A Chinese firebelly newt (Cynops orientalis), the first salamander species found to be infected with the spring viraemia of carp virus.
Jeffrey M Lorch
Jeff Lorch is a Microbiologist at the National Wildlife Health Center.
He received bachelor degrees in Bacteriology and Wildlife Ecology and a Ph.D. in Molecular and Environmental Toxicology from the University of Wisconsin – Madison. Since joining the USGS, Dr. Lorch has devoted his career to investigating and diagnosing wildlife mortality events and studying emerging wildlife diseases. Presently, his work focuses on disease ecology and management of bat white-nose syndrome and snake fungal disease, surveillance for Batrachochytrium salamandrivorans (the fungus that causes salamander chytridiomycosis), and development of molecular methods for detection of wildlife pathogens.
Professional Experience
2015 – Present, Microbiologist, National Wildlife Health Center
2012 – 2015, Research Associate, University of Wisconsin – Madison
Education and Certifications
Ph.D. Molecular and Environmental Toxicology, University of Wisconsin – Madison, 2012
B.S. Bacteriology, University of Wisconsin – Madison, 2005
B.S. Wildlife Ecology, University of Wisconsin – Madison, 2005
Affiliations and Memberships*
2015 – Present, Honorary Associate, Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin – Madison
Science and Products
Diagnostic Microbiology Laboratory (DML)
The USGS National Wildlife Health Center's Diagnostic Microbiology Laboratory (DML) routinely performs a variety of procedures to isolate and identify important pathogenic bacteria and fungi from wildlife. Microbes are identified based upon morphological characteristics, biochemical/physiological properties, molecular assays (e.g., PCR), and DNA sequence analysis.
Prevalence Rates of Snake Fungal Disease and Its Population-level Impacts in a Snake Assemblage in Southwest Louisiana
Snake Fungal Disease
White-Nose Syndrome
Analysis of mitochondrial DNA sequence data from Myotis lucifugus and Myotis occultus
Paranannizziopsis spp. associated with skin lesions in wild snakes in North America and development of a real-time PCR assay for rapid detection of the fungus in clinical samples
Pd qPCR Interlaboratory Testing Results
Population genetic analysis of the snake-infecting fungus, Ophidiomyces ophidiicola, in the eastern United States
Tracking the growth of Ophidiomyces ophidiicola over time in natural and sterile soils using quantitative PCR
Confirmed cases of snake fungal disease in historical museum specimens
Skin mycobiomes of eastern North American bats
Data from Burmese Pythons swabbed for the presence of SFD-causing Ophidiomyces in southwest Florida
Pseudogymnoascus destructans survival at elevated temperatures - Artificial media count data
Emerging fungal pathogen Ophidiomyces ophiodiicola in wild European snakes
Pathogenic lineage of Perkinsea causes mass mortality of frogs across the USA: Data
Snake dermatitis data
A Chinese firebelly newt (Cynops orientalis), the first salamander species found to be infected with the spring viraemia of carp virus.
A Chinese firebelly newt (Cynops orientalis), the salamander species recently found to be infected with the spring viraemia of carp virus, or SVCV.
A Chinese firebelly newt (Cynops orientalis), the salamander species recently found to be infected with the spring viraemia of carp virus, or SVCV.
Fungi growing from soil collected in a cave. Arrow points to Geomyces destuctans, the fungus that causes white-nose syndrome in bats.
Fungi growing from soil collected in a cave. Arrow points to Geomyces destuctans, the fungus that causes white-nose syndrome in bats.
Amount of soil (about 200 mg) from which Geomyces destructans was cultured. This shows the small amount of soil needed to harbor live fungus and the threat that humans might pose in moving it around from cave to cave on their gear, boots, and clothing.
Amount of soil (about 200 mg) from which Geomyces destructans was cultured. This shows the small amount of soil needed to harbor live fungus and the threat that humans might pose in moving it around from cave to cave on their gear, boots, and clothing.
