Category Archives: Food Microbiology Research

Research – Foods implicated in U.S. outbreaks differ from the types most commonly consumed

Journal of Food Protection

Foodborne disease outbreak investigations identify foods responsible for illnesses. However, it is not known the degree to which foods implicated in outbreaks reflect the distribution of food consumption in the U.S. population or the risk associated with their consumption. To examine this, we compared the distribution of foods in 24 categories implicated in outbreaks to the distribution of foods consumed by the U.S. population. Beef, chicken, eggs, fish, herbs, mollusks, pork, sprouts, seeded vegetables, and turkey were implicated in outbreaks significantly more often than expected based on the frequency of their consumption in the general population, suggesting a higher risk of contamination or mishandling from foods in these categories than in others. In contrast, pasteurized dairy, fruits, grains-beans, oils and sugars, and root/underground vegetables were less frequently implicated in outbreaks than they were consumed in the general population, suggesting a lower risk for these food categories.

Research – Bacteria Broadly-Resistant to Last Resort Antibiotics Detected in Commercial Chicken Farms


Resistance to last resort antibiotics in bacteria is an emerging threat to human and animal health. It is important to identify the source of these antimicrobial resistant (AMR) bacteria that are resistant to clinically important antibiotics and evaluate their potential transfer among bacteria. The objectives of this study were to (i) detect bacteria resistant to colistin, carbapenems, and β-lactams in commercial poultry farms, (ii) characterize phylogenetic and virulence markers of E. coli isolates to potentiate virulence risk, and (iii) assess potential transfer of AMR from these isolates via conjugation. Ceca contents from laying hens from conventional cage (CC) and cage-free (CF) farms at three maturity stages were randomly sampled and screened for extended-spectrum β-lactamase (ESBL)-producing Enterobacteriaceae, carbapenem-resistant Acinetobacter (CRA), and colistin resistant Escherichia coli (CRE) using CHROMagar™ selective media. We found a wide-spread abundance of CRE in both CC and CF hens across all three maturity stages. Extraintestinal pathogenic Escherichia coli phylogenetic groups B2 and D, as well as plasmidic virulence markers iss and iutA, were widely associated with AMR E. coli isolates. ESBL-producing Enterobacteriaceae were uniquely detected in the early lay period of both CC and CF, while multidrug resistant (MDR) Acinetobacter were found in peak and late lay periods of both CC and CF. CRA was detected in CF hens only. blaCMY was detected in ESBL-producing E. coli in CC and CF and MDR Acinetobacter spp. in CC. Finally, the blaCMY was shown to be transferrable via an IncK/B plasmid in CC. The presence of MDR to the last-resort antibiotics that are transferable between bacteria in food-producing animals is alarming and warrants studies to develop strategies for their mitigation in the environment. View Full-Text

Research – NIH scientists study salmonella swimming behavior as clues to infection



Salmonella enterica serovar Typhimurium bacteria (S. Typhimurium) commonly cause human gastroenteritis, inflammation of the lining of the intestines. The bacteria live inside the gut and can infect the epithelial cells that line its surface. Many studies have shown that Salmonella use a “run-and-tumble” method of short swimming periods (runs) punctuated by tumbles when they randomly change direction, but how they move within the gut is not well understood.

National Institutes of Health scientists and their colleagues believe they have identified a S. Typhimurium protein, McpC (Methyl-accepting chemotaxis protein C), that allows the bacteria to swim straight when they are ready to infect cells. This new study, published in Nature Communications, describes S. Typhimurium movement and shows that McpC is required for the bacteria to invade surface epithelial cells in the gut.

The study authors suggest that McpC is a potential target for developing new antibacterial treatments to hinder the ability of S. Typhimurium to infect intestinal epithelial cells and colonize the gut. National Institute of Allergy and Infectious Diseases scientists at Rocky Mountain Laboratories in Hamilton, Montana, led the study. Collaborators included groups from the University of Texas A&M campuses in College Station and Kingsville.

