Rodent Health Monitoring

Replace Sentinel Mice

More Accurate Results

Reduce Labor & Cost

Reduce Emotional Fatigue

It is important to ensure that rodent colonies are free of adventitious infectious agents to support high quality, robust research & safety data. Over the last 50 years, health surveillance has been typically performed using sentinel animals. More recently, molecular-based diagnostics combined with environmental monitoring strategies have been adapted by many institutions to either supplement or replace the more traditional methods. These newer approaches have the possibility of significantly reducing/replacing the number of rodents used in maintaining specific-pathogen-free colonies.

Introductory slide deck for environmental monitoring

We recommend starting by giving an introductory presentation to management and other stakeholders about the evidence, advantages, and practicalities of replacing sentinel rodents with environmental health monitoring. We have a 10-15 min slide deck that you are free to use and modify for your facility that you can download by clicking the image below. 

Why use environmental monitoring?

How to use environmental monitoring if you have racks that filter at the rack level (e.g., Allentown or Tecniplast)?

Individually Ventilated Cages (IVCs) + Plenum Swabs

Advantages = Initially less costly than exhaust plenum media holders (i.e. collars mounted media.)

Challenges = Some rack brands/designs are easier to implement environmental monitoring than others (e.g., not effective with rack designs with cage level exhaust air filtration). May not be sensitive enough for pathogens that are at low prevalence.

Individually Ventilated Cages (IVCs) + Collar Mouted Media

Advantages = Operator variability is minimized & minimal handling is required. Detects Helicobacter & MNV with similar sensitivity to swabbing. Media helps increase dust collection. Acceptable for 3-month collection. Provides a history of pathogens that were present over the previous 3 months. Presumably reduced ergonomic effort.

Challenges = Can be physically difficult to place/collect collar mounted media from single-sided racks. Collars/media must be placed AFTER racks are washed & collected BEFORE wash which requires coordination (alternatively you can wait to wash racks until they test positive and then clean once the potential outbreak is resolved). May be costly.

How to use environmental monitoring if you have racks that filter at the cage level (NOT Allentown or Tecniplast), Static Cages, or want to use the same method everywhere?

IVCs or Static Cages + Filter Paper or Flocked Swabs

Exhaust air duct monitoring is not an option for static cages or racks that filter at the cage level (Bauer, 2016; Dubelko, 2018). In this case, PCR material must be collected from the cage. These methods are described in 3 key references: Dubelko, 2018; O’Connel 2021; or Hanson, 2021.

Overall, the best option may be to place 10 flocked swabs or a large piece of filter paper inside an additional cage (where sentinel animals would usually be placed) and then transfer soiled bedding as usual. Soiled bedding should be shaken or stirred with the swabs after cage change. Flocked swabs or filter paper can be tested at 1-3 months after placing them.

Research shows that PCR testing of flocked swabs was as effective or MORE effective than PCR testing from sentinel mice.

Thus far these methods have been used to detect pinworms, fur mites, mouse hepatitis virus (MHV), murine norovirus (MNV, minute virus of mice (MVM), mouse parvovirus (MPV), Theiler murine encephalomyelitis virus (TMEV), Helicobacter spp*, Syphacia obvelata, Aspiculuris tetraptera, Rodentibacter spp.*, Entamoeba muris, and Spironucleus spp.

This method is still reliant on soiled bedding transfer & dependent on personnel shaking cages or stirring. However, it is still an effective replacement for soiled bedding sentinel mice.

Removing Testing Altogether or Testing Individual Animals via PCR

If animals from approved vendors will only be on-site for a short period of time (e.g., <1-2 months) then health monitoring may not be necessary. You could also consider collecting fecal samples, fur swabs +/- oral swabs directly from colony animals.

Addressing Common Concerns & Questions

Is there really enough data on this? There are more than 20 publications supporting environmental monitoring from more than 7 years.

It’s too costly! In fact, in some cases, it may be less expensive to conduct environmental monitoring (Luchins, 2020). Be sure to factor in the cost of housing & caring for sentinel rodents.

I don’t have time to retrain my staff & develop a new program. Although there may be an initial time investment, there are time savings once implemented (Luchins, 2020).

Will other institutions accept our rodents? Reports from institutions currently using only environmental monitoring indicate that yes, other institutions will accept their rodents. In fact, other institutions recognize the increased sensitivity of this type of health monitoring program.

Will there be false positives or ambiguities? This is possible. Always investigate unexpected results further.

Will there be residual nucleic acid after rack washing? There may be some for Helicobacter spp. or MNV though may not (Mailhot, 2019). If seen, you may need to wash racks more than once or even scrub plenums to remove residual nucleic acids.

