Cost Comparison of Rodent Soiled Bedding Sentinel and Exhaust Air Dust Health-Monitoring Programs

Comparison of Plenum and Cage-level Filter Exhaust Dust PCR Testing to Soiled Bedding Sentinel Mice (Mus musculus) on an IVC Rack

The use of soiled-bedded sentinels (SBSs) has historically been the standard for colony health surveillance monitoring at our institution. With the advent of newer technologies in which dust collected from filters is tested by PCR, we compared traditional SBS with PCR testing of both exhaust air dust collected from a filter in the downstream vertical plenum (exhaust dust test [EDT]) and the SBS cage-level exhaust filter (SCEF). Our hypothesis was that both methods of filter testing would identify more pathogens than SBS testing. Twenty-five individually ventilated mouse racks that used disposable caging were sanitized and placed into rotation. Rack plenums were tested by PCR to verify negative results before the study start. Exhaust dust collection media were placed in the exhaust plenum (n = 25). SBS cages were placed on each side of the rack with 2 mice per cage (n = 42 mice), with the remaining cage slots occupied by research animals. At each triweekly cage change, the exhaust air filters were carefully removed from the cage top, placed in sterile 50-mL conical tubes, and pooled for submission. After 3mo, the SBS mice were tested via serology for bacterial and viral agents and by PCR for Helicobacter species, pinworms, and ectoparasites. In addition, the EDT filter and SCEF were collected for PCR to evaluate for the same agents. Our results indicate that the SCEF consistently detected agents more frequently than the EDT filter placed in the plenum and that the EDT filter media detected agents more frequently than did the SBS mice. Our data suggest that both PCR methods of detection are superior to SBS for individually ventilated disposable rodent cages and that the SCEF is superior to EDT. These data supported our movement of institution toward environmental monitoring as a method of rodent colony health surveillance.

Assessing Methods for Replacement of Soiled Bedding Sentinels in Cage-level Exhaust IVC Racks

Soiled bedding sentinel programs have long been the cornerstone of rodent health monitoring surveillance. Many recent studies have evaluated methods to replace live animals in these programs; however, the type of ventilated rack being used greatly influences the detection rate of adventitious pathogens. This study evaluated 4 alternative sampling techniques across 5 distinct vivaria and assessed their accuracy in detecting 5 pathogens. Testing was done in an operational (real-world) setting using IVC racks that vent air at the cage level. The 5 agents surveyed were mouse norovirus, Helicobacter spp., Rodentibacter spp. Entamoeba muris, and Spironucleus muris. Samples were collected for subsequent PCR assays as follows: 1) cages with live sentinels exposed to soiled bedding; 2) filter paper placed on the lid of an unoccupied cage containing soiled bedding; 3) filter paper placed in the bedding of an unoccupied cage that contained soiled bedding; 4) swabs from an unoccupied sentinel cage that contained soiled bedding; and 5) pooled swabs from colony cages admixed with swabs from soiled bedding sentinel mice. Cumulative accuracy for all pathogens of interest was highest with the existing soiled bedding sentinel program, followed by pooled swabs of colony cages mixed with swabs from occupied soiled bedding sentinel cages. Soiled bedding sentinel cages detected mouse norovirus, Helicobacter spp., and S. muris with the highest accuracy; the pooled swabs were best in detecting Rodentibacter spp. and E. muris. The findings suggest that with the type of rack and caging used in our facilities, the soiled bedding sentinel method has highest concurrence with the expected health status of an animal room, and the results from this method can be enhanced with the addition of pooled swabs of colony animals.

Evaluation of exhaust air dust polymerase chain reaction as a supplement method for soiled bedding sentinel monitoring in specific pathogen free mouse facility using two different individually ventilated cage racks

Health monitoring is essential for ensuring animal health and reliable research results. Each animal facility should establish adequate health monitoring methods, and microbiological quality control should be implemented through regular health surveillance. Recently, specific pathogen free (SPF) mice have been housed in individually ventilated cage (IVC) racks in the majority of mouse facilities globally, and health monitoring is implemented using a soiled bedding sentinel (SBS). Even though SBS monitoring is a standard method, it has a limitation in that some pathogens are not sufficiently transmitted to the sentinel housed in the IVC. The exhaust air dust polymerase chain reaction (EAD PCR) method has been reported to be a reliable complementary method to SBS monitoring based on research findings. In Korea, health monitoring programs using EAD PCR have not yet been applied to laboratory animal facilities. The microbiological status of mouse colonies housed in the two IVC racks was compared using SBS and EAD PCR monitoring in our SPF mouse facility. Except for Helicobacter spp. and Staphylococcus aureus, the detection of 16 pathogens did not differ between the two methods. In the detection of Helicobacter spp., EAD PCR was found to be more sensitive than SBS. Helicobacter spp. were not found by SBS, whereas four S. aureus positive samples were detected by either SBS or EAD PCR test. According to our findings, EAD PCR can be used as a supplement to SBS monitoring. Moreover, EAD PCR can reduce the number of animals used, making it a 3R (Replacement, Reduction, Refinement)-consistent method.

