Spatial Assessment of Amphibian Chytrid Fungus (Batrachochytrium dendrobatidis) in South Africa Confirms Endemic and Widespread Infection

Tarrant, Jeanne; Cilliers, Dirk; Preez, Louis H. Du; Weldon, Ché

doi:10.1371/journal.pone.0069591

Cited by 21 publications

(21 citation statements)

References 62 publications

(74 reference statements)

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“…We did not further limit buffer areas by host occurrence because amphibians occur widely (see fig. 1 in [20]) and Bd may survive outside of its usual host species [1,10,11]. We used sampled background points to fit and evaluate all models, even those that are traditionally presence–absence (as in [2,16,18]); presence-only models were trained only on presence points and then evaluated similarly with background points.…”

Section: Methodsmentioning

confidence: 99%

Accuracy of climate-based forecasts of pathogen spread

2017

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Species distribution models (SDMs) are a tool for predicting the eventual geographical range of an emerging pathogen. Most SDMs, however, rely on an assumption of equilibrium with the environment, which an emerging pathogen, by definition, has not reached. To determine if some SDM approaches work better than others for modelling the spread of emerging, non-equilibrium pathogens, we studied time-sensitive predictive performance of SDMs for Batrachochytrium dendrobatidis, a devastating infectious fungus of amphibians, using multiple methods trained on time-incremented subsets of the available data. We split our data into timeline-based training and testing sets, and evaluated models on each set using standard performance criteria, including AUC, kappa, false negative rate and the Boyce index. Of eight models examined, we found that boosted regression trees and random forests performed best, closely followed by MaxEnt. As expected, predictive performance generally improved with the length of time series used for model training. These results provide information on how quickly the potential extent of an emerging disease may be determined, and identify which modelling frameworks are likely to provide useful information during the early phases of pathogen expansion.

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Section: Methodsmentioning

confidence: 99%

Accuracy of climate-based forecasts of pathogen spread

2017

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“…For example, in some areas (e.g. South Korea, Brazil, and South Africa), Bd appears to be in an enzootic state with amphibian hosts [10][11][12], while in others (e.g. western North America [13], Central America and South America) there are repeated examples of epizootics and die offs of hosts.…”

Section: Introductionmentioning

confidence: 99%

Batrachochytrium dendrobatidis infection in amphibians predates first known epizootic in Costa Rica

et al. 2019

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Emerging infectious diseases are a growing threat to biodiversity worldwide. Outbreaks of the infectious disease chytridiomycosis, caused by the fungal pathogen Batrachochytrium dendrobatidis (Bd), are implicated in the decline and extinction of numerous amphibian species. In Costa Rica, a major decline event occurred in 1987, more than two decades before this pathogen was discovered. The loss of many species in Costa Rica is assumed to be due to Bd-epizootics, but there are few studies that provide data from amphibians in the time leading up to the proposed epizootics. In this study, we provide new data on Bd infection rates of amphibians collected throughout Costa Rica, in the decades prior to the epizootics. We used a quantitative PCR assay to test for Bd presence in 1016 anuran museum specimens collected throughout Costa Rica. The earliest specimen that tested positive for Bd was collected in 1964. Across all time periods, we found an overall infection rate (defined as the proportion of Bd-positive individuals) of 4%. The number of infected individuals remained relatively low across all species tested and the range of Bd-positive specimens was shown to be geographically constrained up until the 1980s; when epizootics are hypothesized to have occurred. After that time, infection rate increased threefold , and the range of specimens tested positive for Bd increased, with Bd-positive specimens collected across the entire country. Our results suggest that Bd dynamics in Costa Rica are more complicated than previously thought. The discovery of Bd's presence in the country preceding massive declines leads to a number of different hypotheses: 1) Bd invaded Costa Rica earlier than previously known, and spread more slowly than previously reported; 2) Bd invaded multiple times and faded out; 3) an endemic Bd lineage existed; 4) an earlier Bd lineage evolved into the current Bd lineage or hybridized with an invasive lineage; or 5) an earlier Bd lineage went extinct and a new invasion event occurred causing epizootics. To help

