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Retest Analysis: When Original Sample Results and Retest Results Don’t Correlate

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By Laurie Post, Ph.D.
When undesirable microorganisms are detected in a production lot, root cause analysis often includes testing additional samples from the affected lot or related lots of product. However, upon reanalysis, even when a larger sample size is used, the suspect organism cannot be detected in the retest analysis. Correlation differences between original and retest results can occur for several reasons:

  1. Distribution pattern of the microorganisms
  2. Lack of representative sampling
  3. Organism die-off
  4. Level of contamination and probabilities of detection

Distribution
The distribution pattern of microorganisms in a production lot affects the likelihood of detecting the organism in the product. For instance, distribution patterns can be Random or Non-Random.

Random Distribution: Microorganisms are distributed evenly throughout the entire lot. Microorganisms will likely be detected. This type of microbial distribution is not a factor of time since at any point in the sampling process there is an equal opportunity to detect the organism in question (Example A).


Non-random Distribution: Microorganisms are not distributed evenly throughout the entire lot. Microorganisms may not be detected by random sampling. This type of distribution is dependent on time since the microbial contamination is only represented at certain intervals in the production cycle without equal opportunity for detection (Examples B and C)

Example B shows a non-random distribution pattern of organisms that can be present at the startup of production. In this case, the food actually cleans the line, so that over time the contaminant is reduced to undetectable levels. If a retest sample of this lot of production is pulled from containers made later in the day, then the retest results will be negative for the target organism, even though the organism was present.

Example C is another example of non-random microbial distribution that can occur when condensate drips onto exposed product. Condensate began to drip sometime after startup and continues throughout the rest of the day, increasing toward shutdown. If retain samples taken at the beginning of the day were selected for retest analysis, the retest samples would likely be negative for the target organism even
though the organism was present in that lot of production.


Sampling
Microbiological analyses are only as good as the sampling procedure used to procure the sample. Every effort must be made to obtain a RANDOM SAMPLE. “Spot sampling” or taking a single sample will not yield a representative sample. FDA recommends taking 30 random 25g samples during the entire production run for Ready-to-Eat products that will be consumed without a process lethal to microbial pathogens. These include products such as cereals, confectionary products, cheese, dairy, spices – and many others (FDA Bacteriological Analytical Manual). For fluid and powdered products, most manufacturers employ mechanical or auto-samplers. For discrete products, samples are taken on a time production basis (i.e. one candy bar every half hour) and then the analytical unit (the actual amount tested) is made by compositing. Compositing must be performed carefully and thoughtfully, not only to ensure a representative sample, but also to avoid sample contamination.

Organism Die-off
Organisms contaminating a product may not survive at the same level for long periods of time. For example, Escherichia coli (E. coli) is not capable of long-term survival in an inhospitable matrix, such as chocolate, and will eventually die off. Levels may fall below the ability of an assay to detect the organism.


Levels of Contamination and Probability of Detection
The probability of finding a target organism in a retest sample is based on the probability of finding the target organism in the original sample. If 10 samples are collected for analysis and only one tests positive for a pathogen, the level of contamination is one in ten or 10%. Based on a standard statistical analysis, if there is a 10% chance of finding the target organism in the original sample, then the ability of finding the organism a second time by retest sampling is [10% X 10%] or [0.10 X 0.10 = 0.01] or one in a hundred. Similarly, if the level of contamination is 5%, the probability of finding the positive a second time is one in twenty-five and 1% is one in ten thousand. The short hand version of this is to simply square the level of
contamination, as shown here:

Level of Contamination- Probability of Finding the Target Organism in the Original Sample Probability of Finding the Target Organism in a
Retest Sample
One in two (50%)One in four (25%)
One in four (25%)One in sixteen (6.5%)
One in five (20%)One in twenty five (2.5%)
One in ten (10%)One in a hundred (1%)
One in a hundred (1%)One in ten thousand (0.01%)

There are many factors that can result in correlation differences between original and retest results. But, if a retest is desired, pull many random samples and request a retest as soon as possible.