Analysis of mitochondrial DNA sequence data demonstrates that monophyly of myotis occultus is complicated by greater sampling of myotis lucifugus
Paranannizziopsis spp. infections in wild snakes and a qPCR assay for detection of the fungus
Development and application of a qPCR-based genotyping assay for Ophidiomyces ophidiicola to investigate the epidemiology of ophidiomycosis
Frequent transitions in mating-type locus chromosomal organization in Malassezia and early steps in sexual reproduction
Prevalence of Ophidiomyces ophidiicola and epizootiology of snake fungal disease in free-ranging Northern Pine Snakes (Pituophis melanoleucus melanoleucus) in New Jersey
A cross inoculation experiment reveals Ophidiomyces ophiodiicola and Nannizziopsis guarroi can each infect both snakes and lizards
Wild rodents harbor high diversity of Arthroderma
Epistylis spp. infestation in two species of mud turtles (Kinosternon spp.) in the American Southwest
Ophidiomycosis is related to seasonal patterns of reproduction, ecdysis, and thermoregulatory behavior in a free-living snake species
The future of fungi: Threats and opportunities
Avian-associated Aspergillus fumigatus displays broad phylogenetic distribution, no evidence for host specificity, and multiple genotypes within epizootic events
Salmonella enterica serovar Typhimurium from wild birds in the United States represent distinct lineages defined by bird type
Non-USGS Publications**
**Disclaimer: The views expressed in Non-USGS publications are those of the author and do not represent the views of the USGS, Department of the Interior, or the U.S. Government.
Code for: Small enzootic survival costs mask the potential for long-term population size suppression
Science and Products
- Science
Diagnostic Microbiology Laboratory (DML)
The USGS National Wildlife Health Center's Diagnostic Microbiology Laboratory (DML) routinely performs a variety of procedures to isolate and identify important pathogenic bacteria and fungi from wildlife. Microbes are identified based upon morphological characteristics, biochemical/physiological properties, molecular assays (e.g., PCR), and DNA sequence analysis.
Prevalence Rates of Snake Fungal Disease and Its Population-level Impacts in a Snake Assemblage in Southwest Louisiana
WARC researchers used visual encounter surveys to determine prevalence rates of snake fungal disease in south-central Louisiana.Snake Fungal Disease
Snake fungal disease is an infectious disease confirmed in numerous species of snakes caused by the fungus Ophidiomyces ophidiicola .White-Nose Syndrome
White-nose syndrome (WNS) is an emergent disease of hibernating bats that has spread from the northeastern across United States at an alarming rate. - Data
Analysis of mitochondrial DNA sequence data from Myotis lucifugus and Myotis occultus
The validity of Myotis occultus as a species unique from M. lucifugus has been a source of debate. Most recently, many authorities treat M. occultus as a distinct species, at least in part because a previous study showed that M. occultus and M. l. carissima (the subspecies that occurs in closest proximity to M. occultus) form separate monophyletic clades based on sequences of two mitochondrial genParanannizziopsis spp. associated with skin lesions in wild snakes in North America and development of a real-time PCR assay for rapid detection of the fungus in clinical samples
The emergence of ophidiomycosis (or snake fungal disease) in snakes has prompted increased awareness of the potential impacts of fungal infections on wild reptile populations. Yet, aside from Ophidiomyces ophidiicola, little is known about other mycoses affecting wild reptiles. The closely related genus Paranannizziopsis has been associated with dermatomycosis in snakes and tuataras in captive colPd qPCR Interlaboratory Testing Results
These data were collected as part of a voluntary initiative to create a White-Nose Syndrome Diagnostic Laboratory Network among laboratories participating in research and surveillance for Pseudogymonascus destructans (Pd) - the fungal pathogen causing White-Nose Syndrome in bats. Pd_qPCR_InterlaboratoryLODdata.xlsx is raw qPCR data from multiple laboratories running serial dilutions of Pd gBlock iPopulation genetic analysis of the snake-infecting fungus, Ophidiomyces ophidiicola, in the eastern United States
Snake fungal disease (SFD; ophidiomycosis), caused by the pathogen Ophidiomyces ophidiicola (Oo), has been documented in wild snakes in North America and Eurasia, and is a potentially emerging disease in the eastern USA. However, a lack of historical disease data has made it challenging to determine whether Oo is a recent arrival to the USA or whether SFD emergence is due to other factors. Here, wTracking the growth of Ophidiomyces ophidiicola over time in natural and sterile soils using quantitative PCR
