DNA Extraction Method Affects the Detection of a Fungal Pathogen in Formalin-Fixed Specimens Using qPCR

Chytrid infections exhibit historical spread and contemporary seasonality in a declining stream-breeding frog

Species with extensive geographical ranges pose special challenges to assessing drivers of wildlife disease, necessitating collaborative and large-scale analyses. The imperilled foothill yellow-legged frog (Rana boylii) inhabits a wide geographical range and variable conditions in rivers of California and Oregon (USA), and is considered threatened by the pathogen Batrachochytrium dendrobatidis (Bd). To assess drivers of Bd infections over time and space, we compiled over 2000 datapoints from R. boylii museum specimens (collected 1897-2005) and field samples (2005-2021) spanning 9° of latitude. We observed a south-to-north spread of Bd detections beginning in the 1940s and increase in prevalence from the 1940s to 1970s, coinciding with extirpation from southern latitudes. We detected eight high-prevalence geographical clusters through time that span the species' geographical range. Field-sampled male R. boylii exhibited the highest prevalence, and juveniles sampled in autumn exhibited the highest loads. Bd infection risk was highest in lower elevation rain-dominated watersheds, and with cool temperatures and low stream-flow conditions at the end of the dry season. Through a holistic assessment of relationships between infection risk, geographical context and time, we identify the locations and time periods where Bd mitigation and monitoring will be critical for conservation of this imperilled species.

Response to "Specimen collection is essential for modern science"

Natural history museums are vital repositories of specimens, samples and data that inform about the natural world; this Reply responds to a Formal Comment that queried whether it will ever be possible to completely do away with whole animal specimen collection, inviting open conversations about the ethical implications of specimen collection.

Chytrid fungus in amphibians from the lowland Brazilian Amazon

Infectious diseases are one of the main threats to biodiversity. The fungus Batrachochytrium dendrobatidis (Bd) is associated with several amphibian losses around the globe, and environmental conditions may dictate the success of pathogen spread. The Brazilian Amazon has been considered climatically unsuitable for chytrid fungus, but additional information on Bd dynamics in this ecoregion is still lacking. We sampled 462 amphibians (449 anurans, 4 caudatans and 9 caecilians), representing 57 species from the Brazilian Amazon, and quantified Bd infections using qPCR. We tested whether abiotic variables predicted the risk of Bd infections, and tested for relationships between biotic variables and Bd. Finally, we experimentally tested the effects of Bd strains CLFT 156 and CLFT 102 (from the southern and northern Atlantic Forest, respectively) on Atelopus manauensis. We detected higher Bd prevalence than those previously reported for the Brazilian Amazon, and positive individuals in all 3 orders of amphibians sampled. Both biotic and abiotic predictors were related to prevalence, and no variable explained infection load. Moreover, we detected higher Bd prevalence in forested than open areas, while the host's reproductive biology was not a factor. We detected higher mortality in the experimental group infected with CLFT 156, probably because this strain was isolated from a region characterized by discrepant climatic conditions (latitudinally more distant) when compared with the host's sampling site in Amazon. The lowland Brazilian Amazon is still underexplored and future studies targeting all amphibian orders are essential to better understand Bd infection dynamics in this region.

Use of mammalian museum specimens to test hypotheses about the geographic expansion of Lyme disease in the southeastern United States

