Reducing Pathogens in the Vivarium

Reducing Pathogens in the Vivarium

Whether you’re dealing with immunocompetent or immunocompromised animals, pathogens in the vivarium can pose a serious threat. Viruses, parasites, bacteria, mycoplasma, and fungi can all threaten the health of research animals and negatively affect data.

Your vivarium’s pathogen management plan may be the deciding factor in the success of your next research project. To reduce the likelihood of pathogen transmission, your rodents (or other animals) require routine and diagnostic health monitoring in addition to vivarium-based biosecurity measures.

The Pathogen Management Plan

A pathogen management plan is a key tool in the monitoring of pathogens in a vivarium.

Pathogens are wildly diverse, and their presence can depend heavily on local geography and facilities. Different pathogens pose different risks to animals and/or research; thus, the response will differ based on the severity levels. The pathogen management plan will differ between institutions as classification of risk factors as well as variations in screening capabilities, research animals, research projects, and facility operations are carefully considered. While the response to individual detections will depend on the specific pathogen, options may include:

  • Retesting
  • Culling
  • Rederivation
  • Quarantine
  • Isolation
  • Cage pressurization changes
  • Additional personal protective equipment (PPE) for staff
  • Limited room access
  • Limited animal movement

It’s important that all parties who interact with the vivarium (e.g., veterinarian, facility manager, husbandry technician) are aware of the standard operating procedures (SOPs) in the event of a positive pathogen detection.

Central to Explora BioLabs’ pathogen management is a sentinel program with regular screening of animals and environmental analysis where appropriate. We use a combination of PCR, serology, ATP testing, and additional sampling and testing methods as indicated. Potential pathogens are classified as low, medium, or high risk. Low-risk pathogens are of minimal concern and generally require no proactive response outside of standard biosecurity practices and cleaning/disinfecting measures carried out at regular intervals by Explora BioLabs’ vivarium technicians. In the event of medium-risk pathogen detection, the client is notified and follow-up testing to confirm the pathogen’s presence is recommended. Explora works with each individual client to minimize impact on research. We will discuss appropriate options such as treatment, eradication, and rederivation.

When high-risk pathogens are detected, the quarantine procedure is immediately employed and the client is notified. The quarantine procedure includes

  • a quarantine sign placed on the holding/procedure room,
  • restricted staff access,
  • additional PPE use,
  • and adjustments to the general room service flow to place the quarantined room at the last service of the day to prevent transmission to other holding rooms.

(Note that processes differ for shared rooms.)

In the case of a high-risk pathogen, a discussion with the client regarding follow-up testing, treatment options, eradication, and rederivation is conducted. A consultation with Explora BioLabs’ vet is also included.

Once any pathogen is detected, the origin and transmission should be investigated to tighten biosecurity measures and prevent future exposure.

Pathogen Types & Transmission Risks

As stated above, pathogens come in various forms and at differing risk levels. The types of pathogens screened for by Explora BioLabs can affect a range of systems including respiratory, digestive, dermal, and hematopoietic. Many can be without any clinical presentations and yet still impact the efficacy of the research. Such pathogens can be in the form of parasites, viruses, bacteria, mycoplasma, and fungi.

In terms of parasites, Explora BioLabs screens for enteric protozoa, Spironucleus muris; helminth pinworm parasites (i.e., Aspiculuris tetraptera and Syphacia spp.); mites (i.e., Myobia musculi, Myocoptes musculinus, and Radfordia affinis); and non-pathogenic parasites (i.e., Tritrichomonas muris and Entamoeba muris). More often, parasitic infections are asymptomatic but can create physiological conditions that can affect research outcomes; thus, most parasites are classified as medium- to high-risk pathogens.

The detection of some parasites can help us assess the efficacy of our standard biosecurity measures. For example, the non-pathogenic parasites T. muris and E. muris generally do not significantly affect research results, but we screen for them as indicators of good husbandry and sanitation practices.

