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on February 12, 2007

Get Ready for FDA’s New Rule

A proposed FDA rule will increase the frequency of assays to detect possible Salmonella Enteritidis (SE)infection in flocks.

The proposed FDA rule on prevention of SE (Salmonella Enteritidis), which will probably be finalized in 2007, will increase the frequency of assays to detect possible infection in flocks. The introduction of voluntary Egg Quality Assurance Programs (EQAPs) following the emergence of SE, the USDA mandated post-harvest chilling of product coupled with use of pasteurized products and improved handling at the institutional and consumer levels, has reduced incident cases of SE in the United States.

A decline in outbreaks from a total of 81 in 1990 to a plateau of 30 since the early 2000s attests to the efforts of egg producers, food service and institutional operations. Unfortunately, progress in elimination of SE infection in consumers has stalled at a time when surveillance systems including FoodNet and advanced microbiological techniques have improved the capability to diagnose and record SE in patients.

Of the approximately 960 outbreaks involving 32,000 cases from 1975 through 2002, CDC was able to determine a vehicle of infection in 45% of the investigations. Of these, 79% were attributed to eggs or meals containing egg products. From 1992 through 1999, 76% of 202 outbreaks with a confirmed vehicle of infection were attributable to eggs or egg products. Accepting that 16% of SE infections which are diagnosed each year were acquired outside the USA, the FDA attributes a mid-range estimate of 66% of incident cases of SE in the USA to consumption of contaminated eggs.

The FoodNet database confirmed an SE incidence rate of 2.32 cases per 100,000 of the U.S. population in 2002, indicating persistence of reservoirs in eggs despite the emergence of new vehicles. The CDC confirmed a relatively stable number of confirmed SE isolates from patients during the period 2000 through 2004, with annual values ranging from a low of 4,914 in 2003 to a high of 6,847 in 2000. The FDA calculates that there are approximately 120,000 incident cases of SE annually in the United States. Although this figure is subject to question since it incorporates numerical assumptions relating presumed and diagnosed cases, it is evident that SE infection persists in flocks in the Midwest and Western states and to a lesser degree, in the Mid-Atlantic and Great Lakes regions.

Status of EQAPs

Currently, various state and national voluntary programs cover between 60% and 70% of shell-egg production in the United States. The intensity of sampling varies among programs with the Pennsylvania EQAP the most rigorous. Many of the state EQAPs and the widely-followed United Egg Producers 5‑Star Program require evaluation of the status of flocks by assay of drag swabs from manure two to three weeks before depletion (Figure 1).

Delaying the first sampling age of layers to within two weeks before depletion exposes consumers to the possibility of vertical egg-borne infection by transovarial or transoviductal transmission. Given persistence of infection on a typical 8- to 12-house in‑line complex, hens will become infected shortly after transfer. There will be two peaks of excretion of SE, usually following onset of production during the first and second cycles.

Stress associated with initiation of egg-laying, climatic extremes or exposure to immunosuppressive or intestinal pathogens may activate proliferation of Salmonella in the intestinal tract with the possibility of systemic dissemination of infection to the reproductive tract in susceptible hens.

Sampling flocks within two weeks of depletion obviously absolves the producer of the need to take any direct action such as diversion of eggs to breaking and pasteurization in response to a positive finding. The long period between transfer and depletion after the second cycle effectively allows potentially contaminated eggs to enter the market.

The second problem with current SE surveillance systems relates to the inherent insensitivity of the drag swab assay under commercial conditions. Studies have shown that the moisture content of the manure beneath cages or in pits can affect the rate of recovery of SE in addition to a number of operator and environmental variables.

Not all laboratories function in accordance with the approved NPIP enrichment and isolation protocol and SE isolation is at best dependant on technical and operator variables. In some instances, split samples of drag swabs sent to two different laboratories have yielded negative and positive results.

The National Animal Health Monitoring System Study conducted in 1999 showed that 7% of layer houses were infected with SE. More significant was the revelation that 13% of high-rise units tested positive. Published extracts from the NAHMS survey in peer‑reviewed journals detail risk factors associated with infection including rodent infestation, defective biosecurity and incomplete inter-flock decontamination.

The aim of SE surveillance is not simply to pass a test or to comply with the rules of a self-serving program. The objective should be for our industry to identify infected flocks and complexes and to take appropriate action to suppress as far as possible, the presence of SE in flocks and to reduce the risk to consumers. The various modalities including conforming to NPIP programs to ensure that SE-negative chicks are placed, vaccination, effective biosecurity, and rodent suppression are only part of the continuum which extends beyond farms to include appropriate egg-washing and maintaining a cold chain from the point of production through to sale and implementing safe handling and preparation in domestic and institutional kitchens.

FDA Proposed Rule

The FDA has jurisdiction over aspects of egg production and distribution under both the Federal Food Drug and Cosmetics Act and the Public Health Service Act. The Proposed Rule relating to “SE Prevention Measures” issued in terms of 21 CFR Parts 16 and 118, closely follows the principles promoted by UEP. These encompass purchase of SE-free pullet chicks, biosecurity procedures, suppression of rodents, decontamination of infected farms and appropriate handling and storage of eggs. Environmental testing is regarded as the “cornerstone” of the program.

