Food Safety

Staphylococcus aureus contamination in canned tuna

July 1, 2025

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The canned tuna industry constantly battles Staphylococcus aureus contamination. However, a groundbreaking study by DeBeer et al. (2025) is set to redefine how the industry approaches food safety. This pivotal research offers critical insights into S. aureusburden in frozen precooked tuna loins and its growth under processing conditions.

What makes this study stand out is its direct challenge to the FDA’s Seafood HACCP Guide‘s 3-hour cumulative exposure time limit when product temperature exceeds 21.1°C (70°F). DeBeer et al. (2025) provide empirical evidence that this guideline is operationally unrealistic for large-scale canneries and scientifically overconservative for sealed products. Their findings reveal S. aureus growth is significantly inhibited in sealed cans due to limited oxygen availability — a crucial factor overlooked by current regulations.

The system of rules established in the EU, on the other hand, appears — at least in the view of the present author — to be well suited to preventing and controlling contamination by S. aureus. These findings are therefore of particular relevance to food retailers managing own-labels canned tuna supplies, who may wish to review their HACCP systems and audit programmes for non-EU industrial suppliers.

Methodology

The research employed a comprehensive three-pronged methodological approach to evaluate S. aureus contamination and growth dynamics in industrial tuna processing. The study was conducted at a 22,000 square metre tuna processing facility in Lyons, Georgia, USA, which processes approximately 90 metric tonnes of frozen tuna loins daily.

Certificate of analysis review

The researchers compiled and analysed 48,933 certificates of analysis (COAs) from frozen precooked tuna loin shipments received between 2011 and 2022. These COAs represented shipments from seven suppliers across Thailand, China, Colombia, Ecuador, the Solomon Islands, and Indonesia.

S. aureus enumeration was conducted using either the 3M Petrifilm Staph Express Count Plate Method (AOAC method 2003.11) or the Chinese National Method GB4789.10-2016, with detection limits varying from 3 to 100 CFU/g depending on the analytical method employed (DeBeer et al., 2025).

Typical processing conditions assessment

During a two-month period in 2011, researchers conducted focused sampling to quantify potential S. aureus increased during normal processing operations. Nine unique production lots from five suppliers were monitored systematically.

Samples were collected at three critical control points: after loin thawing (n=6/lot), from packing lines (n=6/lot), and from closed cans at retort entry (n=6/lot).

All samples underwent microbiological analysis using the 3M Petrifilm Staph Express Count Plate Method at accredited laboratories.

Extended processing time trials

To evaluate ‘worst-case’ scenarios, researchers modified standard processing procedures on three production days in August and September 2018.

These modifications included doubling the thawing period to 8-10 hours at 20°C, bypassing the chill room, and extending holding times in the retort staging area up to 5 hours at 26°C.

Both open and sealed cans were evaluated to assess the impact of oxygen availability on S. aureus growth dynamics, with samples collected at 0, 3, and 5-hour intervals.

Major outcomes

The comprehensive analysis yielded several significant findings that challenge current regulatory assumptions about S. aureus prevalence and growth in tuna processing environments.

Contamination frequency in frozen loins

Analysis of the extensive certificate of analysis (COA) database revealed remarkably low contamination rates, with only 2.14% (1,045 of 48,933) of frozen loin shipments containing detectable levels of S. aureus. Detection frequencies varied significantly by tuna species: albacore showed the highest rate at 3.06%, followed by yellowfin at 1.46%, and skipjack at 0.47%. Notably, S. aureus was never detected in bigeye (n=977) or wahoo (n=277) loins throughout the twelve-year study period. When detected, contamination levels typically ranged from 1 to 85 CFU/g, though the researchers noted potential underreporting due to calculation errors in some laboratory results (DeBeer et al., 2025).