When To Revalidate A Process Preventive Control

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By Ryan Maus
FSMA legislation (21 CFR §117.160) requires that preventive controls be validated to assure that they are appropriate to control the hazards identified in the food safety plan. Generally, validation occurs:

  • Prior to, or within 90 days of implementation of the food safety plan
  • Whenever a change to a control measure(s) could impact its ability to control the hazard(s)
  • Whenever a reanalysis of the food safety plan reveals the need to do so

Concerning reanalysis of the food safety plan, according to FSMA legislation (21 CFR §117.170), this is required at least once every 3 years or:

  • Whenever new information about potential hazards associated with the food arise
  • Whenever appropriate after an unanticipated food safety problem
  • Whenever you find that a preventive control, combination of preventive controls, or the food safety plan as a whole is ineffective

So what is considered a significant product/process change? Examples from FSPCA’s PCQI training manual include:

  • Raw material changes, including a new supplier (e.g. change in viscosity, moisture levels, particle size; new pathogen hazard identified; increased microbial load)
  • Product or process changes (e.g. reduced water activity, changes in operating parameters, new equipment, equipment is moved)
  • Increasing production volumes that lead to extended run times, changes in bed depth, increased volumes of material in chambers
  • Adverse finding during review or observation of a recurring deviation (i.e. may suggest the validation is no longer adequate)
  • Emerging scientific information on hazards or control measures
  • Changes in consumers profiles and handling (e.g. marketing to children, infants, or an immunocompromised population)

Often, a food producer must consider changes to equipment, such as a heating element, and whether this would impact the equipment’s efficacy in controlling an identified hazard. The most conservative approach to demonstrate the preventive control’s efficacy would be to revalidate the process. However, another approach is to conduct a heat distribution study to verify that the heat distribution did not change significantly in a way that areas of the roaster see lower temperatures than when the roaster was initially validated. This could include collecting data that supports the initial validation, for example, temperature distribution data pre/post heating element replacement. If the analysis of this data indicates the same temperature profile, then you may be able to conclude that the reanalysis does not indicate the need for a full validation study. If the temperature profile has changed, then some additional study would be warranted.

Regulatory Watch Out!

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Use of Unapproved Food Additives – FDA’s Public Inventory

Any substance used or intended for use in food must be authorized by the FDA for use as a food additive under the Federal Food, Drug, and Cosmetic (FD&C) Act, unless the use of that substance is generally recognized as safe (GRAS) by qualified experts or qualifies for an exemption.


As part of its on-going compliance activities, FDA conducts post-market activities to monitor the food supply for chemical contaminants. FDA identifies foods that contain a substance for which there is no authorization as a food additive and then reviews the regulatory status of this substance. FDA scientists analyze whether there is a basis to conclude that the intended use of the substance is GRAS or meets a
listed exception to the food additive definition. When FDA scientists determine that a substance is an unapproved food additive because it is not GRAS for its intended use (and does not meet a listed exception), they deem the additive to be unsafe and any food that contains the additive is adulterated.

On July 12, 2023, FDA released a public inventory of certain food ingredients that do not have GRAS status as determined by the agency and are therefore deemed unsafe. The inventory is a useful tool to assure the use of authorized ingredients.


The FDA Concludes Voluntary Pilot Program to Evaluate Alignment of Third-Party Food Safety Standards
with FSMA Rules


Food manufacturers may find that they are required to comply with one of the Global Food Safety Initiative standards in addition to the FDA’s Preventive Controls for Human Food or Produce Safety Rules. The FDA recently concluded a voluntary pilot program to evaluate alignment of private third-party food safety audit standards including BRC, FSSC22000, SQF and Global G.A.P. with applicable FDA regulations.


The pilot program was launched to help both FDA and industry gain a better understanding of whether these standards align with FDA regulations. Alignment between these standards may allow a company to structure their food safety plan to eliminate redundancy in their documentation and auditing programs.

Buyers and others in the food supply-chain often use third-party audits to assess the quality and safety of a product. Buyers, such as importers and receiving facilities, might stipulate an audit as part of a purchase agreement. In addition, three FSMA regulations – the Preventive Controls for Human Food rule, Preventive Controls for Animal Food (PC Animal Food) rule, and Foreign Supplier Verification Programs (FSVP) rule – allow for third-party audits to be used as supplier verification activities. Points of alignment would provide confidence that, in general, the third-party standards used to audit suppliers adequately address applicable FDA food safety requirements.