What about missing new & emerging pathogens? This problem can be helped by performing histopathology on any colony animals with unusual phenotypes/signs/illness.

What institutions have made the switch?

Several reputable, large academic, pharmaceutical, and government organizations have replaced live soiled bedding sentinel rodents with environmental monitoring technology. This includes institutions such as University of Washington, University of Florida, University of Colorado Anschutz Medical Campus, Emory University, University of Chicago, Yerkes National Primate Research Center, Medical College of Wisconsin, Northwestern University, Benaroya Research Institute, and many more. 

What should I do if I find something?

This may depend on the pathogen. Ask your diagnostic laboratory what they recommend. They may recommend testing colony animals by cage perimeter swabs, direct fur swabs, blood, or feces to narrow down positive cages. Alternatively they may suggest pooled plenum swabbing for confirmatory testing

If you suspect a false positive or residual nucleic acid, then move cages to a clean rack & re-swab in 2-4 weeks.

Consider submitting to a different diagnostic lab for confirmatory testing.

NA3RsC Webinars & Presentations

PDF of our Presentations from AALAS 2021 click on the image below:

Video fo our presentation on November 9, 2021:


  1. Bauer, B. A., Besch-Williford, C., Livingston, R. S., Crim, M. J., Riley, L. K., & Myles, M. H. (2016). Influence of rack design and disease prevalence on detection of rodent pathogens in exhaust debris samples from individually ventilated caging systems. Journal of the American Association for Laboratory Animal Science55(6), 782-788.
  2. Besselsen, D. G., Wagner, A. M., & Loganbill, J. K. (2000). Effect of mouse strain and age on detection of mouse parvovirus 1 by use of serologic testing and polymerase chain reaction analysis. Comparative medicine50(5), 498-502.
  3. Brielmeier, M., Mahabir, E., Needham, J. R., Lengger, C., Wilhelm, P., & Schmidt, J. (2006). Microbiological monitoring of laboratory mice and biocontainment in individually ventilated cages: a field study. Laboratory animals40(3), 247-260.
  4. Compton, S. R., Homberger, F. R., Paturzo, F. X., & Clark, J. M. (2004). Efficacy of three microbiological monitoring methods in a ventilated cage rack. Comparative medicine54(4), 382-392.
  5. de Bruin, W. C. C., van de Ven, E. M. E., & Hooijmans, C. R. (2016). Efficacy of soiled bedding transfer for transmission of mouse and rat infections to sentinels: a systematic review. PloS one11(8), e0158410.
  6. Dole, V. S., Zaias, J., Kyricopoulos-Cleasby, D. M., Banu, L. A., Waterman, L. L., Sanders, K., & Henderson, K. S. (2011). Comparison of traditional and PCR methods during screening for and confirmation of Aspiculuris tetraptera in a mouse facility. Journal of the American Association for Laboratory Animal Science50(6), 904-909.
  7. Dubelko, A. R., Zuwannin, M., McIntee, S. C., Livingston, R. S., & Foley, P. L. (2018). PCR Testing of Filter Material from IVC Lids for Microbial Monitoring of Mouse Colonies. Journal of the American Association for Laboratory Animal Science57(5), 477-482.
  8. Gerwin, P. M., Ricart Arbona, R. J., Riedel, E. R., Henderson, K. S., & Lipman, N. S. (2017). PCR testing of IVC filter tops as a method for detecting murine pinworms and fur mites. Journal of the American Association for Laboratory Animal Science56(6), 752-761.
  9. Hanson, W. H., Taylor, K., & Taylor, D. K. (2021). PCR Testing of Media Placed in Soiled Bedding as a Method for Mouse Colony Health Surveillance. Journal of the American Association for Laboratory Animal Science: JAALAS.
  10. Ike, F., Bourgade, F., Ohsawa, K., Sato, H., Morikawa, S., Saijo, M., … & Berard, M. (2007). Lymphocytic choriomeningitis infection undetected by dirty-bedding sentinel monitoring and revealed after embryo transfer of an inbred strain derived from wild mice. Comparative medicine57(3), 272-281.
  11. Jensen, E. S., Allen, K. P., Henderson, K. S., Szabo, A., & Thulin, J. D. (2013). PCR testing of a ventilated caging system to detect murine fur mites. Journal of the American Association for Laboratory Animal Science52(1), 28-33.
