Tools, Cores & Labs


Partners and affiliates of the Institute for Infectious and Zoonotic Diseases have access to all standard protocols and procedures through Penn Vet’s Center for Host-Microbial Interactions (CHMI).

Our wildlife health experts have an established network of relationships with wildlife organizations throughout the Mid-Atlantic region and the U.S. Partners and affiliates also have the opportunity to leverage our diagnostic laboratory testing capabilities, our wildlife field operations, as well as the expertise of our wildlife pathologists, epidemiologists, and ecologists.  

The SODAPOP Metacognitive Framework

Choosing an antimicrobial is a complicated clinical task particularly for veterinary students and trainees. The SODAPOP Metacognitive Framework was developed to help future antimicrobial prescribers “think about thinking about” choosing an antimicrobial. Check out the SODAPOP method below!


For instructors interested in incorporating SODAPOP into their classroom, Stephen Cole, VMD, MS, DACVM at PennVet has developed 5 small animal cases and 2 validated rubrics for your use with SODAPOP that are available for use upon request. Please complete the form below to receive access to these tools.

Interest Form

Cores & Labs

Shared laboratories and facilities are an integral part of research and education. They are cost effective and serve as the nexus for productive research collaborations. Penn Vet has several technology-based core facilities and laboratories that offer a variety of research, consultative, and statistical services. 

Research Cores

  • Animal Model Core-CORL

    The Animal Model Core at Penn Vet New Bolton Center at the intersection of science and the rapid advancements in health care technology is an ecosystem supporting the continuum from discovery to invention to innovation in medical translation. We are invested in understanding the value proposition of emerging technologies under consideration and how they target unmet clinical needs. This process informs animal model development to enhance scientific rigor during in vivo studies in experimental or naturally occurring disease models. Studies can be iterative starting on a small scale leading towards pivotal non-clinical IND/IDE-enabling trials in support of FDA or OUS-FDA submissions.  

  • Comparative Pathology Core

    The Comparative Pathology Core (CPC), an Abramson Cancer Center shared resource, provides expert pathological characterization and validation of mouse and other animal models used in biomedical research by offering the expertise of board-certified veterinary pathologists and access to state-of-the-art histology, molecular staining of animal tissues, and digital pathology services.

  • Extracellular Vesicle Core

    Located in the Rosenthal Building at Penn's School of Veterinary Medicine (Penn Vet), the Extracellular Vesicle (EV) Core Facility provides comprehensive or selected services in the necessary isolation, quantification and characterization of EVs.  

    Isolation of EV is based on size exclusion using high-performance (SEC-HPLC) or gravity fed (e.g. iZon column) liquid chromatography, ultracentrifugation, and/or density gradient ultracentrifugation.  We can accurately characterize EV particle size distribution and concentration using resistive pulse sensing techniques (nCS1, Spectradyne, LLC) and Nanoparticle tracking analysis.  Immunophenotype can be accomplished using nanoscale flow cytometry and/or chip array (ExoViewTM) techniques.   

  • Penn Vet Imaging Core

    The Penn Vet Imaging Core (PVIC) provides access to cutting-edge optical imaging capabilities for researchers at the University of Pennsylvania, Children's Hospital of Philadelphia, and Wistar Institute.

    The PVIC includes instruments to perform widefield, confocal, multiphoton, fluorescence lifetime, and total internal reflection fluorescence (TIRF) microscopy, as well as software tools for image analysis. 

  • Referral Center for Animal Models

    For many lethal or debilitating genetic disorders in patients there are no satisfactory therapies. The critical barriers to developing effective treatments for genetic diseases in humans and animals include limited natural history studies, an insufficient understanding of how genotype and phenotype correlate with disease, a paucity of validated surrogate markers, and the dearth of potential therapies that substantially improve disease in animal models. These barriers are partially overcome by studying naturally occurring large animal models (canine and feline) of human genetic disease for which breeding colonies are developed and natural history, clinicopathological, and histological data are collected. Animal models allow for the studies necessary to unravel the pathogenic mechanisms involved in disease progression.