The results of the pilot program can be found in The FDA Concludes Voluntary Pilot Program to Evaluate Alignment of Third-Party Food Safety Standards with FSMA Rules. The FDA’s statements regarding alignment of the standards are referenced in the table below and apply only to the specified audit standards and addenda listed.


The reviews listed in the table focused on assessing third-party food safety standards and not the overall quality of the audit programs or qualifications of auditors. The FDA’s review and the findings from this pilot do not constitute an endorsement of any one food safety audit standard, or audits conducted under such standards. The FDA also adds a qualifying statement that third-party audits are not a substitute for FDA or state regulatory inspections for compliance with FDA regulations, including the Preventive Controls for Human Food Rule or the Produce Safety Rule.

Third-Party Food Safety Audit Standard and Applicable
Addendum		Scope Name
BRC Global Standard Food Safety plus the Global Standard Food Safety,
Issue 9, Interpretation Guideline		Preventive Controls for Human Food (PCHF)
FSSC 22000 Scheme 5.1 for Food Manufacturing plus the FSSC 22000, Version 3 FSMA PCHF Report Addendum
Preventive Controls for Human Food (PCHF
SQF Food Safety Code: Food Manufacturing, Edition 9 plus the SQF
Addendum for the Preventive Controls for Human Food		Preventive Controls for Human Food (PCHF)
GLOBALG.A.P. Integrated Farm Assurance – All Farm Base Crops Base – Fruit and Vegetables Checklist. Version 5.4-1- GFS plus the GLOBALG.A.P. Food Safety Modernization Act Produce Safety Rule Add-on Module Version 1.3Produce Safety Rule (PSR)
*Did not include Subpart E, related to Agricultural Water (as applicable to non-sprout produce) or Subpart M, related to sprouts

Current Recall a Reminder of Past Incident Involving Frozen Vegetables Contaminated with Listeria monocytogenes

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A new recall of frozen vegetables was published on August 23, 2023, due to the finding of Listeria monocytogenes in sweet cut corn. Recalled products were distributed to major retailers across the U.S. having best by dates as far away as December 2024. Listeria monocytogenes, like many pathogens, will not be eliminated by freezing and will persist in the frozen product. While little information is given in the recall, findings from a 2016 listeriosis outbreak involving frozen vegetables is highlighted in the following.


In 2016, the first multistate outbreak of L. monocytogenes involving frozen vegetables occurred in the U.S. Initially three persons reported illness in 2016, but six more illnesses occurring between 2013 – 2015 were identified using PulseNet traceback data. Two outbreak strains were identified in patients ranging in age from 56 to 91 years and three deaths were reported.


Routine sample of frozen vegetables, and the use of whole genome sequencing (WGS), revealed that eight illnesses were closely related to a strain found in frozen organic white sweet cut corn and one illness to a strain found in frozen organic petite green peas produced by CRF Frozen Foods of Pasco, WA. At the same time, an investigation of the Oregon Potato Company of Pasco, WA found that environmental samples matched the whole genome sequence associated with the eight clinical cases and the CRF frozen organic white sweet cut corn. However, a connection between the companies is unknown because the FDA is prohibited by law from releasing publicly certain information about supply chains, which may constitute confidential commercial information.


A recent publication describes the investigational findings by federal and state regulatory agencies at the two frozen vegetable manufacturers. Observations at the CRF Frozen Foods’ facility indicated that the materials and design of equipment and utensils did not allow proper cleaning and maintenance, and could be potential sources of contamination. An investigation of the facility did not find L. monocytogenes in the environment, but L. innocua was found in zones 1 – 3 which FDA considers evidence of conditions that would be suitable for L. monocytogenes.