  12. Kapoor, P., Hayes, Y. O., Jarrell, L. T., Bellinger, D. A., Thomas, R. D., Lawson, G. W., … & Nielsen, J. N. (2017). Evaluation of anthelmintic resistance and exhaust air dust PCR as a diagnostic tool in mice enzootically infected with Aspiculuris tetraptera. Journal of the American Association for Laboratory Animal Science56(3), 273-289.
  13. Körner, C., Miller, M., & Brielmeier, M. (2019). Detection of Murine Astrovirus and Myocoptes musculinus in individually ventilated caging systems: Investigations to expose suitable detection methods for routine hygienic monitoring. PloS one14(8), e0221118.
  14. Leblanc, M., Berry, K., Graciano, S., Becker, B., & Reuter, J. D. (2014). False-positive results after environmental pinworm PCR testing due to rhabditid nematodes in corncob bedding. Journal of the American Association for Laboratory Animal Science53(6), 717-724.
  15. Lindstrom, K. E., Carbone, L. G., Kellar, D. E., Mayorga, M. S., & Wilkerson, J. D. (2011). Soiled bedding sentinels for the detection of fur mites in mice. Journal of the American Association for Laboratory Animal Science50(1), 54-60.
  16. Luchins, K. R., Bowers, C. J., Mailhiot, D., Theriault, B. R., & Langan, G. P. (2020). Cost Comparison of Rodent Soiled Bedding Sentinel and Exhaust Air Dust Health-Monitoring Programs. Journal of the American Association for Laboratory Animal Science59(5), 508-511.
  17. Mahabir, E., Durand, S., Henderson, K. S., & Hardy, P. (2019). Comparison of two prevalent individually ventilated caging systems for detection of murine infectious agents via exhaust air particles. Laboratory animals53(1), 84-88.
  18. Mailhiot, D., Ostdiek, A. M., Luchins, K. R., Bowers, C. J., Theriault, B. R., & Langan, G. P. (2020). Comparing mouse health monitoring between soiled-bedding sentinel and exhaust air dust surveillance programs. Journal of the American Association for Laboratory Animal Science59(1), 58-66.
  19. Manuel, C. A., Pugazhenthi, U., & Leszczynski, J. K. (2016). Surveillance of a ventilated rack system for Corynebacterium bovis by sampling exhaust-air manifolds. Journal of the American Association for Laboratory Animal Science55(1), 58-65.
  20. Manuel, C. A., Pugazhenthi, U., Spiegel, S. P., & Leszczynski, J. K. (2017). Detection and elimination of Corynebacterium bovis from barrier rooms by using an environmental sampling surveillance program. Journal of the American Association for Laboratory Animal Science56(2), 202-209.
  21. Miller, M., Ritter, B., Zorn, J., & Brielmeier, M. (2016). Exhaust air dust monitoring is superior to soiled bedding sentinels for the detection of Pasteurella pneumotropica in individually ventilated cage systems. Journal of the American Association for Laboratory Animal Science55(6), 775-781.
  22. Miller, M., Ritter, B., Zorn, J., & Brielmeier, M. (2016). Exhaust air particle PCR detects Helicobacter hepaticus infections at low prevalence. J Vet Sci Technol7(343), 2.
  23. Miller, M., & Brielmeier, M. (2018). Environmental samples make soiled bedding sentinels dispensable for hygienic monitoring of IVC-reared mouse colonies. Laboratory animals52(3), 233-239.
  24. O’Connell, K. A., Tigyi, G. J., Livingston, R. S., Johnson, D. L., & Hamilton, D. J. (2021). Evaluation of In-cage Filter Paper as a Replacement for Sentinel Mice in the Detection of Murine Pathogens. Journal of the American Association for Laboratory Animal Science.
  25. Pettan-Brewer, C., Trost, R. J., Maggio-Price, L., Seamons, A., & Dowling, S. C. (2020). Adoption of Exhaust Air Dust Testing in SPF Rodent Facilities. Journal of the American Association for Laboratory Animal Science59(2), 156-162.
  26. Perdue, K. A., Copeland, M. K., Karjala, Z., Cheng, L. I., Ward, J. M., & Elkins, W. R. (2008). Suboptimal ability of dirty-bedding sentinels to detect Spironucleus muris in a colony of mice with genetic manipulations of the adaptive immune system. Journal of the American Association for Laboratory Animal Science47(5), 10-17.
  27. Ragland, N. H., Miedel, E. L., & Engelman, R. W. (2019). PCR prevalence of murine opportunistic microbes and their mitigation by using vaporized hydrogen peroxide. Journal of the American Association for Laboratory Animal Science58(2), 208-215.
  28. Zorn, J., Ritter, B., Miller, M., Kraus, M., Northrup, E., & Brielmeier, M. (2017). Murine norovirus detection in the exhaust air of IVCs is more sensitive than serological analysis of soiled bedding sentinels. Laboratory animals51(3), 301-310.