Data-Driven Food Safety: E. coli Testing as a Tool for Process Control in Beef Plants

By John Scanga, Ph.D 

Challenges in the Beef Production Environment 

No matter what interventions we apply in the live animal or production environments—whether it's researching vaccines for Escherichia coli or Salmonella, using chlorinated water, administering probiotics or prebiotics, or any other control strategy—there’s one hard truth: fecal material is inherently dirty, and we will never be able to make it clean. Our priority, then, is to keep it off the carcass to reduce the risk of foodborne illness. 

Foodborne illness often stems from the transfer of fecal material from the animal environment to the final food product. Preventing that transfer is a straightforward goal in theory—but in practice, it's incredibly challenging. This becomes even more complex in high-capacity processing plants, some of which operate at speeds of up to 390 head per hour. The scale, speed, and intricacy of these facilities make effective contamination control a constant and critical challenge. 

Approaches to Food Safety in Beef Production 

To ensure food safety in beef production, we rely on a concept known as multiple hurdle technology. This approach integrates a combination of interventions—such as the application of heat, organic acids, chemical reducers, and physical methods like trimming—to reduce or eliminate physical, chemical, and microbiological contaminants from the carcass. These steps are implemented throughout the process, from the arrival of the live animal to the final beef product, with the goal of minimizing food safety risks at every stage. 

An essential part of this system is the ability to monitor and verify the effectiveness of these interventions. That’s where microbial testing comes into play. Within beef and meat processing plants, samples are routinely collected and submitted for laboratory analysis to ensure ongoing control and compliance. These tests typically fall into four key categories: 

1. Pre-operational sanitation swabs 
   • Used to assess the cleanliness of equipment and surfaces before production begins. 
2. Generic E. coli carcass swabs 
   • Collected from carcasses as part of regulatory compliance (mandated under the HACCP "Mega-Reg") for both pork and beef slaughter operations. 
3. Harvest monitoring 
   • Process verification testing conducted during harvest to evaluate intervention efficacy and process control. 
4. Pathogen verification 
   • Targeted testing to detect and verify the absence of specific pathogens such as Salmonella or E. coli O157:H7. 

These sampling strategies play a critical role in verifying that food safety systems are working as intended and help identify any areas that may require corrective action.

Pre-operational (Pre-op) Swabs 

Pre-operational swabbing is a microbiological sampling method used to verify the effectiveness of cleaning and sanitation procedures before production begins. These swabs are collected throughout the facility to assess environmental cleanliness, with sampling typically conducted across four standardized zones: 

• Zone 1: Direct product contact surfaces (e.g., conveyor belts, cutting tables) 
• Zone 2: Areas adjacent to direct contact surfaces (e.g., equipment framework) 
• Zone 3: Broader areas within the production environment, away from product contact (e.g., floors, walls) 
• Zone 4: Non-production areas (e.g., welfare spaces, locker rooms) 

Pre-op testing is critical—not only for verifying sanitary conditions, but also for enabling production to be segmented into smaller, traceable lots. If sanitation practices are inadequate or documentation is lacking, a product recall may have to include all production since the last documented and verified cleaning, greatly increasing the scale and cost of the recall. 

Pre-op Analytics 

The true value of pre-op testing emerges when data is consistently collected, analyzed, and used to drive continuous improvement. For example, results from monthly pre-op tests can be tracked against an internal hygiene standard to evaluate trends over time. 

In the case illustrated in Figure 1, a target benchmark of 2 log CFU/cm² was established, with an ideal goal of achieving non-detectable levels near the test limit of detection (10 CFU/cm²). While this plant frequently met the target, data analysis revealed specific areas where sanitation could be improved.

These insights are then shared with the sanitation team to identify and correct problem areas—often hard-to-clean locations like belt crevices, cutting board stands, or hidden structural components. This data-driven approach helps maintain a consistently clean environment and reduces the risk of contamination entering the food supply.

E. coli Carcass Swabbing

For beef slaughter operations, regulatory guidelines require the collection of E. coli samples at a minimum rate of one test per 300 carcasses, or at least one test per week, whichever is greater. This swabbing process is conducted using either a sponge stick or cellulose sponge, and samples are taken from three specific areas of the carcass:

• Hind leg
• Flank
• Brisket/forearm

Each of these areas is swabbed over a 100 cm² surface, yielding a total sample size of 300 cm², which is then combined into a single sample for analysis.

