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About the Microbiological Testing Program for E. coli O157:H7 and non-O157 Shiga toxin-producing E. coli (STEC)

About the Testing Program
Objectives of the Testing Program
On October 17, 1994, FSIS began a microbiological testing program to detect Escherichia coli O157:H7 in raw ground beef. The objectives of the testing program have evolved over time. An original objective was to stimulate industry testing and other actions to reduce the presence of the pathogen in raw ground beef.

Today, FSIS considers product sampling to be one of several activities conducted to verify the effectiveness of HACCP systems. Since the initiation of the FSIS testing program, many grinders and suppliers of raw ground beef components have instituted programs to routinely test their ground beef products or raw materials used in ground beef products for E. coli O157:H7.

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Changes Over Time
Over time, FSIS has taken steps to improve the public health effectiveness of this testing program by detection of lower numbers of this pathogen through increased sample size and adoption of new more sensitive methods (see footnotes that accompany summary tables ). All regulatory analyses of raw ground beef and raw ground beef products are performed in FSIS laboratories located in Alameda, CA, St. Louis, MO, and Athens, GA and have been reported as of sample analysis completion date. Therefore, all text, tables and graphs through 2007 were based upon sample analysis completion date. Beginning in 2008, quarterly and annual reports and figures are based upon sample collection date. Weekly reports are still posted by analysis completion date due to overlapping from one week to the next.

Today, there are approximately 1,400 federally inspected establishments producing raw ground beef subject to 9 CFR 319.15 (a), (b), or (c), the raw ground beef products that are currently routinely sampled for E. coli O157:H7 as part of the Agency's HACCP verification program. In recent years most raw ground beef samples have been collected at the federally inspected establishments. The Agency still collects some samples from retail stores, but normally only when (1) the retail store produces raw ground beef using whole muscle or trimmings from a cutting/boning operation conducted at the store, or (2) the retail store does not maintain records of raw beef suppliers or records documenting clear and accurate grinding logs.

In earlier years, FSIS analyzed some samples from State inspected establishments when not all State programs had the capability to test for E. coli O157:H7. All States now have their own testing program for raw ground beef. The number of samples analyzed from imported raw ground beef will vary depending on the volume of imported product.

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Categories of Samples Used in Reporting
In recent years, there has been increasing interest in using the E. coli O157:H7 results as an indicator of industry trends or as a measure of program performance. For this reason, the standard table that has been used since 1994 has been revised to illustrate two categories of samples that are collected at both Federal establishments and at retail stores. The revised table uses the following definitions for categories of samples:
  • Verification Sample from a Federal Plant: Samples that are scheduled each month by randomly selecting establishments from the current population of all raw ground beef producers.

  • Routine Sample from a Retail Store: Samples that are collected by program investigators in the course of making a routine retail store visit.

  • Follow-Up Sample: Samples that are scheduled in response to a positive finding from an initial HACCP verification sample or a routine retail sample. Sample collection may or may not be the same as the location where the initial positive sample was collected. Follow-up samples include both sampling to verify corrective action and sampling to help identify the source of the contamination.

FSIS views results from the "Verification" samples from Federal establishments as the best indicator of the overall trend of the presence of E. coli O157:H7 in raw ground beef. For this reason the Agency uses the percentage of positives in these samples as one of its key performance measures. Figure 1 (PDF Only) shows the graph of this performance measure on an annual basis from 2000 through 2009.

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2007 Results: Actions Taken to Reduce E. coli O157:H7
When the Agency posted the results from 2006, it was noted that the results for the last quarter of 2006 represented the first time a three-month quarter result had been above 0.20 percent since April-June of 2004. Because FSIS had the performance measure aimed at keeping the percentage of ground beef positives below 0.20 percent, the Agency was concerned about the result showing 0.21 percent even though it seemed consistent with other recent quarter patterns and the overall results for 2006 were the same as for 2005. At the time FSIS indicated the Agency would closely monitor the 2007 results to assess whether there is any evidence of an increasing trend. Because the performance measure was clearly exceeded during 2007, FSIS initiated several actions that are summarized at http://www.fsis.usda.gov/News_&_Events/NR_102307_01_att/index.asp .