Lyme disease, caused primarily in North America by the bacterium Borrelia burgdorferi sensu stricto, is the most frequently reported vector-borne disease in North America and its geographic extent is increasing in all directions from foci in the northeastern and north central United States. Several southeastern states, including Virginia and North Carolina, have experienced large increases in Lyme disease incidence in the past two decades, with the biggest changes in incidence occurring in the western portion of each state. We tested the hypothesis that B. burgdorferi s.s. was present in western Virginia and North Carolina Peromyscus leucopus populations prior to the recent emergence of Lyme disease. Specifically, we examined archived P. leucopus museum specimens, sampled between 1900 and 2000, for B. burgdorferi s.s. DNA. After confirming viability of DNA extracted from ear punch biopsies from P. leucopus study skins collected between 1945 and 2000 in 19 Virginia counties and 17 North Carolina counties, we used qPCR of two species-specific loci to test for the presence of B. burgdorferi s.s. DNA. Ten mice, all collected from the Eastern Shore of Virginia in 1989, tested positive for presence of B. burgdorferi; all of the remaining 344 specimens were B. burgdorferi-negative. Our results suggest that B. burgdorferi s.s was not common in western Virginia or North Carolina prior to the emergence of Lyme disease cases in the past two decades. Rather, the emergence of Lyme disease in this region has likely been driven by the relatively recent expansion of B. burgdorferi s.s. in southward-moving ticks and reservoir hosts in the mountainous counties of these two states.

A protocol for good quality genomic DNA isolation from formalin-fixed paraffin-embedded tissues without using commercial kits

BACKGROUND

DNA isolation from formalin-fixed paraffin-embedded (FFPE) tissues for molecular analysis has become a frequent procedure in cancer research. However, the yield or quality of the isolated DNA is often compromised, and commercial kits are used to overcome this to some extent.

METHODS

We developed a new protocol (IARCp) to improve the quality and yield of DNA from FFPE tissues without using any commercial kit. To evaluate the IARCp's performance, we compared the quality and yield of DNA with two commercial kits, namely NucleoSpin® DNA FFPE XS (MN) and QIAamp DNA Micro (QG) isolation kit.

RESULTS

Total DNA yield for QG ranged from 120.0 to 282.0 ng (mean 216.5 ng), for MN: 213.6-394.2 ng (mean 319.1 ng), and with IARCp the yield was much higher ranging from 775.5 to 1896.9 ng (mean 1517.8 ng). Moreover, IARCp has also performed well in qualitative assessments by spectrophotometer, fluorometer, and real-time PCR assay.

CONCLUSION

Overall, IARCp represents a novel approach to DNA isolation from FFPE which results in good quality and significant amounts of DNA suitable for many downstream genome-wide and targeted molecular analyses. This protocol does not require the use of any commercial kits or phenol for isolating DNA from FFPE tissues, making it suitable to implement in low-resource settings such as low and middle-income countries.

Molecular Techniques for Genus and Species Determination of Fungi From Fresh and Paraffin-Embedded Formalin-Fixed Tissue in the Revised EORTC/MSGERC Definitions of Invasive Fungal Infection

The EORTC/MSGERC have revised the definitions for proven, probable, and possible fungal diseases. The tissue diagnosis subcommittee was tasked with determining how and when species can be determined from tissue in the absence of culture. The subcommittee reached a consensus decision that polymerase chain reaction (PCR) from tissue, but not immunohistochemistry or in situ hybridization, can be used for genus or species determination under the new EORTC/MSGERC guidelines, but only when fungal elements are identified by histology. Fungal elements seen in tissue samples by histopathology and identified by PCR followed by sequencing should fulfill the definition of a proven fungal infection, identified to genus/species, even in the absence of culture. This summary discusses the issues that were deliberated by the subcommittee to reach the consensus decision and outlines the criteria a laboratory should follow in order to produce data that meet the EORTC/MSGERC definitions.

Chytridiomycosis-induced mortality in a threatened anuran

Effectively planning conservation introductions involves assessing the suitability of both donor and recipient populations, including the landscape of disease risk. Chytridiomycosis, caused by the fungal pathogen Batrachochytrium dendrobatidis (Bd), has caused extensive amphibian declines globally and may hamper reintroduction attempts. To determine Bd dynamics in potential source populations for conservation translocations of the threatened California red-legged frog (Rana draytonii) to Yosemite National Park, we conducted Bd sampling in two populations in the foothills of the Sierra Nevada Mountains, California, U.S.A. At one of two sites, we observed lethally high Bd loads in early post-metamorphic life stages and confirmed one chytridiomycosis-induced mortality, the first such report for this species. These results informed source population site selection for subsequent R. draytonii conservation translocations. Conservation efforts aimed at establishing new populations of R. draytonii in a landscape where Bd is ubiquitous can benefit from an improved understanding of risk through disease monitoring and ex situ infection studies.

