Application of Microbial and Parasitology Techniques for Diagnosis in Laboratory Rodents

Pathogen diagnosis in rodents through effective health monitoring programs is essential for maintaining high welfare and standards in laboratory animal facilities. Although many animal facilities are increasingly adopting real-time polymerase chain reaction testing of environmental or filter samples for pathogen detection, thereby reducing the need for sentinel animals, classical methods such as microbiological assays and microscopic examination for parasites, remain essential and relevant tools in laboratory animal diagnostics. This article describes protocols for the identification of bacterial, viral, and parasitic agents in mice and rats in accordance with the recommendations of the Federation of European Laboratory Animal Science Associations. The methodologies presented detailed procedures for sample collection from mice and rats and for screening these samples using bacterial, parasitological, and viral panels. In addition, we describe bacterial culture techniques and the use of selective and differential media for pathogen isolation, as well as step-by-step protocols for the detection of pinworms, mites, and parasite eggs. These protocols provide a practical foundation for establishing a basic diagnostic laboratory to support standardized animal husbandry and health monitoring quality. © 2026 The Author(s). Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: Gathering rodent samples for pathogen screening Basic Protocol 2: Inoculation and screening of bacterial cultures from rodent samples Support Protocol 1: Identification of bacteria using differential media Basic Protocol 3: Identification of Helicobacter by PCR targeting the 16S rRNA gene Basic Protocol 4: Pinworm screening by microscopy Support Protocol 2: Confirmation and specification of parasites (pinworms and mites) by PCR Basic Protocol 5: Mite screening by microscopy Basic Protocol 6: Virus identification by serology.