Molecular detection and genotyping of Aphanomyces astaci directly from preserved crayfish samples uncovers the Norwegian crayfish plague disease history

Using eDNA to simultaneously detect the distribution of native and invasive crayfish within an entire country

The introduction of invasive crayfish has led to a decline of many European native species of crayfish across their range. In this study, novel duplex assays for all crayfish occurring in Switzerland were developed. We aimed to identify the distribution of the seven species using a traditional trap surveillance method as well by collecting water samples to detect eDNA by species-specific quantitative real-time PCR. We reveal our overall experience in finding optimal field and laboratory techniques to discover the distribution and abundance of native and invasive species in order to enhance knowledge of early invasive species invasion and highlight important pockets of populations where native species remain, for implementation of conservation strategies. Using eDNA, important populations of native noble and white-clawed crayfish were revealed in multiple waters across various cantons. The successful identification of native and invasive crayfish species in Switzerland using eDNA can be applied to future nationwide projects. This method which has the ability to detect all species simultaneously across an entire country, will allow an improvement in freshwater crayfish conservation management.

Real-Time PCR Assays for Rapid Identification of Common Aphanomyces astaci Genotypes

The oomycete Aphanomyces astaci is the etiologic agent of crayfish plague, a disease that has seriously impacted the populations of European native crayfish species. The introduction of non-indigenous crayfish of North American origin and their wide distribution across Europe have largely contributed to spread of crayfish plague in areas populated by indigenous crayfish. Tracking A. astaci genotypes may thus be a useful tool for investigating the natural history of crayfish plague in its European range, as well as the sources and introduction pathways of the pathogen. In this study, we describe the development of real-time PCR TaqMan assays aiming to distinguish the five genotype groups of A. astaci (A–E) previously defined by their distinct RAPD patterns. The method was evaluated using DNA extracts from pure A. astaci cultures representing the known genotype groups, and from A. astaci-positive crayfish clinical samples collected mostly during crayfish plague outbreaks that recently occurred in Central Italy and Czechia. The assays do not cross-react with each other, and those targeting genotype groups A, B, D, and E seem sufficiently specific to genotype the pathogen from infected crayfish in the areas invaded by A. astaci (particularly Europe). The unusual A. astaci genotype “SSR-Up” documented from crayfish plague outbreaks in Czechia and chronically infected Pontastacus leptodactylus in the Danube is detected by the group B real-time PCR. The assay originally developed to detect group C (one not yet documented from crayfish plague outbreaks) showed cross-reactivity with Aphanomyces fennicus; the A. astaci genotype “rust1” described in the United States from Faxonius rusticus is detected by that assay as well. Analyses of additional markers (such as sequencing of the nuclear internal transcribed spacer or mitochondrial ribosomal subunits) may complement such cases when the real-time PCR-based genotyping is not conclusive. Despite some limitations, the method is a robust tool for fast genotyping of A. astaci genotype groups common in Europe, both during crayfish plague outbreaks and in latent infections.

Simultaneous detection of native and invasive crayfish and Aphanomyces astaci from environmental DNA samples in a wide range of habitats in Central Europe

Crayfish of North American origin are amongst the most prominent high-impact invasive invertebrates in European freshwaters. They contribute to the decline of European native crayfish species by spreading the pathogen causing crayfish plague, the oomyceteAphanomyces astaci. In this study we validated the specificity of four quantitative PCR (qPCR) assays, either published or newly developed, usable for environmental DNA (eDNA) screening for widely distributed native and non-native crayfish present in Central Europe:Astacus astacus,Pacifastacus leniusculus,Faxonius limosusandProcambarus virginalis. We then conducted an eDNA monitoring survey of these crayfish as well as the crayfish plague pathogen in a wide variety of habitat types representative for Central and Western Europe. The specificity of qPCR assays was validated against an extensive collection of crayfish DNA isolates, containing most crayfish species documented from European waters. The three assays developed in this study were sufficiently species-specific, but the published assay forF. limosusdisplayed a weak cross-reaction with multiple other crayfish species of the family Cambaridae. In the field study, we infrequently detected eDNA ofA. astacitogether with the three non-native crayfish species under examination. We never detected eDNA fromA. astacitogether with native crayfish, but in a few locations eDNA from both native and non-native crayfish was captured, due either to passive transport of eDNA from upstream populations or co-existence in the absence of infected crayfish carriers ofA. astaci. In the study, we evaluated a robust, easy-to-use and low-cost version of the eDNA sampling equipment, based mostly on items readily available in garden stores and hobby markets, for filtering relatively large (~5 l) water samples. It performed just as well as the far more expensive equipment industrially designed for eDNA water sampling, thus opening the possibility of collecting suitable eDNA samples to a wide range of stakeholders. Overall, our study confirms that eDNA-based screening for crayfish and their associated pathogen is a feasible alternative to traditional monitoring.

