Food, Water & Environmental Microbiology

With comprehensive expertise and capability, AFL conducts food safety testing, including regulatory food testing for food ingredients, food products, water and environmental samples to determine microbial growth and pathogen risks in the farm-to-fork supply chain. We also serve our clients to validate advanced media and methods/test kits for testing foodborne organisms in various matrices for official acceptance or internal use. We carry out R&D projects or challenge studies to support validation/registration of a new formulation, equipment and process or discovery research. Our professional team of microbiologists and technologists is committed to providing scientifically sound and practical solutions to meet your specific needs.

AFL is accredited to ISO/IEC 17025 standard for many microbiological analyses on our Scope of Accreditation. Click below to learn more about our microbiology services or contact us to learn how we can meet your needs.

Food pathogen testing

  • Bacillus cereus group
  • Campylobacter spp.
  • Clostridium perfringens
  • Cryptosporidium
  • Escherichia coli O157:H7
  • Giardia
  • Listeria monocytogenes
  • Salmonella spp.
  • Salmonella Enteritidis
  • Staphylococcus aureus
  • Shiga toxin-producing E. coli (STEC or VTEC)
  • Top 6 non-O157 STEC O types: O26, O45, O103, O111, O121, O145
  • Vibrio species (V. cholerae, V. vulnificus and V. parahaemolyticus)
  • Yersinia enterocolitica

Water microbiology testing

AFL tests water from a variety of sources, including potable water (tap, well), water used in food processing, surface water (pond, river, stream), irrigation/wash water, waste, recreational and recirculation water. Our water microbial quantitative or qualitative tests include:

  • Generic E. coli
  • Campylobacter
  • Heterotrophic bacteria
  • Salmonella
  • Total coliform
  • Yeast and Mold

AFL is licensed to provide microbiological testing for drinking waters under Ont. Reg 318/319 and Ont. Reg. 170 for E. coli/Total coliforms and Heterotrophic bacteria.

For Small Drinking Water System (SDWS) testing required by the Public Health Unit, please contact us for appropriate testing and submission information.

Environmental monitoring and indicator testing

  • Bacillus cereus group
  • Clostridium perfringens
  • Generic E. coli
  • Heterotrophic bacteria
  • Lactic acid bacteria (LAB)
  • Listeria species
  • Pseudomonas aeruginosa
  • Staphylococcus aureus
  • Total viable bacteria
  • Total coliform
  • Yeast and Mold

Beer, wine and beverage spoilage testing

AFL tests beer products, raw ingredients, water and environmental samples to find contaminants or potential contamination issues. We use various methods from rapid PCR, culture isolation to next generation sequencing technologies to identify organisms of concern. The AFL professional team of scientists and technologists are committed to providing the highest quality results and value to our clients to enhance your product quality and protect your brand.

Comprehensive organism coverage for beer and wine spoilers:

Bacteria:

  • Acetobacter species
  • Brettanomyces species
  • Gluconobacter species
  • Lactobacillus species
  • Leuconostoc species
  • Megasphaera species
  • Oenococcus species
  • Pectinatus species
  • Pediococcus species

Yeast:

  • Brettanomyces/ Dekkeraspecies
  • Hanseniaspora species
  • Hansenula species
  • Metschnikowia species
  • Pichia species
  • Saccharomyces species
  • Saccharomyces cerevisiae (variant diastaticus)
  • Saccharomycodes species
  • Schizosaccharomyces species
  • Wickerhamomyces species
  • Zygosaccharomyces species

Hop resistance genes

High speed to actionable results

  • PCR Rush Results within 48 hours

Regulatory testing for non-alcoholic beverages for meeting food safety regulations

  • Pathogen detection – e.g. E. coli O157:H7, Listeria monocytogenes, Salmonella, Shiga toxin-producing E. coli (STEC)
  • Indicator enumeration – e.g. total viable bacteria, generic E. coli, total coliform, Listeria spp., yeast and mold

Accurate results with peace of mind

  • Comprehensive microorganism and hop resistance genes coverage to minimize the possibility an organism will be missed
  • Testing is engineered to ensure high quality results and conducted following the requirements of ISO/IEC 17025 standards.

