Food Sample Analysis

Food sample testing supports foodborne illness outbreaks and investigations, microbial risk assessment (Hazard Analysis and Critical Control Points (HACCP) or routine surveillance) or complaint investigations.  Public Health Inspectors can review requirements and guidelines before submitting food samples to PHO for testing.

PHO laboratory performs testing of food samples submitted by Ontario’s boards of health (BOH) for microbiological analyses including indicator and pathogenic organisms as well as physicochemical parameters. Food samples may be collected to assist with an outbreak investigation (part of meal, control or follow-up (after remedial action)) or for microbial risk assessment in support of a Hazard Analysis Critical Control Point (HACCP) assessment or routine surveillance. Food samples may also be submitted as a ‘complaint’ submission (food with off-odour, off-colour, texture, etc.) for laboratory evaluations that are not associated with an investigation of foodborne illness.

Analyses available at the PHO Laboratory for food testing are listed below. Test information including testing frequency, turnaround times and reporting limits, is dependent on the specific analysis. [Click on individual testing links for test directory details – see below.]

Routine testing of cooked, ready-to-eat foods includes: Aerobic Colony Count, Bacillus cereus, Total Coliform, Escherichia coli, total gram negative, Salmonella species and Staphylococcus aureus. Other indicator bacteria and foodborne pathogens will be tested depending on the food type, clinical laboratory information and epidemiological details provided on the Food Bacteriology Requisition

Physicochemical testing will be performed upon request. For a list of etiological agents associated with foodborne illness, including incubation periods, symptoms, modes of transmission and associated foods, refer to Appendix C: Major Foodborne Diseases: General Features.

Analyses NOT available at PHO Laboratory as part of the for food testing program:

  • Cryptosporidium
  • Cyclospora
  • Giardia
  • Hepatitis A
  • Norovirus
  • Prion disease
  • Toxoplasma
  • Trichinella
  • Ciguatera poisoning
  • Paralytic shellfish poisoning

The above listed test requests will be referred to CFIA, Ontario-Area Recall Coordinator (ON-ARC), as per Ontario Foodborne Illness Outbreak Response Protocol (ON-FIORP) - Annex 2. Additional information such as commercial product details, reason for test request, clinical implications and priority level will be required by CFIA for the test referral. Contact the environmental laboratory through PHO Laboratory Customer Service Centre at 416-235-6556 or toll free 1-877-604-4567 to discuss any other test request not listed above.

Botulism test requests - contact Health Canada’s Botulism Reference Service directly at (613) 957-0902 or contact the Ministry on-call after hours at 1 (866) 212-2272.

Food Surveys or Studies

If a board of health would like to initiate a special food survey or study that involves laboratory testing, contact the environmental laboratory program microbiologist through PHO Laboratory Customer Service Centre at 416-235-6556 or toll free 1-877-604-4567 to discuss the study outline and impact on the laboratory.

Sample Selection


  • Selection of food items for collection and submission related to a foodborne outbreak should be determined based on all available environmental, epidemiological and clinical laboratory information related to the outbreak. Information about the clinical pathogen, if known or suspected, should be included to facilitate prioritization of food items both collected and tested.
  • If unsafe food-handling practices are identified during the inspection of a food premise, selection of food items for a microbial risk assessment is based on the health inspector’s discretion. The submission of foods is not a requirement in these circumstances but may provide an additional tool available to support the assessment.


  • During a foodborne outbreak investigation, the results of an environmental investigation, such as a Hazard Analysis Critical Control Point (HACCP) review, and epidemiological analyses, such as the calculation of attack rate, will facilitate prioritization of food items that are most likely to be involved. If attack rates are unavailable, incubation period, clinical symptoms and epidemiologic information about related cases should be used.
  • If risk stratification of food sources is not performed by the submitting public health inspector, and there is an abundance of samples submitted for testing, prioritization will be determined by PHO Laboratory Environmental Microbiology section. The communication of all available clinical, epidemiological and environmental information to PHO Laboratory is of great importance in guiding these decisions.
  • Avoid submitting raw foods which require processing or cooking before consumption, unless they are linked to a specific outbreak or a confirmed etiological agent. If testing of raw foods is required, please contact the PHO Laboratory Customer Service Centre at 416-235-6556 or toll free 1-877- 604-4567.

Containers for Sampling


  • Sterile plastic bags with wire closure are the preferred sample container for all food types.
  • Food samples found in the original container can be submitted in the original packaging providing that the container is air-tight and will not leak during transit.
  • If the original container has been opened or if the packaging is fragile and may be damaged during transit, samples should be transferred from the original container to a sterile plastic sampling bag with wire closure.