  • Transgenic Mouse Core

    The Transgenic Mouse Core located in the School of Veterinary Medicine is a state-of-the-art fee-for-service facility that offers a full line of embryological manipulation services, focused on, but not limited to, murine model systems.  These services primarily enable the generation of genetically modified murine models, as well as experimental research in germ cell function and early embryonic development.

Penn Vet Laboratories

  • ASMG Laboratory - Microbial Genomics

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    The Role of Microbes in Mediating Methane Emissions Final Colloquium Report Released

    Increased greenhouse gases leading to climate change are recognized as the main driver of record-breaking global heatwaves, which threaten human health and well-being. Microorganisms are important producers and consumers of major greenhouse gases, including methane (CH4). CH4 is ~80 times as po- tent as CO2 on a mass basis at trapping heat in the atmosphere over a 20-year period, significantly contributing to a warming planet. More.

    Could we breed cows that emit less methane?

    [August 2, 2023; Philadelphia, PA] Reducing methane emissions from livestock would benefit farmers and the environment. In a first step towards breeding low-methane-emitting cows, researchers from the University of Pennsylvania School of Veterinary Medicine and Pennsylvania State University have identified key differences between cows that naturally emit less methane than average. More.

    Dipti Pitta, PhD, Named Mark Whittier and Lila Griswold Allam Associate Professor at the University of Pennsylvania’s School of Veterinary Medicine

    [October 10, 2022; Philadelphia, PA] – Andrew M. Hoffman, DVM, DVSc, DACVIM, Gilbert S. Kahn Dean of the School of Veterinary Medicine at the University of Pennsylvania (Penn Vet) has named Dipti Pitta, PhD, an internationally recognized scholar working at the interface of microbiology, agriculture, and dairy nutrition, the Mark Whittier and Lila Griswold Allam Associate Professor. More.

    The Agricultural Systems and Microbial Genomics (ASMG) Laboratory was established to support Dr. Dou and Dr. Pitta in their research endeavors

    Dr. Pitta is the ruminant nutritionist and microbiologist at the Center for Animal Health and Productivity (CAHP), New Bolton Center, University of Pennsylvania.

    new-bolton-center-asmg-lab-microbial-genomics 400

    Research at the ASMG lab focuses primarily on the gut microbial composition of ruminants utilizing advanced molecular methodologies. The alimentary tract of a ruminant is colonized by millions of microbes living in a symbiotic relationship with the host. Therefore, knowledge of the microbial composition of the entire gut can provide insights into improving the overall health and productivity of the animal.

    The advent of next generation sequencers has greatly enhanced our ability to explore community microbial populations. The ASMG lab has the capabilities to isolate bacteria and methanogens from the gastrointestinal contents of different ruminant species as well as apply multi-omic approaches to better characterize and understand the functional potential of rumen microbiota. The primary areas of focus include deciphering dietary-microbe, microbe-microbe and host-microbe interactions that play essential roles in maintaining health and production while also minimizing negative impacts on the environment. Research efforts at ASMG are to understand the role of microbiota in ruminal methanogenesis and determine the impacts of different inhibitors on enteric methane inhibition, application of precision technologies to advance animal productivity and early life microbial interventions to improve health and welfare, and productivity of dairy cattle. Please research projects for further details.

    In addition, The ASMG group collaborates with other researchers and clinicians both within the University of Pennsylvania as well as at other institutions. Research findings are disseminated via publications and are presented at conferences. The ASMG group strives to educate and train next generation students in application of microbial genomics to help address global issues such as Food Insecurity, Climate Change, Sustainable Agricultural Systems, and Mitigation of Antimicrobial Resistance. Opportunities for students from diverse backgrounds, ranging from high school through postdoctoral are available at ASMG laboratory to further their careers in microbial genomics and its applications

    Read More About The ASMG Laboratory - Microbial Genomics
  • Beiting Laboratory

    We study the biological basis of diseases caused by microbes -- whether it be a parasitic worm, a pathogenic bacterium, or a complex microbial community in the gut. Our group makes up the Center for Host-Microbial Interactions, at Penn Vet, and our research leverages a diverse skill set that cuts across the disciplines of genomics, microbiology and immunology. We engage in collaborative projects that benefit from close interactions with veterinarians and human clinicians alike. Our research embodies the idea of 'One-Health' - that humans, animals and the environment are interconnected, and that we all live in a microbial world. We are located at the The University of Pennsylvania, in The Department of Pathobiology at the School of Veterinary Medicine.

