Category Archives: Whole Genomic Sequencing

Research – Integration of genomics in surveillance and risk assessment for outbreak investigation


Keeping food safe is a challenge that needs continuous surveillance for the sake of consumers’ health. The main issue when a food‐borne pathogen outbreak occurs is represented by the identification of the source(s) of contamination. Delivering this information in a timely manner helps to control the problem, with positive outcomes for everyone, especially for the consumers, whose health is in this way preserved, and for the stakeholders involved in food production and distribution, who could face enormous economic losses if recalls or legal issues occur. Whole genome sequencing (WGS) is a tool recently implemented for the characterisation of isolates and the study of outbreaks because of its higher efficiency and faster results, when compared to traditional typing methods. Lower sequencing costs and the development of many bioinformatic tools helped its spread, and much more attention has been given to its use for outbreak investigation. It is important to reach a certain level of standardisation, though, for ensuring result reproducibility and interoperability. Moreover, nowadays it is possible, if not mandatory for Open Science Practices, to share WGS data in publicly available databases, where raw reads, assembled genomes and their corresponding metadata can be easily found and downloaded. The scope of this Fellowship was to provide the Fellow all the training necessary for successfully integrating genomics to surveillance and risk assessment of food‐borne pathogens from farm to fork.

Research – Frozen Vegetable Processing Plants Can Harbour Diverse Listeria monocytogenes Populations: Identification of Critical Operations by WGS


Frozen vegetables have emerged as a concern due to their association with foodborne outbreaks such as the multi-country outbreak of Listeria monocytogenes serogroup IVb linked to frozen corn. The capacity of L. monocytogenes to colonize food-processing environments is well-known, making the bacteria a real problem for consumers. However, the significance of the processing environment in the contamination of frozen foods is not well established. This study aimed to identify potential contamination niches of L. monocytogenes in a frozen processing plant and characterize the recovered isolates. A frozen vegetable processing plant was monitored before cleaning activities. A total of 78 points were sampled, including frozen vegetables. Environmental samples belonged to food-contact surfaces (FCS); and non-food-contact surfaces (n-FCS). Positive L. monocytogenes samples were found in FCS (n = 4), n-FCS (n = 9), and the final product (n = 1). A whole-genome sequencing (WGS) analysis revealed two clusters belonging to serotypes 1/2a-3a and 1/2b-3b). The genetic characterization revealed the presence of four different sequence types previously detected in the food industry. The isolate obtained from the final product was the same as one isolate found in n-FCS. A multi-virulence-locus sequence typing (MVLST) analysis showed four different virulence types (VT). The results obtained highlight the relevant role that n-FCS such as floors and drains can play in spreading L. monocytogenes contamination to the final product. View Full-Text

Research – Invasive listeriosis outbreaks and salmon products: a genomic, epidemiological study


Invasive listeriosis, caused by Listeria (L.) monocytogenes, is a severe foodborne infection, especially for immunocompromised individuals. The aim of our investigation was the identification and analysis of listeriosis outbreaks in Germany with smoked and graved salmon products as the most likely source of infection using whole-genome sequencing (WGS) and patient interviews.

In a national surveillance program, WGS was used for subtyping and core genome multi locus sequence typing (cgMLST) for cluster detection of L. monocytogenes isolates from listeriosis cases as well as food and environmental samples in Germany. Patient interviews were conducted to complement the molecular typing.

We identified 22 independent listeriosis outbreaks occurring between 2010 and 2021 that were most likely associated with the consumption of smoked and graved salmon products. In Germany, 228 cases were identified, of 50 deaths reported (22%) 17 were confirmed to have died from listeriosis. Many of these 22 outbreaks were cross-border outbreaks with further cases in other countries.

This report shows that smoked and graved salmon products contaminated with L. monocytogenes pose a serious risk for listeriosis infection in Germany. Interdisciplinary efforts including WGS and epidemiological investigations were essential to identifying the source of infection. Uncooked salmon products are high risk foods frequently contaminated with L. monocytogenes. In order to minimise the risk of infection for consumers, food producers need to improve hygiene measures and reduce the entry of pathogens into food processing. Furthermore, susceptible individuals should be better informed of the risk of acquiring listeriosis from consuming smoked and graved salmon products’.

