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Verster R, Ghosh PN, Sewell TR, Garner TWJ, Fisher MC, Muller W, Cilliers D, Weldon C. Environment predicts Batrachochytrium dendrobatidis lineage distribution and zones of recombination in South Africa. Ecol Evol 2024; 14:e11037. [PMID: 38390004 PMCID: PMC10883246 DOI: 10.1002/ece3.11037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Revised: 01/10/2024] [Accepted: 02/02/2024] [Indexed: 02/24/2024] Open
Abstract
The amphibian-infecting chytrid fungus, Batrachochytrium dendrobatidis (Bd), is widespread throughout Africa and is linked to declines of populations and species across the continent. While it is well established that the lineage of Bd encodes traits which determine disease severity, knowledge around how lineages are distributed according to environmental envelope is unclear. We here studied the distribution of Bd in South Africa based on the two lineages found, BdGPL and BdCAPE, in terms of their genome and environmental envelope statistically associated with their distribution. We used Bd surveillance data from published studies, as well as data collected during fieldwork from across South Africa, Lesotho, and eSwatini with samples collected along a transect spanning most of South Africa from Lesotho to the west coast. We utilized lineage-typing qPCR to resolve the spatial distribution of BdGPL and BdCAPE across South Africa and used the resulting surveillance data to create a predictive ecological niche model for Bd lineages in South Africa. Phylogenomic analyses were performed on isolates sourced from across the transect. We show that BdGPL demonstrates a strong isolation by distance suggestive of stepping-stone dispersal, while BdCAPE showed two distinct clusters within their genomic structure that appear geographically and temporally clustered, indicating two separate invasions. Our predictive niche model revealed that the two lineages tended to occur in different ecotypes; BdGPL was associated with lower altitude, arid regions while BdCAPE occurred across cooler, higher altitude environs. Niche predictions identified a zone of lineage contact, where genomics identified inter-lineage recombinants. We argue that this zone of recombination should be prioritized for disease surveillance as it is a potential hotspot for the evolution of variants of amphibian chytrid with novel traits that may be epidemiologically relevant.
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Affiliation(s)
- Ruhan Verster
- Unit for Environmental Sciences and Management North-West University Potchefstroom South Africa
| | - Pria N Ghosh
- Unit for Environmental Sciences and Management North-West University Potchefstroom South Africa
- MRC Centre for Global Infectious Disease Analysis, School of Public Health Imperial College London London UK
| | - Tom R Sewell
- MRC Centre for Global Infectious Disease Analysis, School of Public Health Imperial College London London UK
| | - Trenton W J Garner
- Unit for Environmental Sciences and Management North-West University Potchefstroom South Africa
- Institute of Zoology Zoological Society of London London UK
| | - Matthew C Fisher
- MRC Centre for Global Infectious Disease Analysis, School of Public Health Imperial College London London UK
| | - Wynand Muller
- Unit for Environmental Sciences and Management North-West University Potchefstroom South Africa
| | - Dirk Cilliers
- Unit for Environmental Sciences and Management North-West University Potchefstroom South Africa
| | - Ché Weldon
- Unit for Environmental Sciences and Management North-West University Potchefstroom South Africa
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Ghose SL, Yap TA, Byrne AQ, Sulaeman H, Rosenblum EB, Chan-Alvarado A, Chaukulkar S, Greenbaum E, Koo MS, Kouete MT, Lutz K, McAloose D, Moyer AJ, Parra E, Portik DM, Rockney H, Zink AG, Blackburn DC, Vredenburg VT. Continent-wide recent emergence of a global pathogen in African amphibians. FRONTIERS IN CONSERVATION SCIENCE 2023. [DOI: 10.3389/fcosc.2023.1069490] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/17/2023] Open
Abstract
