Zoonotic Disease Surveillance in Animal Shelters: Methods and Challenges

By Dr. Zubair Khalid, DVM, MS, PhD · 2026-08-11

Key Takeaways

• Animal shelters serve as critical sentinel sites for zoonotic disease surveillance due to high animal density and unknown health histories, necessitating population-level monitoring rather than individual patient diagnosis.
• Surveillance design must align with objectives, employing cross-sectional surveys for prevalence estimation, and repeated or longitudinal sampling to track temporal trends and distinguish pre- vs. intra-shelter transmission.
• Diagnostic platforms vary in sensitivity, specificity, and cost, with serology detecting past exposure (e.g., Leishmania infantum IFAT titers) and molecular methods (e.g., RT-PCR) confirming active infection, requiring careful selection based on pathogen biology and resources.
• One Health integration is paramount, requiring data linkage with human health surveillance systems and clear reporting pathways to public health authorities for effective zoonotic disease control.
• Admission screening protocols should prioritize pathogens with immediate transmission risk to staff and other animals, including fecal flotation for gastrointestinal parasites and dermatophyte culture/PCR for skin lesions, with species-specific considerations for Bartonella in cats and Brucella canis in dogs from high-risk sources.
• Environmental sampling of high-touch surfaces and kennel floors can detect pathogen persistence and identify biosecurity failures, complementing animal-based surveillance by indicating potential transmission risks before clinical cases emerge.

Animal shelters occupy a distinctive position at the human-animal interface. They concentrate animals of unknown health history, frequently house them at high density, and place them in close contact with staff, volunteers, and adopting members of the public. These conditions create opportunities for zoonotic pathogen transmission in both directions, and they make shelters valuable sentinel sites for detecting pathogens that may circulate more broadly in the community. This article examines the methods used to conduct zoonotic disease surveillance in companion animal shelters, the epidemiological logic that underpins those methods, and the operational challenges that limit their implementation. It is written for veterinary researchers, public health veterinarians, and shelter medicine specialists who design or interpret surveillance programs. The scope covers population-level monitoring and pathogen detection, not individual patient diagnosis or treatment.

Surveillance in shelters differs from surveillance in clinical practice in several fundamental ways. The unit of observation is the population instead of the individual, the sampling frame is defined by shelter intake instead of by owner presentation, and the objectives typically include early detection of emerging threats, estimation of prevalence, and identification of risk factors for infection. Shelters also serve as a bridge between free-roaming and owned animal populations, which makes them informative for understanding transmission dynamics that extend beyond the shelter walls. The methods described here draw on established frameworks from veterinary public health, including the One Health approach that links human, animal, and environmental health for zoonotic disease control WHO One Health initiative.

At a Glance

The Epidemiological Rationale for Shelter Surveillance

Shelters provide a sampling convenience that other companion animal populations do not. Animals entering shelters represent a catchment population drawn from a defined geographic area, and they have not been selected on the basis of clinical signs in the way that veterinary hospital patients have. This makes shelter-based prevalence estimates less biased toward symptomatic disease than estimates derived from clinic populations. The study of stray dog and cat shelters in North-East Italy illustrates this point, as it used routine monitoring of shelter populations to investigate the prevalence of known, potential, and emerging zoonotic agents across multiple diagnostic platforms zoonoses in dog and cat shelters in North-East Italy.

The sentinel value of shelters depends on the pathogen in question. For pathogens with environmental reservoirs or vector-borne transmission, shelter animals may reflect exposure risk in the surrounding region. For directly transmitted pathogens, shelter crowding can amplify transmission and reveal infections that would circulate at lower prevalence in less dense populations. The high-density housing typical of shelters also creates conditions analogous to those in other congregate settings, which makes shelter data relevant for understanding transmission dynamics in kennels, boarding facilities, and other group-housing contexts.

Surveillance Design and Sampling Strategies

Cross-Sectional Prevalence Surveys

Cross-sectional surveys estimate the point prevalence of infection or exposure in a shelter population at a single time. They are the simplest surveillance design and are appropriate when the objective is to describe the burden of a specific pathogen. The utility of a cross-sectional survey depends on sample size, sampling method, and the diagnostic characteriztics of the test used. Convenience sampling of animals that are already being handled for other purposes is common but introduces selection bias, because animals with clinical signs may be overrepresented.

