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1. Tracking, Synthesizing, and Sharing Global Batrachochytrium Data at AmphibianDisease.org

   https://doi.org/10.3389/fvets.2021.728232  

   Koo, Michelle S.; Vredenburg, Vance T.; Deck, John B.; Olson, Deanna H.; Ronnenberg, Kathryn L.; Wake, David B. (October 2021, Frontiers in Veterinary Science)

   Emerging infectious diseases have been especially devastating to amphibians, the most endangered class of vertebrates. For amphibians, the greatest disease threat is chytridiomycosis, caused by one of two chytridiomycete fungal pathogens Batrachochytrium dendrobatidis (Bd) and Batrachochytrium salamandrivorans ( Bsal ). Research over the last two decades has shown that susceptibility to this disease varies greatly with respect to a suite of host and pathogen factors such as phylogeny, geography (including abiotic factors), host community composition, and historical exposure to pathogens; yet, despite a growing body of research, a comprehensive understanding of global chytridiomycosis incidence remains elusive. In a large collaborative effort, Bd -Maps was launched in 2007 to increase multidisciplinary investigations and understanding using compiled global Bd occurrence data ( Bsal was not discovered until 2013). As its database functions aged and became unsustainable, we sought to address critical needs utilizing new technologies to meet the challenges of aggregating data to facilitate research on both Bd and Bsal . Here, we introduce an advanced central online repository to archive, aggregate, and share Bd and Bsal data collected from around the world. The Amphibian Disease Portal ( https://amphibiandisease.org ) addresses several critical community needs while also helping to build basic biological knowledge of chytridiomycosis. This portal could be useful for other amphibian diseases and could also be replicated for uses with other wildlife diseases. We show how the Amphibian Disease Portal provides: (1) a new repository for the legacy Bd- Maps data; (2) a repository for sample-level data to archive datasets and host published data with permanent DOIs; (3) a flexible framework to adapt to advances in field, laboratory, and informatics technologies; and (4) a global aggregation of Bd and Bsal infection data to enable and accelerate research and conservation. The new framework for this project is built using biodiversity informatics best practices and metadata standards to ensure scientific reproducibility and linkages across other biological and biodiversity repositories. 

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2. Fungal infection, decline and persistence in the only obligate troglodytic Neotropical salamander

   https://doi.org/10.7717/peerj.9763  

   Olivares-Miranda, Mizraim; Vredenburg, Vance T.; García-Sánchez, Julio C.; Byrne, Allison Q.; Rosenblum, Erica B.; Rovito, Sean M. (January 2020, PeerJ)

   The fungal pathogen Batrachochytrium dendrobatidis ( Bd ) is implicated in global mass die-offs and declines in amphibians. In Mesoamerica, the Bd epidemic wave hypothesis is supported by detection of Bd in historic museum specimens collected over the last century, yet the timing and impact of the early stages of the wave remain poorly understood. Chiropterotriton magnipes , the only obligate troglodytic Neotropical salamander, was abundant in its small range in the decade following its description in 1965, but subsequently disappeared from known localities and was not seen for 34 years. Its decline is roughly coincident with that of other populations of Neotropical salamanders associated with the invasion and spread of Bd . To determine the presence and infection intensity of Bd on C. magnipes and sympatric amphibian species (which are also Bd hosts), we used a noninvasive sampling technique and qPCR assay to detect Bd on museum specimens of C. magnipes collected from 1952 to 2012, and from extant populations of C. magnipes and sympatric species of amphibians. We also tested for the presence of the recently discovered Batrachochytrium salamandivorans ( Bsal ), another fungal chytridiomycete pathogen of salamanders, using a similar technique specific for Bsal . We did not detect Bd in populations of C. magnipes before 1969, while Bd was detected at low to moderate prevalence just prior to and during declines. This pattern is consistent with Bd -caused epizootics followed by host declines and extirpations described in other hosts. We did not detect Bsal in any extant population of C. magnipes . We obtained one of the earliest positive records of the fungus to date in Latin America, providing additional historical evidence consistent with the Bd epidemic wave hypothesis. Genotyping results show that at least one population is currently infected with the Global Panzootic Lineage of Bd , but our genotyping of the historical positive samples was unsuccessful. The lack of large samples from some years and the difficulty in genotyping historical Bd samples illustrate some of the difficulties inherent in assigning causality to historical amphibian declines. These data also provide an important historical baseline for actions to preserve the few known remaining populations of C. magnipes . 

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3. Community-Wide Genotyping of Batrachochytrium dendrobatidis in Ecuadorian Forests

   https://doi.org/10.1007/s10393-025-01716-y  

   Neely, Wesley J; Moretta-Urdiales, M_D M; Smart, Utpal; Lynch, Ryan L; Guayasamin, Juan Manuel; McCracken, Shawn F; Rodriguez, David (May 2025, EcoHealth)

   Abstract The amphibian chytrid fungusBatrachochytrium dendrobatidis(Bd) is a cosmopolitan pathogen with numerous distinct lineages. The global panzootic lineage (Bd-GPL) is the most widespread and virulent lineage and is responsible for many recorded amphibian declines. Mapping the extent ofBd-GPL and other more established lineages is important for predicting disease dynamics in amphibian communities. Ecuador is the most biodiverse country per unit area for amphibian taxa and, thus, a priority for studies on genotypic diversity ofBd. In this study, we tested skin swab samples collected from 464 individual amphibians across coastal, Andean montane, and Amazonian forests, for the presence of twoBdlineages known to be present in South America: the globally-distributedBd-GPL and the Brazilian-endemicBd-Asia2/Brazil lineage. By using a discriminatory qPCR SNP assay, we found widespread prevalence ofBd-GPL in Ecuador in diverse host taxa. Genotyping efficiency was 36% in this study, meaning that one in every three swabs that tested positive forBdin infection assays were successfully genotyped. Through this study, we provide further support for the presence of a singleBdlineage in this neotropical biodiversity hotspot. 