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Scheduling of Samples
The initial HACCP verification samples for federally inspected establishments are randomly scheduled each month from the most current list of establishments producing raw ground beef. The selection process has remained the same since the program was initiated, but the number of samples scheduled for a specific month can change. For example, during 2007, FSIS increased the number of samples for July 2007 after an unusual number of positive results in June. Scheduling remained at an elevated level for August through December where essentially all establishments were scheduled every month. There was also a period from 1998 through 2002 when some scheduled establishments were exempt from sample collection if they met certain criteria that were specified in FSIS Directive 10,010.1, Microbiological Testing Program for Escherichia coli O157:H7 in Raw Ground Beef, which was issued February 1, 1998.

Retail samples are not scheduled from an existing list of facilities that are producing raw ground beef. Program investigators first select retail facilities that will be reviewed. Whether or not a raw ground beef sample will be collected depends on what is observed during a review. FSIS procedures for retail sampling are covered in FSIS Directive 10,010.1, Revision 1, March 31, 2004, and updated through FSIS Notice 43-06, July 20, 2006 and through various Questions and Answers now posted with Directive 10.010.1, Revision 3.

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Seasonal Variations
The addition of 2010 results to Figure 2 (PDF Only) shows quarterly results for samples collected from all raw ground beef sources for years CY 2003 through CY 2010. The fourth quarter in 2007 produced the highest positive results from 2005 through 2007 in FSIS regulatory testing for raw ground beef. This result is anomalous because most positive results peak during the second and third quarters (April-September). Results from 2008 cannot be compared with those of previous years, because starting with CY 2008, annual microbiological results were reported by sample collection date as opposed to analysis end date. The third and fourth quarters in 2008 produced a higher number of positive ground beef samples compared to 2009. A decline in the overall percent positive was observed in CY 2009 (0.32 percent), compared to CY 2008 (0.46 percent). A decline in the overall percent positive was observed in CY 2010 (0.24 percent) compared to CY 2009 (0.32 percent).

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Trim Sampling
On March 19, 2007, FSIS began routine verification sampling of beef manufacturing trimmings intended for use in raw ground beef or beef patty products at the slaughter establishments that produced those trimmings. FSIS considers it extremely critical to keep the percent positive rate for beef trim low in order to affect the percentage of positive raw ground beef samples downward. Trim sampling was initiated with FSIS Notice 18-07, March 1, 2007. During CY 2007, FSIS analyzed 712 trim samples for E. coli O157:H7 and found 2 positive samples (0.28 percent). FSIS Notice 68-07, October 26, 2007, initiated routine verification of other raw ground beef components. Sampling of those other components began in late December.

FSIS recently identified the results of a year-long baseline study on boneless beef manufacturing trimmings designated for use in raw beef and the percent positive rate was 0.68 percent. FSIS will be tracking the percent positive rate for boneless manufacturing trimmings in FSIS verification testing and comparing results with the baseline level. FSIS believes that the percent positive rate for boneless manufacturing trimmings should at a minimum remain below this baseline value in order to reduce the likelihood that E. coli O157:H7 will be identified in ground beef.

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2008 Results
The FSIS Microbiological quarterly and yearly postings for 2008 have been reported by sample collection date. Prior to 2008, results were reported for analyses of samples completed by the end of the calendar year. Beginning January 2008, results were posted to include all samples collected within the calendar year, to better align FSIS' activities with those of other federal partners. The Agency does not anticipate this change to have any effect on the results presented. Therefore the 2008 results can not be compared to results from previous years, since those results were reported by analysis end date. FSIS continues to evaluate its E. coli O157:H7 policy and testing programs using sample results and other data sources. In January 2008, FSIS implemented a targeted sampling program that incorporates production volume and history of sample results in scheduling raw ground beef sampling for E. coli O157:H7 at federally inspected establishments. Under this new verification testing program, larger volume operations are tested more frequently than in the past, and data from the checklists (FSIS Notice 65-07) was used to determine testing frequency for establishments. The Agency also implemented a change in the laboratory testing method. The 2008 results for ground beef have been added to the summary table, and possible effects of the implemented changes are discussed below.