IntroductionEmerging infectious diseases are increasingly recognized as a global threat to wildlife. Pandemics in amphibians, caused by the fungal pathogen Batrachochytrium dendrobatidis (Bd), have resulted in biodiversity loss at a global scale. Genomic data suggest a complex evolutionary history of Bd lineages that vary in pathogenicity. Africa harbors a significant proportion of global amphibian biodiversity, and multiple Bd lineages are known to occur there; yet, despite the decline of many host species, there are currently no described Bd-epizootics. Here, we describe the historical and recent biogeographical spread of Bd and assess its risk to amphibians across the continent of Africa.MethodsWe provide a 165-year view of host-pathogen interactions by (i) employing a Bd assay to test 4,623 specimens (collected 1908–2013); (ii) compiling 12,297 published Bd records (collected 1852–2017); (iii) comparing the frequency of Bd-infected amphibians through time by both country and region; (iv) genotyping Bd lineages; (v) histologically identifying evidence of chytridiomycosis, and (vi) using a habitat suitability model to assess future Bd risk.ResultsWe found a pattern of Bd emergence beginning largely at the turn of the century. From 1852–1999, we found low Bd prevalence (3.2% overall) and limited geographic spread, but after 2000 we documented a sharp increase in prevalence (18.7% overall), wider geographic spread, and multiple Bd lineages that may be responsible for emergence in different regions. We found that Bd risk to amphibians was highest in much of eastern, central, and western Africa.DiscussionOur study documents a largely overlooked yet significant increase in a fungal pathogen that could pose a threat to amphibians across an entire continent. We emphasize the need to bridge historical and contemporary datasets to better describe and predict host-pathogen dynamics over larger temporal scales.
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Bie J, Zheng K, Gao X, Liu B, Ma J, Hayat MA, Xiao J, Wang H. Spatial Risk Analysis of Batrachochytrium dendrobatidis, A Global Emerging Fungal Pathogen. ECOHEALTH 2021; 18:3-12. [PMID: 34212260 DOI: 10.1007/s10393-021-01519-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Revised: 01/21/2021] [Accepted: 03/02/2021] [Indexed: 06/13/2023]
Abstract
Chytridiomycosis, a leading cause for the global decline in the number of amphibians, is caused by the fungal pathogen Batrachochytrium dendrobatidis. In this study, global distribution data of B. dendrobatidis were collected from January 2009 to May 2019. Space-time scan statistics and the maximum entropy (MaxEnt) model were used to analyze the epidemic trends and aggregation of the pathogen, and predict B. dendrobatidis distribution through its relationships with climate factors, wind speed, and solar radiation. The results of space-time scan statistics show seven clusters of data for the distribution of B. dendrobatidis. The time was mainly concentrated in 2009, 2013, 2015, and 2016, and the regions were primarily concentrated in southeastern Canada, southwestern France, Nigeria, Cameroon, eastern Brazil, southeastern Brazil, central Madagascar, and central and eastern Australia. MaxEnt showed that annual precipitation had the largest contribution percentage in the model, and annual mean temperature highly influenced the distribution of B. dendrobatidis. The global high-risk areas of B. dendrobatidis distribution were mainly observed in western Canada, southern Brazil, Chile, the United Kingdom, Japan, the Republic of Korea, eastern South Africa, eastern Madagascar, southeastern Australia, and southern China.
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Affiliation(s)
- Jia Bie
- Heilongjiang Key Laboratory for Laboratory Animals and Comparative Medicine, College of Veterinary Medicine, Northeast Agricultural University, 600 Changjiang Road, Harbin, 150030, People's Republic of China
| | - Keren Zheng
- Heilongjiang Key Laboratory for Laboratory Animals and Comparative Medicine, College of Veterinary Medicine, Northeast Agricultural University, 600 Changjiang Road, Harbin, 150030, People's Republic of China
| | - Xiang Gao
- Heilongjiang Key Laboratory for Laboratory Animals and Comparative Medicine, College of Veterinary Medicine, Northeast Agricultural University, 600 Changjiang Road, Harbin, 150030, People's Republic of China
| | - Boyang Liu
- Heilongjiang Key Laboratory for Laboratory Animals and Comparative Medicine, College of Veterinary Medicine, Northeast Agricultural University, 600 Changjiang Road, Harbin, 150030, People's Republic of China
| | - Jun Ma
- Heilongjiang Key Laboratory for Laboratory Animals and Comparative Medicine, College of Veterinary Medicine, Northeast Agricultural University, 600 Changjiang Road, Harbin, 150030, People's Republic of China
| | - Muhammad Abid Hayat
- Heilongjiang Key Laboratory for Laboratory Animals and Comparative Medicine, College of Veterinary Medicine, Northeast Agricultural University, 600 Changjiang Road, Harbin, 150030, People's Republic of China
| | - Jianhua Xiao
- Heilongjiang Key Laboratory for Laboratory Animals and Comparative Medicine, College of Veterinary Medicine, Northeast Agricultural University, 600 Changjiang Road, Harbin, 150030, People's Republic of China
| | - Hongbin Wang
- Heilongjiang Key Laboratory for Laboratory Animals and Comparative Medicine, College of Veterinary Medicine, Northeast Agricultural University, 600 Changjiang Road, Harbin, 150030, People's Republic of China.
