Persister, I don’t even know her: STEC in produce

Bacterial persistence is a form of phenotypic heterogeneity in which a subpopulation, persisters, has high tolerance to antibiotics and other stresses. Persisters of enteric pathogens may represent the subpopulations capable of surviving harsh environments and causing human infections. Here we examined the persister populations of several shiga toxin-producing Escherichia coli (STEC) outbreak strains under conditions relevant to leafy greens production.

The persister fraction of STEC in exponential-phase of culture varied greatly among the strains examined, ranging from 0.00003% to 0.0002% for O157:H7 strains to 0.06% and 0.08% for STEC O104:H4 strains. A much larger persister fraction (0.1–11.2%) was observed in STEC stationary cells grown in rich medium, which was comparable to the persister fractions in stationary cells grown in spinach lysates (0.6–3.6%). The highest persister fraction was measured in populations of cells incubated in field water (9.9–23.2%), in which no growth was detected for any of the STEC strains examined. Considering the high tolerance of persister cells to antimicrobial treatments and their ability to revert to normal cells, the presence of STEC persister cells in leafy greens production environments may pose a significant challenge in the development of effective control strategies to ensure the microbial safety of fresh vegetables.

Enhanced formation of shiga toxin-producing Escherichia coli persister variants in environments relevant to leafy greens production

Science Direct, Food Microbiology, Volume 84

Sandy Thao, Maria T. Brandl, Michelle Qiu Carter

Was it really the last meal that made you barf? No

Early in a foodborne disease outbreak investigation, illness incubation periods can help focus case interviews, case definitions, clinical and environmental evaluations and predict an aetiology. Data describing incubation periods are limited.

We examined foodborne disease outbreaks from laboratory-confirmed, single aetiology, enteric bacterial and viral pathogens reported to United States foodborne disease outbreak surveillance from 1998–2013. We grouped pathogens by clinical presentation and analysed the reported median incubation period among all illnesses from the implicated pathogen for each outbreak as the outbreak incubation period.

Outbreaks from preformed bacterial toxins (Staphylococcus aureus, Bacillus cereus and Clostridium perfringens) had the shortest outbreak incubation periods (4–10 h medians), distinct from that of Vibrio parahaemolyticus (17 h median). Norovirus, salmonella and shigella had longer but similar outbreak incubation periods (32–45 h medians); campylobacter and Shiga toxin-producing Escherichia coli had the longest among bacteria (62–87 h medians); hepatitis A had the longest overall (672 h median). Our results can help guide diagnostic and investigative strategies early in an outbreak investigation to suggest or rule out specific etiologies or, when the pathogen is known, the likely timeframe for exposure. They also point to possible differences in pathogenesis among pathogens causing broadly similar syndromes.

Incubation periods of enteric illness in foodborne outbreaks, United States, 1998-2013

Cambridge University Press

  1. J. Chai(a1)W. Gu(a1)K. A. O’Connor (a2)L. C. Richardson (a1) and R. V. Tauxe 


Farm-to-fork food safety in Denmark: Campylobacter is prominent

Burden of disease metrics is increasingly established to prioritize food safety interventions. We estimated the burden of disease caused by seven foodborne pathogens in Denmark in 2017: Campylobacter, Salmonella, Shiga toxin–producing Escherichia coli, norovirus, Yersinia enterocolitica, Listeria monocytogenes, and Toxoplasma gondii.

We used public health surveillance data and scientific literature to estimate incidence, mortality, and total disability-adjusted life year (DALY) of each, and linked results with estimates of the proportion of disease burden that is attributable to foods.

Our estimates showed that Campylobacter caused the highest burden of disease, leading to a total burden of 1709 DALYs (95% uncertainty interval [UI] 1665–1755), more than threefold higher than the second highest ranked pathogen (Salmonella: 492 DALYs; 95% UI 481–504). Campylobacter still led the ranking when excluding DALYs attributable to nonfoodborne routes of exposure. The total estimated incidence was highest for norovirus, but this agent ranked sixth when focusing on foodborne burden. Salmonella ranked second in terms of foodborne burden of disease, followed by Listeria and Yersinia. Foodborne congenital toxoplasmosis was estimated to cause the loss of ∼100 years of healthy life, a burden that was borne by a low number of cases in the population. The ranking of foodborne pathogens varied substantially when based on reported cases, estimated incidence, and burden of disease estimates.