The overall percent positive of raw ground beef (RGB) samples tested for E. coli O157:H7 in CY 2008 was 0.46 (Table). Some of the factors identified by FSIS as possibly contributing to the percent positive for 2008 include the following:
  • Test method sensitivity: Analysis of the 2008 data by the FSIS, did not demonstrate any basis for verifying or quantifying an increased sensitivity effect for the January 2008 changes made to the E. coli O157:H7 testing method (i.e., the "new method" FSIS MLG 5.04). The FSIS validation study determined the new method to be as sensitive as the older method, but determining the impact on samples would require much more extensive study.

  • The industry may have implemented some changes in controlling the slaughtering process for some segments of the slaughter, fabrication and/or grinding process.

  • Most ground beef establishments are low volume producers, and a proportionally greater number of E. coli O157:H7 samples and positive test results are associated with these establishments relative to larger establishments. In past years, the percentage of positive samples from the smallest plants (Category 4) was considerably less than largest establishments (Category 1). In CY 2008, FSIS observed an increase in the relative percentage of positive results associated with smaller plants. However, analysis of CY 2008 data for Category 1 and 4 ground beef establishments did not confirm statistically verifiable differences for these establishment categories.

  • There could have been an increase in prevalence at pre-harvest due to unknown factors. Pre-harvest data for hides and feces carriage rate are not available for consideration, and therefore, a definitive conclusion about the prevalence of the pathogen pre-harvest cannot be made.

There were 53 positive samples from federal establishments, which includes follow-up sampling (0.47%). The initial verification sample percent positive rate was 0.45% and the follow-up percent positive rate was 1.12%. It is difficult to completely explain higher percent positive rate in follow-up samples. Positive follow-up samples may indicate a plant with sanitation problems or a supplier with sanitation problems. There was one import sample that tested positive (2.63%). All retail samples were confirmed negative.

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2009: Bench Trim Sampling
On July 31, 2009 the Agency issued a Notice (51-09, Routine Sampling and Testing of Beef Manufacturing Trimmings Derived from Cattle Not Slaughtered in That Establishment (Bench Trim) for Escherichia coli ( E. coli) O157:H7) designed to collect beef manufacturing trimmings and other raw ground beef or patty components in establishments that produce trim derived from cattle not slaughtered on site.

Establishments that produce beef trimmings from cattle slaughtered on site will continue to be subjected to sampling under the Trim Verification program, and establishments that produce other raw ground beef or patty components from cattle slaughtered on site will continue to be subjected to sampling under the Raw Ground Beef Components program.

The purpose of Notice 51-09 is to inform inspection program personnel to begin routine sampling of bench trim for E. coli O157:H7 when they receive a sample request notice with the appropriate project code. Bench Trim results are included in weekly and quarterly Raw Ground Beef and Component Testing Data tables and any positive findings are included in the Individual Positive Results for Raw Ground Beef Components table.

Some additional modifications under development for the FSIS testing method that may be implemented in 2010 and may consequently have some impact on FSIS data in the future include the following:
  • The use of a single 325-gram test portion (although the Agency does not anticipate increased sensitivity for this testing), rather than the current analysis of 5-65g samples.

  • Modifications to N60 sampling to address stakeholder concerns. The industry contends that the FSIS N60 testing is not as representative or robust as the industry's N60 testing. As the FSIS sampling and laboratory sample preparation are refined to more truly represent the N60 sample, there may be potential for some change in the observed positive sample rate.

