Pathogenic Organisms

When it comes to the food supply, pathogenic organisms can be introduced in a number of different ways. Common vectors include water, soil, waste or fecal matter, humans and animals. The ubiquity of pathogenic organisms leaves us open to developing foodborne illness, chronic conditions or deadly diseases. For these reasons, the study and control of pathogenic organisms comprises a large part of our food safety systems. It is impossible to completely eliminate these organisms from the environment, but risk can be minimized through the use of food science as a tool to better understand and detect pathogenic organisms, and measure our success at controlling them. 

pathenogenic-organisms 1The definition of a pathogenic organism is an organism capable of causing disease in its host. A human pathogen is capable of causing illness in humans. Common examples of pathogenic organisms include specific strains of bacteria like Salmonella, Listeria and E. coli, and viruses such as Cryptosporidium.




Bacteria, like other forms of life, constantly evolve to meet new environmental challenges. Changes to the ecology of bacteria, combined with complicated global supply networks, the consolidation of animal and produce operations, and the increasing consumption of convenience foods that lack a cook step before consumption are all examples of the new challenges facing the control of pathogenic organisms.


Testing technologies can discover varying degrees of detail about a bacterium, which is important for forensic investigation. For instance, not all strains of a species of bacteria are not pathogenic organisms. For instance, there are strains of the broader Salmonella species that would not harm a person, while there are many other strains that are pathogenic organisms and can cause massive damage.


In terms of testing technologies, screening methods tend to be fast and efficient, and provide the first step in determining whether contamination is present. Screens can be conducted by external laboratories, but newer tests have been designed to make in-house testing easier and more feasible with rapid technology platforms.


If a screen comes up with a positive result, further sub-typing using molecular methods can determine whether pathogenic organisms are present (specific strains that are clinically significant). Screening tests are also useful for monitoring Critical Control Points, trends and the overall efficacy of sanitation strategies, while molecular methods lend themselves more to in-depth or investigative testing for pathogenic organisms. For instance a company may conduct in-house screening using one of the commercially-available rapid testing platforms, but send their positives to an external lab that can perform a genetic analysis using advanced molecular methods to check for pathogenic organisms. Rapid screening methods are generally available at commercial labs, as well.


Emerging Risks: STECs, Antibiotic Resistance and the Future of Pathogen Control


Regulations and food safety plans need to be responsive to new threats from pathogenic organisms. Changes in the industry landscape can bring ‘new’ pathogenic organisms to light. For instance, the advent of refrigeration as a mode of food preservation provided a friendly environment for the pathogenic organism Listeria monocytogenes in cold, wet ready-to-eat plants.


As new pathogenic organisms have emerged and evolved, so too have regulatory policies and control measures to protect public health and ensure the safety of the food supply.


Science is concerned with developing tests to screen for or confirm the presence of pathogenic organisms to avoid contamination and identify trends, as well as providing early detection for new pathogenic organisms before they can cause food recalls or illness.


The term ‘new’ must be taken loosely. Bacteria, as they evolve and move throughout the environment, may or may not be picked up by diagnostic testing. For instance the strain of E. coli implicated in the 2011 outbreak in Europe in not a new superbug – it had been isolated and identified a number of years earlier. However not all discoveries of new strains are communicated to the international community, and it can be a long time between initial discovery of pathogenic organisms and the realization that they are a food safety concern.


The strain of pathogenic organism that impacted Europe, E. coli O104, is part of a wider group of E. coli strains that can cause serious illness in humans, designated Shiga toxin-producing E. coli, or STECs. Due to the particularly destructive effect these pathogenic organisms have on human health, some companies have taken the initiative to test for multiple strains routinely. In addition, the US Department of Agriculture has announced that a total of six strains of STECs, on top of E. coli O157, will now have mandatory testing requirements. Further, companies will now also be held liable for knowingly releasing products contaminated with any of these six pathogenic organisms (beginning to take effect in 2012). Test kits for E. coli O157:H7 are widely available on the commercial market, making it a feasible industry-wide option to extend those existing tests parameters to include the six new strains. It is expected that routine testing for non-O157 E. coli will grow throughout industry and regulatory requirements.


Antibiotic-resistance is also of great concern to health officials and the public, particularly as modern agriculture leads to widespread use of antibiotics for non-therapeutic reasons such as growth promotion or disease prevention in densely crowded animal operations.


As more and more antibiotics are used routinely, pathogenic organisms develop tolerance by evolving their morphology and becoming immune. Antibiotics that are used to treat important human diseases are also used in food-producing animals, leaving the door open for the treatments to become ineffective should a consumer become infected with a resistant strain. As with STECs, antibiotic-resistance has been around for a long time, however in recent years it has become more and more widely studied and publicized — although data is still lacking on the causality and progress of mitigation strategies. Further collaboration is necessary to determine the best way to regulate the use of antibiotics in food-producing animals and avoid antibiotic-resistant pathogenic organisms.


Control Measures


In order to prevent the contamination of food products with pathogenic organisms, a multi-prong approach is applied:

  • control environmental contamination with a comprehensive sanitation program and regular monitoring to assess the success of the program
  • identify risk level based on production environment and/or product category (for instance ready-to-eat meats) and establish more stringent monitoring for high-risk categories
  • Identify emerging risks through scientific monitoring and long-term trend analysis
  • scientifically validate the efficacy of kill steps or sanitation procedures
  • educate personnel and consumers about their role in preventing contamination

The application of food science is key. Screening methods have fast turnarounds, suitable for test-and-hold procedures or regular environmental monitoring. If screening results come up positive, further information can be gathered using genetic or biochemical methods (for instance determining whether the specific strain is of clinical significance, or to track the potential source).


At the production level, safety measures may be built directly into a product – for instance manipulating the product formula (water activity and/or pH) to make it inhospitable to a particular pathogenic organism of concern. Challenge studies may be conducted by external laboratories to confirm whether a particular pathogenic organism can/cannot grow in a product, based on specific formulas, processing, packaging and storage conditions etc. The results of these studies can be useful in developing a risk-classification for the product, or provide documentation to regulators or auditors confirming that a specific product formula is not susceptible to a particular pathogenic organism.


‘Kill steps’ in processing are also commonly employed to help lessen the risk of pathogenic organisms from reaching the consumer, such as the application of antimicrobials, heat treatments or pasteurization. However they are not fail safes, as product may come into contact with pathogenic organisms post-kill step, on the line or during packaging, storage or distribution. Again, techniques need to be extensively validated by science to confirm their efficacy and acceptance by industry and government. Kills steps are often used on high-risk products, such as ground beef, or products that will be shipped to high-risk populations, such as pasteurized eggs in nursing homes or schools.


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