Our results reinforce the need to continue food safety efforts throughout the food chain in Denmark, with a particular focus on reducing the incidence of Campylobacter infections.

Burden of disease estimates of seven pathogens commonly transmitted through foods in Denmark, 2017

Foodborne Pathogens and Disease

Sara Monteiro PiresLea Sletting JakobsenJohanne Ellis-IversenJoana Pessoa, and Steen Ethelberg

Salmonella most common cause of foodborne illness in EU

The European Food Safety Agency (EFSA) reports nearly one in three foodborne outbreaks in the EU in 2018 were caused by Salmonella. This is one of the main findings of the annual report on trends and sources of zoonoses published today by the European Food Safety Authority (EFSA) and the European Centre for Disease Prevention and Control (ECDC).

In 2018, EU Member States reported 5,146 foodborne outbreaks affecting 48,365 people. A foodborne disease outbreak is an incident during which at least two people contract the same illness from the same contaminated food or drink.

Slovakia, Spain and Poland accounted for 67% of the 1,581 Salmonella outbreaks. These outbreaks were mainly linked to eggs.

“Findings from our latest Eurobarometer show that less than one third of European citizens rank food poisoning from bacteria among their top five concerns when it comes to food safety. The number of reported outbreaks suggests that there’s room for raising awareness among consumers as many foodborne illnesses are preventable by improving hygiene measures when handling and preparing food” said EFSA’s chief scientist Marta Hugas.

Salmonellosis was the second most commonly reported gastrointestinal infection in humans in the EU (91,857 cases reported), after campylobacteriosis (246,571).

White Castle frozen food division announces voluntary recall of a limited production of frozen sandwiches due to Listeria monocytogenes

Any excuse to write about White Castle means I get to recall the great movie, Harold and Kumar Go To White Castle.

I had a hockey friend over for lunch one day, we ate steak and watched Harold and Kumar, and it was one of the best times ever.

White Castle has initiated a voluntary recall of a limited number of frozen 6 pack cheeseburgers, frozen 6 pack hamburgers, frozen 6 pack jalapeno cheeseburgers, and 16 pack hamburgers, 16 pack cheeseburgers for the possible presence of Listeria monocytogenes. 

The voluntary recall will impact product on shelves at select retailers with best by dates ranging from 04 Aug 2020 to 17 Aug 2020. Any product with these dates on shelves is presently being removed. Any product with a best by date before or after these best by dates is not included in the voluntary recall.

To date, public health officials have not reported any illness associated with these products.

“Our number one focus is the safety of our customers and our team members, and as a family owned business, we want to hold ourselves to the absolute highest standards of accountability in all aspects of our business – and especially food safety,” said White Castle Vice President, Jamie Richardson.

Uh huh.

Chicago looks back on restaurant inspection

The Chicago Department of Public Health (CDPH) conducts routine food inspections of over 15,000 food establishments to ensure the health and safety of their patrons.

In 2015, CDPH deployed a machine learning model to schedule inspections of establishments based on their likelihood to commit critical food code violations.

The City of Chicago released the training data and source code for the model, allowing anyone to examine the model. We provide the first independent analysis of the model, the data, the predictor variables, the performance metrics, and the underlying assumptions. We present a summary of our findings, share lessons learned, and make recommendations to address some of the issues our analysis unearthed.

Hindsight analysis of the Chicago food inspection forecasting model, 2019

Illinois Institute of Technology

Vinesh Kannan, Matthew Shapiro, and Mustafa Bilgic

Raw is risky: Eating raw pig liver from Singapore market may increase risk of hepatitis E

Danielle Ann of Alvinology reports researchers at the Singapore General Hospital have found definite similarities between the virus strains of Hepatitis E virus or (HEV) in pig liver and human liver.

This means that ingesting raw pork liver could mean you’re ingesting a strain of HEV that’s similar enough to human HEV that it could cause you get infected.

The same report said that people who have contracted HEV has risen steadily over the years. While the researchers could not say if the ingestion of raw pig liver is the main cause of the rise in cases, many local dishes feature this ingredient and do not cook the meat thoroughly.

The same report said that you can acquire the disease from eating contaminated food or substances. Ingesting water that is laced with the disease or accidentally drinking water that has trace amounts of faeces. Eating raw or half-cooked meat that is infected can also transmit the virus to you.