Microbiota and environmental health monitoring of mouse colonies by metagenomic shotgun sequencing

Metagenomic next-generation sequencing (mNGS) allows the monitoring of microbiota composition of murine colonies employed for scientific purposes in a single test by assessing the composition of gut microbiome and the detection of pathogens from fecal pellets. In this study, we tested the potential use of mNGS for monitoring both microbiota composition and the presence of pathogens through Environmental Health Monitoring, by using exhaust dust collection filters derived from individually ventilated cages (IVC) systems.mNGS analysis was performed on nucleic acids isolated from filters collecting air from the exhaust of: (1) cages with mice housed in a non-pathogen free facility; (2) animal-free cages with clean chow and bedding from the same facility; (3) cages housing mice from a specific-pathogen free (SPF) facility. mNGS results revealed correspondence between microbiome composition from fecal pellets and filter, including pathogenic bacteria (Helicobacter hepaticus, Helicobacter typhlonius, Chlamydia muridarum, Rodentibacter pneumotropicus, Citrobacter rodentium), intestinal protozoa (Tritrichomonas muris, Spironucleus muris) nematoda (Aspiculuris tetraptera) and eukaryotic parasites (Myocoptes musculinus), present in the colony. Entamoeba muris and Syphacia obvelata were detected in fecal pellets but not in filter. The animal free exhaust dust filter, exposed to clean cages (no mice) placed in the IVC after removal of all mice, exhibited the presence of the same pathogens due to contaminated connecting pipes, confirming the sensitivity of the approach. Conversely, the filter from SPF colony revealed the absence of pathogens.The current use of exhaust dust collection filters in health surveillance requires multiple molecular tests to identify specific pathogens and does not provide information on the colony microbiome. This work provides the proof-of-principle that assaying exhaust dust collection filters by mNGS for microbiota monitoring of laboratory mice is feasible. In its daily application, results suggest the usefulness of the test in SPF facilities, where pathogenic micro-organisms are expected to be absent. mNGS analysis of exhaust dust collection filters allows the analysis of multiple cages, reducing the number of tests required for pathogen detection and corresponding costs, and avoiding the use of sentinel mice.

Confirmation of Pathogen 'Burnout' in Mouse Colonies with Previous Evidence of Infection with Parvovirus and Rotavirus

Pathogen monitoring and colony health management are critical components of any rodent research program. From an operational perspective, rodent facilities are protected from unwanted infectious agents by facility-specific bioexclusion criteria, sanitation of the physical environment, and personal protective equipment. Another important preventative measure is the use of room health levels to provide traffic patterns for animal care and research staff as they move between rooms of differing health status. For mice, our institution uses a tiered room level system with 6 defined categories, ranging from level 1 (strictest entry criteria) to 6 (least stringent entry criteria). Level 6 is defined as rooms with mice that have tested positive for mouse parvovirus (MPV) or mouse rotavirus (MRV) or both on sentinel serology at any point in time in the past and no decontamination. Because many of our mouse rooms had historically been positive for MPV and/or MRV and because of the high financial and logistic challenges of using repeated test-and-cull for elimination, we had tolerated the potential presence of MPV and MRV and had developed management practices that would promote 'burnout' (that is, elimination of infectious agents due to absence of susceptible hosts) of these pathogens. Analysis of sentinel data showed that we had 28 rooms in 4 facilities for which excluded pathogens had not been identified in 3 y or more. We therefore developed a hybrid testing strategy involving both PCR analysis and serology and implemented it in sentinels and in select colony mice to determine whether the rooms had undergone successful burnout and were free of MPV and MRV. All test results obtained during the assessment were negative for both viruses, and the rooms were subsequently upgraded to level 5 (free from excluded pathogens and allowing two-way movement in and out of housing room). All upgraded rooms have remained negative on subsequent quarterly routine sentinel serology for over 3 y. Our testing strategy for confirming pathogen burnout may be a useful and cost-efficient model for other academic rodent research programs that face a similar situation.

