Authored by: Rimkus Forensics Marketing Team
The Centers for Disease Control and Prevention (CDC) estimates that six major pathogens cause about 9.9 million domestically acquired foodborne illnesses in the United States each year, and that those six pathogens, together with Toxoplasma gondii, account for an estimated 53,300 hospitalizations and 931 deaths. The method used to detect those pathogens, the standard applying to that method, and the chain of documentation connecting sample to result may all influence whether analytical findings can withstand regulatory scrutiny or courtroom challenge.
Claims professionals and attorneys evaluating contamination evidence must consider which microorganisms laboratories test, how laboratories detect them, what standards apply to the methods, and how microbial analysis may function as evidence in forensic investigations and litigation.
Key takeaways: Microbial analysis methods and evidentiary standards
Microbial analysis of food products can generate the laboratory evidence underlying contamination claims, recalls, and regulatory enforcement actions.
What microbial analysis measures
- Pathogens such as Salmonella, Listeria monocytogenes, and E. coli O157:H7 each carry distinct regulatory classifications that may affect liability exposure
- Indicator organisms like aerobic plate count and coliforms may support negligence claims even without detected pathogens
How detection methods affect evidentiary weight
- Culture-based methods provide the regulatory benchmark for validating other methods; positive results from rapid or molecular methods typically require culture confirmation
- Whole genome sequencing (WGS) has become a primary outbreak traceback tool and may help link and exclude potential sources
Rimkus forensic experts evaluate microbial analysis behind food contamination claims and litigation. Contact Us to discuss a matter.
What is microbial analysis of food products?
Microbial analysis is the laboratory process of detecting, identifying, and quantifying microorganisms in food matrices, spanning pathogenic bacteria, indicator organisms that may signal process failures, and spoilage organisms relevant to product quality.
Under 21 CFR Part 117, Food Safety Modernization Act (FSMA) Preventive Controls for Human Food require verification activities, which may include product testing for pathogens or indicator organisms where such testing is appropriate to the preventive control, including for ready-to-eat (RTE) foods when contamination is a hazard requiring a preventive control. Section 402(a)(1) of the Federal Food, Drug, and Cosmetic Act deems a food adulterated if it contains any poisonous or deleterious substance that may render it injurious to health.
What microorganisms do laboratories typically test in food products?
Target organisms fall into two functional categories: pathogens with direct public health significance, and indicator organisms that may signal sanitary conditions, process control, or fecal contamination.
Pathogens
Listeria monocytogenes has been classified as an adulterant in RTE meat and poultry products since 1989. E. coli O157:H7 received adulterant classification in raw ground beef in 1994, and in 2012 USDA classified six additional non-O157 Shiga toxin-producing E. coli (STEC) serogroups as adulterants in raw non-intact beef products. Cronobacter spp. carries zero tolerance in infant formula under 21 CFR 106.55.
A single positive test result for any zero-tolerance adulterant may constitute adulteration under the applicable legal framework, depending on the product and jurisdiction.
Salmonella presents the most legally complex distinction. In Food and Drug Administration (FDA)-regulated foods, a positive may support an enforcement action under Section 402(a)(1).
In Food Safety and Inspection Service (FSIS)-regulated raw meat and poultry, Salmonella has historically not been classified as an adulterant. FSIS has issued a final determination effective May 1, 2025, declaring not-ready-to-eat breaded and stuffed raw chicken products adulterated when the raw chicken component contains Salmonella at 1 colony-forming unit (CFU) per gram or higher. As of late 2025, FSIS has delayed verification and enforcement of this determination while it reevaluates available test methods, and the agency’s broader proposed Salmonella framework for other raw poultry products has been withdrawn.
Indicator organisms
A commonly described progression of fecal-contamination indicators runs from broader groups such as total coliforms to fecal coliforms and then to generic E. coli, while pathogenic E. coli refers to specific disease-causing strains. Elevated aerobic plate counts in a finished product may support an inference of process failure or temperature abuse, potentially supporting negligence claims even absent a detected pathogen.
How do laboratories detect microorganisms in food products?
Three principal method categories operate at different points in the detection workflow. Culture-based methods provide the validation benchmark for other methods, while laboratories often use rapid and molecular methods as alternative or complementary approaches.
Sampling and sample preparation
Representative sampling is foundational to defensible results. Sampling plans define the number of units laboratories test, the maximum allowable defective units, and the concentration limits that distinguish acceptable from unacceptable lots. FDA Bacteriological Analytical Manual (BAM) Chapter 1 describes sampling principles and procedures, emphasizing that samples must be representative of the lot and properly collected and handled.
Sample preparation varies by matrix. BAM Chapter 5 specifies complete soaking without homogenization for fresh leafy greens, while ground beef and powdered infant formula each require distinct protocols. Applying the wrong preparation protocol may affect pathogen recovery and may compromise the validity of results.
Chain of custody documentation, including temperature logs, seal integrity records, and transport conditions, may affect whether results are positioned to withstand challenge.
Culture-based methods
The FDA describes the Bacteriological Analytical Manual as its “preferred laboratory procedures for microbiological analyses of foods and cosmetics.” The workflow progresses through pre-enrichment, selective enrichment, selective plating, and biochemical and serological confirmation.
FDA BAM Chapter 5 describes the Salmonella culture as a multi-day, stepwise process, with presumptive identification reached only after pre-enrichment, selective enrichment, plating, and initial biochemical testing. The method can detect very low levels of contamination, validated to approximately 1 CFU per analytical portion, and can produce live isolates for serotyping, antimicrobial resistance testing, and whole genome sequencing.