Repeated and Longitudinal Sampling

Repeated cross-sectional sampling at defined intervals allows surveillance programs to detect changes in prevalence over time. This design is particularly important for pathogens with seasonal transmission. The Leishmaniosis Surveillance Program in the Madrid community sampled stray dogs twice annually, in April and November, to detect infections acquired before and after the sandfly risk season Leishmania infantum infection serosurveillance in stray dogs in Madrid. The timing of samples relative to vector activity is critical for interpreting serological results, because antibody detection reflects exposure that may have occurred weeks to months before sampling.

Longitudinal designs that follow individual animals through their shelter stay can distinguish infections acquired before intake from those transmitted within the shelter. This distinction matters for biosecurity planning, because within-shelter transmission indicates a failure of infection control, whereas pre-existing infection indicates a need for intake screening or community-level intervention.

Diagnostic Platforms and Their Limitations

Serological surveillance detects evidence of past exposure or current infection depending on the pathogen and the antibody class measured. Immunofluorescence antibody tests and enzyme-linked immunosorbent assays are commonly used for pathogens such as Leishmania infantum and Leptospira species. Seroprevalence data are useful for risk mapping and for identifying endemic areas, but they cannot distinguish active infection from resolved exposure, and they are affected by the background seroprevalence in the source population. The serosurveillance program for Leishmania infantum in Madrid used an IFAT cut-off of 1:100 and reported an overall seroprevalence of 6.1% across 3,225 stray dogs from 17 shelters Leishmania infantum infection serosurveillance in stray dogs in Madrid.

Molecular methods such as polymerase chain reaction detect pathogen nucleic acid and can confirm active infection, but they are more expensive and require laboratory infrastructure that may not be available in all settings. Microbiological culture remains necessary for antimicrobial resistance surveillance and for pathogens where viability matters. The choice of diagnostic platform should be guided by the surveillance objective, the pathogen biology, and the resources available, and it should be documented explicitly in the surveillance protocol.

One Health Integration and Cross-Sector Coordination

Shelter surveillance generates data that are relevant to human health authorities, wildlife agencies, and veterinary practitioners. The One Health framework provides the conceptual basis for integrating these data across sectors CDC One Health and zoonotic disease resources. In practice, integration requires data sharing agreements, compatible case definitions, and clear reporting pathways. Shelters are rarely part of formal government surveillance programs, and the absence of regular official programs was identified as a limitation in the North-East Italy study zoonoses in dog and cat shelters in North-East Italy. This gap means that much shelter surveillance is conducted opportunistically, with results published in the research literature instead of feeding into real-time public health decision-making.

The One Welfare framework extends this integration to include animal welfare and human wellbeing as interdependent outcomes exploring the One Health-One Welfare nexus and zoonoses. Overcrowded shelters with inadequate sterilization programs and uncontrolled companion animal populations create conditions that increase zoonotic risk while simultaneously compromising animal welfare. Surveillance programs that address only pathogen detection without considering the welfare context may miss the underlying drivers of transmission.

Surveillance Protocols for High-Risk Shelter Populations

Shelter surveillance programs must stratify animals by exposure risk and clinical status. The highest yield comes from systematic sampling of newly admitted animals, animals with clinical signs compatible with zoonotic infection, and animals originating from known endemic areas. Shelters that serve as intake points for free-roaming cats or confiscated dogs face different risk profiles than shelters receiving only owned relinquishments, and the protocol should reflect that difference.

For vector-borne pathogens, seasonal timing determines diagnostic sensitivity. In regions where sandfly activity is seasonal, sampling twice yearly, once before and once after the transmission period, detects both chronic infections and newly acquired ones. The Leishmaniasis Surveillance Program in Madrid applied this design, testing a minimum of 100 dogs per shelter in April and November each year to capture infections acquired during the preceding sandfly season. Shelters in endemic regions should adopt this two-point annual sampling frame instead of relying on single opportunistic testing.

