In this article, you'll learn:
• Why the biological characteristics of Salmonella, Cronobacter, Listeria monocytogenes, pathogenic E. coli, and Bacillus cereus—stress tolerance, cold growth, environmental persistence, and toxin stability—make reliable detection technically demanding
• How ISO and FDA BAM workflows differ in practice for each of these organisms
• Where chromogenic media sit within standardized regulatory workflows and what they can—and can’t—replace
• Why culture-based methods remain indispensable even where rapid molecular screening is in use
• What the 2025–2026 cereulide in infant formula incident signals for ingredient-level testing and risk control
• Answers to FAQ regarding the detection of foodborne pathogens in food manufacturing
Ensuring microbiological safety in food manufacturing requires more than procedural compliance with a reference method. It depends on understanding how target pathogens survive processing, persist in production environments, and respond to the recovery and selective culture conditions. For food and beverage laboratories, that makes media selection more than a purchasing decision: it’s a direct part of method performance, workflow reliability, and confidence in results.
Five organisms are of greatest regulatory and public health concern in food manufacturing: Salmonella spp., Cronobacter spp., Listeria monocytogenes, pathogenic Escherichia coli, and Bacillus cereus. These organisms are particularly challenging for food manufacturers because the microbiological characteristics that make them hazardous also make reliable detection technically demanding. Stress tolerance, cold growth, environmental persistence, and toxin stability all have direct implications for enrichment strategy, media selection, and workflow design.
Salmonella spp.: Recovery of stressed cells drives method performance
Salmonella remains one of the most significant bacterial hazards in food production. In the European Union, salmonellosis consistently ranks among the most frequently reported zoonotic infections, and is a leading cause of foodborne outbreaks across multiple product categories, including poultry, eggs, fresh produce, and low-moisture foods.
The public health significance of salmonellosis reflects a low infectious dose, high desiccation tolerance, and the organism’s ability to persist through complex processing and distribution chains—characteristics that make reliable recovery of sub-lethally injured cells central to effective laboratory detection.
Detection is performed under ISO 6579-1 or FDA Bacteriological Analytical Manual (BAM) Chapter 5. In both frameworks, pre-enrichment in Buffered Peptone Water (BPW) is used to recover injured cells prior to application of selective pressure.
Under ISO 6579-1, selective enrichment typically proceeds through Rappaport-Vassiliadis Soya Peptone Broth (RVS) or Modified Semi-solid Rappaport-Vassiliadis (MSRV) medium, alongside a second selective enrichment, such as Mueller Kauffman tetrathionate novobiocin broth (MKTTn). FDA BAM Chapter 5 employs a comparable enrichment-then-isolation logic, although specific media and procedural details differ by product type and analytical context.
Isolation in both approaches uses selective and differential agars. Xylose Lysine Deoxycholate (XLD) is commonly used, alongside other media selected according to the method and matrix, such as Hektoen Enteric (HE) agar. Chromogenic formulations are also increasingly used to improve presumptive differentiation. In practice, method performance for Salmonella detection is driven less by the choice of plating media, and more by effective recovery of stressed cells during pre-enrichment.
Cronobacter spp.: Desiccation persistence and infant nutrition risk
Cronobacter spp. are of particular concern in powdered infant formula, and other low-moisture products such as infant cereals, due to their association with severe neonatal infections, and ability to survive for extended periods under desiccated conditions. That persistence is relevant to both finished product and dry-processing environments, where hygienic zoning, dry-cleaning strategy, and environmental monitoring are critical components of risk management.
Detection is defined in ISO 22964 and FDA BAM Chapter 29. Following non-selective recovery in BPW, selective enrichment is used to improve recovery of Cronobacter spp. from competing background flora. Under ISO 22964:2017, Cronobacter Selective Broth (CSB) and Chromogenic Cronobacter Isolation (CCI) agar define the core workflow.
In the 2023 update to FDA BAM Chapter 29, Enterobacter sakazakii agar (DFI formulation) is widely used, with CCI agar and Enterobacter sakazakii Isolation Agar (ESIA) listed as alternative or optional media within the method. As with Salmonella, the biological challenge of robust recovery of stress-damaged cells directly shapes method requirements with regard to Cronobacter spp..
Listeria monocytogenes: Cold growth and environmental persistence in ready-to-eat food production
Listeria monocytogenes represents one of the most significant hazards in ready-to-eat (RTE) food production. Although listeriosis has lower case numbers than salmonellosis, it carries high rates of hospitalization and mortality among vulnerable populations, making it disproportionately important from a public health perspective.