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4. Inhibitory Bacterial Diversity and Mucosome Function Differentiate Susceptibility of Appalachian Salamanders to Chytrid Fungal Infection

   https://doi.org/10.1128/aem.01818-21  

   Jiménez, Randall R.; Carfagno, Amy; Linhoff, Luke; Gratwicke, Brian; Woodhams, Douglas C.; Chafran, Liana Soares; Bletz, Molly C.; Bishop, Barney; Muletz-Wolz, Carly R. (April 2022, Applied and Environmental Microbiology)

   Reguera, Gemma (Ed.)

   ABSTRACT Mucosal defenses are crucial in animals for protection against pathogens and predators. Host defense peptides (antimicrobial peptides, AMPs) as well as skin-associated microbes are key components of mucosal immunity, particularly in amphibians. We integrate microbiology, molecular biology, network-thinking, and proteomics to understand how host and microbially derived products on amphibian skin (referred to as the mucosome) serve as pathogen defenses. We studied defense mechanisms against chytrid pathogens, Batrachochytrium dendrobatidis (Bd) and B. salamandrivorans (Bsal), in four salamander species with different Batrachochytrium susceptibilities. Bd infection was quantified using qPCR, mucosome function (i.e., ability to kill Bd or Bsal zoospores in vitro ), skin bacterial communities using 16S rRNA gene amplicon sequencing, and the role of Bd-inhibitory bacteria in microbial networks across all species. We explored the presence of candidate-AMPs in eastern newts and red-backed salamanders. Eastern newts had the highest Bd prevalence and mucosome function, while red-back salamanders had the lowest Bd prevalence and mucosome function, and two-lined salamanders and seal salamanders were intermediates. Salamanders with highest Bd infection intensity showed greater mucosome function. Bd infection prevalence significantly decreased as putative Bd-inhibitory bacterial richness and relative abundance increased on hosts. In co-occurrence networks, some putative Bd-inhibitory bacteria were found as hub-taxa, with red-backs having the highest proportion of protective hubs and positive associations related to putative Bd-inhibitory hub bacteria. We found more AMP candidates on salamanders with lower Bd susceptibility. These findings suggest that salamanders possess distinct innate mechanisms that affect chytrid fungi. IMPORTANCE How host mucosal defenses interact, and influence disease outcome is critical in understanding host defenses against pathogens. A more detailed understanding is needed of the interactions between the host and the functioning of its mucosal defenses in pathogen defense. This study investigates the variability of chytrid susceptibility in salamanders and the innate defenses each species possesses to mediate pathogens, thus advancing the knowledge toward a deeper understanding of the microbial ecology of skin-associated bacteria and contributing to the development of bioaugmentation strategies to mediate pathogen infection and disease. This study improves the understanding of complex immune defense mechanisms in salamanders and highlights the potential role of the mucosome to reduce the probability of Bd disease development and that putative protective bacteria may reduce likelihood of Bd infecting skin. 

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5. Environmental DNA ‐based detection of pathogens in trade and captive settings: Best practices and validation for Batrachochytrium salamandrivorans

   https://doi.org/10.1111/2041-210x.14217  

   Brunner, Jesse L; Yarber, Christian M; Pearhill, Robert_A I; Goldberg, Caren S (November 2023, Methods in Ecology and Evolution)

   Abstract Detecting pathogens in the live animal trade is critical for tracking and preventing their movement, introduction and spillover into susceptible fauna. However, the scale of the live animal trade makes individually testing animals infeasible for all but the most economically important taxa. For instance, while the fungal pathogen,Batrachochytrium salamandrivorans(Bsal), threatens amphibian, particularly caudate diversity, in Europe and the Americas, screening even a fraction of the millions of live amphibians imported into the United States, alone, is impractically laborious and expensive. A promising alternative to individual‐level sampling (e.g. swabbing the skin of salamanders) is to instead collect DNA from the animals' environment (e.g. housing container or water) which allows us to screen a whole group of animals at a time.We used a series of experiments withBsal‐spiked water and substrates and experimentally infected rough‐skinned newts (Taricha granulosa) to determine which methods yield the mostBsalenvironmental DNA (eDNA) and evaluate the capacity of these methods to detectBsal‐infected animals in conditions found in captive settings and trade.We found that filtering water housing infected animals for even an hour can consistently recover detectable levels ofBsaleDNA, that there is little evidence ofBsaleDNA being clumped in housing containers or swamped or inhibited by dirty housing containers, and that eDNA‐based methods achieves an equivalent or higher chance of detectingBsalinfections in a (virtual) population of co‐housed newts with fewer samples than individual swabs.By sampling the genetic materials accumulated from a whole group of animals, eDNA‐based methods are a powerful means of detecting pathogens, such asBsal, in shipments and captive populations. These methods bring routine pathogen surveillance into reach in many more contexts and can thus be an important tool in conservation and disease control. 

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