Detection of Myocoptes musculinus in Fur Swab and Fecal Samples by Using PCR Analysis

A comprehensive approach for microbiota and health monitoring in mouse colonies using metagenomic shotgun sequencing

Background

Health surveillance of murine colonies employed for scientific purposes aim at detecting unwanted infection that can affect the well-being of animals and personnel, and potentially undermine scientific results. In this study, we investigated the use of a next-generation sequencing (NGS) metagenomic approach for monitoring the microbiota composition and uncovering the possible presence of pathogens in mice housed in specific pathogen-free (SPF) or conventional (non-SPF) facilities.

Results

Analysis of metagenomic NGS assay through public and free algorithms and databases allowed to precisely assess the composition of mouse gut microbiome and quantify the contribution of the different microorganisms at the species level. Sequence analysis allowed the uncovering of pathogens or the presence of imbalances in the microbiota composition. In several cases, fecal pellets taken from conventional facilities were found to carry gene sequences from bacterial pathogens (Helicobacter hepaticus, Helicobacter typhlonius, Chlamydia muridarum, Streptococcus pyogenes, Rodentibacter pneumotropicus, Citrobacter rodentium, Staphylococcus aureus), intestinal protozoa (Entamoeba muris, Tritrichomonas muris, Spironucleus muris) nematoda (Aspiculuris tetraptera, Syphacia obvelata), eukaryotic parasites (Myocoptes musculinus) and RNA virus (Norwalk virus). Thus, the use of NGS metagenomics can reduce the number of tests required for the detection of pathogens and avoid the use of sentinel mice.

Conclusions

In summary, in comparison with standard approaches, which require multiple types of test, NGS assay can detect bacteria, fungi, DNA and RNA viruses, and eukaryotic parasites from fecal pellets in a single test. Considering the need to protect animal well-being and to improve the success and reproducibility of preclinical studies, this work provides the proof-of-concept that the use of NGS metagenomics for health monitoring of laboratory mice is a feasible and dependable approach, that is able to broaden the current concept of health monitoring of laboratory mice from “pathogen surveillance” to a more inclusive “microbiota surveillance”.

Supplementary Information

The online version contains supplementary material available at 10.1186/s42523-021-00113-4.

PCR Testing of Media Placed in Soiled Bedding as a Method for Mouse Colony Health Surveillance

Rodent colony health surveillance has traditionally been accomplished by testing sentinel animals that have been exposed to soiled bedding from colony animals. Collecting samples from exhaust plenums on ventilated caging systems, followed by PCR analysis, has emerged as another promising method for health surveillance. However, environmental testing at the rack level is not effective for all ventilated rack designs. In this study, we tested whether media placed in soiled bedding is effective in detecting 3 adventitious agents: mouse norovirus (MNV), Helicobacter spp., and fur mites. Soiled bedding was collected from pathogen-positive colony mice and distributed to traditional sentinel mouse cages and mouse-free experimental cages every 1 to 2 wk for static and ventilated cages, respectively. Experimental cages contained 10 flocked swabs ('passive swabs') and 1 piece of filter media. After 90 d, fresh feces, pelage swabs, and blood were collected from the sentinel cages, and the passive swabs and filter media were collected from the experimental cages. Concurrently, 10 additional flocked swabs ('active swabs') were stirred through the cumulated soiled bedding of each experimental cage. Sentinel mice were positive for MNV and Helicobacter spp., but negative for fur mites by pelage swab PCR. All samples from experimental cages were positive for Helicobacter spp. and fur mites in both caging types. For MNV, passive swabs were most effective at detection (100%), followed by active swabs (80% to 100%) and filter media (60% to 80%). These findings suggest that testing media in pooled soiled bedding samples is more effective than traditional sentinel methods for colony health surveillance and is a viable option when sampling at the rack level is ineffective.

PCR and RT-PCR in the Diagnosis of Laboratory Animal Infections and in Health Monitoring

Molecular diagnostics (PCR and RT-PCR) have become commonplace in laboratory animal research and diagnostics, augmenting or replacing serological and microbiologic methods. This overview will discuss the uses of molecular diagnostics in the diagnosis of pathogenic infections of laboratory animals and in monitoring the microbial status of laboratory animals and their environment. The article will focus primarily on laboratory rodents, although PCR can be used on samples from any laboratory animal species.