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Zimkus BM, Baláž V, Belasen AM, Bell RC, Channing A, Doumbia J, Fokam EB, Gonwouo LN, Greenbaum E, Gvoždík V, Hirschfeld M, Jackson K, James TY, Kusamba C, Larson JG, Mavoungou LB, Rödel MO, Zassi-Boulou AG, Penner J. Chytrid Pathogen (Batrachochytrium dendrobatidis) in African Amphibians: A Continental Analysis of Occurrences and Modeling of Its Potential Distribution. HERPETOLOGICA 2020. [DOI: 10.1655/0018-0831-76.2.201] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Affiliation(s)
- Breda M. Zimkus
- Museum of Comparative Zoology, Harvard University, Cambridge, MA 02138, USA
| | - Vojtech Baláž
- University of Veterinary and Pharmaceutical Sciences Brno, Faculty of Veterinary Hygiene and Ecology, Department of Biology and Wildlife Diseases, 612 42 Brno, Czech Republic
| | - Anat M. Belasen
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY 14853, USA
| | - Rayna C. Bell
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC 20560, USA
| | - Alan Channing
- Unit for Environmental Sciences and Management, North-West University, Potchefstroom, 2520, South Africa
| | - Joseph Doumbia
- ONG EnviSud Guinée Commune Ratoma 030BP:558 4720 Conakry, Guinée
| | - Eric B. Fokam
- Department of Zoology and Animal Physiology, University of Buea, 00237, Cameroon
| | - LeGrand N. Gonwouo
- Laboratory of Zoology, Faculty of Sciences, University of Yaoundé I, P.O. Box 812, Yaoundé, Cameroon
| | - Eli Greenbaum
- Department of Biological Sciences, University of Texas at El Paso, 500 W. University Ave., El Paso, TX 79968, USA
| | - Václav Gvoždík
- Institute of Vertebrate Biology of the Czech Academy of Sciences, 603 65 Brno, Czech Republic
| | - Mareike Hirschfeld
- Museum für Naturkunde Berlin, Leibniz Institute for Evolution and Biodiversity Science, Invalidenstr. 43, 10115 Berlin, Germany
| | - Kate Jackson
- Department of Biology, Whitman College, 345 Boyer Avenue, Walla Walla, WA 99362, USA
| | - Timothy Y. James
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Chifundera Kusamba
- Centre de Recherche en Sciences Naturelles, Département de Biologie, Lwiro, The Democratic Republic of the Congo
| | - Joanna G. Larson
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Lise-Bethy Mavoungou
- Institut National de Recherche en Sciences Exactes et Naturelles (IRSEN), Cité Scientifique (Ex-ORSTOM), 2400, République du Congo
| | - Mark-Oliver Rödel
- Museum für Naturkunde Berlin, Leibniz Institute for Evolution and Biodiversity Science, Invalidenstr. 43, 10115 Berlin, Germany
| | - Ange-Ghislain Zassi-Boulou
- Institut National de Recherche en Sciences Exactes et Naturelles (IRSEN), Cité Scientifique (Ex-ORSTOM), 2400, République du Congo
| | - Johannes Penner
- Museum für Naturkunde Berlin, Leibniz Institute for Evolution and Biodiversity Science, Invalidenstr. 43, 10115 Berlin, Germany
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De León ME, Zumbado-Ulate H, García-Rodríguez A, Alvarado G, Sulaeman H, Bolaños F, Vredenburg VT. Batrachochytrium dendrobatidis infection in amphibians predates first known epizootic in Costa Rica. PLoS One 2019; 14:e0208969. [PMID: 31821326 PMCID: PMC6903748 DOI: 10.1371/journal.pone.0208969] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2018] [Accepted: 10/18/2019] [Indexed: 11/19/2022] Open
Abstract
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 three-fold, 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 visualize areas where future studies should take place, we provide a Bd habitat suitability model trained with local data. Studies that provide information on genetic lineages of Bd are needed to determine the most plausible spatial-temporal, host-pathogen dynamics that could best explain the epizootics resulting in amphibian declines in Costa Rica and throughout Central America.