  • If a commercial packaged product has been submitted, record the following product information on the Food Bacteriology Requisition: brand name, lot number, best before date, expiry date, use by date, Universal Product Code (UPC), name of manufacturer/importer/legal agent, unit size, non-intact (open) and intact (closed). Photographs may also be taken and maintained by the public health inspector to capture this information at the time of sample collection which may facilitate a food recall if required. Photographs should not be submitted to the laboratory.
  • For foodborne outbreak investigations: when collecting an opened commercial packaged product, collection of a closed sample with the same lot may be useful to determine if the product was contaminated prior to consumer handling. PHO Laboratory will only analyze closed samples in conjunction with a foodborne outbreak investigation and only following consultation and approval by the laboratory. Please consult with the CFIA prior to submission as appropriate.
  • Styrofoam and box-board packaging used for fast-food products are examples of containers that are not suitable for microbiological testing. They are not air tight and may leak, potentially resulting in cross contamination of sample(s). These containers should not be put inside a sterile sample bag since the outside surfaces of the containers are a potential source of contamination and the sample will be compromised.

Sample Preparation


The following steps are recommended to organize and minimize food sample collection time:

  • Investigate before sampling to determine a sampling plan.
  • Ensure all materials required are available prior to collection.
  • Label sample bags using a permanent marker.
  • Complete requisition(s) before or after, never during, sample collection.
  • After collection, double check to ensure the food sample unique identifier on the sample bag and requisition are legible and match.

Sample Collection


  • Use aseptic technique at all stages of sample collection. If sterile gloves or tongs are not available, an inverted sampling bag may be used as a glove to collect the sample.
  • Collect samples that are representative of each item of food that is being investigated.
  • Meals that contain multiple discreet items (e.g. rice and chicken) may be collected individually or combined as a single sample. If collected as a single sample, components should be collected in approximately equal amounts and will be tested as one sample.
  • Foods that contain multiple items (e.g., sandwiches) may be collected as a single sample.
  • If an individual component is of greater interest than other components of a meal or mixed food, sample the items individually so they can be tested as individual samples.
  • Once collection is completed, close the mouth of the sterile plastic sampling bag with the wire closure, and roll down several times twisting the ends together tightly to prevent leaking during transport.
  • Submit a minimum of 200 grams of each sample if possible, as multiple tests may be required. Samples that are less than 10 grams will not be tested.


  • Failure to follow these instructions will compromise the sample integrity and the laboratory results.
  • Separation of meals or mixed foods must be performed at the sampling stage. The laboratory will not separate components of a sample once received in the laboratory.
  • Leaking samples will not be accepted by the laboratory. Refer to the Food – Laboratory Acceptance Criteria section for a complete list of acceptance criteria.



For large lots of food
(greater than 200 grams)

For small quantities of food
(Less than 200 grams)

  Most pre-packaged foods are produced in very large lots (a batch or production unit which may be identified by the same code; i.e., lot number, production code or other unique identifiers). During some investigations, it may be determined that there is very little sample available for analysis.
  • Where possible, mix the same lot of food before sampling.
  • In foodborne outbreak investigations, small quantity samples can be processed by the laboratory, but complete analysis may not be possible. Tests performed will be prioritized based on the type of food/suspected etiological agent.
  • Samples that are less than 10 grams will not be tested.
  • If a lot of food is larger than 2 kilograms, take five sub-samples of 200 grams each and submit as individual samples for analysis.
  • Ensure sub-samples are clearly and distinctly labeled with a unique identifier for tracking purposes on both the sampling bag and requisition.
  • If a particular etiological agent(s) is suspected or confirmed, indicate the information on the requisition form and the analysis for this agent(s) will be given priority. In the absence of such information, the laboratory will aim to perform those analyses most likely to provide information useful to the investigation.


Completion of the Food Bacteriology Requisition

The information below outlines the instructions for completing the Food Bacteriology Requisition. Complete instructions are also located on the reverse or page 2 of the requisition and include, submitter information, sample collection, reason for test request, sample details and shipping instructions.


  • Complete all areas of the Food Bacteriology Requisition.The information included on the requisition will also be provided on the final laboratory report.


  • Ship dry foods and other shelf stable foods in a closed container at ambient temperature.
  • Ship frozen foods in an insulated container with sufficient ice packs to maintain the frozen state.
  • Ship perishable foods in an insulated container with sufficient cold packs to maintain a temperature as close to 4°C as possible. If ice is used, contain the ice in a manner that does not allow water contact with the samples.
  • Submit all food samples to the closest PHO laboratory as soon as possible after collection.


  • Foods that exhibit temperature abuse during shipping may be rejected and not processed. If the product appears to have undergone a change of state such as from a frozen state to a liquid state, the product will be rejected.