Research – Possibility, duration, and molecular predictors of sanitizer tolerance in Listeria monocytogenes

Centre For Produce Safety


Due to concerns over bacterial tolerance to sanitizers, FDA and FSIS recommend rotating sanitizers in RTE food processing facilities to better control foodborne pathogens, in particular, Listeria monocytogenes (Lm). These recommendations are nonbinding; whether Lm develops tolerance to common sanitizers remains
inconclusive and debated. Even if Lm develops tolerance through sub-lethal exposure to sanitizers, how long and how strong the tolerance can last should be considered in determining whether sanitizer rotation is needed and how often it should be applied. Lack of consensus and quantitative data on possibility and duration of sanitizer tolerance creates confusions and dilemmas, especially when sanitizer rotation presents considerable challenges in training, compliance, and cost control to the industry. This proposal describes studies to help settle the debate and fill critical knowledge gaps regarding Lm tolerance to chlorine and quaternary ammonium compounds. We will measure residual sanitizer levels in produce processing facilities. We will perform laboratory assays to investigate tolerance development and persistence. We will explore machine-learning-aided tolerance prediction and identify evolutionary signals (or lack thereof) of tolerance development from whole genome sequencing data. Our results will provide the industry and regulators with scientific evidence for substantiating, better implementing, or justifiably shelving sanitizer rotational programs.

Technical Abstract

There is still no scientific consensus on whether Listeria monocytogenes (Lm) develops sanitizer tolerance. We hypothesize that development of two types of sanitizer tolerance may occur in Lm. First, short-term adaptation to sub-lethal levels of sanitizers induces acquired tolerance, which is transient and not hereditary. Second, long- term selection by sanitizers causes intrinsic tolerance, which is established in Lm populations by evolutionary changes to Lm genomes. To help settle the debate, we will test our hypothesis by distinguishing and investigating both types of tolerance in Lm using chlorine and a quaternary ammonium compound as example sanitizers.

In this study, we will survey residual sanitizer levels in a leafy green and a tomato processing facilities to evaluate if laboratory-derived sanitizer levels optimal for tolerance development are relevant to produce processors. We will assess the possibility of acquired tolerance by measuring the difference in minimum inhibition concentrations (MIC) before and after sanitizer adaptation. We will study how different sanitizer levels and exposure time affect the development of acquired tolerance, including how long the tolerance can last after exposure to sanitizers. We will explore the mechanisms behind the development of acquired sanitizer tolerance by characterizing temporal shifts in Lm transcriptome throughout the duration of the tolerance.

We will assess intrinsic tolerance in a collection of 200-300 strategically selected Lm strains using high-throughput growth kinetics assays. We will search for evolutionary evidence that suggests the development of intrinsic tolerance in recent history by analyzing whole genome sequencing (WGS) data of these strains. We
will build a machine-learning classifier to predict tolerance levels and identify key tolerance predictors from WGS.

This research will provide valuable prerequisite information for determining if sanitizer rotation is necessary for preventing the development of Lm tolerance to sanitizers. Scientific data from the project will also help optimize sanitation practices to mitigate tolerance development and determine frequency for sanitizer rotation if rotation is needed.

Research – The presence of microbial contamination and biofilms at a beer can filling production line

Journal of Food Protection

Contamination of beer arises in 50% of all events at the late stages of production, the filling area. Hereby, biofilms, being consortia of microorganisms embedded in a matrix composed of extracellular polymeric substances, play a critical role. To date, most studies have focused on the presence of (biofilm forming) microorganisms within this filling environment. Our aim was to characterize the microbial status as well as the presence of possible biofilms at a can filling line for beer by determining the presence of microorganisms and their associated matrix components (carbohydrates, proteins and extracellular DNA (eDNA)). Targeted qPCR confirmed the presence of microorganisms at ten sites during operation and three after cleaning (from 23 sites respectively). The evaluation of carbohydrates, eDNA and proteins showed that 16 sites were positive for at least one component during operation and four after cleaning. We identified one potential biofilm hotspot, namely the struts below the filler, harboring high loads of bacteria and yeast, eDNA, carbohydrates and proteins. The protein pattern was different than that of beer. This work deepens our understanding of biofilms and microorganisms found at the filling line of beer beverages at sites critical for production.

USA – FDA CORE Response Team Update


A new Salmonella Miami outbreak has been announced by the FDA in their CORE Table. The only information given is that 48 people are sick.   

