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1. Leveraging machine learning to uncover multi-pathogen infection dynamics across co-distributed frog families

   https://doi.org/10.7717/peerj.18901  

   Wiley, Daniele_L F; Omlor, Kadie N; Torres_López, Ariadna S; Eberle, Celina M; Savage, Anna E; Atkinson, Matthew S; Barrow, Lisa N (January 2025, PeerJ)

   BackgroundAmphibians are experiencing substantial declines attributed to emerging pathogens. Efforts to understand what drives patterns of pathogen prevalence and differential responses among species are challenging because numerous factors related to the host, pathogen, and their shared environment can influence infection dynamics. Furthermore, sampling across broad taxonomic and geographic scales to evaluate these factors poses logistical challenges, and interpreting the roles of multiple potentially correlated variables is difficult with traditional statistical approaches. In this study, we leverage frozen tissues stored in natural history collections and machine learning techniques to characterize infection dynamics of three generalist pathogens known to cause mortality in frogs. MethodsWe selected 12 widespread and abundant focal taxa within three ecologically distinct, co-distributed host families (Bufonidae, Hylidae, and Ranidae) and sampled them across the eastern two-thirds of the United States of America. We screened and quantified infection loadsviaquantitative PCR for three major pathogens: the fungal pathogenBatrachochytrium dendrobatidis(Bd), double-stranded viruses in the lineageRanavirus(Rv), and the alveolate parasite currently referred to as Amphibian Perkinsea (Pr). We then built balanced random forests (RF) models to predict infection status and intensity based on host taxonomy, age, sex, geography, and environmental variables and to assess relative variable importance across pathogens. Lastly, we used one-way analyses to determine directional relationships and significance of identified predictors. ResultsWe found approximately 20% of individuals were infected with at least one pathogen (231 single infections and 25 coinfections). The most prevalent pathogen across all taxonomic groups was Bd (16.9%; 95% CI [14.9–19%]), followed by Rv (4.38%; 95% CI [3.35–5.7%]) and Pr (1.06%; 95% CI [0.618–1.82%]). The highest prevalence and intensity were found in the family Ranidae, which represented 74.3% of all infections, including the majority of Rv infection points, and had significantly higher Bd intensities compared to Bufonidae and Hylidae. Host species and environmental variables related to temperature were key predictors identified in RF models, with differences in importance among pathogens and host families. For Bd and Rv, infected individuals were associated with higher latitudes and cooler, more stable temperatures, while Pr showed trends in the opposite direction. We found no significant differences between sexes, but juvenile frogs had higher Rv prevalence and Bd infection intensity compared to adults. Overall, our study highlights the use of machine learning techniques and a broad sampling strategy for identifying important factors related to infection in multi-host, multi-pathogen systems. 

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2. Novel skin defense peptides and microbiota contribute to disease resilience of the Ngäbe-Buglé leopard frog

   https://doi.org/10.3389/famrs.2024.1458731  

   Woodhams, Douglas C; Muñiz-Torres, Aura; Hertz, Andreas; Kearns, Patrick; McDonnell, Nina; Reinert, Laura; Rollins-Smith, Louise A; LaBumbard, Brandon; Voyles, Jamie; Richards-Zawacki, Corinne L; et al (December 2024, Frontiers in Amphibian and Reptile Science)