Can a smartphone stop a norovirus outbreak?

Rebecca Trager of Chemistry World reports U.S. researchers have created a handheld detection system that is sensitive enough to catch just a few particles of norovirus.

University of Arizona biomedical engineer Jeong-Yeol Yoon and his team have created a highly sensitive portable detection system capable of spotting norovirus at levels that can make people sick. The work was presented the American Chemical Society’s national meeting in San Diego, California on 27 August.

As few as 10 norovirus particles can cause vomiting and diarrhoea in humans and the virus is extremely contagious so early detection is vital to prevent outbreaks. However, the virus does not grow in laboratory cultures and current detection methods rely on specialised and time-consuming PCR (polymerase chain reaction) techniques.

Yoon’s research team previously developed a smartphone-based device that measured light-scattering from norovirus-bound polystyrene beads in a paper microfluidic chip. It has now improved the device’s detection limit by changing to a fluorescence-based method.

‘I looked at and saw that they sell a lot of these smartphone attachments – smartphone microscope attachments – that turn your phone turns into a microscope, and by adding a couple of other components, I could convert the smartphone-based microscope into a fluorescence microscope,’ Yoon explains.

The setup uses a microscope accessory with a separate light source and two optical filters. He and colleagues also designed a 3D printed case to house the components.

To test a sample, it is first added to the paper microfluidic chip, followed by a suspension of fluorescent beads labelled with norovirus antibodies. After three to five minutes, the antibodies bind to any norovirus particles in the sample, creating aggregates of the fluorescent beads that spread out along the channels of the chip. The resulting increase in fluorescence intensity around each norovirus particle can be detected by taking a picture of the chip with the smartphone’s camera.

An app that the team has also developed then analyses the picture to calculate the sample’s norovirus concentration from the pixel count in the image. So far, the lowest detection limit corresponded to about 5 or 6 norovirus particles per sample, Yoon says. He estimates that the material costs of this system, aside from the cell phone and app development costs, are about $200.

13 sick pulling mussels from the shell

I love my shellfish – mussels and scallops (oysters are sorta gross) – but the kid was diagnosed with a shellfish allergy so they’re an occasional lunch while she’s at school.

Health types in the UK report on six cases of diarrhetic shellfish poisoning (DSP) following consumption of mussels in the United Kingdom (UK). The mussels contained high levels of heat-stable okadaic acid (OA)-group toxins. Here we describe the environmental and epidemiological investigation carried out in response to the outbreak.

In June 2019 (day 0), Public Health England South West was notified by the local authority of three diners who were unwell following consumption of mussels in a restaurant 5 days earlier. The local authority had determined that the restaurant had had received a batch recall notice, also 5 days earlier, from the shellfish producer for the mussels because of elevated toxin levels but this was not seen before the mussels were served that day. On day 1, PHE South West received a report from the county neighbouring the first of gastrointestinal illness linked to mussels from the same producer. A multi-agency outbreak control team was therefore convened on day 2 and led by the PHE South West health protection team.

An alert was sent to all health protection teams across England on day 2 asking about any reported cases of gastrointestinal illness following consumption of mussels. Local authorities in areas of product distribution were informed of the identified risk by email. Persons reporting illness who were identified by local authorities as having consumed the affected mussels were asked by PHE to complete a bespoke questionnaire on exposure and clinical data.

A probable case of DSP was defined as an individual with diarrhoea, three or more loose stools in 24 h, or vomiting or abdominal cramps or nausea, with date of onset from 7 days before to 1 day after notification of the outbreak, and time of onset 30 min to 24 h following consumption of mussels harvested from the affected site. Confirmed cases were as probable, but with an absence of pathogens in a stool sample that would otherwise explain illness.

Thirteen individuals reported to have been unwell after consumption of mussels were contacted. Completed questionnaires were received from seven individuals, of which three were confirmed, and three probable cases. The cases ate at four separate venues. One respondent did not meet the case definition as symptom onset was more than 24 h following consumption.

The mean age of cases was 59 years (range: 37–76 years); three were male and three were female. All cases reported eating steamed mussels. Five cases ate mussels as a main course and one as a starter. Reported portion sizes ranged from 11 to 50 mussels.