Viruses in research mice are a serious concern due to the potential for a widespread outbreak throughout the facility, possible subsequent diseases, and the significant impact on research outcomes. The severity and risk ratings of individual viruses are dependent on the infection passage, host characteristics, and virus properties. Transmission varies across viruses but can include the fecal-oral route, direct contact, vertical transmission, and exposure to contaminated materials. Explora BioLabs screens for the following viral infections among sentinels relating to:

  • The respiratory system: SENDAI (Sendai virus) and PVM (pneumonia virus of mice).
  • The digestive system: REO3 (respiratory enteric virus).
  • The hematopoietic system: LCMV (lymphocytic choriomeningitis virus) and MNV (murine norovirus).
  • Multiple or miscellaneous systems: MAD (mouse adenovirus), ECTRO (ectromelia or mousepox), MVM (minute virus of mice), MHV (mouse hepatitis virus), EDIM (epizootic diarrhea of infant mice or mouse rotavirus), MPV (mouse parvovirus), NS-1 (nonstructural protein—parvovirus), MKPV (mouse kidney parvovirus), and TMEV (GDVII) (Theiler’s murine encephalomyelitis virus).

(Note that Explora BioLabs rates almost all viral infections as high-risk pathogens. Some pathogens are only screened for in immunodeficient mice.)

For bacteria, mycoplasma, and fungi, Explora BioLabs screens sentinels for such infections in:

  • The respiratory system, with the following bacteria rated as medium risk: Cilia-Associated Respiratory Bacillus (CAR Bacillus) or Filobacterium rodentium, Klebsiella pneumoniae (and Klebsiella oxytoca), Mycoplasma pulmonis (MPUL), Streptococcus pneumoniae, Bordetella bronchiseptica, Beta hemolytic Streptococcus (non-group D), and Pneumocystis carinii.
  • The digestive system, with the following bacteria rated as low to medium risk: Helicobacter spp., Clostridium piliforme (Tyzzer’s disease), and Pseudomonas aeruginosa.
  • The dermal system, with the following bacteria rated as medium to high risk: Pasteurella pneumotropica, Staphylococcus aureus, Corynebacterium kutscheri, and Corynebacterium bovis.
  • Multiple systems: HAC-2 (Hyperkeratosis-associated coryneform 2), rated as high risk.

(Note that some pathogens are screened for in only immunodeficient mice.)

The factors that influence the susceptibility of mice to certain bacterial species include the genetics, age, and immune status of the mice in addition to heating, ventilation, air conditioning, human traffic flow and contact, husbandry protocols, and newly introduced mice. In general, fungal infections are not as common as bacterial infections, though they do pose a high risk to research mice and should be screened for regularly.

Explora clients receive a comprehensive breakdown of parasite ratings, screenings, and responses.

Biosecurity Measures

Biosecurity measures are at the forefront of vivarium pathogen defense for research mice and the research studies that depend on them. Almost all objects that interact with the mice are required to undergo some form of cleaning or disinfection to limit the spread of potential pathogens. These factors include (but are not limited to) human contact, other research animals, research biologics, feed, bedding, water, caging, equipment, droplets, and dust.

Direct human exposure is not recommended due to a higher transmission risk of opportunistic bacteria from human to animal via the skin, breath, and nasal or oral secretions. Protective measures include the use of adequate PPE. Furthermore, disinfected forceps and gloves should be used when handling mice.

The greatest risk of pathogen transmission in the vivarium is in the handling of mice during cage changes and experimental use. There should be a physical separation of mice based on health status and traffic-restricting protocols for humans and mice. Newly introduced mice not sourced from the four commercial breeders (i.e., Jax, CRL, Taconic, and ENVIGO) should be prescreened and quarantined before being introduced to the vivarium to prevent outside pathogens from entering the system. Research biologics should be pre-screened (e.g., PCR tested) to ensure proper contents, with approval as a part of the study or as an agent without significant impacts on the study. Feed, bedding, water, caging, and equipment require thorough cleaning and sterilization.

In addition, the most secure caging systems for research mice include individually ventilated cages that reduce the spread of airborne pathogens and protect the mice from exposure to unfiltered room air. Explora BioLabs uses individually ventilated cages with HEPA-filtered air inlets to provide reliable protection to research mice. Pressurization options are also available for such ventilation systems and can be enabled in quarantine situations to further prevent the spread of contaminated air to other mice.

Explora BioLabs is rigorously committed to animal health and the safety of your studies. We have detailed internal protocols in place for testing and response to any detection. We protect your studies so you can focus on getting strong, repeatable results. It’s your science: powered by Explora.


Don’t see the information you’re looking for? Visit Explora BioLabs’ News & Resources page for an archive of past articles and more.

Explora BioLabs provides a network of AAALAC-accredited vivarium facilities and preclinical research services in the U.S. Explora’s Vivarium-as-a-Service™ and CRO solutions offer clients the ability to initiate in vivo studies in as little as two weeks with proper husbandry management and crucial regulatory oversight. For more information about how Explora BioLabs can benefit your research studies, contact us today.

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