Admission Screening Protocols

Admission screening should target pathogens that pose immediate transmission risk to staff, volunteers, and other animals. The minimum dataset for dogs includes fecal flotation for gastrointestinal parasites, dermatophyte culture or PCR on animals with skin lesions, and serology for regionally endemic vector-borne pathogens. Cats require the same fecal and dermatophyte evaluation, with additional testing for Bartonella species in animals with fever, lymphadenopathy, or a history of flea infestation. Serological positivity for Bartonella henselae reached 70% in cats in one Italian shelter survey, which underscores the importance of flea control as a surveillance intervention instead of a purely clinical one.

The decision to test for Brucella canis should be guided by intake source. Shelters accepting intact dogs from uncontrolled breeding environments or seized from commercial breeding facilities should screen all animals, because the bacterium transmits horizontally through breeding and contact with reproductive secretions. Shelters receiving only neutered pets from private owners can test selectively, targeting dogs with a history of reproductive abnormalities or known exposure to positive animals.

Diagnostic Test Selection and Interpretation

Test choice depends on whether the surveillance question is prevalence estimation, individual animal risk classification, or early outbreak detection. Serological surveys estimate population exposure but cannot distinguish active infection from past exposure. Molecular methods detect current infection but lose sensitivity when pathogen load is low or when sampling occurs during the incubation period. The discrepancy between these platforms is substantial. In a study of dogs in eastern Colombia, 17.8% were seropositive for Leishmania antibodies while only 4.3% were PCR-positive for L. infantum. A surveillance program that relies on serology alone will overestimate the number of infectious animals, while a program that relies on PCR alone will miss animals in the seroconversion window.

For shelters, the practical approach is a tiered algorithm. Serology serves as the primary screening tool because it is inexpensive and amenable to batch processing. Animals that test positive undergo confirmatory molecular testing when the pathogen is one for which treatment or euthanasia decisions will follow. For pathogens where seropositivity itself carries public health significance, such as Leptospira in dogs, the serological result is sufficient to trigger biosecurity measures regardless of PCR confirmation. Leptospira seropositivity reached 44.3% in dogs in the Italian shelter survey, a figure that should prompt review of rodent control and urine handling protocols in any shelter with comparable endemic pressure.

Environmental Sampling and Biosecurity Monitoring

Surveillance extends beyond the animals themselves. Environmental sampling detects pathogens that persist in the shelter environment and identifies failures in cleaning and disinfection protocols. High-touch surfaces, food preparation areas, and isolation ward floors should be sampled on a rotating schedule. The sampling frequency should increase when new animals are admitted from high-risk sources or when a zoonotic infection has been confirmed in the population.

The choice of environmental sample type depends on the target pathogen. Swabs of surfaces detect bacteria and some viruses, while dust and litter samples are more appropriate for dermatophytes. Fecal contamination monitoring requires sampling of kennel floors, runs, and outdoor exercise areas. Results should be interpreted with caution, because environmental detection does not prove transmission to animals or humans. The value of environmental sampling lies in trend detection: a rising frequency of positive samples indicates biosecurity breakdown before clinical cases appear.

Data Management and Thresholds for Action

A surveillance program generates value only when data are analyzed and acted upon. Shelters should maintain a centralized database that records for each animal: intake date, source, clinical signs, test results, and disposition. Prevalence calculations should be performed quarterly, stratified by species, intake source, and season. The denominator must be clearly defined, because prevalence estimates based on tested animals only will overestimate true prevalence if testing is targeted at clinically affected animals.

Action thresholds should be established in advance and tied to specific responses. The table below provides a framework for interpreting surveillance findings.

Sentinel animals, defined as long-stay residents tested at regular intervals, provide the most reliable indicator of active transmission. Their housing history is known, their exposure is limited to the shelter environment, and their serological status can be tracked over time. Shelters should designate a small cohort of sentinel animals and test them at the same frequency as the seasonal sampling schedule.

Documentation and Reporting Obligations

Surveillance records must be structured to support both internal decision-making and external reporting. Each animal record should include the specific test used, the laboratory performing the test, the date of sampling, and the result with the laboratory's reference range or cutoff. For serological tests, the titer or optical density value should be recorded, also the positive or negative interpretation, because titer trends over time carry more information than a single result.

