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While epizootics increasingly affect wildlife, it remains poorly understood how the environment shapes most host–pathogen systems. Here, we employ a three‐step framework to study microclimate influence on ectotherm host thermal behaviour, focusing on amphibian chytridiomycosis in fire salamanders (Salamandra salamandra) infected with the fungal pathogen Batrachochytrium salamandrivorans (Bsal). Laboratory trials reveal that innate variation in thermal preference, rather than behavioural fever, can inhibit infection and facilitate salamander recovery under humidity‐saturated conditions. Yet, a 3‐year field study and a mesocosm experiment close to the invasive Bsal range show that microclimate constraints suppress host thermal behaviour favourable to disease control. A final mechanistic model, that estimates range‐wide, year‐round host body temperature relative to microclimate, suggests that these constraints are rule rather than exception. Our results demonstrate how innate host defences against epizootics may remain constrained in the wild, which predisposes to range‐wide disease outbreaks and population declines.

Biodiversity loss is one major outcome of human-mediated ecosystem disturbance. One way that humans have triggered wildlife declines is by transporting disease-causing agents to remote areas of the world. Amphibians have been hit particularly hard by disease due in part to a globally distributed pathogenic chytrid fungus (Batrachochytrium dendrobatidis [Bd]). Prior research has revealed important insights into the biology and distribution of Bd; however, there are still many outstanding questions in this system. Although we know that there are multiple divergent lineages of Bd that differ in pathogenicity, we know little about how these lineages are distributed around the world and where lineages may be coming into contact. Here, we implement a custom genotyping method for a global set of Bd samples. This method is optimized to amplify and sequence degraded DNA from noninvasive skin swab samples. We describe a divergent lineage of Bd, which we call BdASIA3, that appears to be widespread in Southeast Asia. This lineage co-occurs with the global panzootic lineage (BdGPL) in multiple localities. Additionally, we shed light on the global distribution of BdGPL and highlight the expanded range of another lineage, BdCAPE. Finally, we argue that more monitoring needs to take place where Bd lineages are coming into contact and where we know little about Bd lineage diversity. Monitoring need not use expensive or difficult field techniques but can use archived swab samples to further explore the history-and predict the future impacts-of this devastating pathogen.

[EN] The infectious chytrid fungus Batrachochytrium salamandrivorans (Bsal) has been responsible for severe population declines of salamander populations in Europe. Serious population declines and loss of urodelan diversity may occur if appropriate action is not taken to mitigate against the further spread and impact of Bsal. We provide an overview of several potential mitigation methods, and describe their possible advantages and limitations. We conclude that long-term, context-dependent, multi-faceted approaches are needed to successfully mitigate adverse effects of Bsal, and that these approaches should be initiated pre-arrival of the pathogen. The establishment of ex situ assurance colonies, or management units, for species threatened with extinction, should be considered as soon as possible. While ex situ conservation and preventive measures aimed at improving biosecurity by limiting amphibian trade may be implemented quickly, major challenges that lie ahead are in designing in situ disease containment and mitigation post-arrival and in increasing public awareness.

Parasitic chytrid fungi have emerged as a significant threat to amphibian species worldwide, necessitating the development of techniques to isolate these pathogens into culture for research purposes. However, early methods of isolating chytrids from their hosts relied on killing amphibians. We modified a pre-existing protocol for isolating chytrids from infected animals to use toe clips and biopsies from toe webbing rather than euthanizing hosts, and distributed the protocol to researchers as part of the BiodivERsA project RACE; here called the RML protocol. In tandem, we developed a lethal procedure for isolating chytrids from tadpole mouthparts. Reviewing a database of use a decade after their inception, we find that these methods have been applied across 5 continents, 23 countries and in 62 amphibian species. Isolation of chytrids by the non-lethal RML protocol occured in 18% of attempts with 207 fungal isolates and three species of chytrid being recovered. Isolation of chytrids from tadpoles occured in 43% of attempts with 334 fungal isolates of one species (Batrachochytrium dendrobatidis) being recovered. Together, these methods have resulted in a significant reduction and refinement of our use of threatened amphibian species and have improved our ability to work with this group of emerging pathogens.

Globalized infectious diseases are causing species declines worldwide, but their source often remains elusive. We used whole-genome sequencing to solve the spatiotemporal origins of the most devastating panzootic to date, caused by the fungus Batrachochytrium dendrobatidis, a proximate driver of global amphibian declines. We traced the source of B. dendrobatidis to the Korean peninsula, where one lineage, BdASIA-1, exhibits the genetic hallmarks of an ancestral population that seeded the panzootic. We date the emergence of this pathogen to the early 20th century, coinciding with the global expansion of commercial trade in amphibians, and we show that intercontinental transmission is ongoing. Our findings point to East Asia as a geographic hotspot for B. dendrobatidis biodiversity and the original source of these lineages that now parasitize amphibians worldwide.