Wildlife diseases pose an ever-growing threat to global biodiversity. Understanding how wildlife pathogens are distributed in the environment and the ability of pathogens to form environmental reservoirs is critical to understanding and predicting disease dynamics within host populations. Snake fungal disease (SFD) is an emerging conservation threat to North American snake populations. The causatiConfirmed cases of snake fungal disease in historical museum specimens
Snake fungal disease (SFD) represents a conservation threat to wild snake populations. The disease was reported in North America early in the 21st century, but the history of SFD has not been investigated. We examined museum specimens and confirmed cases of SFD based on clinical signs, histopathologic lesions, and detection of the causative agent Ophidiomyces ophidiicola. The first confirmed casesSkin mycobiomes of eastern North American bats
North American bats have experienced catastrophic population declines from white-nose syndrome (WNS), a fungal disease caused by Pseudogymnoascus destructans (Pd). Although Pd can infect many hibernating bat species, population-level impacts of WNS vary by host species. Microbial skin assemblages, including the fungal component (mycobiome), can influence host resistance to infectious diseases; howData from Burmese Pythons swabbed for the presence of SFD-causing Ophidiomyces in southwest Florida
The size and sex of each of the Burmese pythons swabbed in this study for the SFD-causing (snake fungal disease) Ophidiomyces ophiodiicola pathogen is given along with the real time PCR swab result.Pseudogymnoascus destructans survival at elevated temperatures - Artificial media count data
The survival of Pseudogymnoascus destructans (Pd) was evaluated at temperatures outside of its thermal range of growth on three different artificial growth media; Sabouraud dextrose agar (SD), brain-heart infusion agar (BHI), and brain-heart infusion agar supplemented with 10% sheep red blood cells (BHI+B). Pd was harvested from starting cultures grown of MEA agar at 7?C for 60 days. Harvested conEmerging fungal pathogen Ophidiomyces ophiodiicola in wild European snakes
Snake fungal disease (SFD) is an emerging disease of wild snakes in eastern North America caused by the fungus Ophidiomyces ophiodiicola. Recently, the disease has also been detected in wild snake in Europe. The data presented here describe: 1) culture, PCR, and histopathology results of wild European snakes opportunistically sampled for O. ophiodiicola, 2) colony expansion rates of various isolatPathogenic lineage of Perkinsea causes mass mortality of frogs across the USA: Data
Severe perkinsea data was based on the observation of characteristic gross and microscopic lesions and the morphological identification of Perkinsea organisms within the lesions. Necropsies and gross evaluation of carcasses were carried out under a dissecting microscope. Specimen were collected and submitted to the NWHC as part of mortality investigations and collection of specimen from apparentlySnake dermatitis data
Snake fungal disease (SFD) is an emerging disease of wild snakes in eastern North America caused by the fungus Ophidiomyces ophiodiicola. The data presented here describe: 1) the types of fungi recovered in culture from the skin of snakes with and without fungal skin infections, 2) the presence or absence of skin lesions in populations of snakes surveyed at several sites in Wisconsin and Minnesota - Multimedia
Chinese Firebelly Newt
A Chinese firebelly newt (Cynops orientalis), the first salamander species found to be infected with the spring viraemia of carp virus.
A Chinese firebelly newt (Cynops orientalis), the first salamander species found to be infected with the spring viraemia of carp virus.
Chinese Firebelly NewtA Chinese firebelly newt (Cynops orientalis), the salamander species recently found to be infected with the spring viraemia of carp virus, or SVCV.
A Chinese firebelly newt (Cynops orientalis), the salamander species recently found to be infected with the spring viraemia of carp virus, or SVCV.
Fungal Growth on Petri DishFungi growing from soil collected in a cave. Arrow points to Geomyces destuctans, the fungus that causes white-nose syndrome in bats.
Fungi growing from soil collected in a cave. Arrow points to Geomyces destuctans, the fungus that causes white-nose syndrome in bats.
Soil Next to a DimeAmount of soil (about 200 mg) from which Geomyces destructans was cultured. This shows the small amount of soil needed to harbor live fungus and the threat that humans might pose in moving it around from cave to cave on their gear, boots, and clothing.
Amount of soil (about 200 mg) from which Geomyces destructans was cultured. This shows the small amount of soil needed to harbor live fungus and the threat that humans might pose in moving it around from cave to cave on their gear, boots, and clothing.