Reporting obligations vary by jurisdiction and by pathogen. Some zoonotic diseases are notifiable to public health authorities, and shelters must know which pathogens in their region trigger mandatory reporting. The CDC One Health resources provide guidance on zoonotic disease prioritization and cross-sector collaboration, and shelters should align their reporting protocols with the requirements of their local public health agency. The World Health Organization One Health initiative similarly frames zoonotic disease surveillance as a shared responsibility across human and animal health sectors. Shelters that maintain standing relationships with public health veterinarians before an outbreak occurs will find the reporting pathway faster and less contentious when a notifiable pathogen is detected.

Protocol Review and Adaptive Management

Surveillance protocols require periodic revision as endemic pathogen prevalence changes, as new diagnostic tests become available, and as the shelter's intake population shifts. An annual review should examine whether the pathogens targeted by the protocol still match the regional risk profile. The Italian shelter survey noted that no regular official programs were ongoing to allow efficient risk surveillance for companion animal zoonoses, which suggests that many shelters operate without external oversight and must therefore conduct their own periodic risk reassessment.

The review should also assess diagnostic yield. If a test has returned no positive results for several consecutive sampling periods, the shelter should consider whether the test remains cost-effective or whether sampling should be redirected to a different pathogen. Conversely, a rising prevalence in a previously low-prevalence pathogen should trigger investigation of the cause, including changes in animal sources, vector populations, or environmental conditions.

Shelters should also monitor for emerging pathogens that were not part of the original surveillance design. Influenza A virus has been detected with increasing frequency in companion animals, and shelters with high-density dog housing create conditions that favor respiratory virus transmission. Surveillance programs should include a mechanism for ad hoc testing when clinical signs suggest a pathogen outside the routine panel, and the protocol should specify which clinical presentations trigger expanded diagnostic testing.

Recognized Complications and Failure Modes

Surveillance programs in shelters fail through predictable mechanisms. Passive surveillance, which relies on clinical recognition of disease, underdetects subclinical zoonoses such as Leishmania infantum and Bartonella henselae because infected animals may appear healthy for months or years. Serosurveys from shelter populations in North-East Italy illustrate this gap: serological positivity for Leishmania infantum reached 25% in dogs and Bartonella henselae 70% in cats, figures that clinical observation alone would never generate Mazzotta et al., institutional publication on zoonoses in dog and cat shelters in North-East Italy. Active sampling protocols are therefore the only reliable route to prevalence estimates, yet they consume staff time and diagnostic budget that many shelters cannot sustain.

Sample degradation constitutes a second failure mode. Molecular assays for RNA viruses, including influenza A virus and SARS-CoV-2, require cold chain integrity from collection to laboratory. A convenience sampling study across Ohio animal populations found no viral RNA in shelter animals, but the authors noted that sampling logistics and transport conditions constrained the interpretability of negative results Ehrlich et al., institutional publication on SARS-CoV-2 surveillance in Ohio animals. Negative surveillance data are only as credible as the pre-analytic handling that produced them.

Threshold drift is a third problem. When prevalence falls below the action threshold, programs tend to reduce sampling frequency, which then delays detection of resurgence. The Madrid leishmaniosis surveillance program avoided this by mandating a minimum of 100 dogs tested twice annually, in April and November, to capture infection before and after the sandfly risk season Müller et al., institutional publication on Leishmania infantum serosurveillance in stray dogs in Madrid. Fixed minimum sample sizes, independent of recent prevalence, prevent this decay.

Common Errors and Corrective Actions

Less experienced personnel frequently confuse seroprevalence with active infection. A positive IgG titre indicates exposure, not necessarily current infectiousness. In the Bucaramanga metropolitan area study, 17.8% of dogs were seropositive by IFAT but only 4.3% were PCR-positive for L. infantum, a discrepancy that matters for risk communication and for decisions about isolation or treatment Jaimes-Dueñez et al., institutional publication on Leishmania infantum in dogs in eastern Colombia. The corrective action is to pair serology with molecular testing when the surveillance objective is to estimate transmission risk instead of historical exposure.

A second error is sampling convenience populations without documenting their relationship to the source population. Shelters that receive animals from multiple municipalities produce prevalence estimates that reflect admission geography, not local transmission. The North-East Italy study drew animals from seven provinces and reported results as regional surveillance, which is valid only because the sampling frame was explicitly described Mazzotta et al., institutional publication on zoonoses in dog and cat shelters in North-East Italy. Records of origin, duration of stay, and prior vaccination status must accompany every sample.

