Researchers monitor amphibians for chytrid fungus by combining repeated population surveys with pathogen testing, most often using individually collected skin swabs and real-time PCR assays for Bd, Bsal, or both. The tests show whether a pathogen was detected in the sampled animals; understanding what that means for a population also requires information such as host species, life stage, survival, habitat, and sampling dates.
What researchers are trying to measure
Population monitoring and pathogen surveillance are related but distinct. A population survey may track where amphibians occur, how many are observed, survival, or change over time. Pathogen surveillance asks whether infection is present and how it varies among sampled animals or locations. A positive test by itself does not show that a population is declining or that infection caused a decline.
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Researchers can connect these lines of evidence. For example, USGS describes work examining Bd prevalence and pathogen load alongside environmental stressors and green treefrog survival. The measures help address different parts of the question: infection data characterize the pathogen, while repeated observations and survival data describe host outcomes. USGS research on amphibian chytrid fungus
How field surveillance is conducted
Choose sites and sampling times
Researchers define which sites, species, and periods to sample according to the question. Repeated surveys across places and years make comparisons possible, while targeted surveillance can focus effort where introduction or spread is a concern.
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For Bsal, an emerging salamander chytrid, USGS risk assessments consider fungal ecology, trade-related information, salamander diversity, mitigation, and earlier surveillance when identifying higher-risk counties. A 2016 USGS workshop report also recommended early detection at key import locations, among high-risk wild populations, and through archived samples. USGS Bsal surveillance and risk assessment 2016 USGS workshop report
Observe and sample amphibians
Field teams may capture amphibians by hand, traps, or nets, then collect an individual skin swab. Keeping samples separate and following contamination-control procedures helps reduce the risk of transferring pathogen material between animals. Depending on the question, USGS research also uses non-lethal tissue samples, soil or water samples, and environmental measurements.
Test samples for the pathogen
In a USGS national survey, DNA extracted from individual amphibian swabs was tested with real-time TaqMan PCR for Bd and Bsal. This is a documented surveillance approach, not a single universal protocol: the appropriate sample, assay, and handling procedures depend on the study and the organisms being sampled. USGS national amphibian chytrid fungus survey
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“Chytrid” can refer to more than one pathogen in amphibian surveillance. Bd is associated with amphibian chytridiomycosis. Bsal is a distinct chytrid fungus that is an emerging concern for salamanders and is the focus of targeted US surveillance. Reports should name the pathogen tested rather than implying that a result for one covers the other.
How to interpret results in context
Prevalence—the proportion of sampled animals that test positive—depends in part on which hosts and life stages were sampled and when. In a study of boreal toads in southeast Alaska and northwest British Columbia, Bd prevalence peaked in June. Adult prevalence was 37.5%, compared with 11.2% for juveniles and metamorphs. Those figures describe that study’s sampled toads; they are not general rates for amphibians. Hossack et al., 2020
For results to be interpretable, reports should identify the pathogen, host species and life stages, sampling locations and dates, sample type, assay, and relevant features of the sampling design. A negative result means the pathogen was not detected in the tested material under those conditions; it does not establish that the pathogen is absent everywhere or from unsampled animals.
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- AUDBN FG: REPTILES/AMPHIBIANS
- Detection is not a population trend: infection results need demographic observations to support conclusions about abundance, survival, or decline.
- Sampling composition matters: season and life stage can affect measured prevalence.
- There is no one-size-fits-all field recipe: the sources do not establish a universal sample size, swabbing stroke count, storage method, or assay threshold for every species and study. Teams should use a validated protocol and follow laboratory requirements.
What current US Bsal surveillance says—and does not say
As reported by the U.S. Geological Survey National Wildlife Health Center on its January 2026 page, its surveillance program had tested more than 15,000 samples from 39 states and over 55 species since 2016, with no Bsal detected in that program. This is a result for the stated U.S. program, samples, and reporting period—not proof of global absence or a guarantee about later sampling. USGS Bsal surveillance and risk assessment
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Where to find general amphibian survey methods
For population-survey planning, the USGS record for Measuring and Monitoring Biological Diversity: Standard Methods for Amphibians describes ten standard amphibian sampling procedures, along with implementation protocols, equipment and personnel needs, and data-analysis suggestions. It is a general field-methods reference, not a diagnostic manual for Bd or Bsal. USGS standard methods for amphibians
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