Parasitic chytrid fungi have emerged as a significant threat to amphibian species worldwide, necessitating the development of techniques to isolate these pathogens into culture for research purposes. However, early methods of isolating chytrids from their hosts relied on killing amphibians. We modified a pre-existing protocol for isolating chytrids from infected animals to use toe clips and biopsies from toe webbing rather than euthanizing hosts, and distributed the protocol to researchers as part of the BiodivERsA project RACE; here called the RML protocol. In tandem, we developed a lethal procedure for isolating chytrids from tadpole mouthparts. Reviewing a database of use a decade after their inception, we find that these methods have been applied across 5 continents, 23 countries and in 62 amphibian species. Isolation of chytrids by the non-lethal RML protocol occured in 18% of attempts with 207 fungal isolates and three species of chytrid being recovered. Isolation of chytrids from tadpoles occured in 43% of attempts with 334 fungal isolates of one species (Batrachochytrium dendrobatidis) being recovered. Together, these methods have resulted in a significant reduction and refinement of our use of threatened amphibian species and have improved our ability to work with this group of emerging pathogens.

Aim Identifying hosts and regions susceptible to invasion by an emerged pathogen is vital to inform early risk assessments. We here show how differences between a pathogen's native and invasive observed niche and their underlying environments affect this process, using the recent emergence of Batrachochytrium salamandrivorans (Bsal) as a critical, empirical example. Location Palaearctic. Methods To quantify observed niches, we first gathered occurrences from the native Asian and invasive European distribution of Bsal. Through ordination in PCA‐bound environmental space, we then applied overlap tests to compare native and invasive Bsal niches with those of 56 putative Western Palaearctic host species. At last, we ensembled bivariate niche models (ESMs) for each Bsal niche to assess how differences in observed niches influenced suitability predictions. Results The observed invasive Bsal niche is a conservative, partially filled subset of its wider native niche. Pathogen–host overlap measured using the narrow invasive niche was nevertheless found to be significantly higher than that of the native niche, which is partly situated in subtropical conditions absent from the Western Palaearctic. ESMs created using the native niche predict high suitability for Bsal throughout Europe. Conversely, a more restricted range was predicted using the invasive niche, which coincides with the presence of oceanic climates in north‐western Europe and several Mediterranean mountain ranges. Main conclusions Unequal relative availability of environments in native and invasive ranges may lead to underestimation of observed niche overlap between native pathogen populations and putative hosts in the invasive range. The existence of partially filled niches may add uncertainty to overlap measurements, and predictions of potential further spread. Results based on the invasive niche therefore provide a conservative estimate; yet demonstrate, in our case, that Bsal is already present in conditions

The close contact between household pets and people offers favourable conditions for bacterial transmission. In this article, the aetiology, prevalence, transmission, impact on human health and preventative measures are summarized for selected bacterial zoonoses transmissible by household pets. Six zoonoses representing distinct transmission routes were selected arbitrarily based on the available information on incidence and severity of pet-associated disease caused by zoonotic bacteria: bite infections and cat scratch disease (physical injuries), psittacosis (inhalation), leptospirosis (contact with urine), and campylobacteriosis and salmonellosis (faecal-oral ingestion). Antimicrobial resistance was also included due to the recent emergence of multidrug-resistant bacteria of zoonotic potential in dogs and cats. There is a general lack of data on pathogen prevalence in the relevant pet population and on the incidence of human infections attributable to pets. In order to address these gaps in knowledge, and to minimize the risk of human infection, actions at several levels are recommended, including: (1) coordinated surveillance of zoonotic pathogens and antimicrobial resistance in household pets, (2) studies to estimate the burden of human disease attributable to pets and to identify risk behaviours facilitating transmission, and (3) education of those in charge of pets, animal caretakers, veterinarians and human medical healthcare practitioners on the potential zoonotic risks associated with exposure to pets. Disease-specific recommendations include incentives to undertake research aimed at the development of new diagnostic tests, veterinary-specific antimicrobial products and vaccines, as well as initiatives to promote best practices in veterinary diagnostic laboratories and prudent antimicrobial usage.

The global amphibian trade is suspected to have brought several species to the brink of extinction, and has led to the spread of amphibian pathogens. Moreover, international trade is not regulated for ~98 % of species. Here we outline patterns and complexity underlying global amphibian trade, highlighting some loopholes that need to be addressed, focusing on the European Union. In spite of being one of the leading amphibian importers, the EU’s current legislation is insufficient to prevent overharvesting of those species in demand or the introduction and/or spread of amphibian pathogens into captive and wild populations. We suggest steps to improve the policy (implementation and enforcement) framework, including (i) an identifier specifically for amphibians in the World Customs Organisation’s harmonised system, (ii) Parties to CITES should strive to include more species in the CITES appendices, and (iii) restriction or suspension of trade of threatened species, restricted-range species, and species protected in their country of origin. Commercial trade should not put survival of amphibian species further at risk.