The accuracy of the test results may be affected by improper collection, handling and/or shipping. Food samples that do not meet the acceptance criteria may be rejected by the laboratory and a new sample would be required to be re-submitted with a newly completed requisition. The acceptance criteria are outlined below.

Description Acceptance Reason
  • Sample must be received from an authorized board of health.
Sample Type
  • Food samples are collected to assist with an outbreak investigation (part of meal, control or follow-up (after remedial action)), complaint or for a routine monitoring microbial risk assessment (HACCP or routine surveillance).
  • PHO Laboratory may analyze raw food samples (e.g., raw chicken), which require processing or cooking before consumption, to support a foodborne outbreak investigation with a confirmed etiological agent.
Sample Requisition
  • The requisition must be completed when it is received at the laboratory including date, time and location of collection. The requisition must have a unique identifier that matches the identifier on the sample collection bag.
  • If a sample is received without a requisition it will not be processed; however, the sample will be held for two weeks.
Sample Collection
  • The sampling container must not compromise the integrity of the sample. Refer to the Containers for sampling section.
  • The full panel of tests may not be performed if a small amount of food (<200 grams) is received. At least 25 grams of sample is required for each analysis. Please contact the PHO laboratory Customer Service Centre at 416-235-6556 or toll free 1-877-604-4567, if collecting a small amount of food.
Sample Transport
  • The sample container must be secure to avoid leaks during transport.
    The sample temperature must meet the requirements listed below when received at the laboratory: 
    • Frozen foods should be received frozen (≤ 0°C); if frozen foods have a temperature ≥ 15°C when received at the laboratory, they will not be tested.
    • Foods normally held at refrigeration temperatures should be between 2.0 to 8.0°C when received at the laboratory and must not be at or < 0°C or ≥ 25 °C.

Satisfactory microbial limits for a food sample will be dependent on the food preparation, conditions (raw, ready-to-eat, and frozen, refrigerated, shelf stable) and commodity type (e.g., dairy, meat, etc.) in relation to a specific analysis. Refer to Health Canada’s Health Products and Food Branch (HPFB).

Standards and Guidelines for Microbiological Safety of Food - An Interpretive Summary for food commodity type details.

The tables below describe the reporting limit and unsatisfactory level for ready-to- eat foods for indicator bacteria and foodborne pathogens according to Health Canada, and physicochemical testing available at PHO Laboratory. If a board of health would like further interpretation on food results, contact PHO Laboratory Customer Service Centre at 416-235-6556 or toll free 1-877-604-4567, and provide the sample identification number.


Testing Type Reporting Limit (CFU/g)a Unsatisfactory Level (CFU/g)a, c
Aerobic Colony Count < 1,000 to > 200,000

Category 1: ≥ 105,
Category 2: ≥ 107,
Category 3: N/A

Total Coliform < 3 to > 1,100 b ≥ 103
Escherichia coli < 3 to > 1,100 b ≥ 100
Total gram negative < 1,000 to > 200,000  ≥ 10 4 d
Yeast and mould < 10 to > 200,000   No reportable limit available

CFU (colony forming units)
MPN (most probable number) is used for this test method
Microbial guidelines as per Health Canada
Microbial guidelines as per Alberta Health Services 

Unsatisfactory levels of indicator bacteria indicate improper food preparation, handling, storage or holding conditions, temperature abuse, and/or sanitation. Refer to specific test details below for more information.

Aerobic Colony Count (ACC): It is reasonable to expect properly prepared and handled ready-to-eat processed or cooked foods, where no additional food handling was required after food preparation, to have an ACC of < 104 CFU per gram. An ACC of > 105 CFU per gram is usually evidence of post processing temperature abuse, inadequate cooking or improper storage conditions. ACC cannot be applied to raw, uncooked, unprocessed foods (e.g., fruits or vegetables), cultured or fermented products (e.g., cheese, yogurt or salami, etc.) since these foods are known and expected to have naturally occurring microbial flora. There are three categories of ACC listed in the table above, which are based on food type and the processing/handling the food has undergone.

Category 1 – cooked foods that do not require handling or processing; i.e., soups, bread, quiche, cooked meat, fish & seafood, vegetables, etc.

Category 2 – cooked foods that require further handling prior to or during the preparation of the final product; i.e., hot dogs, sandwiches, burgers, etc.

Category 3 – foods that have a high ACC due to the normal microbial flora associated; i.e., pitas, potato or pasta salad, salad rolls, fresh fruits, raw vegetables, cheese, yogurt, deli meats, etc.