    Read More About The Beiting Laboratory
  • Dou Laboratory

    Nitrogen, Phosphorus, and Integrated Management

    Nitrogen and phosphorus are essential nutrients for growing plants and animals. Insufficient nutrients diminish yields; excessive applications translate to wasted resources and environmental pollution. The work of Dr. Dou’s group features an integrated system nutrient management approach, coupling nutrient optimization in animal feeding with manure management and targeted nutrient application to crops for enhanced production efficiency and reduced environmental footprint.

    • Please see relevant projects and publications in 'Research Projects' and 'Publications' tab below.

    Integrated whole farm management based on nutrients (pathogen) flow pathway


    Whole Farm Management 

    Pathogens, Antimicrobial Resistance (AMR), and Livestock Farming 

    Livestock animals are important reservoirs of zoonotic pathogens as well as antimicrobial resistant determinants (antibiotic residues, AMR microbes, and AMR genes).  What happens to these “microbial pollutants” in the post-shed environment? How long do they survive under different management conditions? What is their distribution pattern in the intrinsically linked farming sectors and the dissemination pathways to the broader terrestrial and aquatic ecosystems? What intervention may help mitigate relevant risks associated with animal farming concerning food safety and public health? The research of Dr. Dou’s group addresses some of these critical issues.

    • Please see relevant projects and publications in 'Research Projects' and 'Publications' tab below.

    Food Waste, Food Security, and Sustainability

    Sustainable food security is an issue that intersects many of the contemporary challenges the world is struggling to deal with today, e.g. water scarcity, water pollution, resource limitation, land degradation, habitat and biodiversity loss, climate change, and hunger and poverty.  Dr. Dou collaborates with national and international experts to examine sustainable food security issues from multiple dimensions, such as food waste reduction and reuse, engaging, and empowering smallholder farmers, etc. 

    • Please see relevant projects and publications in 'Research Projects' and 'Publications' tab below.

    Developing Novel Feeds from Food Waste and Crop Residue Biomass from Cows

    Livestock farming is at a crossroads, its sustainable future challenged by competing interests for limited resources and urgent need to mitigate environmental and climate footprints, amid a rapidly growing global demand for animal protein. One viable solution overlooked, is to leverage the innate ability of animals as nature’s most effective recyclers, able to utilize a wide variety of plant biomass materials as feed resources in producing meats, milk, and eggs. This project will deploy an innovative sequential fermentation approach to create novel feeds for dairy cows using food waste of fruit and vegetable discards and post-harvest crop residues such as wheat straw and spent mushroom substrates, abundantly available but currently wasted or landfilled. 

    • Please see relevant projects and publications in 'Research Projects' and 'Publications' tab below.
    Read More About The Dou Laboratory
  • Harty Laboratory

    At the Harty Laboratory, we focus our research on three main areas:

    1. The molecular dynamics and biological significance of virus-host interactions during late stages of RNA virus assembly and egress.
    2. The identification and development of host-oriented therapeutics as a new class of antiviral inhibitors.
    3. The interplay between the host innate immune response and RNA virus infection.

    Our model virus systems to interrogate these topics include:

    • Filoviruses (Ebola and Marburg viruses)
    • Arenaviruses (Lassa fever and Junín viruses)
    • Rhabdoviruses (VSV)
    • Retroviruses (HIV-1 and HTLV-1)
    Read More About The Harty Laboratory
  • Hunter Laboratory

    T gondii in the retina, Hunter Lab

    Dr. Christopher Hunter's research team has been working on various aspects of basic parasitology since 1984.