Seven L. monocytogenes positive zone 1 swabs, two positive zone 2 swabs, ten positive zone 3 were found in the Oregon Potato Company’s facility. Two of these positives, one zone 1 swab and one zone 3 swab,- matched an outbreak strain also found in CRF’s frozen organic white sweet cut corn. Inspectional observations made include:

  • failure to clean food‐contact surfaces as frequently as necessary to protect against contamination
  • facility construction that did not prevent condensate from contaminating food‐contact surfaces
  • food‐contact surfaces not adequately cleaned and sanitized
  • failure to maintain physical facilities in a sanitary condition
  • facility construction not allowing adequate cleaning of floors and walls

A FDA warning letter was issued and noted the presence of L. monocytogenes in the facility as being indicative of inadequate sanitation efforts to effectively control pathogens in the facility. Although these products are considered not ready‐to‐eat, many consumers may use these products
without proper cooking. Cooking instructions should be clear and validated, and consumers should be informed that consuming undercooked or uncooked frozen vegetables could lead to foodborne illness.

A Recent Soft Serve Ice Cream Outbreak and a Look Back at Past Incidents Involving Pathogen Contamination

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A recent outbreak of listeriosis has been linked to Soft Serve On The Go ice cream cups, resulting in 2 illnesses. An investigation by the Pennsylvania Department of Agriculture detected the presence of Listeria monocytogenes in an unopened sample of ice cream taken from a patient’s home. The product isolate was matched to the clinical L. monocytogenes outbreak strain by whole genome sequencing. Five positive samples of finished product obtained from the production facility by the New York State Department of Agriculture and Markets also matched the outbreak strain.

A recall of products distributed nationally is currently ongoing. However, this is not the first outbreak or recall associated with ice cream and many others have occurred as shown in the tables below.

YearLocationPathogenIllnessesDeathsProducer
2022MultistateL. monocytogenes281Big Olaf Creamery
2014WashingtonL. monocytogenes22Snoqualmie Ice Cream
2010-2015MultistateL. monocytogenes103Blue Bell
2005MultistateSalmonella260Cold Stone Creamery
1994MultistateSalmonellaEstimated 224,0000Schwan’s
Past ice cream outbreaks are shown in the following table.
DatePathogenPathogen SourceProducer
07/13/2022L. monocytogenesEnvironmentBig Olaf Creamery, LLC
06/06/2022SalmonellaPeanut ButterTaharka Brothers Ice Cream
02/12/2022L. monocytogenesEnvironmentThe Royal Ice Cream Company, Inc.
04/27/2021L. monocytogenesNot MentionedVelvet Ice Cream
05/14/2020L. monocytogenesNot MentionedRamar Foods
03/17/2020L. monocytogenesEnvironmentWorking Cow Homemade Ice Cream
Recent ice cream recalls due to pathogen contamination are shown in the following table.

Contamination of ice cream products generally occurs after pasteurization, resulting from sources that include the addition of contaminated inclusions (e.g. fruits, nuts, candy, or bakery pieces) to the finished product, contamination from the production environment, and inadequate sanitation of equipment such as filling heads. Freezing ice cream can prevent pathogen outgrowth, but it will not eliminate pathogen presence. Low levels of pathogens causing illness were identified in the 1994 Schwan’s outbreak (Salmonella 0.004-0.46 MPN/g) and 2015 Blue Bell outbreak (L. monocytogenes 3.9-7.1 MPN/g).

Supplier verification programs are critical to evaluate inclusions and reduce the risk associated with them. Inclusions and flavors must be ready-to-eat and any required Process Preventive Controls must have been applied at the supplier, unless the ice cream manufacturer assumes this responsibility.

Sanitation controls are critical to prevent post pasteurization pathogen contamination of finished ready to-eat ice cream products. This is especially true for L. monocytogenes. Cross contamination with L. monocytogenes from the environment is identified in Blue Bell’s 2015 outbreak and numerous recalls. Ice cream processes can be hard to clean, leaving behind nutrients for microbial growth. Listeria can grow,
form biofilms, and persist in harborage sites such as drains leading to cross contamination. Biofilm formation is a constant problem in ice cream producing facilities and requires proper cleaning and sanitizing procedures for their removal and prevention. The effectiveness of sanitation programs are verified by the results attained from a well-designed environmental monitoring program

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