Listeria monocytogenes has the ability to grow at refrigeration temperatures, including typical chilled storage conditions around 4 °C. Its ability to establish persistent niches in drains, equipment joints, and wet-processing environments, means control of this organism is heavily dependent on environmental monitoring, not just finished product testing. When positives are detected, rapid escalation is essential.
ISO 11290-1 and FDA BAM Chapter 10 describe the standard detection frameworks, with meaningfully different workflows. ISO 11290-1 uses a two-stage enrichment—half-Fraser broth followed by Fraser broth—before plating onto ALOA, a chromogenic Listeria agar developed by Ottaviani & Agosti, together with a second selective agar such as Oxford or PALCAM agar—a selective medium containing polymyxin, acriflavine, lithium chloride, ceftazidime, esculin and mannitol.
FDA BAM Chapter 10 enriches in Buffered Listeria Enrichment Broth (BLEB), followed by plating onto one esculin-based selective agar (Oxford, Modified Oxford, or PALCAM) combined with one chromogenic selective agar (e.g. CHROMagar Listeria), where permitted within the method. In both workflows, chromogenic media support faster presumptive recognition of positives—a meaningful operational advantage in facilities where timely corrective action is critical.
Pathogenic E. coli: Molecular screening and the non-O157 challenge
Pathogenic E. coli—particularly Shiga toxin-producing E. coli (STEC)—are major food safety hazards capable of causing severe gastrointestinal disease and complications, including hemolytic uremic syndrome (HUS).
Regulatory focus has expanded well beyond E. coli O157:H7 to include six major non-O157 serogroups—O26, O45, O103, O111, O121, O145—because of their recognized association with severe illness. Isolating non-O157 strains presents a persistent analytical challenge: they are more biochemically variable than O157:H7, and may not display the phenotypic markers targeted by traditional selective media.
ISO/TS 13136 is a polymerase chain reaction (PCR)-based method centered on detection of Shiga toxin genes (stx1/stx2), and the intimin adhesion gene (eae), together with selected serogroup-associated genes, with culture isolation attempted from PCR-positive samples. It should be noted that ISO/TS 13136 defines a gene-based detection framework, and doesn’t directly correspond to the full set of serogroup targets used in some regional regulatory programs (e.g. U.S. “non-O157 STEC” classifications).
Enrichment in regulatory context commonly uses modified Tryptone Soy Broth (mTSB) supplemented with novobiocin. FDA BAM Chapter 4A uses an enrichment, screening, and isolation workflow for O157 detection by using modified Buffered Peptone Water with pyruvate (mBPWp) for enrichment and selective differential media, including CHROMagar O157, for isolation.
Chromogenic media can improve presumptive colony differentiation for non-O157 strains, but are most effective as part of a broader workflow that integrates molecular screening and confirmatory testing, given the limitations of phenotypic approaches for biochemically variable strains.
Bacillus cereus: Spore survival, toxin stability, and the limits of microbiological detection
Bacillus cereus is a spore-forming organism of particular concern in cooked foods, rice and pasta dishes, dairy-based products, dehydrated ingredients, and reconstituted powdered foods. Spores can survive conventional processing conditions and germinate in foods subjected to inadequate time-temperature control, particularly during slow cooling or warm holding.
The emetic toxin cereulide, produced by some strains during the late exponential to stationary growth phase, is highly resistant to heat, acidic conditions, and digestive enzymes. Its formation is influenced by temperature, pH, water activity, oxygen availability, and food matrix composition, and remains relevant in psychrotrophic populations under chilled conditions. This means that thermal inactivation of vegetative cells after toxin formation doesn’t eliminate the toxicological risk. The highest-risk scenarios involve slow cooling, extended ambient storage, temperature abuse in the danger zone (5–60 °C in most regulatory frameworks), or reheating of foods in which cereulide may already be present.
ISO 7932 and FDA BAM Chapter 14 primarily describe enumeration rather than mandatory pre-enrichment. Mannitol Egg Yolk Polymyxin (MYP) agar is the standard plating medium in both frameworks. Where low-level or stressed-cell detection is relevant, laboratories may use Tryptic Soy Broth (TSB) for recovery and Tryptic Soy-Polymyxin Broth (TSPB) for selective enrichment before subculture, particularly in Most Probable Number (MPN) workflows. Critically, microbiological detection of B. cereus doesn’t address the presence of pre-formed cereulide toxin: direct toxin analysis requires the LC-MS/MS method specified in ISO 18465.
The importance of this distinction became acute during the 2025–2026 multi-country infant formula incident, in which cereulide contamination was traced to arachidonic acid oil used in infant nutrition products—a scenario in which viable B. cereus in the finished product was not the primary finding.