Research – Pulsed ultraviolet light technology to improve egg safety, help poultry industry

Science Daily

Salmonella Eggs Food Poisoning Food Safety

Pulsed ultraviolet light can be an effective alternative to some of the antimicrobial technologies now used by the poultry industry to kill pathogens on eggshells, according to Penn State researchers, who simulated production conditions to test the technology.

Researcher Paul Patterson, professor of poultry science, College of Agricultural Sciences, suggests the technology has merit for commercial application in the egg industry.

“This study is unique because it scaled-up and applied components of standard egg processing to a conveyor and sanitizing eggs in a commercial setting,” he said. “In the absence of water or other chemical sanitizers, this technology has the potential to achieve significant — equal or greater — microbial reductions than some currently available technologies.”

Every year in the United States, an average of 287 eggs are consumed per person, and more than 14.1 billion eggs are set in hatchery incubators to produce chicks destined for the egg and meat bird industries. By reducing the microbial load on eggs, foodborne illness outbreaks associated with eggs and poultry meat can be reduced while chick health is maintained.

Research – Growth and Survival of Attached Listeria on Lettuce and Stainless Steel Varies by Strain and Surface Type


The foodborne pathogen Listeria monocytogenes lives as a saprophyte in nature and can adhere to and grows on surfaces as diverse as leaves, sediment, and stainless steel. To discern the mechanisms used by L. monocytogenes for attachment and growth on various surfaces, we studied interactions between the pathogen on lettuce and stainless steel. A panel of 24 strains (23 of Listeria monocytogenes and 1 L. innocua ) was screened for attachment and growth on lettuce at 4 o C and 25 o C and on stainless steel at 10 o C and 37 o C. Overnight growth of attached cells resulted in a 0 – 3 log increase on lettuce, depending on the strain and the temperature. Among the worst performing strains on lettuce were two from a large cantaloupe outbreak, indicating that factors important for interactions with cantaloupe may be different from those required on lettuce tissue. Strains that grew the best on lettuce belonged to serotypes 1/2a, 1/2b, and 4b and were from cheese, potatoes, and water/sediment near produce fields. Confocal microscopy of L. monocytogenes tagged with constitutively expressed green fluorescent protein indicated associations with the cut edges and veins of lettuce leaves. On stainless steel coupons, there was a 5 – 7 log increase at 10 o C after 7 d and a 4 – 7 log increase at 37 o C after 40 h. Statistically, surface growth on stainless steel was better for serotype 1/2a than for serotype 4b strains, even though certain serotype 4b strains grew well on the coupons. The latter included strains that originated from produce and water/sediment. Some strains were fit in both environments, while others showed variability between the two different surfaces. Further analysis of these strains should reveal molecular factors needed for adherence and surface growth of L. monocytogenes on different biotic and abiotic surfaces.

Spain – Mycotoxin update on the Hazard Map


In the Hazard Map database, we have updated all the sheets corresponding to the mycotoxins of the chemical hazards block:

  • Aflatoxins
  • Ochratoxins
  • Zearalenone
  • Deoxynivalenol
  • Fumonisins
  • Trichothecenes T-2 and HT2
  • Patulin

Mycotoxins are products of fungal metabolism and their ingestion, inhalation or skin absorption can cause disease or death in animals and people. The most important mycotoxins are produced by molds of the genera Aspergillus , Penicillium and Fusarium .

Among the most common mycotoxins are aflatoxins, ochratoxin A, patulin, fumonisins, zearanelone, deoxynivalenol, and T-2 and HT-2 toxins.

Research – 95% of banknotes are covered in harmful bacteria

Yahoo Finance

Some 95% of banknotes are covered in harmful bacteria that can cause a variety of serious illnesses, including MRSA, urinary tract infections, pneumonia, and even anthrax.

That is according to a new study by in conjunction with microbiologists, which swabbed 20 of the most-used currencies from around the world. The swabs were used to inoculate agar plates, which were then incubated at room temperature for one week.

The study revealed that the Canadian dollar was the dirtiest and most dangerous banknote in the world, with 209 microbe colonies discovered, spread with the harmful bacillus, a microbe with strains that can cause food poisoning, sepsis, and in rare cases, anthrax.