Improved method for genotyping the causative agent of crayfish plague (Aphanomyces astaci) based on mitochondrial DNA

Aphanomyces astaci causes crayfish plague, which is a devastating disease of European freshwater crayfish. The likely first introduction of A. astaci into Europe was in the mid-19th century in Italy, presumably with the introduction of North American crayfish. These crayfish can carry A. astaci in their cuticle as a benign infection. Aphanomyces astaci rapidly spread across Europe causing the decline of the highly susceptible indigenous crayfish species. Random amplified polymorphic DNA-PCR analysis of A. astaci pure cultures characterized five genotype groups (A, B, C, D and E). Current A. astaci genotyping techniques (microsatellites and genotype-specific regions, both targeting nuclear DNA) can be applied directly to DNA extracted from infected cuticles but require high infection levels. Therefore, they are not suitable for genotyping benign infections in North American crayfish (carriers). In the present study, we combine bioinformatics and molecular biology techniques to develop A. astaci genotyping molecular markers that target the mitochondrial DNA, increasing the sensitivity of the genotyping tools. The assays were validated on DNA extracts of A. astaci pure cultures, crayfish tissue extractions from crayfish plague outbreaks and tissue extractions from North American carriers. We demonstrate the presence of A. astaci genotype groups A and B in UK waters.

A tentative new species Aphanomyces fennicus sp. nov. interferes with molecular diagnostic methods for crayfish plague

Several isolates of an unknown oomycete resembling the genus Aphanomyces were obtained into laboratory culture from samples of noble crayfish (Astacus astacus) in 2016-2017. The crayfish were kept in cages in connection with a study on an eventually persistent crayfish plague infection in a small Finnish lake, following an acute episode of the disease in 2010. Despite the close resemblance of the isolates to the causative agent of crayfish plague, Aphanomyces astaci, and the positive results obtained in OIE recommended A. astaci-specific ITS-based conventional PCR and qPCR molecular assays, the isolates can be distinguished from A. astaci by morphological features concerning hyphal structure and chlamydospore formation, as well as using the randomly amplified polymorphic DNA-polymerase chain reaction (RAPD-PCR) method, microsatellite-based genotyping, the pathogenicity test and phylogenetic analysis based on ITS sequencing. The name Aphanomyces fennicus sp. novum is proposed for this close relative of A. astaci. The detection of this tentative novel species giving false-positive results in existing diagnostic assays for the crayfish plague highlights the importance of careful interpretation of the results from molecular methods, especially concerning crayfish with low-level infections, excluding the possibility to verify the results from clinical or sequencing data.

Aphanomyces astaci genotypes involved in recent crayfish plague outbreaks in central Italy

The oomycete Aphanomyces astaci is the causative agent of crayfish plague in native European freshwater crayfish. Molecular analyses showed that several distinct genotype groups of this pathogen, apparently associated with different original host taxa, are present in Europe. Tracking their distribution may contribute to understanding the introduction pathways of A. astaci. We used microsatellite markers to genotype the pathogen strains involved in 7 mass mortalities of the endangered indigenous crayfish Austropotamobius pallipes that occurred between 2009 and 2016 in the Abruzzi and Molise regions, central Italy. Three A. astaci genotype groups (A, B, and D, with the latter represented by 2 distinct multilocus genotypes) were identified, suggesting the existence of multiple infection sources even in a relatively small area. Most crayfish plague episodes were due to genotype groups associated with the North American host species Pacifastacus leniusculus and Procambarus clarkii, although these crayfish are not widespread in the study area. A. astaci genotype group A was detected not only in crayfish plague outbreaks but also in apparently healthy Astacus leptodactylus imported for human consumption from Armenia and kept alive in an aquaculture facility. Imports of chronically infected A. leptodactylus from Armenia, Turkey, and possibly Eastern Europe are an underestimated introduction pathway for A. astaci. Although we cannot exclude the presence of latently infected native populations of A. pallipes in the region, A. astaci infections in legally imported crayfish species considered vulnerable to crayfish plague may represent further reservoirs of A. astaci; this should be reflected in the policies regulating the trade of live crayfish.