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“…For example, in some areas (e.g. South Korea, Brazil, and South Africa), Bd appears to be in an enzootic state with amphibian hosts [10–12], while in others (eg. western North America [13], Central America and South America) there are repeated examples of epizootics and die offs of hosts.…”

Section: Introductionmentioning

confidence: 99%

Prevalence of the fungal pathogen Batrachochytrium dendrobatidis in amphibians of Costa Rica predated first-known epizootic

León

Zumbado‐Ulate

García‐Rodríguez

et al. 2018

Preprint

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25 Emerging infectious diseases are a growing threat to biodiversity worldwide. Outbreaks of the 26 infectious disease chytridiomycosis, caused by the fungal pathogen Batrachochytrium 27 dendrobatidis (Bd), have caused the decline and extinction of numerous amphibian species. In 28 Costa Rica, a major decline event occurred in 1987, more than two decades before this pathogen 29 was discovered. The loss of many species in Costa Rica is assumed to be due to Bd-epizootics, 30 but there are few studies that provide data from amphibians in the time leading up to the 31 proposed epizootics. In this study, we provide new data on Bd infection rates of amphibians 32 collected throughout Costa Rica, in the decades prior to the epizootics. We used a quantitative 33 PCR assay to test for Bd infection in 1016 specimens collected throughout Costa Rica. We found 34 Bd-infected hosts collected as early as 1964, and a infection prevalence average per decade of 35 just 4%. The infection prevalence remained relatively low and geographically constrained until 36 the 1980s when epizootics are hypothesized to have occurred. After that time, infection 37 prevalence increased three-fold and Bd-infected hosts we collected throughout the entire country.38 Our results, suggest that Bd may either have invaded Costa Rica earlier than previously known, 39 and spread more slowly than previously reported, or that an endemic lineage of the pathogen 40 may exists. To help visualize areas where future studies should take place, we provide a Bd 41 habitat suitability model trained with local data. Studies that provide information on genetic 42 lineages of Bd are needed to determine whether an endemic lineage of Bd or the Global 43 Panzootic Lineage (identified from mass die off sites globally) was present in Costa Rica and 44 responsible for the epizootics that caused amphibian communities to collapse. 45 46 Introduction 3 47 Amphibians are experiencing a global extinction event [1,2]. Though many factors contribute to 48 population declines, the emergence of the fungal pathogen Batrachochytrium dendrobatidis (Bd) 49 is one of the most important [3]. The disease chytridiomycosis, caused by the fungal pathogen 50 Batrachochytrium dendrobatidis (hereafter Bd), was first described in 1999 and has since been 51 found all over the world [3][4][5]. Interestingly, Bd is composed of many genetic lineages that vary 52 in virulence and affect host species differently. The panzootic disease is attributed to Bd-GPL, a 53 Global Panzootic Lineage of Bd associated with Bd epizootics and host population collapse [6].54 Other lineages of Bd have been shown to be less virulent and have been identified in areas 55 lacking epizootics [7]. Bd infects the skin of the amphibian and causes hyperkeratosis, the 56 thickening of skin which disrupts the amphibian's osmotic balance; leading to death by cardiac 57 arrest in highly infected individuals [8,9]. 58The dynamics of Bd and its hosts, including pathogen invasion and the host-pathogen 59 interactions that follow, ar...

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Spatial Assessment of Amphibian Chytrid Fungus (Batrachochytrium dendrobatidis) in South Africa Confirms Endemic and Widespread Infection

Cited by 21 publications

References 62 publications

Accuracy of climate-based forecasts of pathogen spread

Accuracy of climate-based forecasts of pathogen spread

Batrachochytrium dendrobatidis infection in amphibians predates first known epizootic in Costa Rica

Prevalence of the fungal pathogen Batrachochytrium dendrobatidis in amphibians of Costa Rica predated first-known epizootic

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