Invasive African clawed frogs in California: A reservoir for or predator against the chytrid fungus?

Amphibian species are experiencing population declines due to infection by the fungal pathogen, Batrachochytrium dendrobatidis (Bd). The African clawed frog (Xenopus laevis), an asymptomatic carrier of Bd, has been implicated in the spread of this pathogen through global trade and established invasive populations on several continents. However, research has not explored the relationships of both life stages of this amphibian with Bd. While the post-metamorphic individuals may act as a reservoir, spreading the infection to susceptible species, the filter-feeding larvae may consume the motile Bd zoospores from the water column, potentially reducing pathogen abundance and thus the likelihood of infection. We explore these contrasting processes by assessing Bd prevalence and infection intensities in field populations of post-metamorphic individuals, and performing laboratory experiments to determine if larval X. laevis preyed upon Bd zoospores. The water flea, Daphnia magna, was included in the Bd consumption trials to compare consumption rates and to explore whether intraguild predation between the larval X. laevis and Daphnia may occur, potentially interfering with control of Bd zoospores by Daphnia. Field surveys of three X. laevis populations in southern California, in which 70 post-metamorphic individuals were tested for Bd, found 10% infection prevalence. All infected individuals had very low infection loads (all Bd loads were below 5 zoospore equivalents). Laboratory experiments found that larval X. laevis consume Bd zoospores and therefore may reduce Bd abundance and transmission between amphibians. However, metamorphic and juvenile X. laevis exhibited intraguild predation by consuming Daphnia, which also prey upon Bd zoospores. The results suggest that X laevis is not a large reservoir for Bd and its larval stage may offer some reduction of Bd transmission through direct predation.

Historical amphibian declines and extinctions in Brazil linked to chytridiomycosis

The recent increase in emerging fungal diseases is causing unprecedented threats to biodiversity. The origin of spread of the frog-killing fungus Batrachochytrium dendrobatidis (Bd) is a matter of continued debate. To date, the historical amphibian declines in Brazil could not be attributed to chytridiomycosis; the high diversity of hosts coupled with the presence of several Bd lineages predating the reported declines raised the hypothesis that a hypervirulent Bd genotype spread from Brazil to other continents causing the recent global amphibian crisis. We tested for a spatio-temporal overlap between Bd and areas of historical amphibian population declines and extinctions in Brazil. A spatio-temporal convergence between Bd and declines would support the hypothesis that Brazilian amphibians were not adapted to Bd prior to the reported declines, thus weakening the hypothesis that Brazil was the global origin of Bd emergence. Alternatively, a lack of spatio-temporal association between Bd and frog declines would indicate an evolution of host resistance in Brazilian frogs predating Bd's global emergence, further supporting Brazil as the potential origin of the Bd panzootic. Here, we Bd-screened over 30 000 museum-preserved tadpoles collected in Brazil between 1930 and 2015 and overlaid spatio-temporal Bd data with areas of historical amphibian declines. We detected an increase in the proportion of Bd-infected tadpoles during the peak of amphibian declines (1979-1987). We also found that clusters of Bd-positive samples spatio-temporally overlapped with most records of amphibian declines in Brazil's Atlantic Forest. Our findings indicate that Brazil is post epizootic for chytridiomycosis and provide another piece to the puzzle to explain the origin of Bd globally.