    For nearly 25 years, Dr. Hunter's team has focused on understanding how the immune response to Toxoplasma gondii is regulated to allow the development of protective immunity as well as to limit T cell mediated pathology in multiple sites including the gut and brain.

    Read More About The Hunter Laboratory
  • Lennon Mucosal Immunology Laboratory

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    Welcome to the Lennon Mucosal Immunology Laboratory where we study Inflammatory Bowel Disease (IBD).

    We believe that by studying naturally occurring IBD in dogs and cats we can improve treatment for people and pets with this debilitating condition. 

    Interested in Working With Us?

    We are always seeking highly motivated students, post-doctoral fellows, or veterinarians who are interested in becoming involved in research.

    Read More About The Lennon Mucosal Immunology Laboratory
  • Povelones Laboratory

    Research Interests


    Our main research interest is innate immune recognition and elimination of pathogens. Our work focuses on the interaction between mosquitoes and the animal and human pathogens they transmit. As the most species-rich group of animals on the planet occupying a vast array of ecological niches, insects are a fantastic example of the potency of innate defenses.

    PoveLab on TV and in the news:
    ★ The changing landscape of mosquito- and tick-borne diseases
    ★ News piece by Tom Avril in
    ★ TV spot by John McDevitt for CBS 3 Philly
    ★ See us on Xploration Awesome Planet "Insects" (Season 3 Episode 10)
    ★ View UPenn Spotlight on Our Work

    Rather than passive or willing carriers of pathogenic organism, mosquitoes are actually amazing pathogen killers. Taking mosquito interactions with malaria parasites as an example, the vast majority of the parasites ingested when a mosquito bites a malarious person are attacked and eliminated before they can mount an infection in the mosquito. It is the few parasites that survive (even one is sufficient), that are ultimately responsible for disease transmission. Similar interactions occur between mosquitoes and the other pathogens they transmit, like canine heartworm (Dirofilaria) and arboviruses (Zika, Dengue, Yellow Fever, West Nile, and Chikungunya).

    Arthropod vectors such as mosquitoes, sand flies and ticks are responsible for transmission of a large number of animal and human diseases worldwide. Studying these organisms may reveal general insights about innate immune defense mechanisms as well as provide novel avenues for controlling the terrible diseases they spread.

    Some of the questions we are addressing:

    • What is the basis of pathogen recognition by the mosquito innate immune system and how do some pathogens manage to escape?
    • What is the biochemical mechanism leading from innate recognition to pathogen killing?
    • How is mosquito complement regulated?
    • How does steroid hormone signaling regulate mosquito immunity?
    Read More About The Povelones Laboratory
  • Reference Andrology Laboratory

    The Reference Andrology Laboratory provides complete testing of neat, cooled and frozen-thawed semen from mammalian and avian species. The primary purpose of these services is to aid practitioners in their differential diagnosis of individual/herd/flock reproductive problems.

    These services are also frequently used by practitioners and studs as a third-party quality control component in an ongoing stud auditing process.

    The laboratory strives to perform objective, validated techniques for assessing samples for the basic spermiogram parameters of sample volume, motility, morphology, and concentration. With advanced notification, we will also try to accommodate requests for supplemental assessment techniques on sperm subcellular structures. We also offer semen extender analysis and microbiological testing of the extended semen product and purified water used in extenders. 

    Read More About The Reference Andrology Laboratory
  • Scott Laboratory

    Dr. Scott's current research is focused on understanding the development, regulation and maintenance of CD4+ and CD8+ T cells in order to design new vaccines and immunotherapies for infectioleishmaniaus diseases.

    The laboratory primarily focuses on experimental murine infections with the protozoan parasite, Leishmania, which provides a well-characterized model of T helper cell differentiation.

