In-Depth Longitudinal Study of Listeria monocytogenes ST9 Isolates from the Meat Processing Industry: Resolving Diversity and Transmission Patterns Using Whole-Genome Sequencing

Abstract

<jats:title>ABSTRACT</jats:title> <jats:p><jats:named-content content-type="genus-species">Listeria monocytogenes</jats:named-content> is a pathogen mostly associated with the consumption of ready-to-eat foods and can cause severe disease and death. It can be introduced into 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 <jats:named-content content-type="genus-species">L. monocytogenes</jats:named-content> sequence types, and for effective source tracking, the divergence and spread of ST9 must be understood. In this study, whole-genome sequencing (WGS) was used to characterize and track 252 <jats:named-content content-type="genus-species">L. monocytogenes</jats:named-content> 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 that diverged from its ancestor in the late 1990s 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- to 6-year period; entry through the 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 9-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.</jats:p> <jats:p><jats:bold>IMPORTANCE</jats:bold> <jats:named-content content-type="genus-species">Listeria monocytogenes</jats:named-content> is a deadly foodborne pathogen that is widespread in the environment, and certain types can be established in food factories. The sequence type ST9 dominates in meat processing environments, and this work was undertaken to obtain data needed for the tracking of this subtype. By using whole-genome sequencing (WGS), we revealed 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 time frame of persistence in the factory, as well as when and how new clones had entered. The present work contributes valuable information about the diversity of ST9 and exemplifies the potential power of WGS in food safety management, allowing the determination of relationships between strains both in an international context and locally between and within factories.</jats:p>

Molecular Typing of Listeria monocytogenes IVb Serogroup Isolated from Food and Food Production Environments in Poland

“…It has been previously shown that the cgMLST analysis is a very useful molecular tool to assess the L. monocytogenes structure population [ 5 , 6 , 27 , 30 , 34 , 35 , 36 ]. In the present study, genetically closely related strains of the SL2-ST145-CT375 type were isolated in nine administrative provinces (voivodeships) of Poland during 2015-2018, mostly from raw meat ( Table S1 ).…”

“…In the present study, genetically closely related strains of the SL2-ST145-CT375 type were isolated in nine administrative provinces (voivodeships) of Poland during 2015-2018, mostly from raw meat ( Table S1 ). This fact can be explained by, e.g., the ability of such isolates to persist in food production environments or introduction of the bacteria from outside sources, e.g., from the meat supplying slaughterhouses [ 35 ].…”

“…The broad tools used to analyse the WGS data for the determination of the genetic relationship between isolates are multi-locus sequence typing (MLST) and analysis of core genome (cgMLST), which allow clonal complexes (CCs) with sequence types (STs) and cgMLST complex types (CTs) to be identified, respectively [ 32 , 33 ]. cgMLST for L. monocytogenes has been demonstrated as a highly reproducible method and is widely used for molecular typing of isolates classified to the same serotypes and lineages and to identify hypervirulent clones [ 5 , 29 , 31 , 34 , 35 , 36 , 37 ].…”

Hypo- and Hyper-Virulent Listeria monocytogenes Clones Persisting in Two Different Food Processing Plants of Central Italy

“…Considering the possible evolution over time of a population of persistent strains in its environment, a relaxed 25-SNPs threshold was applied to define strains as belonging to the same cluster [ 35 , 36 ].…”

Genetic Listeria monocytogenes Types in the Pork Processing Plant Environment: From Occasional Introduction to Plausible Persistence in Harborage Sites

“…Also, CC8 clones were associated with human listeriosis cases and outbreaks across Canada for more than two decades [26]. Several studies reported the favorable settlement and the persistence of CC9 in meat processing environments and equipment for several years [6,24,[27][28][29][30]. This clone possesses higher stress resistance and benzalkonium chloride tolerance genes and a biofilm formation ability that contributes to its persistence [29,30].…”