The mussels were produced in an offshore marine area. A routine shellfish monitoring programme is in place throughout England and Wales, including at the affected site. As a part of this programme, the water column is sampled every 2 weeks from April to September and cell counts of potentially harmful algal species are measured. Shellfish flesh samples are also tested for the presence of selected European Union (EU)-regulated biotoxins every 4 weeks during April to September each year unless phytoplankton counts and/or shellfish toxins are quantified above specified warning limits that require further precautions, including re-testing and closure.

Lipophilic toxin determination, including that for OA-group toxins, is routinely carried out using the method specified in in the EU-Harmonised Standard Operating Procedure for determination of lipophilic marine biotoxins in molluscs by LC-MS/MS [1]. Additional flesh and water samples were taken in advance of the planned sampling date following a report to the local authority from a local fisherman of a red-coloured algal bloom six miles offshore from the production site.

The local authority determined the source of the mussels by questioning venues linked to reports of illness. Subsequently, the shellfish producer provided the outbreak control team with a complete list of all businesses who had received the affected mussels. Mussels from the site were harvested daily from 9 to 5 days before notification of the outbreak for commercial sale. The mussels were not tested by the producer for the presence of toxins. A large volume of mussels was distributed to seafood wholesalers, restaurants and pubs, and subject to the recall notice distributed by the producer 5 days before reports of illness to PHE. A limited number of businesses not linked to any known cases, including wholesalers, retailers, restaurants and pubs, responded to the recall stating they had sold some of the affected produce. No produce was found to still be in circulation at the time of the outbreak response.

Water column and shellfish flesh sampling results are summarised in Table 2. Measured densities of Dinophysis spp. in the water column increased rapidly from being undetectable 16 days before outbreak notification to 1,600 cells per litre 7 days before, coinciding with the time of harvesting of the affected batch and exceeding the England, Wales and Northern Ireland Food Standards Agency trigger level of 100 cells per litre. The level of total OA-group lipophilic toxins in mussel flesh was 338 µg OA equivalents (eq) per kg, following application of measurement uncertainty, 7 days before outbreak notification. This exceeded the maximum permitted limit (MPL) of 160 µg OA eq per kg defined by European Commission (EC) regulation 853/2004 [2]. Toxin concentrations quantified showed that an average of 94% of the OA-group toxins present in the mussels consisted of OA itself, with the remainder being dinophysistoxin 2 (DTX2).

Water column sampling 7 days before outbreak notification did not detect other harmful algal species apart from Pseudo-nitzschia spp., the causative diatom for domoic acid responsible for amnesic shellfish poisoning, at 1,320 cells per litre. This is below the trigger level of 150,000 cells per litre for this species.

Routine shellfish sampling at the same site during the same time period did not detect paralytic shellfish poisoning toxins. Trace levels of yessotoxins were detected, but along with traces of azaspiracids, they were well below regulatory levels. Amnesic shellfish poisoning toxins were below the limit of quantitation (LOQ).

In response to the elevated toxin levels quantified and reported 5 days before outbreak notification, the shellfish bed was immediately closed for harvesting as per standard practice in England. The Food Standards Agency urgently contacted local authorities of places where the affected product had been distributed to ensure that wholesalers and venues had acted upon the recall. Venues were asked whether any product had been frozen, for example in the form of stock, as this would not deactivate the toxin, but there was no evidence this had been done.


We report on six cases of DSP associated with consumption of mussels harvested in the South West of England. Without an available validated test for relevant toxins in human samples, the diagnosis was made based on characteristic clinical symptoms, including diarrhoea, abdominal pain, nausea and fever/chills, elevated levels of OA-group toxins in the flesh of mussels from the same batch as those consumed, the absence of faecal pathogens in stool of cases and epidemiological evidence of exposure to the produce.

DSP occurs following consumption of seafood containing high levels of the heat-stable OA-group toxins produced by dinoflagellates including Dinophysis spp., and is characterised by a rapid-onset of self-limiting gastrointestinal illness [3,4]. Recognised outbreaks of DSP are rare. Seventy cases were identified in 2013 following consumption of mussels harvested around the Shetland Islands [5] and 49 cases were identified in 1998 following consumption of UK-harvested mussels in London [6]. Outbreaks have been recorded in recent years in China, the United States, France and Canada [4,79].

