary: This study extends current understanding of the genetic diversity among L. monocytogenes isolates within various food products and in the production environment of two related food processing environments. Application of WGS based strategies facilitated tracking of this pathogen of importance to human health along the production chain, whilst providing an assessment of the pathogenic potential for all L. monocytogenes isolates recovered. These analyses enabled the grouping of isolates into three virulence categories according to their genotypes along with assessment of their pathogenicity using the zebrafish embryo model. It also facilitated the identification of those isolates with genes conferring tolerance to commercially applied biocides. Findings from this study highlighted the potential for the application of WGS as a proactive tool to support food safety controls as applied to L. monocytogenes. A similar surveillance approach could be used for other pathogens of relevance to public health.

Technical Abstract: Listeria monocytogenes is frequently found in food and processing facilities, where it can persist creating a large concern for the food industry. Its ability to survive under a wide range of environmental conditions enhances the potential for cross contamination of final food products, leading to possible outbreaks of listeriosis. In this study, whole-genome sequencing (WGS) was applied as a surveillance tool to track and characterize L. monocytogenes in two related food processing environments. One hundred L. monocytogenes isolates from environmental and food samples were sequenced and subsequently used to (i) assess the genomic diversity of L. monocytogenes isolates, (ii) identify possible source(s) of contamination, cross contamination routes and persistence, (iii) detect presence/absence of antimicrobial resistance-encoding genes, (iv) assess their virulence profiles and (v) assess in vivo pathogenicity of L. monocytogenes isolates with different virulence profiles. The predominant L. monocytogenes sublineages (SL) were SL101 (21%), followed by SL9 (17%), SL121 (12%) and SL5 (12%). Benzalkonium chloride tolerance genes were found in 62% of the isolates, which increased to 73% when just considering putative persistent subgroups; the most predominant gene was emrC followed by bcrABC, qacH-Tn6188 and qacC. The L. monocytogenes major virulence factor inlA was truncated in 31% of the isolates and one environmental isolate harboured all major virulence factors, including LIPI-4, which has been shown to confer hypervirulence. Zebrafish infection assay results showed a low (3%) zebrafish survival rate for all the hypervirulent isolates and higher survival rates for intermediate (20%) and hypovirulent isolates (53-83%), suggesting that they have different pathogenic potentials