- Publications
Filter Total Items: 66
Analysis of mitochondrial DNA sequence data demonstrates that monophyly of myotis occultus is complicated by greater sampling of myotis lucifugus
The validity of Myotis occultus as a species unique from Myotis lucifugus has been a source of debate. Most recently, many authorities treat M. occultus as a distinct species, at least in part because a previous study showed that M. occultus and M. l. carissima (the subspecies that occurs in closest geographic proximity to M. occultus) form separate monophyletic clades based on sequences of two miAuthorsJeffrey M. Lorch, Antoinette J. Piaggio, Daniel R. TaylorParanannizziopsis spp. infections in wild snakes and a qPCR assay for detection of the fungus
The emergence of ophidiomycosis (or snake fungal disease) in snakes has prompted increased awareness of the potential effects of fungal infections on wild reptile populations. Yet, aside from Ophidiomyces ophidiicola, little is known about other mycoses affecting wild reptiles. The closely related genus Paranannizziopsis has been associated with dermatomycosis in snakes and tuataras in captive colAuthorsJeffrey M. Lorch, Megan Winzeler, Julia S. Lankton, Stephen Raverty, Heindrich N Snyman, Helen M. Schwantje, Caeley Thacker, Susan Knowles, Hugh Y Cai, Daniel A. GrearDevelopment and application of a qPCR-based genotyping assay for Ophidiomyces ophidiicola to investigate the epidemiology of ophidiomycosis
Ophidiomycosis (snake fungal disease) is an infectious disease caused by the fungus Ophidiomyces ophidiicola to which all snake species appear to be susceptible. Significant variation has been observed in clinical presentation, progression of disease, and response to treatment, which may be due to genetic variation in the causative agent. Recent phylogenetic analysis based on whole-genome sequenciAuthorsEllen Haynes, Jeffrey M. Lorch, Matthew C. AllenderFrequent transitions in mating-type locus chromosomal organization in Malassezia and early steps in sexual reproduction
Fungi in the basidiomycete genus Malassezia are the most prevalent eukaryotic microbes resident on the skin of human and other warm-blooded animals and have been implicated in skin diseases and systemic disorders. Analysis of Malassezia genomes revealed that key adaptations to the skin microenvironment have a direct genomic basis, and the identification of mating/meiotic genes suggests a capacityAuthorsMarco A. Coelho, Giuseppe Ianiri, Márcia David-Palma, Bart Theelen, Rohit Goyal, Aswathy Narayanan, Jeffrey M. Lorch, Kaustuv Sanyal, Teun Boekhout, Joseph HeitmanPrevalence of Ophidiomyces ophidiicola and epizootiology of snake fungal disease in free-ranging Northern Pine Snakes (Pituophis melanoleucus melanoleucus) in New Jersey
Snake fungal disease, caused by Ophidiomyces ophidiicola, is recognized as a potential concern for North American snakes. We tested skin swabs from Northern Pine Snakes (Pituophis melanoleucus melanoleucus) in the New Jersey pinelands for the presence of O. ophidiicola before emergence from hibernation. We used qPCR to test the collected swabs for the presence of O. ophidiicola, then determined paAuthorsJoanna Burger, Michael Gochfeld, Robert T. Zappalorti, John F. Bunnell, Christian Jeitner, David Schneider, Kelly Ng, Emile DeVito, Jeffrey M. LorchA cross inoculation experiment reveals Ophidiomyces ophiodiicola and Nannizziopsis guarroi can each infect both snakes and lizards
Host range and specificity are key concepts in the study of infectious diseases. However, both concepts remain largely undefined for many influential pathogens, including many fungi within the Onygenales order. This order encompasses reptile-infecting genera (Nannizziopsis, Ophidiomyces, and Paranannizziopsis) formerly classified as the Chrysosporium anamorph of Nannizziopsis vriesii (CANV). The rAuthorsSavannah L Gentry, Jeffrey M. Lorch, Julia S. Lankton, Anne PringleWild rodents harbor high diversity of Arthroderma
Arthroderma is the most diverse genus of dermatophytes, and its natural reservoir is considered to be soil enriched by keratin sources. During a study on the diversity of dermatophytes in wild small rodents in the Czech Republic, we isolated several strains of Arthroderma. To explore the diversity and ecological significance of these isolates from rodents (n = 29), we characterised the strains genAuthorsŠtěpánka Moulíková, Miroslav Kolařík, Jeffrey M. Lorch, Daniela Kolarczyková, Vit Hubka, Adéla ČmokováEpistylis spp. infestation in two species of mud turtles (Kinosternon spp.) in the American Southwest