Growth during typical processing

Under normal operating conditions, S. aureus populations remained relatively stable throughout processing. The overall detection frequency across all sampling points was 21.6% (35/162), with no significant difference in cell density between thawed loins, packed cans, and retort entry for most production lots. The highest cell density observed during typical processing was 360 CFU/g, remaining well below the 5 log CFU/g threshold associated with enterotoxin production. As DeBeer et al. (2025) conclude, ‘normal operating conditions in the packing facility do not pose a risk for SA increase for most products and production lots between loin receipt and retort staging‘.

Critical findings from extended processing trials

The most striking discovery emerged from the extended processing trials comparing open versus sealed cans. After 3 hours at 26°C, S. aureus levels in open cans reached a median of 615 CFU/g (range: 40-7,200 CFU/g), whilst sealed cans showed significantly lower levels with a median of 205 CFU/g (range: 60-460 CFU/g). After 5 hours, open cans exhibited continued growth to a median of 6,350 CFU/g, whilst sealed cans surprisingly showed decreased S. aureus levels, with only 30% containing detectable amounts (DeBeer et al., 2025).

EU regulatory framework for S. aureus control in tuna processing

The European Union’s approach to managing Staphylococcus aureus in tuna processing differs significantly from US regulations, reflecting a risk-based framework that emphasises prerequisite programmes and HACCP principles.

The primary legislative framework comprises Regulation (EC) No 852/2004 on general food hygiene, supplemented by Regulation (EC) No 853/2004, which lays down specific hygiene rules for food of animal origin, along with industry-specific guidance and standards.

Microbiological criteria, PRPs, and HACCP

Commission Regulation (EC) No 2073/2005 establishes certain microbiological criteria for foodstuffs, without providing harmonized limits for S. aureus.

The EU’s risk-based approach recognises that S. aureus control is more effectively managed through prerequisite programmes (PRPs) and HACCP-based procedures rather than end-product testing.

PRPs are not specific for a given hazard, but apply generally, addressing the environmental and operational conditions necessary to prevent contamination throughout the production chain.

HACCP Implementation Requirements

Under Regulation (EC) No 852/2004, all food business operators must implement procedures based on HACCP principles. The European Commission’s guidance document (2022/C 355/01) provides a comprehensive framework for implementing food safety management systems that integrate PRPs with HACCP-based procedures (Dongo, 2022).

For tuna processing facilities, the HACCP approach to S. aureus prevention typically identifies several critical control points:

temperature control during thawing and staging;
time limits for exposed product at ambient temperatures;
personnel hygiene and handling procedures;
environmental monitoring of processing areas;
verification of thermal processing parameters.

Good manufacturing practices and prerequisite programmes

The EU framework emphasises prerequisite programmes as the foundation for effective S. aureus control. These programmes encompass:

personnel hygiene requirements. Hands must be washed with bactericidal soap prior to handling fish and after a visit to the toilet. Workers must undergo health screening, and those with skin infections or wounds must be excluded from direct product contact areas. Regular training on hygiene practices – i.e. food safety culture, provided by Regulation (EU) 2021/382 (Dongo, 2021) – ensures consistent implementation of control measures;
environmental controls. Processing facilities must maintain sanitary conditions through validated cleaning and disinfection programmes. Personal hygiene, as well as fishery harbour sanitation, are CCPs preventing contamination of products with micro-organisms and filth. Environmental monitoring programmes should include regular sampling of food contact surfaces for indicator organisms;
temperature management. The EU approach aligns with maintaining the cold chain throughout processing. Facilities must establish and validate time-temperature combinations that prevent S. aureus growth whilst ensuring operational feasibility. Temperature monitoring systems with continuous recording provide verification of the effectiveness of control.