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Affiliation(s)
- Marina E. De León
- Department of Microbiology and Molecular genetics, University of California, Davis, United States of America
| | - Héctor Zumbado-Ulate
- Department of Biological Sciences, Purdue University, West Lafayette, IN, United States of America
| | - Adrián García-Rodríguez
- Escuela de Biología, Universidad de Costa Rica, San Pedro, Costa Rica
- Departamento de Zoología, Instituto de Biología, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Gilbert Alvarado
- Escuela de Biología, Universidad de Costa Rica, San Pedro, Costa Rica
- Faculdade de Medicina Veterinária e Zootecnia, Universidade de São Paulo, São Paulo, Brazil
| | - Hasan Sulaeman
- Department of Biology, San Francisco State University, San Francisco, California, United States of America
| | - Federico Bolaños
- Escuela de Biología, Universidad de Costa Rica, San Pedro, Costa Rica
| | - Vance T. Vredenburg
- Department of Biology, San Francisco State University, San Francisco, California, United States of America
- Museum of Vertebrate Zoology, University of California Berkeley, Berkeley, California, United States of America
- * E-mail:
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Doherty‐Bone TM, Cunningham AA, Fisher MC, Garner TWJ, Ghosh P, Gower DJ, Verster R, Weldon C. Amphibian chytrid fungus in Africa – realigning hypotheses and the research paradigm. Anim Conserv 2019. [DOI: 10.1111/acv.12538] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Affiliation(s)
- T. M. Doherty‐Bone
- Conservation Programs Royal Zoological Society of Scotland Edinburgh UK
- Department of Life Sciences Natural History Museum London UK
| | | | - M. C. Fisher
- School of Public Health Imperial College London London UK
| | - T. W. J. Garner
- Institute of Zoology Zoological Society of London London UK
- Unit for Environmental Sciences and Management North‐West University Potchefstroom South Africa
| | - P. Ghosh
- School of Public Health Imperial College London London UK
- Unit for Environmental Sciences and Management North‐West University Potchefstroom South Africa
| | - D. J. Gower
- Department of Life Sciences Natural History Museum London UK
| | - R. Verster
- Unit for Environmental Sciences and Management North‐West University Potchefstroom South Africa
| | - C. Weldon
- Unit for Environmental Sciences and Management North‐West University Potchefstroom South Africa
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de Jong MS, van Dyk R, Weldon C. Antifungal efficacy of F10SC veterinary disinfectant against Batrachochytrium dendrobatidis. Med Mycol 2018; 56:60-68. [PMID: 28371902 DOI: 10.1093/mmy/myx023] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2016] [Accepted: 02/28/2017] [Indexed: 11/13/2022] Open
Abstract
The Infectious disease chytridiomycosis, which is caused by the fungal pathogen Batrachochytrium dendrobatidis, has been identified as one of the most important drivers of amphibian declines and extinction. In vitro B. dendrobatidis is susceptible to a range of disinfectants, but not all have been tested on animals and some that have been proven effective have harmful side effects on the surrounding environment or the animals being treated. We tested the efficacy of F10SC veterinary disinfectant to treat B. dendrobatidis in experimentally infected tadpole and juvenile Sclerophrys gutturalis and tadpoles of Sclerophrys poweri and Amietia hymenopus. The minimum inhibitory concentration for F10SC on in vitro B. dendrobatidis ranged between 1:7000 for 5-min contact time and 1:10000 for 10-min contact time. Based on the survival data of test animals the no observed effect concentration for 15-min contact time was estimated to be 1:2000 dilution for juveniles, and 1:10000 for tadpoles. In S. gutturalis juveniles an 86% infection clearance rate was achieved after five 15-min doses of 1:3000 dilution. A 100% clearance was achieved in A. hymenopus tadpoles after seven 15-min doses of 1:10000 dilution, and after nine doses of the same treatment in S. poweri tadpoles. F10SC has the benefit of being a concentrated compound that provides a treatment protocol which is nontoxic to tadpoles and post-metamorphic individuals, has a short half-life and is effective against B. dendrobatidis during short contact times, but further testing on different species of amphibians is advised.