Immunoassay and rapid methods
Enzyme-Linked Immunosorbent Assay (ELISA) and lateral flow devices detect pathogen proteins, toxins, and metabolic substances through antibody-antigen interactions. ELISA can identify staphylococcal enterotoxin even after bacteria have been killed by heat treatment, directly relevant to processed-food liability cases. Under FDA BAM methods policy, immunoassay methods are screening tools. The policy accepts negative results but typically requires culture-based confirmation for positive results.
Molecular methods
Polymerase chain reaction (PCR)-based methods detect specific DNA sequences using primers designed for pathogen-unique genetic targets. In the FDA workflow, real-time quantitative PCR (qPCR) screens 24-hour pre-enrichment cultures on Day 2, before the culture method’s Day 4 to 5 result.
WGS can determine the complete genetic makeup of a pathogen. The CDC PulseNet network switched from pulsed-field gel electrophoresis (PFGE) to WGS because WGS provides substantially greater discriminatory power, distinguishing isolates that PFGE classified as indistinguishable.
What standards and regulations typically govern microbial analysis?
Applying the wrong agency’s methods to a regulated product may present a significant issue with potential implications for admissibility, because the standards governing food microbial analysis vary by jurisdiction and involve a mix of regulatory requirements and voluntary consensus standards.
The FDA BAM covers food and cosmetic products, while USDA FSIS is responsible for meat, poultry, and processed egg products. AOAC International Official Methods of Analysis is a widely recognized framework for validated analytical methods, while AOAC programs such as Performance Tested Methods specifically address validation of rapid and molecular testing kits. Internationally, ISO 7218:2024, published by the International Organization for Standardization (ISO), supersedes ISO 7218:2007 as the general requirements standard for food microbiology.
Under the FSMA Laboratory Accreditation for Analyses of Foods (LAAF) final rule, accredited laboratories must comply with ISO/IEC 17025:2017 and pass proficiency testing for each method at least every 12 months. Results from accredited laboratories using AOAC-validated or BAM-designated methods may carry stronger evidentiary weight than results from non-accredited laboratories using unvalidated methods.
How does microbial analysis support forensic investigations and litigation?
Microbial analysis can generate scientific evidence that may help connect contaminated food to reported illness in regulatory enforcement actions, product liability claims, and outbreak investigations. PulseNet’s DNA fingerprinting has accelerated that process: before PulseNet, identifying an outbreak could take up to 39 days, whereas today an outbreak can be identified in approximately 16 days.
FDA’s GenomeTrakr network archives pathogen genomic data in publicly accessible databases, so all parties in litigation can access the same reference data. WGS data carry a critical limitation: CDC notes that WGS is only one clue in a foodborne disease outbreak investigation, and that investigators also need information gathered outside the laboratory.
Under In re Paoli Railroad Yard PCB Litigation, a Third Circuit decision interpreting Rule 702, any step that renders an otherwise reliable analysis unreliable can render the expert’s testimony inadmissible.
How do microbial analysis results typically hold up in the courtroom?
A single positive test for a zero-tolerance adulterant may create strict liability exposure under the applicable regulatory framework, while WGS data can link illness clusters to specific products or exclude facilities from suspicion. Method deviations and chain of custody gaps may provide grounds to challenge the analytical record.
What does this mean for contamination disputes?
Microbial analysis may carry significant evidentiary weight, but that weight often depends in part on the target organism, analytical method, governing agency framework, and documentation linking sample to result. In many cases, the sampling, preparation, validation, and chain of custody determine whether a reported positive supports reliable interpretation.
How can forensic support help clarify contamination questions?
Rimkus toxicology and food safety professionals, including microbiologists, toxicologists, and food safety consultants, offer expertise in evaluating hospitality, restaurant, and manufacturing contamination claims and other food safety matters through evaluation of laboratory results, root cause investigation, and expert testimony grounded in Life Sciences disciplines.
Contact us to discuss a matter involving microbial analysis of food products.
Frequently asked questions about microbial analysis of food products
What are the legal consequences of using FDA BAM methods instead of USDA FSIS MLG methods when testing meat or poultry products for pathogens?
Using FDA BAM methods instead of USDA FSIS Microbiology Laboratory Guidebook (MLG) methods for meat, poultry, or egg products may create regulatory risk if establishments use those methods for FSIS-related regulatory purposes without scientific support or validation, because FSIS uses MLG methods as its reference methods and expects scientifically supportable alternatives when establishments use other methods. When contamination disputes escalate to litigation, opposing counsel may challenge the admissibility of test results under Federal Rules of Evidence 702 and Daubert standards if the selected methods do not match the regulatory framework governing the specific product matrix at issue.
How can parties challenge or defend whole genome sequencing (WGS) data in food contamination litigation, and what are its key evidentiary limitations?
Parties may challenge or defend whole genome sequencing data in litigation through disputes over database completeness, interpretation methodology, and epidemiological context gaps. Courts may increasingly scrutinize the gap between laboratory correlation and causation proof, requiring plaintiffs to supplement WGS evidence with traceback documentation, purchase records, consumption histories, and epidemiological linkage demonstrating temporal and geographic plausibility.
Can elevated indicator organism counts like aerobic plate counts alone support a negligence claim in court without evidence of a specific pathogen?
Elevated indicator organism counts can potentially support negligence claims even without pathogen detection because they may demonstrate breach of sanitary standards, process control failures, or temperature abuse that violates the duty of care owed to consumers. The evidentiary weight depends on whether the counts exceed established regulatory action levels, whether the counts violate the defendant’s own specifications, and whether expert testimony can connect the elevated counts to specific process breakdowns that created unreasonable risk.
This article is intended to provide general information and insights into prevailing industry practices. It is not intended to constitute, and should not be relied upon as, legal, technical, or professional advice. The content does not replace consultation with a qualified expert or professional regarding the specific facts and circumstances of any particular matter.