The proposed rule requires purchase of “U.S. S. Enteritidis Monitored” pullets, conforming to NPIP guidelines and regulations. Section 118.5(a) of 21 CFR will mandate assay of the environment of flocks, presumably by drag swabs, at 40 to 45 weeks of age and then 20 weeks after the completion of a molting program if the flock is retained for a second cycle. Combining the proposed FDA Rule with current industry practice, following the UEP “5-Star Program,” an integrated producer would assay pullet chicks (paper in boxes at delivery), pullets at 14 weeks, hens at 40-45 weeks, and finally, 2 weeks prior to depletion for single-cycle flocks. Second-cycle hens would be re-sampled 20 weeks after onset of production and approximately two weeks before depletion.

SE Case Study

The problem of insensitive detection is illustrated by the diagnostic sequence encountered by a commercial operation depicted in Figure 2. The history of the eight-house complex is shown in Figure 2.1, confirming isolation in four of the houses monitored over a six- year period. The infrequent pattern of sampling was determined following the EQAP, which required testing of a flock only two weeks before depletion, coupled with a benign indifference on the part of management to monitoring for SE.

On review of the farm records including the positive result on one of 14 drag swabs from house #8, management was requested to repeat drag swabs on house #8 which was SE-suspect and on house #5, which was previously negative. Split samples collected in November 2005 were assayed by the owner’s designated laboratory and also by a nationally recognized commercial reference laboratory.

The results as shown in Figure 2.2 confirm the presence of SE in 1 row from each of the houses sampled, as assayed by one of the two laboratories. A structured sampling of four adjacent houses (#5-#8) was conducted in February 2006 (Figure 2.3), incorporating drag swabs from manure beneath cage rows, pools of mouse droppings, newly emerged house flies in the pits and dust from fan louvers.

The samples were subjected to a rapid specific SE Polymerase Chain Reaction assay and to conventional double enrichment bacteriological examination by a state diagnostic laboratory. The results as shown in Figure 2.4 confirm SE in various samples from houses #6-#8. There was general correspondence between the SE-PCR and conventional microbiological assays (results not shown) confirming the SE positive status of the complex. It is important to note the inherent insensitivity of drag swab sampling which yielded only 5 positives from 24 drag swabs. Submission of ancillary samples including flies, mouse droppings and dust from fan louvers obviously contributes to identifying positive houses and complexes.

Given the relatively low level of recovery of SE from a structured survey, it is evident that sampling individual houses on a complex at infrequent intervals will fail to recognize that the intestinal tracts of a high proportion of hens in the flocks on a complex are colonized with SE. Within the context of U.S. in-line units, especially those using deep pit housing and two-cycle programs, entire complexes are either free of SE or are contaminated.

It is impossible to prevent lateral dissemination of infection from older flocks to newly transferred susceptible pullets in adjacent houses. Movement of personnel and equipment, rodent migration and particulates entrained in air will inevitably spread SE throughout a complex given current U.S. production practices.

It is erroneously held by many in the industry that SE is ubiquitous and a positive diagnosis is a function of surveillance intensity and diligent laboratory procedures. This contention is not supported by field experience. Following the intensive sampling on the subject farm, the same procedure was followed in March 2006 on a six-house complex with no history of SE on drag swabs extending back for seven years. There was no evidence of SE from the same set of samples and swabs as previously examined, in addition to egg belts which were assayed by the same state laboratory using both PCR and conventional microbiology.


The imminence of FDA surveillance requirements with increased frequency and rigorous procedures will detect currently unrecognized SE infection in cage-free flocks and in-line complexes subjected to “end-of-cycle” sampling programs. The consequences of detection of SE in currently “negative” flocks will be both financially severe and disruptive, given the powers to be exercised by the FDA and the tort system. The industry therefore should do all that is possible in the coming 12 to 18 months to anticipate intensified FDA surveillance and reduce the level of infection. This can be achieved by stringent control of rodents and especially mice, thorough decontamination between flocks and depletion of hens which are positive at the end of the first cycle, as these hens will serve as a reservoir of infection for the entire complex.

Additional research is required on vaccines and methods to improve their effectiveness. It is possible that immunosuppression during the early brooding period by Marek’s and infectious bursal disease viruses compromise subsequent immunity to SE induced by vaccines. Industry practices such as administration of tetracyclines and tylosin to flocks in production affect the balance of intestinal flora and may predispose to proliferation of Salmonella in the intestinal tract.

During the past 10 years the industry has made considerable strides in reducing the prevalence of SE infection. Perpetuating insensitive and infrequent surveillance protocols and applying deficient microbiological procedures have in all probability contributed to the plateau of SE infection in consumers. This has generated concern among public health authorities who are intent on eliminating shell eggs as a major source of SE infection.

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