The close contact between household pets and people offers favourable conditions for bacterial transmission. In this article, the aetiology, prevalence, transmission, impact on human health and preventative measures are summarized for selected bacterial zoonoses transmissible by household pets. Six zoonoses representing distinct transmission routes were selected arbitrarily based on the available information on incidence and severity of pet-associated disease caused by zoonotic bacteria: bite infections and cat scratch disease (physical injuries), psittacosis (inhalation), leptospirosis (contact with urine), and campylobacteriosis and salmonellosis (faecal–oral ingestion). Antimicrobial resistance was also included due to the recent emergence of multidrug-resistant bacteria of zoonotic potential in dogs and cats. There is a general lack of data on pathogen prevalence in the relevant pet population and on the incidence of human infections attributable to pets. In order to address these gaps in knowledge, and to minimize the risk of human infection, actions at several levels are recommended, including: (1) coordinated surveillance of zoonotic pathogens and antimicrobial resistance in household pets, (2) studies to estimate the burden of human disease attributable to pets and to identify risk behaviours facilitating transmission, and (3) education of those in charge of pets, animal caretakers, veterinarians and human medical healthcare practitioners on the potential zoonotic risks associated with exposure to pets. Disease-specific recommendations include incentives to undertake research aimed at the development of new diagnostic tests, veterinary-specific antimicrobial products and vaccines, as well as initiatives to promote best practices in veterinary diagnostic laboratories and prudent antimicrobial usage.

The emerging infectious disease chytridiomycosis is one of the major factors triggering global amphibian declines. A recently discovered species of chytrid fungus, Batrachochytrium salamandrivorans( Bsal), likely originated in East Asia, has led to massive declines in populations of fire salamanders ( Salamandra salamandra) after its apparent introduction to the Netherlands and Belgium. Here, we report the first detection of this pathogen in Germany where it caused mass mortality of fire salamanders in a captive collection. Salamanders from this collection showed an almost 100% prevalence of infection with Bsal. Supposed Bsal-induced mortality occurred in multiple Salamandraspecies ( S. salamandra, S. algira, S. corsica, and S. infraimmaculata), while Bsalinfection was confirmed in nine subspecies of S. salamandraand in S. algira. Our study indicates that this pathogen can potentially infect all fire salamander species and subspecies. If Bsalspreads from captive collections to wild populations, then a similar devastating effect associated with high mortality should be expected.

Emerging infectious diseases are reducing biodiversity on a global scale. Recently, the emergence of the chytrid fungus Batrachochytrium salamandrivorans resulted in rapid declines in populations of European fire salamanders. Here, we screened more than 5000 amphibians from across four continents and combined experimental assessment of pathogenicity with phylogenetic methods to estimate the threat that this infection poses to amphibian diversity. Results show that B. salamandrivorans is restricted to, but highly pathogenic for, salamanders and newts (Urodela). The pathogen likely originated and remained in coexistence with a clade of salamander hosts for millions of years in Asia. As a result of globalization and lack of biosecurity, it has recently been introduced into naïve European amphibian populations, where it is currently causing biodiversity loss.

Amphibian diseases are acknowledged as significant contributors to the decline and extinction of amphibian species. The main culprits currently considered are chytridiomycosis and Ranavirus. In Central America, highly endemic and geographical restricted terrestrial species may be at risk from these diseases. We collected 49 Agalychnis callidryas larvae, one Lithobates forrei and five unidentified larvae on the Nicaraguan Island Ometepe, all deceased, and skin samples were taken. The presence of Ranavirus was determined using PCR. Ranavirus was found involved in 41 of 55 tadpoles. Forty-one Agalychnis callidryas, one Lithobates forrei and another five unidentified anuran tadpoles.

Research on emerging infectious wildlife diseases has placed particular emphasis on host-derived barriers to infection and disease. This focus neglects important extrinsic determinants of the host/pathogen dynamic, where all barriers to infection should be considered when ascertaining the determinants of infectivity and pathogenicity of wildlife pathogens [1, 2 and 3]. Those pathogens with free-living stages, such as fungi causing catastrophic wildlife declines on a global scale [4], must confront lengthy exposure to environmental barriers before contact with an uninfected host [5, 6, 7 and 8]. Hostile environmental conditions therefore have the ability to decrease the density of infectious particles, reducing the force of infection and ameliorating the impact as well as the probability of establishing an infection [9]. Here we show that, in nature, the risk of infection and infectious burden of amphibians infected by the chytrid fungus Batrachochytrium dendrobatidis (Bd) have a significant, site-specific component, and that these correlate with the microfauna present at a site. Experimental infections show that aquatic microfauna can rapidly lower the abundance and density of infectious stages by consuming Bd zoospores, resulting in a significantly reduced probability of infection in anuran tadpoles. Our findings offer new perspectives for explaining the divergent impacts of Bd infection in amphibian assemblages and contribute to our understanding of ecosystem resilience to colonization by novel pathogens.