Research allows the Hygiene and Environment sector to continuously update its knowledge and technical expertise, which can then be put to use in internal projects or those requested by third parties, such as:

• Rapid identification of microorganisms
• Detection of microbial contaminants in production processes
• Detection of pathogenic micro-organisms
• Qualitative and quantitative analysis of pathogenic and environmental microorganisms in different matrices
• Molecular fingerprinting for epidemiological applications such as determining the origin of contamination

In accordance with the Institute's quality guidelines, the department offers the following services:

• Isolation of bacteria, yeasts, or filamentous fungi (molds) from various samples by culturing them on specific media
• Rapid identification of bacteria, yeasts, or filamentous fungi using MALDI-TOF mass spectrometry
• Molecular identification of microorganisms by sequencing specific regions of DNA or RNA
• Specific amplification of DNA or RNA regions using PCR (Polymerase Chain Reaction)
• Identification of specific microorganisms through real-time DNA or RNA amplification (Real Time PCR)
• Upon request, personalized consulting for environmental investigations related to microbiology (sampling in various environments or on specific instruments, analysis of new organisms using MALDI-TOF mass spectrometry, use of next-generation sequencing for population studies, etc.)

Environmental investigations currently carried out by the Hygiene and Environment Department:
Microbiology applied to the natural and built environment

• Analysis of air or water samples for the quantification of bacteria, yeasts, or filamentous fungi
• Determination of the resistance of bacteria to specific antibiotics, using disc diffusion tests (antibiogram)
• Detection of various genes responsible for antibiotic resistance, starting from bacterial cultures or water samples
• Analysis of surfaces (walls, works of art, workbenches, etc.) for the detection and identification of microorganisms such as bacteria, yeasts, or molds
• Detection of xylophagous fungi Coniophora puteana and Serpula lacrymans
• Rapid identification of mosquito eggs (genus Aedes) using MALDI-TOF mass spectrometry

Microbiology applied to the animal environment

• Direct detection of bacteria of the genus Flavobacterium in fish, using fluorescence in situ hybridization (FISH)
• Search for pathogenic bacteria in fish, using specific culture media, identification by MALDI-TOF mass spectrometry, and determination of their resistance to various antibiotics
• Detection of the pathogenic fungus Ophidiomyces ophidiicola in snake samples, using MALDI-TOF mass spectrometry (after isolation of the strain on specific media) or specific DNA amplification (PCR, real-time PCR)
• Detection of bacteria of the genus Mycoplasma in reptile samples (swabs and organs), through specific DNA amplification (PCR) and sequencing
• Detection of viral agents (Adenovirus, Herpesvirus, and Rana virus) in samples from amphibians and reptiles (swabs and organs) using specific DNA amplification (PCR) and sequencing
• Research and selection of bacteriophage viruses to combat infections in animals

Microbiology applied to the human environment 

• Identification of bacteria in the human microbiome using MALDI-TOF mass spectrometry
• Identification of Legionella bacteria using MALDI-TOF mass spectrometry

Miscellaneous

• Vegetative cultures used in cheese production: weekly determination of the ratio between lactobacilli and lactococci-streptococci, using microscopic analysis

The list of procedures in the Hygiene and Environment sector is constantly evolving, as it is based on customized requests, specific environmental situations, and the results of research projects.