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Affiliation(s)
- M S de Jong
- Unit for Environmental Research and Management, North-West University, Potchefstroom 2520, South Africa
| | - R van Dyk
- Unit for Environmental Research and Management, North-West University, Potchefstroom 2520, South Africa
| | - C Weldon
- Unit for Environmental Research and Management, North-West University, Potchefstroom 2520, South Africa
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8
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Miller CA, Tasse Taboue GC, Ekane MMP, Robak M, Sesink Clee PR, Richards-Zawacki C, Fokam EB, Fuashi NA, Anthony NM. Distribution modeling and lineage diversity of the chytrid fungus Batrachochytrium dendrobatidis (Bd) in a central African amphibian hotspot. PLoS One 2018; 13:e0199288. [PMID: 29924870 PMCID: PMC6010240 DOI: 10.1371/journal.pone.0199288] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Accepted: 06/05/2018] [Indexed: 11/18/2022] Open
Abstract
The amphibian disease chytridiomycosis in amphibians is caused by the chytrid fungus Batrachochytrium dendrobatidis (Bd) and has resulted in dramatic declines and extinctions of amphibian populations worldwide. A hypervirulent, globally-dispersed pandemic lineage (Bd-GPL) is thought to be largely responsible for population declines and extinctions, although numerous endemic lineages have also been found. Recent reports of amphibian declines have been linked to the emergence of Bd in Cameroon, a major hotspot of African amphibian diversity. However, it is not known whether Bd-GPL or other lineages have been found in this region. This study therefore aims to examine Bd lineage diversity in the region and predict the distribution of this pathogen under current and future climate conditions using data from this study and from historical records. Almost 15% (52/360) of individuals tested positive for Bd using a standard quantitative PCR diagnostic. Infected amphibians were found at all eight sites sampled in this study. Species distribution models generated in BIOMOD2 indicate that areas with highest predicted environmental suitability occur in the Cameroon highlands and several protected areas throughout the country. These areas of high environmental suitability for Bd are projected to shift or decrease in size under future climate change. However, montane regions with high amphibian diversity are predicted to remain highly suitable. Phylogenetic analysis of the ITS sequences obtained from a set of positive Bd samples indicate that most fall within the Bd-GPL lineage while the remainder group with isolates from either Brazil or South Korea. Although more in depth phylogenetic analyses are needed, identification of Bd-GPL lineages in areas of high amphibian diversity emphasizes the need to continue to monitor for Bd and develop appropriate conservation strategies to prevent its further spread.
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Affiliation(s)
- Courtney A. Miller
- Department of Biological Sciences, University of New Orleans, New Orleans, Louisiana, United States of America
| | - Geraud Canis Tasse Taboue
- Department of Zoology and Animal Physiology, University of Buea, Buea, Cameroon
- Institute of Geological and Mining Research, Yaoundé, Cameroon
| | - Mary M. P. Ekane
- Department of Zoology and Animal Physiology, University of Buea, Buea, Cameroon
| | - Matthew Robak
- Department of Ecology and Evolutionary Biology, Tulane University, New Orleans, Louisiana, United States of America
| | - Paul R. Sesink Clee
- Department of Biology, Drexel University, Philadelphia, Pennsylvania, United States of America
| | - Corinne Richards-Zawacki
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Eric B. Fokam
- Department of Zoology and Animal Physiology, University of Buea, Buea, Cameroon
| | | | - Nicola M. Anthony
- Department of Biological Sciences, University of New Orleans, New Orleans, Louisiana, United States of America
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Antwis RE, Weldon C. Amphibian skin defences show variation in ability to inhibit growth of Batrachochytrium dendrobatidis isolates from the Global Panzootic Lineage. MICROBIOLOGY-SGM 2017; 163:1835-1838. [PMID: 29095686 DOI: 10.1099/mic.0.000570] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The fungal pathogen Batrachochytrium dendrobatidis has caused declines and extinctions in hundreds of amphibian species across the world. Virulence varies among and within lineages; the Global Panzootic Lineage (GPL) is the most pathogenic, although there is also variation in lethality among GPL isolates. Amphibians have a number of defences against pathogens, and skin products including the microbiota and host peptides have considerable influence over disease progression. Here we demonstrate that the collective skin products (the mucosome) of two amphibian species show significant variation in their ability to inhibit different globally distributed isolates of GPL. This may in part explain the variation in disease susceptibility of hosts to different strains of B. dendrobatidis. More work is required to identify particular traits associated with mucosomes that confer broad-spectrum inhibition across GPL in order to facilitate the development of prophylaxis and/or treatments for chytridiomycosis in situ.
