Safe Guarding Your Food from Harmful Microorganisms and the Impact of Our Changing Climate

We’ve all seen those signs posted throughout restaurants, and public restrooms “All employees must wash their hands before returning to work”. That being said, how many of us have seen people walk out of a bathroom stall and bypass the sinks? A study at Michigan State University (MSU) reports that despite posted signs and proper employee training, hand washing practices of individuals on campus still fail to meet recommended standards, with only 5.3% of individuals washing hands with soap and water for >15 seconds (1). Carl Borchgrevink, the Interim School Director-Management for the The School of Hospitality Business at MSU, comments that he “was surprised by the overall findings. In part because their study’s numbers differed significantly from the numbers other researcher[s] had reported. As they typically used self-report! I was also surprised by the low numbers given our surroundings. People should be more concerned and diligent in the college setting (many people together/using the same spaces and touching the same surfaces).” What does this mean for the food we buy in grocery stores and restaurants?

Measures to Reduce Harmful Microorganisms in Food

According to government agencies tasked with safe guarding our foods (such as the United States Department of Agriculture (USDA), U.S. Food and Drug Administration (FDA), and Agriculture and Agri-Food Canada (AAFC)), there are simple steps we can take to protect ourselves and prevent hazardous microbes entering our food. These include: 1- properly washing hands (2) and surfaces frequently; 2- keep foods separate (don’t cross-contaminate); 3- cook all foods as directed; and 4- refrigerate as soon as possible.  These steps apply at all stages of food preparation – production, harvest, as well as preparation in restaurants and your own kitchen. Washing your hands and kitchen surfaces is an easy task, but the agricultural and husbandry industries need to apply these practices on a much larger scale (tractor autoclave anyone!?), whilst also considering the land’s current and previous usage/condition (i.e. organic manure that’s been properly aged/treated or chemical fertilizer, frequency of fertilizer usage, presence of toxic compounds in the soil, etc), and water quality. 

Moussa Diarra, a researcher at AAFC, says that “We will need to change animal production or food processing practices. For example we are trying to decrease antibiotic use during animal production which will help decrease the emergence of antimicrobial resistant bacteria in the food chain. The market is switching from conventional production, to organic production, which means we have more environmentally and animal friendly practices, with less chemicals or antibiotics.”

An additional perspective provided by James Tiedje, who’s been Director of the Center for Microbial Ecology at MSU since it was established in 1989 and involved in agricultural farming for many years, states that: "Food safety includes two principles: keeping food production systems free of pathogens, and keeping the natural, non-pathogenic populations healthy since they can also be a barrier to pathogen establishment. Climate change, especially moisture and temperature extremes, open opportunities for a shift in the normal microbial community to ones that can include pathogens."

Detecting Microbial Hazards

What happens when following the preventative steps outlined above aren’t enough? How can one determine if hazardous microbes have been introduced? Generally speaking, two main methods of microbial detection exist: 1- the traditional microbiological technique of culturing for known or expected pathogens and 2- molecular methods such as analyzing for microbial nucleic acids (DNA or RNA) (3-7). Traditional microbiological methods can be time consuming, sometimes taking 4 – 6 days for target microbes to grow. Culturing is not always straight forward, as <1% of microbes will grow in the lab environment (8) – the difficulty mainly lies in mimicking a microbe’s natural environment (preferred nutrients at ideal concentrations, chemical and physical conditions, community reliance, inhibiting the faster growing microbes). That being said, culturing is somewhat simplified when you know what microbes you’re looking for (especially when the conditions required for growth have already been worked out).

Genetic detection and understanding microbial genomes is of increasing importance, as microorganisms efficiently adapt to changing conditions, often facilitated by horizontal gene transfer (9). A key part of molecular detection includes extracting DNA or RNA from the sample, the methodologies of which vary depending on sample type (10-14). Screening for nucleic acids is quicker than culturing, as typical DNA extraction methods (though the method used should be optimal for target nucleic acids and sample type (15-18)), PCR amplification and electrophoresis can normally be completed in a day. On the other hand, quantitative-PCR can speed up the process even further with on-instrument analysis which removes the need for an electrophoresis step (19, 20). Though an important note of consideration for any PCR method is the quality of template and primer design methodology (21). Shotgun or whole-genome sequencing can provide more in depth information regarding the microorganisms present in a sample (22-24). However, in most cases the FDA still requires that pathogenic microbes be cultured for identity confirmation and regulatory purposes (3). An alternative becoming more popular is the use of mass-spectrometry for pathogen identification (25), but as with any technique it has its own limitations (26) and requires expensive equipment for labs looking to establish it.

Impacts of climate change on microbial food safety

In order to survive, both animals and plants must be able to adapt and evolve in response to changing conditions. This is also true for pathogens as they respond and adapt to our changing climate allowing them to persist and flourish (27-29). Our climate is experiencing changes in temperature and precipitation patterns, an increase in frequency and intensity of extreme weather, as well as oceanic warming and acidification, which also result in changes in the way complex contaminants are transported– all of which impact our food safety (28, 30). 

As many pathogenic microbes demonstrate increased survival in wetter and warmer conditions, there are numerous studies demonstrating a correlation between the impacts of climate change and incidents of foodborne illness (27, 28, 31). To consider one example, Vibrio species are common estuarine and marine organisms typically associated with shellfish. Vibrio related infections in humans typically occur through exposure to seawater or contaminated undercooked shellfish. Baker-Austin et al (2017) discuss the steady increase of Vibrio infections from late 1990s to mid-2000s, and propose that given the connection of Vibrio infections with warmer marine temperatures, Vibrio species detection could serve as a benchmark of sorts for global warming (32). 

Food safety in the future?

Researchers continue working on better understanding current and evolving methods for safe-guarding our food. USDA scientists are investigating how pathogens typically associated with table grapes are impacted during shipping by ~90% moisture, antimicrobial SO2-generating pads that are shipped with commercial table grapes, while at transit temperatures of ~1.1 °C – their results indicate that shipping conditions have varying growth reduction capabilities depending on the pathogen (33). AAFC researchers are even looking into the use of cranberry or blueberry extracts in place of antibiotics for both maintaining health and preventing bacteria-related illnesses in broiler chickens – Diarra says: “We started with cranberry juice in 2005 and found that cranberry by-products/extracts are even more affordable and contain increased amounts of bioactives when compared to cranberry juice. This project is ongoing, and so far shows promising results indicating that cranberry by-products seem to be as effective as an antibiotic in maintaining the chicken’s gut health. We are also studying other fruit by-products, like those from blueberry for example. Both cranberry and blueberry extracts/by-products have potential to be effective in controlling chicken’s gut microbiota during production.” 

With continual advances in science, we can anticipate that quicker and more efficient methods of microbial detection are inevitably ‘just around the corner’ (34-36). Diarra says “climate change can provide an opportunity for pathogenic bacteria to spread, or to enter a new habitat, detection and monitoring bacteria in the environment is really a challenge. We need to be able to detect bacteria quickly, even in real-time if possible, during agri-food production. Understanding the extent to which bacteria are present in the food production environment in relation to weather conditions, is important for food safety.” An ideal solution would be simply being able to add a sample (such as a tissue section of fruit/vegetables or post-butchered meat) to a small handheld device (37), and receive an output telling you whether the food is safe for consumption, what foodborne pathogen(s) may be present, the potential source of contamination, and possibly even a method for removing that pathogen. An important aspect for the feasibility and efficiency of any such device in the future will also depend on cooperation and global input of pathogenic information to databases (37, 38).

No matter what the future holds, properly wash those hands and surfaces!

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