The lowest-observed-adverse-effect level of OA is 45 to 50 µg OA eq per person [4,10]. In our study, an average main course portion of mussels (500 g in shell) would provide 41 µg OA eq., using a flesh weight yield of 24% [11]. This level of exposure is consistent with DSP as the cause of illness considering variability in portion sizes, flesh yield, body weight and toxin levels at the production site. Individual mussel sizes served were unavailable but would likely vary. Therefore, overall estimated portion weight was used to calculate the exposure dose. A limitation is that body weight (bw) was not recorded for cases and because of this, OA eq per kg bw could not be calculated.

A shellfish biotoxin programme monitoring the occurrence of harmful algal blooms and toxins in classified shellfish production areas in the UK, alongside food business operator checks, remains a robust system to protect population health. Nonetheless, a rapid increase in concentrations of Dinophysis spp. cells within the waters of the production site may have contributed to the outbreak, in tandem with shellfish harvesting occurring before official control results were reported and site closure. Whyte et al. (2014) demonstrated that a similar rapid increase in Dinophysis levels, resulting from a change in prevailing wind direction, occurred in the 2013 Shetland Islands origin outbreak [5]. Transdisciplinary research is required to predict future risk and inform monitoring, particularly given likely changes in the distribution of potentially-toxic species particularly if temperature of ocean water increases [12]. Our investigation suggested that affected produce may have been sold by restaurants and pubs with no known linked cases. Given that DSP is a self-limiting illness that may be under-reported by cases and has low awareness among clinicians, the actual number of persons affected in this outbreak is likely to be higher [13].

This outbreak highlights that clinicians and public health professionals should be aware of algal-derived toxins as a potential cause of illness following seafood consumption, and that the need for effective end-product testing of shellfish to ensure food safety remains.

Outbreak of diarrhetic shellfish poisoning associated with consumption of mussels, United Kingdom, May to June 2019



Nick Young, Charlotte Robin, Et al

E. coli O157: Which typing is better?

Due to the potential of enterohemorrhagic Escherichia coli (EHEC) serogroup O157 to cause large food borne outbreaks, national and international surveillance is necessary.

For developing an effective method of molecular surveillance, a conventional method, multilocus variable-number tandem-repeat analysis (MLVA), and whole-genome sequencing (WGS) analysis were compared. WGS of 369 isolates of EHEC O157 belonging to 7 major MLVA types and their relatives were subjected to comprehensive in silico typing, core genome single nucleotide polymorphism (cgSNP), and core genome multilocus sequence typing (cgMLST) analyses. The typing resolution was the highest in cgSNP analysis. However, determination of the sequence of the mismatch repair protein gene mutS is necessary because spontaneous deletion of the gene could lead to a hypermutator phenotype. MLVA had sufficient typing resolution for a short-term outbreak investigation and had advantages in rapidity and high throughput. cgMLST showed less typing resolution than cgSNP, but it is less time-consuming and does not require as much computer power. Therefore, cgMLST is suitable for comparisons using large data sets (e.g., international comparison using public databases). In conclusion, screening using MLVA followed by cgMLST and cgSNP analyses would provide the highest typing resolution and improve the accuracy and cost-effectiveness of EHEC O157 surveillance.

IMPORTANCE Intensive surveillance for enterohemorrhagic Escherichia coli (EHEC) serogroup O157 is important to detect outbreaks and to prevent the spread of the bacterium. Recent advances in sequencing technology made molecular surveillance using whole-genome sequence (WGS) realistic. To develop rapid, high-throughput, and cost-effective typing methods for real-time surveillance, typing resolution of WGS and a conventional typing method, multilocus variable-number tandem-repeat analysis (MLVA), was evaluated. Nation-level systematic comparison of MLVA, core genome single nucleotide polymorphism (cgSNP), and core genome multilocus sequence typing (cgMLST) indicated that a combination of WGS and MLVA is a realistic approach to improve EHEC O157 surveillance.

Effective surveillance using multilocus variable-number tandem-repeat analysis and whole-genome sequencing for enterohemorrhagic Escherichia coli O157

Applied and Environmental Microbiology

Kenichi Lee, Hidemasa Izumiya, Sunao Iyoda, Makoto Ohnishi and EHEC Working Group

DOI: 10.1128/AEM.00728-19