Microorganisms play pivotal roles in food production, safety, and preservation. Their interactions with food can render it unsuitable for consumption, posing risks to food safety and public health. With over 200 identified foodborne diseases, including those caused by bacteria like Bacillus cereus, Clostridium botulinum, and Listeria monocytogenes, as well as fungi such as Penicillium and Aspergillus, and viruses like Norovirus and Hepatitis A, foodborne illnesses remain significant threats to human health.
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Advancements in food preservation techniques, such as low-temperature storage, chemical preservatives, and modified atmosphere packaging, aim to extend shelf-life and eliminate microbial contamination. However, some pathogens may survive these methods, existing as metabolically injured or dormant cells, presenting challenges to food safety. Despite improvements in food manufacturing and safety, foodborne pathogens remain significant public health risks. Various detection methods, including culture-dependent and independent approaches like polymerase chain reactions (PCR), DNA microarray, and next generation sequencing (NGS), have been developed to safeguard public health.
Fig. 1 Nucleic acid-based methods for detecting and identifying foodborne pathogens (Bosch A., et al. 2016).
Outbreaks of Foodborne Illnesses
While bacterial foodborne illnesses are more prevalent, fungal and viral pathogens also pose significant risks to public health. Continued surveillance and preventive measures are essential to mitigate the impact of these pathogens on food safety and human health.
Bacterial Foodborne Illnesses
Foodborne illnesses caused by bacteria are a global concern, contributing to significant hospitalizations, fatalities, and economic losses annually. In the USA alone, an estimated 76 million cases of foodborne illnesses occur each year, resulting in 128,000 to 325,000 hospitalizations and 3,000 to 5,000 deaths, costing the economy up to $83 billion. In the EU, there were 20,017 human cases and 3,086 foodborne outbreaks in 2020, with Salmonella being the most prevalent causative agent, particularly in eggs and egg products. Other common bacterial pathogens include Campylobacter, Yersinia, Shiga toxin-producing Escherichia coli (STEC), and Listeria monocytogenes, with L. monocytogenes-related illnesses resulting in high fatalities. Globally, foodborne bacterial pathogens contribute to around 3 million cases of diarrhoea annually.
Fungal Foodborne Illnesses
Although outbreaks of fungal foodborne illnesses are rare compared to bacteria and viruses, they still pose risks, especially to vulnerable populations. Fungal secondary metabolites, such as toxins, can lead to outbreaks, affecting individuals with suppressed immunity or undergoing immunosuppressive treatments. For instance, in 2013, over 200 people experienced gastroenteritis after consuming contaminated yoghurts with Mucor circinelloides in the USA. Similarly, an outbreak of food poisoning caused by Rhizopus microsporus affected 7 hospital patients in Hong Kong. Key filamentous fungi like Aspergillus, Fusarium, and Mucor can cause localized infections in immunocompetent individuals when consumed with contaminated food or inhaled. While invasive pulmonary diseases are common in immunocompromised patients, gastrointestinal routes can also lead to infections, emphasizing the importance of avoiding foods contaminated with fungi.
Viral Foodborne Illnesses
Viral outbreaks of food poisoning are less frequently reported but remain significant. Noroviruses and Hepatitis A viruses are among the most common foodborne viral pathogens. Noroviruses, responsible for up to 21 million cases of acute gastroenteritis annually in the USA, were a major cause of food outbreaks in the EU in 2020. Enteric viruses contribute to a significant percentage of foodborne illness outbreaks in both the EU and the US. Recent outbreaks, such as the 2018 Winter Olympics gastroenteritis outbreak in South Korea and the consumption of frozen raspberry-linked outbreak in Canada in 2017, were linked to Noroviruses. Hepatitis A virus cases, such as the 162 cases in the US in 2011 and over 1,100 cases in China in 2012, highlight the global impact of viral foodborne illnesses.
Methods for Detecting Foodborne Pathogens
Ensuring food safety by accurately and sensitively detecting pathogens in food is crucial. However, this remains a challenging task due to factors such as interference from other non-target microorganisms, low abundance of target microorganisms, and difficulty in extracting microorganisms from food matrices. Currently, there are various methods used for detecting and identifying foodborne pathogens. These methods include culture-based methods, immunological assays, and nucleic acid-based methods (such as PCR and NGS).
Culture-Based Methods
Culture-based methods, although traditional, remain the gold standard for detecting foodborne pathogens. They rely on the growth of bacteria and fungi on culture media, allowing for subsequent identification. However, they have limitations such as low sensitivity and time-consuming protocols. Yet, they are still widely used, especially when combined with other methods like PCR and MALDI TOF MS for faster and more accurate identification.
Immunological Assays
Immunological assays leverage the affinity between microbial antigens and antibodies for detection. enzyme-linked immunosorbent assay (ELISA) is a prominent method, known for its speed and specificity. Despite being prone to false positives, ELISA, along with lateral flow devices, has been extensively used for detecting bacteria and their toxins, as well as fungal pathogens and mycotoxins.
Nucleic Acid-Based Methods
PCR and its variants are highly sensitive and reproducible methods for detecting specific DNA or RNA sequences of pathogens. Variants like real-time PCR (RT-PCR) and reverse transcriptase PCR (RT-PCR) offer advantages in terms of speed and accuracy. Multiplex PCR allows for the simultaneous detection of multiple pathogens, while methods like viable PCR (vPCR) differentiate between live and dead pathogens, enhancing food safety assessments.
Next-Generation Sequencing (NGS) Methods
NGS approaches, including whole genome sequencing (WGS) and metagenomics, are powerful tools in food safety. WGS allows for the determination of whole genome sequences of isolates, aiding in pathogen surveillance. Metagenomics helps in identifying various microorganisms present in a sample. Although less applied to fungi and viruses in food, NGS has shown promise in detecting and characterizing these pathogens.
In conclusion, each method for detecting foodborne pathogens has its advantages and limitations. Combining multiple techniques can enhance sensitivity, accuracy, and speed, thereby ensuring better food safety practices. Standardized protocols and continuous advancements in technology are essential for further improving pathogen detection methods and safeguarding public health.
References
- Aladhadh M. A review of modern methods for the detection of foodborne pathogens. Microorganisms. 2023, 11(5): 1111.
- Bosch A., et al. Foodborne viruses. Current Opinion in Food Science. 2016, 8: 110-9.
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