Total Coliform: Presence of coliforms in a processed, cooked, ready-to-eat food is indicative of inadequate processing or post processing contamination resulting from poor handling of the product. A satisfactory limit cannot be applied to uncooked or raw foods such as salads and salad ingredients, raw fruits and vegetables, raw meats as well as some fermented foods, etc., since coliforms are regularly found in and/or on these foods.

Escherichia coli: The presence of Escherichia coli in food is indicative of direct or indirect contamination of the food product with fecal material, thus, enteric pathogens may also be present. The presence may be indicative of inadequate processing, post processing contamination and poor sanitation.

Total gram negative: Total gram negative (TGN) count has the same significance as presence of coliforms. Elevated TGN count should not be detected in cooked or processed ready-to-eat foods. Absence of gram negative organisms in a food sample is another indicator of food safety.

Yeast and mould: The presence of yeast and moulds can cause various degrees of deterioration and decomposition of food, resulting in abnormal odours, flavours and colours. Both yeast and mould can also be added intentionally to a product for a desirable flavour such as mould for blue and brie cheeses and yeast for beer, ciders and wines.


Testing Type Reporting Limit (CFU/g)a Unsatisfactory Level (CFU/g)a, c
Bacillus cereus < 100 to > 200,000
≥ 104 potentially hazardous
Campylobacter species Not Detected / Detected
Clostridium perfringens < 100 to > 200,000
≥ 104 potentially hazardous
Escherichia coli O157:H7 Not Detected / Detected
Listeria monocytogenes Not Detected / Detected
Salmonella species Not Detected / Detected
Shigella species Not Detected / Detected
Staphylococcus aureus < 100 to > 200,000
≥ 104 potentially hazardous
Staphylococcus aureus toxin Not Detected / Detected
Vibrio species Not Detected / Detected
Yersinia enterocololitica Not Detected / Detected Detected

a CFU (colony forming units)
b Microbial guidelines as per Health Canada

Foodborne pathogens should not be detected from a ready-to-eat food and would indicate improper food preparation, poor handling, inadequate sanitation practices or possible contamination from a positive food source or an ill food handler. Appendix C: Major Foodborne Diseases: General Features provide additional information regarding the organisms incubation period, clinical symptoms, mode of transmission and associated foods.


Testing Type Reporting Limit (CFU/g)a
pH 1.00 to 14.00
Phosphatase Not Detected / Detected
Water activity (aw) 0.000 to 1.000 IU/L

pH: The pH is a function of the hydrogen ion concentration in the food and is a measure of food acidity and alkalinity, which varies with food type. pH is measured on a scale of 1 to 14, with 7 being neutral, lower numbers indicating greater acidity and higher numbers indicating greater alkalinity. pH is just one factor that influences bacterial growth, and can interact with the following to inhibit growth of pathogens and other organisms: water activity (aw), salt, redox potential, preservatives and temperature. As the pH decreases, a lower temperature is needed to inactivate microbes.5 Foods with an equilibrium pH ≤ 3.7 will not support the growth of bacterial foodborne pathogens, regardless of the aw. However, if the pH of the food (jarred/canned products) is ≤ 4.6, microorganisms are inhibited providing the aw is ≤ 0.85. According to Public Health Ontario’s Home Canning Literature Review, June 2014, a hermetically sealed acidic canned or jarred food with an equilibrium pH ≤ 4.6 that has gone through sufficient heat treatment to eliminate vegetative microorganisms (bacteria, yeasts and molds), will not support the germination and growth of botulinum spores and production of the toxin.

Phosphatase: The enzyme alkaline phosphatase (ALP) is associated with the cream or fat globules of raw milks. It is inactivated below the detection limit of conventional methods following complete pasteurization. The detection of residual alkaline phosphatase indicates a reduction in pasteurization temperature of at least 1.5°C, a 5 minute reduction in holding time, or the presence of ≥ 0.3% raw milk. Since ALP is more heat stable than most pathogens (which may be present in milk), it is used as an indicator of pasteurization; however, a negative ALP test does not guarantee that the product is pathogen free.

Water activity (aw): The availability of water for microbial, enzymatic or chemical activity determines the shelf life of foods. This water availability is measured as water activity (aw). Water activity is the ratio of water vapor pressure of the food substrate to the vapor pressure of pure water at the same temperature. Water activity is measured on a scale of 0 to 1; pure water has an aw of 1.00 and the aw of a completely dehydrated food is 0.00. For most foods to be considered safe to store at room temperature, they should have an aw ≤ 0.85. Bacterial foodborne pathogens are inhibited at this aw; however, for those microorganisms that can cause spoilage (e.g., yeasts and moulds), the aw should be  < 0.60 to prevent food spoilage by inhibiting growth of these organisms.

contact lab

Contact Laboratory Customer Service

Laboratory Services

Updated 22 April 2022