    Read More About The Scott Laboratory
  • Striepen Laboratory

    Welcome to the Striepen lab

    We study the cell and molecular biology of parasites, and use our findings to develop new treatments. Most of our research is focused on Cryptosporidium and Toxoplasma, two protozoan parasites that threaten small children and those with weakened immune systems.

    For the latest updates on our research, please visit

    Read More About The Striepen Laboratory
  • Vaughan Laboratory

    Check out the new Vaughan Laboratory Website

    Dr. Vaughan’s research is focused on defining and understanding the relevant cell types and molecular mechanisms by which the mammalian lung is able to regenerate after severe injury. He is especially interested in elucidating the means by which epithelial progenitors contribute to repaired airway and alveolar units after various lung insults (influenza, ARDS, fibrosis). His studies suggest that physiological lung function is in fact dictated by progenitor cell fate choices after injury.

    Dr. Vaughan and his group have developed a novel orthotopic cell transplantation assay which allows for the direct assessment of engraftment, proliferation, and differentiation potential of these stem cells. Further, he is actively investigating the roles of the Notch, Wnt, and BMP pathways in regulating the differentiation potential and fate of expanded progenitor cells post-injury.

    Dr. Vaughan is part of the CAMB (DSRB) graduate group, and is a member of the Penn Institute for Regenerative Medicine (IRM).

    Interested in Working in the Vaughan Lab?

    Dr. Vaughan is currently seeking new graduate students to join his laboratory team. He welcomes inquiries for potential rotations from incoming students. Contact Dr. Vaughan directly at

    Read More About The Vaughan Laboratory
  • Wildlife Futures
    The Wildlife Futures Program, a science-based, wildlife health program serves to increase disease surveillance, management and research to better protect wildlife across the Commonwealth of Pennsylvania and beyond. Read More About The Wildlife Futures

Pennsylvania Animal Diagnostic Laboratory System (PADLS)

  • Aquaculture-PADLS

    PADLS AquacultureThe Aquaculture Laboratory provides necropsy and diagnostic testing of commercial and ornamental fish. With facilities at both NBC and the Manheim Field Office, the Aquaculture Laboratory is easily accessible for live fish drop-off.  The laboratory provides testing for diagnostics purposes only. Any regulatory testing should be submitted through the Pennsylvania Veterinary Laboratory. More information can be found on the PADLS website.

    As part of PADLS, the Aquaculture Laboratory supports PADLS’ program objectives and mission. The combined resources and technical expertise of leading scientists at PADLS laboratories provide state-of-the-art diagnostic technology supporting veterinarians’ efforts to advance animal and public health initiatives and support producers in assuring a safe, secure, and abundant food supply.

    Read More About The Aquaculture-PADLS
  • Avian Pathology Laboratory-PADLS

    Avian Pathology smallThe Avian Pathology service strives to provide the best possible diagnostic service to Pennsylvania and regional producers, hatcheries, service personnel, feed companies, and breeder companies. Over the past decade, the service has expanded to include pet bird cases submitted by regional veterinarian, pigeons, waterfowl and birds of prey cases submitted by local wildlife organizations, backyard poultry flocks, and exhibition/show birds. Services include avian necropsies, serologic testing, virus isolation, and PCR. The board certified veterinary staff is not only qualified to provide accurate diagnostics but also advise on the treatment, control, and eradication of infectious diseases. Avian field investigation also adds to the array of services available.

    As part of PADLS, the Avian Pathology service supports PADLS’ program objectives and mission. The combined resources and technical expertise of leading scientists at PADLS laboratories provide state-of-the-art diagnostic technology supporting veterinarians’ efforts to advance animal and public health initiatives and support producers in assuring a safe, secure, and abundant food supply.

    Read More About The Avian Pathology Laboratory-PADLS
  • Field Office Lancaster County-PADLS

    PADLS Field Office Lancaster CountyLocated in the northwest part of Lancaster County, the Field Office is a convenient location for veterinarians, farmers, and wildlife rehabilitators living in the western part of the county. The Field Office provides services in both avian pathology and aquaculture including necropsies of birds and fish and sample drop-off for microbiological testing, serology, and toxicology. Clinical and environmental samples received at the Field Office are taken to New Bolton Center for testing.