For infant food manufacturers, the implications are clear: robust supplier qualification, targeted ingredient and finished-product testing for cereulide, strong traceability, recall readiness, and rapid communication with competent authorities are essential risk controls, and can’t be substituted by routine microbiological enumeration alone.
How chromogenic media support food microbiology workflows
Chromogenic media contain enzyme substrates linked to a chromogenic group that is released or activated by target microbial enzymes, producing a visible color change.
When the substrate is cleaved by the target enzyme, a colored product is released or generated, producing a visible colony color change during growth. For example, in E. coli detection, β-glucuronidase activity can yield colored colonies on suitable chromogenic media; in detection of Listeria monocytogenes, phospholipase-related enzymatic reactions can produce characteristic coloration and halo formation on appropriate chromogenic formulations.
Because enzymatic color development occurs during colony growth, chromogenic media often enable faster presumptive recognition than conventional differential media. This can simplify colony selection, reduce interpretive ambiguity, and improve workflow efficiency.
They are not universally mandated and not always direct replacements for reference method agars; their use depends on method allowances and validation data demonstrating equivalent performance. Where they are suitable, they contribute meaningfully to specificity, and to reducing interference from background flora, particularly in complex food matrices.
Culture-based methods and rapid technologies: complementary, not competing
Culture-based methods remain central in food microbiology because they recover viable isolates needed for confirmation, characterization, and strain typing, none of which are available from molecular detection alone. Positive PCR screening results often require culture follow-up where a viable isolate is needed within reference-method frameworks, precisely because nucleic acid detection doesn’t establish viability.
This isn’t an argument against rapid methods. Molecular screening can accelerate decision-making, but in reference-method workflows a live isolate is often still required for downstream confirmation or subtyping. This makes culture and molecular methods complementary rather than competing approaches.
Factors to look for when choosing prepared media for food pathogen testing
For food and beverage laboratories running high sample volumes, the choice of media format matters as much as the method itself.
Ready-to-use broths and agars can reduce preparation variability, simplify workflow standardization across operators and sites, improve traceability, and help laboratories stay aligned with validated testing procedures.
When purchasing prepared media, evaluation criteria extend beyond organism selectivity and recovery performance:
In practice, laboratories benefit most from suppliers that can provide complete workflow coverage—from pre-enrichment through to confirmatory plating—within validated, ready-to-use formats. This reduces variability between steps, simplifies procurement, and supports standardization across sites.
Method, media, and microbiological confidence
Detection of foodborne pathogens in food manufacturing isn’t a single problem with a single solution. It consists of organism-specific challenges shaped by how each pathogen survives, where it persists, and how reliably it can be recovered under the conditions of a standardized reference method. These challenges must be addressed through a combination of sound methodology, appropriate media selection, and well-designed workflow.
ISO and FDA BAM provide a reliable structural foundation, but performance within those frameworks depends on the quality of the tools used, and the laboratory’s understanding of why each step exists.
Pre-enrichment recovers stressed cells that selective pressure would otherwise suppress, selective enrichment suppresses background flora, differential and chromogenic media enable presumptive identification during isolation, and confirmation closes the loop. Rapid technologies accelerate screening, but don’t replace the need for culture-based confirmation in most reference-method contexts.
The 2025–2026 case of cereulide in infant formula is a useful reminder that microbiological detection and food safety risk aren’t always aligned. Where hazards arise from pre-formed toxins or ingredient-borne contamination, effective control requires expanding the detection strategy beyond viable-organism enumeration to targeted chemical analysis, supplier qualification, and traceability.
For food testing labs operating across multiple matrices and pathogen targets, validated culture methods, validated chromogenic media, and standardized ready-to-use formats, provide technical reliability and operational consistency in high-throughput regulated environments.
Our Redipor® range of ready-to-use culture media is designed to support standardized food microbiology workflows, from routine environmental monitoring through to complex pathogen detection programs requiring reliable enrichment, selective isolation, and confirmatory culture steps. If you'd like to discuss how specific media formats can support your current detection workflows, or explore our tailor-made products for specific food matrices, contact our team of experts.
FAQ: Detecting Key Foodborne Pathogens in Food Manufacturing
References
EFSA and ECDC (2024). The European Union One Health 2023 Zoonoses Report. EFSA Journal, 22, e9106. https://doi.org/10.2903/j.efsa.2024.9106
U.S. Food and Drug Administration (2024). Bacteriological Analytical Manual (BAM). https://www.fda.gov/food/laboratory-methods-food/bacteriological-analytical-manual-bam