   Some of the amphibian populations in Panama are demonstrating slow recovery decades after severe declines caused by the invasion of the fungal pathogenBatrachochytrium dendrobatidis(Bd). However, new species remain to be described and assessed for the mechanisms of disease resilience. We identified seven skin defense peptides from a presumably novel leopard frog species in the Tabasará range, at Buäbti (Llano Tugrí), Ngäbe-Buglé Comarca, and Santa Fe, Veraguas, Panama, herein called the Ngäbe-Buglé leopard frog. Two of the peptides were previously known: brevinin-1BLb fromRana (Lithobates) blairiand a previously hypothesized “ancestral” peptide, ranatuerin-2BPa. We hypothesized that the peptides are active againstBdand shape the microbiome such that the skin bacterial communities are more similar to those of other leopard frogs than of co-occurring host species. Natural mixtures of the collected skin peptides showed a minimum inhibitory concentration againstBdof 100 μg/ml, which was similar to that of other leopard frogs that have been tested. All sampled individuals hosted high intensity of infection withBd. We sampled nine other amphibian species in nearby habitats and found lower prevalence and intensities ofBdinfection. In addition to the pathogen load, the skin microbiomes were examined using 16S rRNA gene targeted amplicon sequencing. When compared to nine co-occurring amphibians, the Ngäbe-Buglé leopard frog had similar skin bacterial richness and anti-Bdfunction, but the skin microbiome structure differed significantly among species. The community composition of the bacterial skin communities was strongly associated with theBdinfection load. In contrast, the skin microbiome composition of the Ngäbe-Buglé leopard frog was similar to that of five North American leopard frog populations and the sympatric and congenericRana (Lithobates) warszewitschii, with 29 of the 46 core bacteria all demonstrating anti-Bdactivity in culture. Because of the highBdinfection load and prevalence in the Ngäbe-Buglé leopard frog, we suggest that treatment to reduce theBdload in this species might reduce the chytridiomycosis risk in the co-occurring amphibian community, but could potentially disrupt the evolution of skin defenses that provide a mechanism for disease resilience in this species. 

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3. Host Genus and Habitat Use Shape the Distribution of Batrachochytrium dendrobatidis Lineages in a Hyper‐Diverse Tropical Amphibian Community

   https://doi.org/10.1002/ece3.73250  

   Buttimer, Shannon; Neely, Wesley J; Boyette, Jack M; Lambertini, Carolina; Martins, Renato; Paniagua_Torres, Karen A; Rodriguez, David; Becker, C Guilherme (March 2026, Ecology and Evolution)

   ABSTRACT Pathogens often exploit ecological and evolutionary opportunities created by anthropogenic change, with profound consequences for host communities. In Brazil's Atlantic Forest, the amphibian chytrid fungusBatrachochytrium dendrobatidis(Bd) exemplifies this dynamic, with two co‐occurring lineages: the enzootic Bd‐Brazil lineage and the invasive Global Panzootic Lineage (Bd‐GPL), implicated in historical amphibian declines and Bd hybridization events. To investigate how host taxonomy and habitat use influence Bd lineage distribution, we sampled 3836 amphibians representing 42 species across paired aquatic and terrestrial transects over a two‐year period. We successfully genotypedn = 252 out of 777 Bd‐positive samples using nuclear and mitochondrial SNP assays to differentiate between Bd‐GPL, Bd‐Brazil, hybrids, and coinfections. Our results reveal that Bd lineage distribution is nonrandomly associated with host genus and habitat type. Stream‐dwelling frogs, particularly those in the genusHylodes, had higher rates of coinfection with Bd‐GPL and Bd‐Brazil than most other genera. This pattern may reflect their lifelong association with streams, which might increase their exposure to zoospores from multiple Bd lineages. In contrast, terrestrial transects were dominated by single‐lineage Bd‐GPL infections, even when accounting for differences in amphibian species composition and host genus among transect types. These findings suggest that aquatic habitats could serve as refugia for Bd‐Brazil, while Bd‐GPL may exhibit more desiccation tolerance. Methodological limitations of this study, including biases towards successfully genotyping high‐load infections and limited genomic resolution, underscore the need for more high‐resolution sequencing approaches to fully understand pathogen dynamics in the Atlantic Forest. 