A third error is overinterpreting single-timepoint negative results for pathogens with seasonal transmission. Influenza A virus transmission in dogs occurs through respiratory droplets in high-density settings such as shelters, and detection probability varies with outbreak timing Lee et al., institutional publication on influenza A virus in companion animals. A negative swab in summer does not exclude introduction during winter peaks. Repeated sampling across seasons is the corrective framework.

Limitations of the Evidence Base

The published literature on shelter zoonosis surveillance is geographically concentrated in Europe and parts of Latin America. Prevalence figures from North-East Italy or the Madrid community cannot be extrapolated to other regions because vector distribution, stray animal management, and climate differ substantially. The One Health framework endorsed by the World Health Organization and the Centers for Disease Control and Prevention recognizes that surveillance priorities must be regionally determined, yet most shelters operate without any formal risk assessment WHO One Health Initiative CDC One Health and Zoonotic Disease Resources.

Expert opinion diverges on the value of universal admission screening versus targeted testing based on clinical signs and origin. Proponents of universal screening argue that subclinical shedders of agents such as Leptospira or dermatophytes escape targeted protocols. Opponents note that screening every admission for a broad panel is financially unsustainable and generates false positives that lead to unnecessary isolation. The One Welfare framework adds a further dimension, arguing that surveillance design must account for animal welfare consequences of prolonged isolation and for the ethical obligations shelters hold toward the animals in their care Vidal et al., institutional publication on One Health-One Welfare nexus and zoonoses. No consensus exists on the optimal balance, and shelter capacity, local epidemiology, and available diagnostics should determine the choice.

Escalation and Referral Criteria

Referral to a specialist or diagnostic laboratory is warranted when surveillance findings exceed predefined thresholds, when a novel or emerging pathogen is suspected, or when routine testing produces discordant results that cannot be resolved locally. Influenza A virus detection in shelter cats or dogs should trigger immediate consultation with public health authorities because of the pandemic potential of mammalian-adapted strains Lee et al., institutional publication on influenza A virus in companion animals. Similarly, detection of Leishmania in a non-endemic area, or of any agent with reportable status, requires notification through the appropriate jurisdictional channel.

Regulatory reporting obligations vary by jurisdiction and by pathogen. The World Organization for Animal Health terrestrial code provides international standards for notification of listed diseases, and shelters should maintain a current list of reportable agents for their region WOAH terrestrial animal health code. When in doubt, the laboratory that performed the diagnostic testing is the appropriate first contact for confirmation and for guidance on reporting pathways.

Troubleshooting Table

Frequently Asked Questions

How Should Surveillance Priorities Be Set When Funding and Staffing Are Severely Limited?

Prioritize pathogens by local endemicity, human health consequence, and feasibility of intervention. Serological and molecular surveys from comparable regions can guide agent selection, as demonstrated by the multi-pathogen screening of shelter dogs and cats in North-East Italy, which ranked agents by prevalence and public health relevance Mazzotta et al., institutional publication. When resources permit testing for only one or two agents, select those with direct human transmission potential, such as dermatophytes or gastrointestinal parasites, over agents requiring vector bridges. Use passive surveillance, recording clinical signs and necropsy findings, as a low-cost complement. Coordinate with public health authorities to access regional prevalence data and avoid duplicating existing surveillance CDC One Health resources.

What Is the Minimum Viable Sampling Protocol When Molecular Diagnostics Are Unavailable?

Serology and basic microscopy remain serviceable. For Leishmania infantum, IFAT with a cut-off of 1:100 has supported long-term shelter surveillance programs, with biannual sampling before and after the sandfly season Müller et al., institutional publication. Fecal flotation and direct smear identify most gastrointestinal parasites. Fungal culture on dermatophyte test medium is inexpensive. Store serum and swabs frozen for retrospective PCR testing if funding later appears. Document storage conditions and sample identifiers meticulously so archived material retains diagnostic value. Interpret serology cautiously in endemic areas, since exposure does not equal active infection, and confirm positive results with a second platform when possible MSD Veterinary Manual.

How Should Surveillance Results Be Communicated to Shelter Staff and Adopting Families?