Detection of unknowns beyond the above list

  • Culture isolation – bacteria, yeast or mold; anaerobic and aerobic
  • Rapid identification of species by MALDI-TOF mass spectrometry, advanced biochemical-based system or DNA sequencing – the gold standard
  • Comprehensive detection of all microorganisms using high throughput (next generation) sequencing

Strain identification and tracking

  • Custom strain typing (including Saccharomyces cerevisiae strain typing)
  • Custom whole genome sequencing – the ultimate method

Probiotic testing (species or strain)

Probiotic organisms are bacteria species or strains that are used in many probiotic health products due to their potential health benefits. Species or strain-level identification of probiotic organisms is of paramount importance to ensure probiotic efficacy and safety. Our methods cover over 50 strains/species for the following organisms.

  • Bacillus subtilis
  • Bifidobacterium bifidum
  • Bifidobacterium breve
  • Bifidobacterium infantis
  • Bifidobacterium lactis
  • Bifidobacterium longum
  • Lactobacillus acidophilus
  • Lactobacillus brevis
  • Lactobacillus casei
  • Lactobacillus delbrueckii subsp. bulgaricus
  • Lactobacillus fermentum
  • Lactobacillus gasseri
  • Lactobacillus helveticus
  • Lactobacillus paracasei
  • Lactobacillus plantarum
  • Lactobacillus reuteri
  • Lactobacillus rhamnosus
  • Lactobacillus salivarius
  • Pediococcus pentosaceus
  • Streptococcus thermophilus

Cannabis microbial testing

  • E. coli
  • Salmonella
  • Pseudomonas aeruginosa
  • Staphylococcus aureus
  • Bile-Tolerant Gram-Negative (BTGN) bacteria
  • Total aerobic bacteria counts
  • Yeast and mold counts

Microbial identification testing (bacteria, yeasts and fungi)

AFL conducts routine identification of unknown microorganisms (bacteria, yeasts and fungi) from pure cultures using MALDI-TOF mass spectrometry, DNA sequencing or advanced biochemical reactions. While the MALDI-TOF mass spectrometry or biochemical reactions can provide genus/species level of results on most fresh bacterial cultures, the DNA-based gold standard method will provide rapid, objective and reproducible results on any unknown bacteria, yeasts, or fungi without relying on growth.

Pathogen typing service

If you have concerns about microbial contamination or a pathogen outbreak, our highly educated and dedicated scientists may provide the key to solving your food safety, plant/animal health or environmental issues. Subtyping is often used to investigate microbial transmission of a pathogen during a production process, along a supply chain or in outbreak investigations. We conduct routine subtyping using MLVA and other methodologies for various pathogens or indicators, including but not limited to:

  • Campylobacter
  • E. coli O157:H7
  • Haemophilus parasuis
  • Lactococcus lactis
  • Listeria innocua
  • Listeria monocytogenes
  • Coxiella burnetii
  • Cryptosporidium
  • Giardia
  • Legionella pneumophila
  • Mycoplasma
  • Phytophthora infestans
  • Salmonella
  • Shiga toxin-producing E. coli (STEC or VTEC)
  • Staphylococcus aureus

Microbiome analysis service

Microbiome analysis aims to reveal a complete list of microbial genus/species contained in a sample via targeted deep DNA sequencing. The analysis will provide information on overall microbial community signatures, diversity, dominance or important taxa in foods, water, soil and other samples. The analysis can be used to garner or reveal invaluable insights:

  • Identify gaps/deficiencies in control procedures or agriculture practices
  • Monitor and control abnormal microbial population and prevent potential issues
  • Monitor and manage food-microbe and plant-soil-microbe interactions
  • Proactively identify potential pathogens before becoming an issue
  • Identify the root cause of complex and persistent microbes of concern
  • Develop new biocontrol strategies to minimize usage of chemicals in agriculture

Whole genome sequencing service

We offer services for whole genome sequencing of microorganisms, or sequencing of targeted regions of microbial communities. Whole genome sequences can be used for high-resolution comparison of bacterial strain relatedness while targeted metabarcode sequences can be used to identify genus/species or even Salmonella serotypes in complex samples.

Water activity, pH, moisture and alkaline phosphatase testing

  • Pasteurization confirmation by alkaline phosphatase in milk and dairy products
  • Lab pasteurization count
  • Preliminary incubation count
  • Water activity and pH
  • Moisture content