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Affiliation(s)
- Rachael Ellen Antwis
- School of Environment and Life Sciences, University of Salford, Salford, UK
- Unit for Environmental Sciences and Management, North-West University, Potchefstroom, South Africa
| | - Ché Weldon
- Unit for Environmental Sciences and Management, North-West University, Potchefstroom, South Africa
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Schatz AM, Kramer AM, Drake JM. Accuracy of climate-based forecasts of pathogen spread. ROYAL SOCIETY OPEN SCIENCE 2017; 4:160975. [PMID: 28405387 DOI: 10.5061/dryad.3p121] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 11/29/2016] [Accepted: 03/03/2017] [Indexed: 05/26/2023]
Abstract
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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Affiliation(s)
- Annakate M Schatz
- Odum School of Ecology , University of Georgia , 140 East Green Street, Athens, GA 30602 , USA
| | - Andrew M Kramer
- Odum School of Ecology, University of Georgia, 140 East Green Street, Athens, GA 30602, USA; Center for the Ecology of Infectious Diseases, University of Georgia, 140 East Green Street, Athens, GA 30602, USA
| | - John M Drake
- Odum School of Ecology, University of Georgia, 140 East Green Street, Athens, GA 30602, USA; Center for the Ecology of Infectious Diseases, University of Georgia, 140 East Green Street, Athens, GA 30602, USA
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Schatz AM, Kramer AM, Drake JM. Accuracy of climate-based forecasts of pathogen spread. ROYAL SOCIETY OPEN SCIENCE 2017; 4:160975. [PMID: 28405387 PMCID: PMC5383844 DOI: 10.1098/rsos.160975] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2016] [Accepted: 03/03/2017] [Indexed: 05/13/2023]
Abstract
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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Affiliation(s)
- Annakate M. Schatz
- Odum School of Ecology, University of Georgia, 140 East Green Street, Athens, GA 30602, USA
| | - Andrew M. Kramer
- Odum School of Ecology, University of Georgia, 140 East Green Street, Athens, GA 30602, USA
- Center for the Ecology of Infectious Diseases, University of Georgia, 140 East Green Street, Athens, GA 30602, USA
| | - John M. Drake
- Odum School of Ecology, University of Georgia, 140 East Green Street, Athens, GA 30602, USA
- Center for the Ecology of Infectious Diseases, University of Georgia, 140 East Green Street, Athens, GA 30602, USA
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Seimon TA, Ayebare S, Sekisambu R, Muhindo E, Mitamba G, Greenbaum E, Menegon M, Pupin F, McAloose D, Ammazzalorso A, Meirte D, Lukwago W, Behangana M, Seimon A, Plumptre AJ. Assessing the Threat of Amphibian Chytrid Fungus in the Albertine Rift: Past, Present and Future. PLoS One 2015; 10:e0145841. [PMID: 26710251 PMCID: PMC4692535 DOI: 10.1371/journal.pone.0145841] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2015] [Accepted: 12/09/2015] [Indexed: 11/18/2022] Open
Abstract
Batrachochytrium dendrobatidis (Bd), the cause of chytridiomycosis, is a pathogenic fungus that is found worldwide and is a major contributor to amphibian declines and extinctions. We report results of a comprehensive effort to assess the distribution and threat of Bd in one of the Earth’s most important biodiversity hotspots, the Albertine Rift in central Africa. In herpetological surveys conducted between 2010 and 2014, 1018 skin swabs from 17 amphibian genera in 39 sites across the Albertine Rift were tested for Bd by PCR. Overall, 19.5% of amphibians tested positive from all sites combined. Skin tissue samples from 163 amphibians were examined histologically; of these two had superficial epidermal intracorneal fungal colonization and lesions consistent with the disease chytridiomycosis. One amphibian was found dead during the surveys, and all others encountered appeared healthy. We found no evidence for Bd-induced mortality events, a finding consistent with other studies. To gain a