CPS Funded Projects 2022 – Microbiology of Irrigation Water


Microbial characterization of irrigation waters using rapid, inexpensive and portable next generation sequencing technologies

New microbial detection approaches utilizing whole genome sequencing are being increasingly applied for tracing microbial contaminants entering the food chain. The produce industry can directly benefit from powerful new methods such as shotgun metagenomics, which allows for the rapid identification of all the bacterial, viral, fungal, and protozoan pathogens in irrigation water, soil, or food samples in a single test. Furthermore, whole genome sequencing technologies are quickly becoming less expensive, and compact sequencing technologies like the Oxford Nanopore MinION device could potentially allow testing directly on-site in produce fields or other processing facilities for food safety surveillance programs. However, the application of these new whole genome sequencing technologies and approaches need to be verified and validated for use by the produce industry. The goal of this project is to investigate two technologies that offer slightly different approaches for pathogen detection, to identify the benefits and limitations of each, verify the results, and validate their applications by the produce industry for use in rapid pathogen detection in agricultural waters. The results of this study will provide recommendations, protocols and guidelines to the produce industry regarding the proper implementation of these technologies for pathogen surveillance.

Denmark – Listeria outbreak has sickened 9 in Denmark

Food Safety News

Danish officials are investigating a years-long outbreak of Listeria infections that has affected nine people from 2018 through this month.

The Statens Serum Institut (SSI), Danish Veterinary and Food Administration (Fødevarestyrelsen) and DTU Food Institute are trying to find the source of the infections.

The same type of Listeria monocytogenes has been found in nine people from late 2018 to November 2021. The four patients this year have all only recently become ill. Two people fell sick in both 2018 and 2019 and one case was recorded in 2020.

Among those sick are seven women aged from 35 to 95 years old and two children younger than age 5. They live all over the country. All nine Danish patients have been hospitalized but there have not been any deaths.

Whole genome sequencing (WGS) showed samples from outbreak patients to be closely related, which means it is likely they came from the same source.

Research – Application of Whole Genome Sequencing to Understand Diversity and Presence of Genes Associated with Sanitizer Tolerance in Listeria monocytogenes from Produce Handling Sources


Recent listeriosis outbreaks linked to fresh produce suggest the need to better understand and mitigate L. monocytogenes contamination in packing and processing environments. Using whole genome sequencing (WGS) and phenotype screening assays for sanitizer tolerance, we characterized 48 L. monocytogenes isolates previously recovered from environmental samples in five produce handling facilities. Within the studied population there were 10 sequence types (STs) and 16 cgMLST types (CTs). Pairwise single nucleotide polymorphisms (SNPs) ranged from 0 to 3047 SNPs within a CT, revealing closely and distantly related isolates indicative of both sporadic and continuous contamination events within the facility. Within Facility 1, we identified a closely related cluster (0–2 SNPs) of isolates belonging to clonal complex 37 (CC37; CT9492), with isolates recovered during sampling events 1-year apart and in various locations inside and outside the facility. The accessory genome of these CC37 isolates varied from 94 to 210 genes. Notable genetic elements and mutations amongst the isolates included the bcrABC cassette (2/48), associated with QAC tolerance; mutations in the actA gene on the Listeria pathogenicity island (LIPI) 1 (20/48); presence of LIPI-3 (21/48) and LIPI-4 (23/48). This work highlights the potential use of WGS in tracing the pathogen within a facility and understanding properties of L. monocytogenes in produce settings. View Full-Text

Research -Application of Whole Genome Sequencing to Aid in Deciphering the Persistence Potential of Listeria monocytogenes in Food Production Environments


Listeria monocytogenes is the etiological agent of listeriosis, a foodborne illness associated with high hospitalizations and mortality rates. This bacterium can persist in food associated environments for years with isolates being increasingly linked to outbreaks. This review presents a discussion of genomes of Listeria monocytogenes which are commonly regarded as persisters within food production environments, as well as genes which are involved in mechanisms aiding this phenotype. Although criteria for the detection of persistence remain undefined, the advent of whole genome sequencing (WGS) and the development of bioinformatic tools have revolutionized the ability to find closely related strains. These advancements will facilitate the identification of mechanisms responsible for persistence among indistinguishable genomes. In turn, this will lead to improved assessments of the importance of biofilm formation, adaptation to stressful conditions and tolerance to sterilizers in relation to the persistence of this bacterium, all of which have been previously associated with this phenotype. Despite much research being published around the topic of persistence, more insights are required to further elucidate the nature of true persistence and its implications for public health.