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4. Environmental detection of the amphibian chytrid fungus in water bodies is associated with host infection along a deforestation gradient

   https://doi.org/10.1111/1365-2664.70497  

   de_Assis, Ananda Brito; Rodriguez, David; Neely, Wesley J; Lopes, Carla Martins; Prist, Paula R; Navas, Carlos Arturo; Martins, Renato A; Buttimer, Shannon; Haddad, Célio_Fernando Baptista; Becker, C Guilherme (July 2026, Journal of Applied Ecology)

   Abstract Many wildlife pathogens can persist in the environment independently of their hosts, with the habitat itself serving as a reservoir and potential source of transmission. However, reliably detecting and quantifying free‐living pathogen stages across heterogeneous landscapes using environmental DNA methods remains challenging. Understanding how landcover and habitat structure drive pathogen distribution at the environmental and host levels is critical for advancing disease surveillance and ecology.Amphibian chytridiomycosis, caused by the fungal pathogenBatrachochytrium dendrobatidis(Bd), provides a useful model system to address these broader challenges, yet most studies have focused on host–pathogen interactions, with less emphasis onBdwithin environmental reservoirs. UsingBdas a model system, we investigated whether pathogen distribution in natural aquatic environments is associated with host infection patterns across gradients of habitat loss. We sampled four tropical amphibian species across eight rainforest landscapes and quantifiedBdin paired water and host samples using a high‐capacity water filtration method coupled with digital and real‐time quantitative polymerase chain reaction detection assays.Our results revealed a strong positive correlation betweenBdDNA concentrations in water and infection loads on amphibian skin, indicating that environmentalBdDNA is associated with host infection patterns.Forest cover and habitat split (i.e. spatial separation between forests and aquatic breeding sites) were the primary predictors ofBdoccurrence, concentration and infection load across environmental and host‐associated forms, and bothBd‐GPL andBd‐Asia‐2/Brazil lineages were detected across our study landscapes.Our study introduces and validates a robust protocol for detecting environmentalBd, providing a scalable approach to quantify pathogen–environment associations across multiple landscapes and environmental gradients.Synthesis and applications: Linking environmental pathogen detection with host infection patterns can improve surveillance of diseases involving environmental transmission, particularly where direct host sampling is logistically challenging. This approach enables the identification of areas of elevated transmission risk and supports targeted monitoring and management under habitat loss and degradation. It also provides a practical tool to guide conservation actions in landscapes undergoing rapid land‐use change. 

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5. Bromeliads as environmental pathogen reservoirs and disease dynamics of Batrachochytrium dendrobatidis in equatorial forests

   Moretta-Urdiales, MDM; McCracken, SF; Guayasamin, JM; Lynch, RL; Tenorio, M; Neely, WJ; Rodriguez, D (September 2026, Royal Society open science)

   The amphibian chytrid fungus Batrachochytrium dendrobatidis (Bd) is widely distributed across tropical ecosystems, yet the microhabitats that facilitate its environmental persistence remain poorly understood. We evaluated Bd detection in bromeliad tank contents and infection in amphibian communities across an elevational gradient in Ecuadorian forests. We sampled amphibians at eight sites using skin swabs and canopy and subcanopy bromeliads at five sites using eDNA. Overall, Bd prevalence was 23.0% in amphibians and 11.3% in bromeliads. Subcanopy bromeliads showed a significantly lower probability of Bd detection than amphibians, whereas canopy bromeliads did not differ significantly from amphibians or subcanopy bromeliads. Mid-elevation sites showed higher probability of being Bd-positive compared to high-elevation sites, while low-elevation sites did not differ significantly. Amphibian Bd prevalence also increased with precipitation and followed a nonlinear relationship with temperature, suggesting higher prevalence under intermediate thermal conditions. In contrast, Bd detection in bromeliads was not significantly associated with abiotic factors. Bd infection intensity among amphibians did not differ significantly across host taxonomy or sampling sites. Together, these results suggest that bromeliad tanks may provide aquatic microhabitats for Bd detection and short-term persistence, but host infection patterns appear more associated with amphibian taxonomic identity, site-level variation, and local climatic conditions. 

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