Testing & Data Analysis

These carcass swabs are tested primarily for total coliform counts and generic E. coli. The results are intended to verify the effectiveness of sanitary dressing procedures and overall process control within the plant.

In practice, however, the majority of results fall below detectable limits—meaning they return as zero. This leads to a situation where, from a data perspective, the results are difficult to interpret or utilize. You can't compute meaningful averages or standard deviations from zeros, which limits the value of this data for statistical process control.

When these results are plotted on a control chart, you often end up with a flat line of zeros. Occasionally, a detectable colony may appear, but it’s rare. From a regulatory standpoint, the upper control limit is set at 2 log CFU/cm². Plants consistently exceeding that threshold are likely facing serious issues—not just with compliance, but with overall viability.

So, while this testing is mandatory, it’s often of limited practical value when it comes to driving process improvements or verifying food safety interventions. Plants must perform this testing daily, but its usefulness in monitoring real-time process control is minimal.

Harvest Monitoring in Beef Processing

A harvest monitoring program in a large beef processing facility is designed to look at bacteria throughout the process. It measures the transference of contamination from the hide to the carcass through the sanitary dressing process.

The incoming load that's on the hide will vary based on many conditions and uncontrollable variables – season, cattle type, production environment, whether they're grass fed or grain fed, if it rains outside and pen conditions are wet, and more.

At the end of the day, a beef packer doesn't get to choose when to slaughter cattle and must deal with what comes in the back door. Sometimes the bacterial load is high and sometimes it's lower, but regardless of what it is, it's important to understand that ebb and flow of that microbial load and how control measures address this throughout the process.

4-site Sampling Protocol for Harvest Monitoring

To evaluate microbial reduction and control, a standardized 4-point sampling process is used during harvest:

1. Hide-on Sample
   • Area: 100 cm² (shoulder)
   • Purpose: Measures incoming microbial load. The shoulder is typically the highest contamination point on the hide.
2. Pre-Evisceration Sample
   • Area: ~8000 cm² (hindquarter/round)
   • Purpose: Taken after hide removal but before splitting or evisceration; indicates how much contamination transfers from the hide to the carcass.
3. Post-Evisceration Sample
   • Area: 4000 cm² (brisket and fore shank)
   • Purpose: Collected after carcass washing, splitting, and evisceration, before final antimicrobial interventions.
4. Post-Final Intervention Sample
   • Area: 4000 cm² (brisket and fore shank)
   • Purpose: Taken after final interventions such as hot water washes, organic acids, or trimming. Reflects the final microbial status before chilling.

Using Harvest Monitoring for Process Improvement

The data collected from these four sampling points allows processors to visualize the effectiveness of their intervention strategies across the harvest process.

In this example shown in Figure 4, top to bottom demonstrates the microbial load reduction at each stage.

• Blue Line (Hide-on): Represents initial load, typically measured using Aerobic Plate Count (APC) and Enterobacteriaceae (EB) as a fecal contamination indicator. Expect high counts here.
• Purple Line (Pre-Evisceration): Reflects sanitary dressing effectiveness. A strong reduction (e.g., 6–6.5 log drop) indicates successful contamination control.
• Red Line (Post-Evisceration): Captures remaining bacteria after internal organ removal and washing.
• Green Line (Post-Final Intervention): Demonstrates how well the last interventions perform—ideally showing near-complete reduction before the carcass enters the cooler.

This full-profile approach allows facilities to track microbial reduction from entry to exit—e.g., from ~10 logs on the hide to ~1 log at final intervention.

The fluctuations in the data show that processors don't always get to full reduction of bacteria. There are days where those post-intervention carcasses don't perform as well as they would like, and those are opportunities for plants to understand where opportunities are for training, best practice implementation, and process improvements.

Interpreting APC vs. EB Results

• Enterobacteriaceae (EB): Acts as a fecal contamination indicator—a direct reflection of sanitary dressing performance.
• Aerobic Plate Count (APC): Represents overall bacterial presence, including environmental and non-fecal organisms.