    As part of PADLS, the Field Office supports PADLS’ praquaculture285ogram objectives and mission. The combined resources and technical expertise of leading scientists at PADLS laboratories provide state-of-the-art diagnostic technology supporting veterinarians’ efforts to advance animal and public health initiatives and support producers in assuring a safe, secure, and abundant food supply.

    Read More About The Field Office Lancaster County-PADLS
  • Mammalian Pathology Laboratory-New Bolton Center-PADLS

    The Mammalian Pathology Laboratory Service at New Bolton Center is a constituent of the Pennsylvania Animal Diagnostic Lab System (PADLS) and provides complete autopsy and biopsy services to the patients of New Bolton and referrals from veterinarians throughout the state. Out-of-state cases are accepted for an additional fee (see PADLS fee schedule). Specialties include orthopedic pathology, infectious disease, veterinary forensics and translational animal models. Various histochemical and immunohistochemical techniques are employed to identify a variety of infectious agents and specific cell components in histology sections.

    Large Animal Pathology

    The combined resources and technical expertise of leading pathologists and scientists of New Bolton Center's Mammalian Pathology Laboratory Service, in conjunction with PADLS, provide state-of-the-art diagnostic technology supporting veterinarians’ efforts to advance animal and public health initiatives and support animal producers to ensure a safe, secure, and abundant food supply.

    Read More About The Mammalian Pathology Laboratory-New Bolton Center-PADLS
  • Microbiology Laboratory-PADLS

    PADLS MicrobiologyThe microbiology laboratory is separated into three subgroups: Clinical Microbiology, Molecular Microbiology, and PEQAP.

    Located in the Myrin Building on the New Bolton Campus, the Clinical Microbiology laboratory is equipped with the latest technology and a knowledgeable support staff to provide diagnostic microbiology testing. Consultation and field investigation are also available. Testing includes aerobic, anaerobic, and fungal culture, and antibiotic susceptibility testing. 

    Molecular Microbiology uses sophisticated techniques to isolate and identify viruses and bacteria including polymerase chain reaction (PCR) and real-time reverse transcriptase-PCR. These methods are commonly used to identify Avian Influenza, Salmonella spp., and Streptococcus equi (Strangles).

    In addition to standard microbiological testing, the microbiology laboratory also performs egg testing as part of the Pennsylvania Egg Quality Assurance Program (PEQAP) and the FDA Egg Safety Rule. Farms that participate in these programs demonstrate their concern about food safety and produce a quality egg which helps to assure consumer confidence in eggs.

    As part of PADLS, the microbiology laboratory supports PADLS' program objectives and mission. The combined resources and technical expertise of leading scientists at PADLS laboratories provide state-of-the-art diagnostic technology supporting veterinarians’ efforts to advance animal and public health initiatives and support producers in assuring a safe, secure, and abundant food supply. 

    Read More About The Microbiology Laboratory-PADLS
  • Toxicology Laboratory-PADLS

    PADLS ToxicologyLocated in the Myrin Building on the New Bolton Campus, the toxicology laboratory is equipped with the latest technology and a knowledgeable support staff to provide full veterinary diagnostic toxicology services. Animals can be exposed to toxic chemicals in a number of ways: ingestion of contaminated feed or foreign objects, inhalation, or skin contact. Through identification of such toxic chemicals, the toxicology laboratory helps to diagnose and prevent toxicosis in agricultural animals, pets, and wildlife. In addition to toxins, the laboratory has the ability to identify the levels of nutritionally relevant compounds including metals and vitamin E in animal samples.

    As part of PADLS, the toxicology lab supports PADLS' program objectives and mission. The combined resources and technical expertise of leading scientists at PADLS laboratories provide state-of-the-art diagnostic technology supporting veterinarians’ efforts to advance animal and public health initiatives and support producers in assuring a safe, secure, and abundant food supply.

    Read More About The Toxicology Laboratory-PADLS