Industry standards and certification schemes

Beyond regulatory requirements, the European tuna industry widely adopts private certification standards that provide additional S. aureus control measures. FSSC 22000, IFS, and BRC are the most common food safety certifications that the tuna industry follows, implements, and certifies. These standards include:

FSSC 22000 (Food Safety System Certification 22000). FSSC 22000 – based on ISO 22000 standard, ISO/TS 22002-x (Prerequisite programmes by sector) and FSSC Additional Requirements (specific criteria beyond ISO standards, e.g. food fraud prevention, allergen management) – requires tuna processors to ensure continual improvement of the effectiveness of the food safety management system. This standard provides flexibility in determining operational prerequisite programmes (oPRPs) versus CCPs, potentially reducing the number of critical control points whilst maintaining equivalent safety levels;
International Featured Standards (IFS): Emphasises process control and verification activities, requiring documented evidence that time-temperature combinations prevent pathogen growth. IFS (as FSSC 22000 and BRC) certification requires annual third-party audits to verify implementation effectiveness;
British Retail Consortium (BRC) Global Standard: Requires comprehensive microbiological monitoring programmes, including environmental sampling for pathogens. Like the other schemes mentioned above and all others recognized by GFSI (Global Food Safety Initiative), this certification system requires a risk assessment of all processing steps and the validation of control measures tailored to each specific operation.

Specific control measures for tuna processing

European tuna processors are used to implement multiple barriers to prevent S. aureus contamination and growth:

raw material controls. Suppliers must provide certificates of analysis demonstrating compliance with agreed specifications. Using the HACCP decision tree, eight CCPs are usually identified, namely: fish receipt, frozen storage, racking and staging, metal detection, vacuum sealing, thickness rolling, retorting, and bulk incubation/seal testing;
processing controls. Time limits for product exposure at temperatures above 10°C must be established based on validated studies. The incorporation of modified atmosphere packaging or vacuum sealing can provide additional hurdles to S. aureus growth, as demonstrated in recent research;
verification activities. Regular microbiological testing of in-process and finished products validates control effectiveness. The incorporation of PrPs in the ISO 22000 made the system more flexible by reducing the number of CCPs (8 in the HACCP system) to 4 without compromising the safety of the product.

Harmonisation with international standards

The EU framework is aligned with the principles of the Codex Alimentarius, while also allowing flexibility in its implementation by the industry. The Codex Alimentarius‘ standard CAC/RCP 1-1969 ‘General principles of food hygiene’ is the basic document to protect public health from hazards in food and to promote international trade of food through harmonised FSMS requirements at a global level. This harmonisation facilitates international trade whilst ensuring consistent food safety standards across global supply chains.

The European approach demonstrates that effective S. aureus control relies on comprehensive preventive measures rather than prescriptive end-product standards. By integrating regulatory requirements with industry best practices and certification schemes, European tuna processors maintain high safety standards whilst adapting controls to specific operational conditions. This flexibility, combined with robust verification systems, provides a model for risk-based food safety management applicable across international markets.

Discussion

The study’s findings provide crucial evidence supporting a re-evaluation of current regulatory guidance for tuna processing operations. The dramatic difference in S. aureus growth between open and sealed cans represents a paradigm shift in understanding microbial behaviour in this context.

The researchers attribute the reduced growth in sealed cans to limited oxygen availability, noting that sealed tuna cans contain minimal headspace oxygen (2.1-2.3%), insufficient to support aerobic respiration. This finding aligns with previous research demonstrating decreased S. aureus growth rates under anaerobic conditions (Belay & Rasooly, 2002). The dynamic shift from aerobic to anaerobic conditions during can sealing appears to significantly impact metabolic efficiency and replication rates of S. aureus.

The current FDA guidance, based primarily on data from steak and kidney pie mix under aerobic conditions, may not accurately reflect the unique conditions present in sealed tuna cans. The study highlights that the reference data used to establish regulatory limits were ‘provided to the ICMSF in 1990 as a personal communication from C. Adair, Unilever, with very limited information related to the experimental methodology‘ (DeBeer et al., 2025). This lack of transparency and product-specific data underscores the need for evidence-based regulations tailored to specific food processing operations.

