In depth longitudinal study of Listeria monocytogenes ST9 isolates from meat processing industry: Resolving diversity and transmission patterns using WGS.

Listeria monocytogenes is a pathogen mostly associated with consumption of ready-to-eat foods and can cause severe disease and death. It can be introduced to food chains from raw materials, but often the contamination source is the food production environment where certain clones can persist for years. In the meat chain, ST9 is one of the most commonly encountered L. monocytogenes sequence types, and for effective source tracking, the divergence and spread of ST9 must be understood. In this study, WGS was used to characterize and track 252 L. monocytogenes ST9 isolates collected from four Norwegian meat processing plants between 2009 and 2017. The isolates formed distinct clusters relative to genomes found in public databases, and all but three isolates clustered into two major clonal populations. Different contamination patterns were revealed, e.g.: Evidence of contamination of two factories with a clone diverged from its ancestor in the late 19909s through a common source of raw materials; breach of hygienic barriers within a factory leading to repeated detection of two clones in the high-risk zone during a 4-6 year period; entry through purchase and installation of second-hand equipment harboring a previously established clonal population; and spreading and diversification of two clones from two reservoirs within the same production room over a nine year period. The present work provides data on the diversity of ST9 which is crucial for epidemiological investigations and highlights how WGS can be used for source tracking within food processing factories. IMPORTANCEListeria monocytogenes is a deadly foodborne pathogen that is widespread in the environment, and certain types establish in food factories. The sequence type ST9 dominates in meat processing environments, and this work was undertaken to obtain data needed for tracking of this subtype. By using whole genome sequencing (WGS) we could reveal the presence of cross-contamination routes between meat factories as well as within a single factory, including the spread from different reservoirs within the same room. It was also possible to estimate the timeframe of persistence in the factory, as well as when and how new clones had entered. The present work contributes with valuable information about the diversity of ST9 and exemplifies the potential power of WGS in food safety management, allowing determination of relationships between strains both in an international context and locally between and within factories.