The protistan genus Epistylis contains freshwater colonial species that attach to aquatic organisms in an epibiotic or parasitic relationship. They are known to attach to the epidermis and shells of aquatic turtles, but have not been reported to cause heavy infestations or morbidity in turtles. We documented heavy infestations of Epistylis spp. in several populations of Sonoran mud turtles (KinostAuthorsAudrey K. Owens, Jennifer A. Smith, Rebecca A. Cole, Jeffrey M. Lorch, Daniel A. GrearOphidiomycosis is related to seasonal patterns of reproduction, ecdysis, and thermoregulatory behavior in a free-living snake species
Informed and effective management of emerging infectious diseases can be improved by a clear understanding of host–pathogen–environment interactions. Impacts of the seasonal environment on pathogen dynamics and host responses are poorly described in most reptile host–fungal pathogen systems. Here, we describe seasonal patterns of ophidiomycosis, a disease caused by the fungus Ophidiomyces ophidiicAuthorsC. M. Lind, J. Agugliaro, Jeffrey M. Lorch, T. M. FarrellThe future of fungi: Threats and opportunities
The fungal kingdom represents an extraordinary diversity of organisms with profound impacts across animal, plant, and ecosystem health. Fungi simultaneously support life, by forming beneficial symbioses with plants and producing life-saving medicines, and bring death, by causing devastating diseases in humans, plants, and animals. With climate change, increased antimicrobial resistance, global traAuthorsNicola T. Case, Judith Berman, David S. Blehert, Robert A. Cramer, Christina A. Cuomo, Cameron R. Currie, Iuliana V. Ene, Matthew C. Fisher, Lillian K. Fritz-Laylin, Aleeza C. Gerstein, N. Louise Glass, Neil A. R. Gow, Sarah J. Gurr, Chris Todd Hittinger, Tobias M. Hohl, Iliyan D. Iliev, Timothy Y. James, Hailing Jin, Bruce S. Klein, James W. Kronstad, Jeffrey M. Lorch, Victoria McGovern, Aaron P. Mitchell, Julia A. Segre, Rebecca S. Shapiro, Donald C. Sheppard, Anita Sil, Jason E. Stajich, Eva E. Stukenbrock, John W. Taylor, Dawn Thompson, Gerard D. Wright, Joseph Heitman, Leah E. CowenAvian-associated Aspergillus fumigatus displays broad phylogenetic distribution, no evidence for host specificity, and multiple genotypes within epizootic events
Birds are highly susceptible to aspergillosis, which can manifest as a primary infection in both domestic and wild birds. Aspergillosis in wild birds causes mortalities ranging in scale from single animals to large-scale epizootic events. However, pathogenicity factors associated with aspergillosis in wild birds have not been examined. Specifically, it is unknown whether wild bird-infecting strainAuthorsLotus A. Lofgren, Jeffrey M. Lorch, Robert A. Cramer, David S. Blehert, Brenda M. Berlowski-Zier, Megan Winzeler, Cecilia Gutierrez-Perez, Nicole E. Kordana, Jason E. StajichSalmonella enterica serovar Typhimurium from wild birds in the United States represent distinct lineages defined by bird type
Salmonella enterica serovar Typhimurium is typically considered a host generalist; however, certain isolates are associated with specific hosts and show genetic features of host adaptation. Here, we sequenced 131 S. Typhimurium isolates from wild birds collected in 30 U.S. states during 1978-2019. We found that isolates from broad taxonomic host groups including passerine birds, water birds (AequoAuthorsYezhi Fu, Nkuchia M. M’ikanatha, Jeffrey M. Lorch, David S. Blehert, Brenda M. Berlowski-Zier, Chris A. Whitehouse, Shaoting Li, Xiangyu Deng, Jared C. Smith, Nikki W. Shariat, Erin M. Nawrocki, Edward G. DudleyNon-USGS Publications**
Kapfer, J.M., Sloss, B.L., Schuurman, G.W., Paloski, R.A., and Lorch, J.M. 2013. Evidence of hybridization between common gartersnakes (Thamnophis sirtalis) and Butler's gartersnake (Thamnophis butleri) in Wisconsin (USA). Journal of Herpetology 47:400-405.**Disclaimer: The views expressed in Non-USGS publications are those of the author and do not represent the views of the USGS, Department of the Interior, or the U.S. Government.
- Software
Code for: Small enzootic survival costs mask the potential for long-term population size suppression
This repository contains all of the scripts to reproduce the analyses, figures, and tables associated with the manuscript Glorioso et al. in review. The scripts are organized into folders, and the folders are numbered in the order in which they should be executed. Briefly, there are six folders that do the following: (1) format the data, (2) fit the model, (3) run the population projections, (4) r - News
*Disclaimer: Listing outside positions with professional scientific organizations on this Staff Profile are for informational purposes only and do not constitute an endorsement of those professional scientific organizations or their activities by the USGS, Department of the Interior, or U.S. Government