The research also reveals important insights about supplier variability in S. aureus contamination. While one major supplier responsible for 96% of shipments maintained consistently low contamination rates, two minor suppliers showed dramatically higher detection frequencies (94.3% and 100% respectively). This variability emphasises the importance of robust supplier verification programmes and regular monitoring of incoming raw materials.

Implications for industry practice

The findings have significant implications for commercial tuna processors and regulatory bodies. The data support extending cumulative exposure times beyond the current 3-hour limit for sealed products, where oxygen limitation provides an additional hurdle to S. aureus growth. However, the study emphasises that any relaxation of requirements must be accompanied by stringent hygiene practices and regular verification testing.

For open cans, the rapid S. aureus growth observed reinforces the need for immediate sealing after filling. The study notes that under normal operations, facilities pack and seal 1,200-1,500 cans per minute with only 1-2 minutes between packing and sealing, effectively minimising exposure time and associated risks. The researchers conclude that ‘potential SA growth and SE production risks related to extended dwell times in open cans are not reasonably likely to occur and, thus, do not warrant consideration in HACCP plan development‘ (DeBeer et al., 2025).

The research underscores the importance of maintaining the 2-hour maximum staging time for sealed cans, whilst suggesting this provides an adequate safety margin. The data indicate that the current 3-hour cumulative exposure time recommendation is ‘an overly conservative estimate that is unnecessarily restrictive and should be adjusted‘ for sealed can operations.

Conclusions

This comprehensive analysis of S. aureus behaviour in commercial tuna processing provides compelling evidence for reconsidering current regulatory guidance. The key findings demonstrate that sealed cans present a significantly lower risk for S. aureus growth compared to open cans, primarily due to oxygen limitation. The extensive industry data showing low contamination frequencies and levels in incoming frozen loins, combined with minimal growth during typical processing conditions, support the feasibility of extending cumulative exposure times while maintaining food safety.

The research highlights the critical need for product-specific regulations based on empirical data rather than generalised models. As DeBeer et al. (2025) emphasise, ‘future research is needed to quantify and model SA growth rates in various tuna types and in sealed cans to support confident and accurate recommendations of cumulative exposure times during tuna processing‘. The study provides a robust foundation for developing science-based regulations that ensure food safety whilst avoiding unnecessarily restrictive requirements that challenge operational feasibility in commercial tuna processing.

The implications extend beyond the tuna industry, suggesting that regulatory frameworks should consider the unique characteristics of different food processing operations, including factors such as oxygen availability, product composition, and processing conditions. This research exemplifies the importance of industry-academic collaboration in generating the empirical evidence necessary to inform effective food safety policies that protect public health without imposing impractical constraints on food processors.

For food retailers developing private label canned tuna products, these findings offer crucial insights for supplier management and quality assurance protocols. The demonstrated safety of sealed cans under extended processing times provides retailers with scientific justification to work with suppliers on optimising production efficiency without compromising food safety standards. The variability in S. aureus contamination between suppliers also underscores the importance of rigorous supplier auditing programmes and the value of partnering with processors who maintain robust HACCP systems and verification procedures.

Dario Dongo

References

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Commission Regulation (EC) No 853/2004 of 29 April 2004 laying down specific hygiene rules for food of animal origin. Consolidated text: 09/11/2024 http://data.europa.eu/eli/reg/2004/853/2024-11-09
Commission Regulation (EC) No 2073/2005 of 15 November 2005 on microbiological criteria for foodstuffs. Current consolidated version: 08/03/2020 http://data.europa.eu/eli/reg/2005/2073/oj
Commission Regulation (EU) 2021/382 of 3 March 2021 amending the Annexes to Regulation (EC) No 852/2004 of the European Parliament and of the Council on the hygiene of foodstuffs as regards food allergen management, redistribution of food and food safety culture. http://data.europa.eu/eli/reg/2021/382/oj
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