Recommendations on diagnostic tools for Batrachochytrium salamandrivorans

Batrachochytrium salamandrivorans (Bsal) poses a major threat to amphibian, and more specifically caudata, diversity. Bsal is currently spreading through Europe, and mitigation measures aimed at stopping its spread and preventing its introduction into naïve environments are urgently needed. Screening for presence of Bsal and diagnosis of Bsal-induced disease in amphibians are essential core components of effective mitigation plans. Therefore, the aim of this study was to present an overview of all Bsal diagnostic tools together with their limitations and to suggest guidelines to allow uniform interpretation. Here, we investigate the use of different diagnostic tools in post-mortem detection of Bsal and whether competition between Bd and Bsal occurs in the species-specific Bd and Bsal duplex real-time PCR. We also investigate the diagnostic sensitivity, diagnostic specificity and reproducibility of the Bsal real-time PCR and show the use of immunohistochemistry in diagnosis of Bsal-induced chytridiomycosis in amphibian samples stored in formaldehyde. Additionally, we have drawn up guidelines for the use and interpretation of the different diagnostic tools for Bsal currently available, to facilitate standardization of execution and interpretation.

Rapid extirpation of a North American frog coincides with an increase in fungal pathogen prevalence: Historical analysis and implications for reintroduction

As extinctions continue across the globe, conservation biologists are turning to species reintroduction programs as one optimistic tool for addressing the biodiversity crisis. For repatriation to become a viable strategy, fundamental prerequisites include determining the causes of declines and assessing whether the causes persist in the environment. Invasive species-especially pathogens-are an increasingly significant factor contributing to biodiversity loss. We hypothesized that Batrachochytrium dendrobatidis (Bd), the causative agent of the deadly amphibian disease chytridiomycosis, was important in the rapid (<10 years) localized extirpation of a North American frog (Rana boylii) and that Bd remains widespread among extant amphibians in the region of extirpation. We used an interdisciplinary approach, combining interviews with herpetological experts, analysis of archived field notes and museum specimen collections, and field sampling of the extant amphibian assemblage to examine (1) historical relative abundance of R. boylii; (2) potential causes of R. boylii declines; and (3) historical and contemporary prevalence of Bd. We found that R. boylii were relatively abundant prior to their rapid extirpation, and an increase in Bd prevalence coincided with R. boylii declines during a time of rapid change in the region, wherein backcountry recreation, urban development, and the amphibian pet trade were all on the rise. In addition, extreme flooding during the winter of 1969 coincided with localized extirpations in R. boylii populations observed by interview respondents. We conclude that Bd likely played an important role in the rapid extirpation of R. boylii from southern California and that multiple natural and anthropogenic factors may have worked in concert to make this possible in a relatively short period of time. This study emphasizes the importance of recognizing historical ecological contexts in making future management and reintroduction decisions.

The Emerging Amphibian Fungal Disease, Chytridiomycosis: A Key Example of the Global Phenomenon of Wildlife Emerging Infectious Diseases

The spread of amphibian chytrid fungus, Batrachochytrium dendrobatidis, is associated with the emerging infectious wildlife disease chytridiomycosis. This fungus poses an overwhelming threat to global amphibian biodiversity and is contributing toward population declines and extinctions worldwide. Extremely low host-species specificity potentially threatens thousands of the 7,000+ amphibian species with infection, and hosts in additional classes of organisms have now also been identified, including crayfish and nematode worms.Soon after the discovery of B. dendrobatidis in 1999, it became apparent that this pathogen was already pandemic; dozens of countries and hundreds of amphibian species had already been exposed. The timeline of B. dendrobatidis's global emergence still remains a mystery, as does its point of origin. The reason why B. dendrobatidis seems to have only recently increased in virulence to catalyze this global disease event remains unknown, and despite 15 years of investigation, this wildlife pandemic continues primarily uncontrolled. Some disease treatments are effective on animals held in captivity, but there is currently no proven method to eradicate B. dendrobatidis from an affected habitat, nor have we been able to protect new regions from exposure despite knowledge of an approaching "wave" of B. dendrobatidis and ensuing disease.International spread of B. dendrobatidis is largely facilitated by the commercial trade in live amphibians. Chytridiomycosis was recently listed as a globally notifiable disease by the World Organization for Animal Health, but few countries, if any, have formally adopted recommended measures to control its spread. Wildlife diseases continue to emerge as a consequence of globalization, and greater effort is urgently needed to protect global health.