If APC levels spike but EB remains low, the issue may stem from environmental contamination rather than fecal transfer from the hide. Conversely, elevated EB levels signal potential breakdowns in sanitary dressing or fecal contamination control.

Some facilities may consistently control EB so effectively that results read as zeros. In these cases, monitoring APC trends can provide more nuanced insight into broader sanitation performance and highlight areas for ongoing improvement.

Pathogen Verification Testing

Although daily trim testing for E. coli is not explicitly required by regulation, it functions as a “pseudo-requirement.” In practice, if a facility were to omit this testing, it would prompt intense scrutiny from regulatory agencies. To that end, the FSIS Directive 10,010.1 – Sampling Verification Activities for Shiga Toxin-Producing Escherichia coli (STEC) in Raw Beef Products – provides clear guidance on how these verification activities should be conducted.

Under the Federal Meat Inspection Act (FMIA) (21 U.S.C. 601(m)(1)), any raw, non-intact beef—or intact beef intended for use in non-intact products—that is contaminated with one of the seven regulated STEC serogroups (O157, O26, O45, O103, O111, O121, O145), and tests positive for Shiga toxin (stx) and Intimin (eae) genes, is considered adulterated.

Trim Sampling Methodologies

Most facilities now treat a single 2,000 lb combo bin of beef trimmings as an individual lot. If testing detects a pathogen in a bin, only that bin is affected. Even if hundreds of bins are tested daily, a single positive result does not impact the others—unless a pattern of consecutive failures emerges, which may prompt broader investigation.

There are two primary means to sample the trim:

• Surface Excision – N60 and N60 plus
  • 60 individual pieces of trim in a bag that weighs a minimum of 375 grams.
• Manual (MSD) and Continuous Sampling Devices (CSD) - the MicroTally Cloth
  • Sample verification using a cloth material that is rubbed across the top of that combo bin for 90 seconds, in the case of the MSD process, or mounted on a cassette at the end of a trim belt to allow the trim to rub across the surface of the swab as the trim falls off the belt.

As of February 2023, FSIS revised Directive 10,010.1 to officially adopt the manual sampling device for all their verification sampling; however, surface excision is still commonly performed.

Analytics – Virulence Target Index Reporting

Data from PCR testing can be leveraged to track not just presence or absence of STEC but also patterns in virulence gene expression. These include:

• O-antigen targets (serogroups)
• Shiga toxin 1 (stx1)
• Shiga toxin 2 (stx2)
• Intimin (eae)

By calculating a Virulence Target Index Ratio—comparing the number of gene targets detected to the number tested—plants can gain valuable insight into microbial activity within their process.

An increasing index ratio often correlates with positive results, which is logical – positives cannot occur without a detectable signal.

By trending this data over time, facilities can identify:

• Sudden spikes or unusual patterns in virulence markers
• Early indicators of process control breakdowns
• Effectiveness of sanitation and intervention protocols

This index serves as a powerful process control tool that enables proactive decision-making and reinforcing confidence in the plant’s sanitary dressing and food safety systems.

Conclusion: Beef E. coli Control Through Better Data

As the beef industry continues to refine its food safety systems, one thing remains clear: consistent monitoring and analysis of Escherichia coli test results are vital. From pre-op swabs to harvest monitoring and STEC testing, each data point adds to a broader picture of risk—and opportunity.

By leveraging E. coli test results not just for compliance, but as a strategic tool for beef E. coli control, processors can create safer food, build consumer trust, and stay ahead of regulatory expectations.

Questions on how to apply these tools to your operation?

Connect with an expert.

References

1. Authur, T.M., Bosilevac, J.M., Nou, X., Shackelford, S.D., Wheeler, T.L., Kent, M.P., Jaroni, D., Pauling, B., Allen, D.M., & Koohmaraie, M. (2004). International Association for Food Protection Escherichia coli O157 Prevalence and Enumeration of Aerobic Bacteria, Enterobacteriaceae, and Escherichia coli O157 at Various Steps in Commercial Beef Processing Plants. Journal of Food Protection, Vol. 67, No. 4, 2004, Pages 658–665 Copyright Q.

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