A Silver Lining of the Pandemic: Whole-Genome Sequencing and Food Safety


Zooming out and taking a broader perspective, WGS benefits are particularly visible in microbiology: WGS provides rapid identification and characterization of microorganisms with a level of precision that no tool has ever reached before. Through WGS, specific novel antibiotic targets (resistance genotypes) are being identified in the area of antimicrobial resistance (AMR)studies. It is a significant stepping-stone because more focused surveillance and more targeted diagnostics and drug development are made possible by identifying them and correlating them to the observed phenotypes. The level of detail provided by WGS makes it possible to refine case definitions precisely, which in turn allows for faster investigation of outbreak clusters, thus preventing additional cases of diseases sooner. For example, in 2014, a multinational Salmonella outbreak investigation was conducted in Europe where WGS was used to identify the root cause, and the data collected pointed to some egg farms in a specific location. While WGS was essential in the investigation, it was the international data-sharing efforts that made the investigation successful and conclusive. Another example is the outbreak investigation of Listeria linked to enoki mushrooms in Canada where the specific sequence of the Listeria strain was internationally shared, resulting in successfully tracing the multinational food safety outbreak and the rapid recall of the affected products.

Research – Economic evaluation of whole genome sequencing for pathogen identification and surveillance – results of case studies in Europe and the Americas 2016 to 2019 separator


Whole genome sequencing (WGS) is transforming the work of microbiological reference laboratories across the globe. Complete genomic sequences from an isolate or sample have the potential to improve infectious disease surveillance programmes and strengthen epidemiological investigations. Examples include the potential to identify outbreaks earlier through the added value of genome-based cluster detection, the tracking of strains with specific markers relevant for health (for instance antigenicity, virulence, transmissibility, resistance markers) and the monitoring of effectiveness of control measures (for instance vaccination, elimination programmes) [1]. Development of pathogen genomics and the tools, infrastructure and necessary analytics for WGS can be used across sectors (public health, veterinary health or food safety) and pathogen types (viruses, bacteria or parasites), providing potential for further integration of surveillance activities and thus for economies of scale [1,2].

However, in practice, a model currently favoured involves the introduction of WGS into individual pathogen-focused programmes, where the costs of implementing WGS in routine diagnostics and surveillance remain high in comparison to the mainly phenotypic testing currently in use [2]. To better understand the cost differential between conventional methods and WGS in the context of pathogen identification and surveillance, and to identify the main factors affecting the costs and benefits of WGS-based surveillance systems, we conducted an economic evaluation in eight reference laboratories in seven countries (Argentina, Canada, Germany, Italy, the Netherlands, the United States (US) and two institutes from the United Kingdom (UK)). In a second step, we wanted to understand whether the benefits derived from the additional information obtained through the sequencing of pathogens is likely to balance out the additional cost of WGS. For this purpose, we estimated for the example of salmonellosis the number of cases of illness that would need to be prevented each year through the use of WGS in order to ‘break even’ on costs, i.e. in order to make the use of WGS cost-neutral.

UK – An outbreak of human listeriosis associated with frozen sweet corn consumption: Investigations in the UK

Science Direct

The use of Whole genome sequencing (WGS) identified a multi-country outbreak of human listeriosis associated with consumption of frozen sweet corn produced in Hungary. The purpose of this report was to summarise information on the cases occurring in the UK which were part of this outbreak and outline investigations on the presence of Listeria monocytogenes in the affected food chain.

Prior to the international recall of this product in 2018, 12 UK cases of listeriosis were identified as infected by the outbreak strain between 2015 and 18. Epidemiological and microbiological investigations confirmed these cases as belonging to the outbreak. A further case occurred in 2019 and a contaminated frozen pack from one of the implicated batches of sweet corn was recovered from the patient’s domestic freezer.

The outbreak strain was also detected in products from a sandwich manufacturer in 2018 which added frozen sweet corn directly to sandwich fillings. The sandwich manufacturer’s sweet corn was supplied by a distributor in England which obtained frozen products from the Hungarian manufacturer implicated in the outbreak. Within the distributor’s premises, 208 food and environmental samples were taken: L. monocytogenes was detected in 44% of 70 samples of frozen sweet corn and 5% of 79 other foods.

The outbreak strain was detected in the frozen sweet corn, in one other frozen food (mixed vegetables) and in the factory environment. The outbreak strain was also recovered from frozen beans on retail sale in the first four months of 2019. Five other L. monocytogenes strains together with two other Listeria species were detected in samples from the importer’s premises. One of the L. monocytogenes strains in the importer’s factory, which was distinct from the outbreak strain, was also recovered from sweet corn collected from the sandwich manufacturer, sweet corn tested in England in 2013 and 2016 and the blood of two cases of human listeriosis which occurred in England in 2014. This report shows how analysis by WGS provides evidence to understand complex food chains.

This report also highlights risks for transmission of human listeriosis from frozen sweet corn and the potential for misuse of this food as a ready-to-eat product.