historical perspective about Bd in the Albertine Rift, skin swabs from 232 museum-archived amphibians collected as voucher specimens from 1925–1994 were tested for Bd. Of these, one sample was positive; an Itombwe River frog (Phrynobatrachus asper) collected in 1950 in the Itombwe highlands. This finding represents the earliest record of Bd in the Democratic Republic of Congo. We modeled the distribution of Bd in the Albertine Rift using MaxEnt software, and trained our model for improved predictability. Our model predicts that Bd is currently widespread across the Albertine Rift, with moderate habitat suitability extending into the lowlands. Under climatic modeling scenarios our model predicts that optimal habitat suitability of Bd will decrease causing a major range contraction of the fungus by 2080. Our baseline data and modeling predictions are important for comparative studies, especially if significant changes in amphibian health status or climactic conditions are encountered in the future.
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Affiliation(s)
- Tracie A. Seimon
- Wildlife Conservation Society, Bronx, NY, United States of America
- * E-mail:
| | - Samuel Ayebare
- Wildlife Conservation Society, Bronx, NY, United States of America
| | - Robert Sekisambu
- Department of Environmental Sciences, Makerere University, Kampala, Uganda
| | - Emmanuel Muhindo
- Wildlife Conservation Society, Bronx, NY, United States of America
| | - Guillain Mitamba
- Wildlife Conservation Society, Bronx, NY, United States of America
| | - Eli Greenbaum
- Department of Biological Sciences, University of Texas at El Paso, El Paso, TX, United States of America
| | - Michele Menegon
- Tropical Biodiversity Section, MUSE, The Science Museum of Trento, Trento, Italy
| | - Fabio Pupin
- Tropical Biodiversity Section, MUSE, The Science Museum of Trento, Trento, Italy
| | - Denise McAloose
- Wildlife Conservation Society, Bronx, NY, United States of America
| | | | - Danny Meirte
- Department of African Biology, Royal Museum for Central Africa, Tervuren, Belgium
| | - Wilbur Lukwago
- Department of Environmental Sciences, Makerere University, Kampala, Uganda
| | - Mathias Behangana
- Department of Environmental Sciences, Makerere University, Kampala, Uganda
| | - Anton Seimon
- Wildlife Conservation Society, Bronx, NY, United States of America
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Abstract
AbstractRose's mountain toad Capensibufo rosei survives in a few isolated montane populations in the south-western Cape of South Africa. It comprises several cryptic species but it is uncertain whether the lineage on the Cape Peninsula is distinct. We tested the hypothesis that toads from the Peninsula form a single genetic lineage but that different breeding sites are divergent at a population level as a result of limited dispersal abilities. Directed surveys were carried out to locate breeding sites and samples obtained were analysed in a phylogenetic and population genetic framework, using two mitochondrial markers. We found toads breeding at only one of five known historical breeding sites, although one new breeding site was also recorded. No toads were observed at 15 other non-breeding localities where they were historically observed. Toads from the two active breeding sites formed a single lineage that was sufficiently distinct to be given species status. However, these were discrete at a population level, with no shared haplotypes, suggesting no gene flow between sites. One site was particularly low in genetic diversity, implying increased vulnerability to stochastic events and elevated risk of extinction. These results, coupled with the failure to locate historically known sites on the Cape Peninsula, make this newly recognized Peninsula endemic a conservation priority. Efforts should focus on the protection and expansion of the two known surviving populations and the patches of habitat upon which they rely.
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