Using Sterile Flocked Swabs as an Alternative Method for Rodent Health Monitoring

Routine health monitoring is an integral part of managing SPF rodent colonies. In recent years, rack-level environmental sampling has been introduced as an adjunct method or replacement for exposure of sentinel rodents to soiled bedding. However, rack-level environmental monitoring is not compatible with rodent housing systems that have cage-level filtration. The current study investigated whether exposure of sterile flocked swabs to soiled bedding can be an alternative sampling method for routine health monitoring in mice, thus replacing the use of sentinels in soiled-bedding cages. Flocked swabs were placed in cages containing pooled samples of soiled bedding but no mice; swabs remained there for 90 d, with weekly agitation and biweekly swabbing of the cage floor to mimic the agitation of soiled bedding by sentinel mice and facilitate the collection of dust particles. Fecal samples were collected from both colony and sentinel mice. For environmental samples, exhaust debris was collected from the rack plenum, and dust samples were collected from the exhaust hose. All samples were collected on days 88 through 91 and were tested for multiple pathogens by using real-time PCR assays. To determine the diagnostic agreement of flocked swab sampling with the other methods, we used κ statistics to compare the test results from flocked swabs with those from sentinel feces, exhaust debris, and colony animal feces; we found excellent agreement between the colony feces and the flocked swab methods. The sterile flocked swab method detected all enzootic pathogens in the colonies tested. Results from flocked swab samples had the least agreement with sentinel feces, which also failed to detect the presence of fur mites. This study supports the use of sterile flocked swabs as alternative to using sentinel mice, thus conforming to the guiding principles of replacement and reduction in the use of animals for routine colony health monitoring.

Using Filter Media and Soiled Bedding in Disposable Individually Ventilated Cages as a Refinement to Specific Pathogen-free Mouse Health Monitoring Programs

Molecular-based methods have shown potential for improving pathogen detection and reducing animal use. While increasing evidence supports rodent-free environmental health PCR pathogen detection, limited information is available regarding efficacy for disposable individually ventilated caging systems. In such systems, testing of plenum exhaust air dust is ineffective, and the use of collection media is optimal. We performed a series of studies to compare PCR infectious agent detection with dust collected on media placed in a mouse-free soiled bedding cage, the cage exhaust filter of an occupied sentinel cage, and direct sampling from colony and sentinel mice with traditional soiled bedding mouse sentinels. We hypothesized that after a 3-mo period, testing of filter media agitated in a soiled bedding cage would be equal to or more sensitive than more traditional methods. Agitated media detected Astrovirus-1, segmented filamentous bacteria and Helicobacter ganmani to a degree comparable to testing lid exhaust filter PCR from a sentinel mouse cage, but opportunists such as Staphylococcus aureus and Proteus mirabilis were not detected consistently, and H. hepaticus was not detected at all. Direct sampling of pooled fecal pellets and body swabs from sentinel mice and testing using PCR also failed to reliably detect opportunists and Helicobacter spp. While further work is needed to refine use of filter media in soiled bedding for detection of lower prevalence opportunists, this report provides evidence that a rodent-free method of reliably detecting murine agents in a disposable individually ventilated cage system with cage-level filtration outperforms direct sampling of soiled bedding sentinel mice.

Health Monitoring of Laboratory Rodent Colonies-Talking about (R)evolution

The health monitoring of laboratory rodents is essential for ensuring animal health and standardization in biomedical research. Progress in housing, gnotobiotic derivation, and hygienic monitoring programs led to enormous improvement of the microbiological quality of laboratory animals. While traditional health monitoring and pathogen detection methods still serve as powerful tools for the diagnostics of common animal diseases, molecular methods develop rapidly and not only improve test sensitivities but also allow high throughput analyses of various sample types. Concurrently, to the progress in pathogen detection and elimination, the research community becomes increasingly aware of the striking influence of microbiome compositions in laboratory animals, affecting disease phenotypes and the scientific value of research data. As repeated re-derivation cycles and strict barrier husbandry of laboratory rodents resulted in a limited diversity of the animals' gut microbiome, future monitoring approaches will have to reform-aiming at enhancing the validity of animal experiments. This review will recapitulate common health monitoring concepts and, moreover, outline strategies and measures on coping with microbiome variation in order to increase reproducibility, replicability and generalizability.

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.