Frame results as population-level risk information, not individual diagnoses. Provide staff with a written summary listing detected agents, transmission routes, and required personal protective equipment. For adopting families, prepare a one-page handout naming the agent, explaining whether it poses risk to immunocompetent humans, and listing hygiene measures. Avoid alarming language for low-risk findings. When a reportable zoonosis is detected, follow jurisdictional reporting pathways before any public communication WOAH terrestrial animal health standards. Document all communications in the shelter record, including date, recipient, and content, to maintain an audit trail.

Can Surveillance Findings From One Shelter Be Generalized to Another Shelter in the Same Region?

Only with caution. Shelter prevalence is shaped by admission source, average length of stay, housing density, and vector exposure. A serosurvey of stray dogs in the Madrid community found prevalence varied with age, breed, and shelter location, indicating that even within one region, shelter populations are not epidemiologically uniform Müller et al., institutional publication. Similarly, shelter dogs in eastern Colombia showed higher infection prevalence than owned dogs, suggesting shelter conditions themselves modify risk Jaimes-Dueñez et al., institutional publication. Use published regional data to formulate initial hypotheses, then validate with local sampling before changing protocols.

What Records Must Be Kept for a Shelter Surveillance Program to Be Defensible?

Maintain a central log linking each sampled animal to a unique identifier, admission date, source, clinical findings, sample type, test performed, laboratory, and result. Record the test kit lot number and expiry date for point-of-care assays. Retain raw laboratory reports, also transcribed results. Document the surveillance protocol version in effect at each sampling date, since protocols evolve. Record staff training on sample collection and biosecurity. Keep these records for a period consistent with local statute of limitations for liability, typically several years. Digital records with automated backup are preferable, but a bound paper log is acceptable if entries are made in permanent ink and corrections are initialled.

How Does Surveillance Differ for Shelters Housing Species Other Than Dogs and Cats?

Feline and canine shelters have established serological and molecular panels, but other species require different agents and sampling strategies. Cats in shelters warrant attention to influenza A virus, given alimentary transmission through raw poultry and environmental exposure, whereas dogs transmit influenza primarily by respiratory droplets in high-density housing Lee et al., institutional publication. For shelters housing wildlife or agricultural species, consult species-specific references and regional veterinary authorities, since the agent list and sample types differ substantially MSD Veterinary Manual. Always verify that the diagnostic laboratory accepts the species in question and that test validation covers it, as many commercial assays are validated only for dogs and cats.

Related Clinical & Scientific Guides

• Wildlife Disease Surveillance: Designing and Implementing a One Health Program
• Biosecurity Risk Assessment for Livestock Operations: A Practical Framework
• Rabies Post-Exposure Prophylaxis in Veterinary Personnel

References and Further Reading

• Zoonoses in dog and cat shelters in North-East Italy: update on emerging, neglected and known zoonotic agents.. 2024.
• Exploring the One Health-One Welfare nexus and zoonoses.. 2025.
• Leishmania infantum infection serosurveillance in stray dogs inhabiting the Madrid community: 2007-2018.. 2022.
• Epidemiological features of Leishmania infantum in dogs (Canis lupus familiaris) suggest a latent risk of visceral leishmaniasis in the metropolitan area of Bucaramanga, Santander, Eastern Colombia.. 2023.
• Mammalian adaptation and zoonotic risk of influenza A viruses in companion animals.. 2025.
• Lack of SARS-CoV-2 Viral RNA Detection among a Convenience Sampling of Ohio Wildlife, Companion, and Agricultural Animals, 2020-2021.. 2023.
• WHO One Health Initiative. WHO.
• CDC One Health and Zoonotic Disease Resources. CDC.
• MSD Veterinary Manual, Professional Edition. MSD Veterinary Manual.

Related Articles

• Zoonotic Disease Risk Assessment in Animal Shelters: Protocols and Best Practices
• Comparative Zoonotic Disease Surveillance: Wildlife, Livestock, and Human Health Interfaces
• Zoonotic Disease Risk Assessment in Veterinary Practice
• Antimicrobial Resistance Surveillance in Wildlife: Methods and Gaps
• Veterinary Epidemiology: Study Designs for Zoonotic Disease Research

This article is educational professional reference material for veterinary audiences. It is not a substitute for veterinary diagnosis, individual clinical judgment, current product labeling, or applicable regulatory requirements.