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2009: Raw Ground Beef Sampling
A total of 12,797 raw ground beef samples were analyzed and 41 E. coli O157:H7 positives were observed in CY 2009 ( Table). There were 36 positive samples from federal establishments, which includes one follow-up sample (out of 492) and 35 (out of 11,573) analyzed from the verification testing program. From the retail stores, out of the 631 samples tested, there were 2 positive samples. The 2 positive samples were from the 619 verification samples tested. None of the 12 follow-up samples resulted in a positive E. coli O157:H7. Of the 101 imported samples tested, there were 3 positive results. The overall percent positive of raw ground beef tested for E. coli O157:H7 in CY 2009 was 0.30 percent (Figure 1, PDF Only). There was a decrease in the percent positive of raw ground beef samples in CY 2009 (0.30 percent) compared to CY 2008 (0.44 percent). The Agency did not implement any new changes to the raw ground beef sampling program in CY 2009.

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2010 Results
In CY 2010, ammoniated beef products were added to the E. coli O157:H7 verification programs. This change in the sampling frame added 4 additional beef products establishments. In addition, discussions associated with N60 sampling are on going with the goal of making this sampling method more robust.

2010 Trim and Other Components of Raw Ground Beef Sampling
Federal establishment testing collected 2,751 samples, which were analyzed from trim and components. From these samples, 13 E. coli O157:H7 positives were detected in CY 2010 (Year-End Results, 2010). Percent positive of raw ground beef components decreased by 52% in CY 2010 (0.47 percent) compared to CY 2009 (0.99 percent). The bench trim verification program analyzed 547 samples. No positives were detected resulting in a reduction from CY 2009 (0.67 percent). Import testing collected 580 samples, which produced 3 positives. The percent positive for imports increased by 27% in CY 2010 (0.52 percent) compared to CY 2009 (0.38 percent).

2010 Raw Ground Beef Sampling
A total of 12,550 raw ground beef samples were analyzed and 30 E. coli O157:H7 positive samples were detected in CY 2010 (Table). Due to a logistical error with the August scheduling, no sampling forms were sent out between August 5 and September 2. This resulted in approximately 1,100 fewer sampling forms being sent into the field than were scheduled.

The percent positive of raw ground beef verification testing for E. coli O157:H7 at federal establishments in CY 2010 was 0.23 percent (Figure 1, PDF Only). There was a 23% reduction in the percent positive of raw ground beef samples in CY 2010 (0.23 percent) compared to CY 2009 (0.30 percent). Three out of 325 analyzed samples from follow-up testing were positive, and 26 out of 11,291 analyzed samples were positive for the verification testing program (Year-End Results, 2010). A total of 905 samples were analyzed from retail stores and no positives were detected; therefore, there were no follow-up samples tested. This was a reduction from CY 2009 (0.32 percent) at retail. Twenty-nine samples were analyzed from imports and 1 positive was found resulting in a 14% increase in the percent positive of imports in CY 2010 (3.45 percent) compared to CY 2009 (2.97 percent).

Summary Tables

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2012: Testing for non-O157 Shiga toxin-producing E. coli
FSIS considers raw, non-intact beef products or the components of these products found to have six Shiga toxin-producing Escherichia coli (STEC) to be adulterated, in addition to E. coli O157:H7. (Refer to the Federal Register notice Shiga Toxin-Producing Escherichia coli in Certain Raw Beef Products | PDF). These six non-O157 STECs are O26, O45, O103, O111, O121, and O145.

On June 4, 2012, FSIS began verification testing for these non-O157 STEC in domestic and imported beef manufacturing trimmings from cattle slaughtered on or after June 4, 2012. Beef manufacturing trimmings collected from cattle slaughtered before June 4, 2012, or that contain other components such as cheek meat are analyzed for E. coli O157:H7 only.

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Last Modified Jun 08, 2013