Changes in microbial prevalence in mice within Japanese academic animal facilities between 2011 and 2024

The microbiological quality of laboratory animals evolves along with changes in the research environment. To identify recent trends in modern Japanese research facilities, this study analyzed longitudinal contamination data for 16 major pathogens (including Helicobacter hepaticus, Pseudomonas aeruginosa, Staphylococcus aureus, Mycoplasma pulmonis, Mouse hepatitis virus (MHV), Murine norovirus (MNV) and various protozoa) collected over a 14-year period from 2011 to 2024. Our analysis revealed a significant decline in the testing request-level positivity rates (the number of positive testing requests per total requests) for most pathogens, including Helicobacter hepaticus, Pasteurella pneumotropica, Staphylococcus aureus, MHV, MNV and several intestinal protozoa and pinworms. Notably, the highest positivity rate, recorded for Staphylococcus aureus, decreased from 21.45% in 2011 to 13.65% in 2024. Similarly, the rate for Entamoeba dropped from 9.75% to 5.76%. Spironucleus muris, which maintained a low prevalence, showed a slight increase from 0.05% to 0.09% during the same period. These results demonstrate that the overall microbiological quality of mice from academic institutions has improved significantly over the past 14 years. While this progress reflects the success of modern bio-exclusion strategies, the data indicate that certain microorganisms persist at low levels and are not easily eradicated. These findings suggest that maintaining this high standard of quality requires continuous vigilance and the further refinement of quality control protocols to safeguard the integrity and reproducibility of biomedical research.