New genotyping method for the causative agent of crayfish plague (Aphanomyces astaci) based on whole genome data

The oomycete Aphanomyces astaci causes crayfish plague, the most important disease of European freshwater crayfish species. Presumably introduced into Europe 150 years ago with the import of North American crayfish, A. astaci is highly pathogenic to European crayfish species. Five genotypes (A, B, C, D, and E) have been defined based on random amplified polymorphic DNA analysis (RAPD-PCR) from A. astaci pure cultures. The distinction of genotypes is an essential tool to conduct molecular epidemiological studies on crayfish plague and it has been used to clarify and better understand the history and spread of this disease in Europe. Whereas RAPD-PCR requires DNA from pure culture isolates, the development of genotyping tools that can be applied to DNA extracted from clinical samples allows a much wider application of genotyping studies, including revisiting historic samples. In this study, we present a new approach that adds to currently available methods for genotyping A. astaci strains directly from clinical crayfish samples. Whole-genome sequencing of A. astaci strains representing all currently known genotypes was employed, genomic regions unique to the respective genotype identified, and a PCR-based genotyping assay designed, which focuses on the presence/absence of PCR product after amplification with the genotype-specific primers. Our diagnostic methodology was tested using DNA extracts from pure A. astaci cultures, other Aphanomyces species and additional oomycetes, samples from a recent Italian crayfish plague outbreak and additional historical samples available in the Centre for Environment, Fisheries and Aquaculture Science laboratory. The new markers were reliable for pure culture and clinical samples from a recent outbreak and successfully discriminated genotype A, B, D, and E. The marker for genotype C required an additional sequencing step of the generated PCR product to confirm genotype.

Hosts and transmission of the crayfish plague pathogen Aphanomyces astaci: a review

The crayfish plague pathogen, Aphanomyces astaci Schikora, has become one of the most well-studied pathogens of invertebrates. Since its introduction to Europe in the mid-19th century, it has caused mass crayfish mortalities, resulting in drastic declines of local populations. In contrast, North American crayfish usually serve as latent carriers, although they may also be negatively affected by A. astaci infections under some circumstances. Recent research benefiting from molecular tools has improved our knowledge about various aspects of A. astaci biology. In this review, we summarize these advances, particularly with respect to the host range and transmission. We highlight several aspects that have recently received particular attention, in particular newly confirmed or suspected A. astaci hosts, latent A. astaci infections in populations of European crayfish, and the relationship between A. astaci genotype groups and host taxa.

Prevalence of the pathogen Aphanomyces astaci in freshwater crayfish populations in Croatia

The Oomycete Aphanomyces astaci is an obligate crayfish parasite that co-evolved with American crayfish species, and they therefore generally live in a balanced relationship. On the contrary, European native crayfish are highly susceptible to A. astaci, and infestation with it causes development of the lethal disease termed crayfish plague. Until now, 5 A. astaci strains have been described from the freshwater crayfish present in Europe. In this study we aimed to investigate the occurrence of the pathogen A. astaci in Croatian native and non-native crayfish populations, as well as to genotype established strains using microsatellite markers and obtain information on the pathogen's epidemiology. Our results showed that the pathogen is widespread in both native and non-native crayfish populations. Agent level, when positive, in non-native crayfish was generally low; in native species it was higher. Genotyping from microsatellites proved the presence of the B (Ps) strain in non-native species (Pacifastacus leniusculus), while the A (As) strain was detected from viable native species (Astacus astacus and Austropotamobius torrentium) that are distributed in areas lacking non-native crayfish. The genotype from A. torrentium differed from a typical A (As) by 1 allele. Strain B (Ps) was identified in native Astacus leptodactylus from the population that co-occurs with P. leniuscuslus. Interestingly, in 1 A. leptodactylus population both A (As) and B (Ps) strains were present.

Gyrodactylus spp. diversity in native and introduced minnow (Phoxinus phoxinus) populations: no support for "the enemy release" hypothesis

BACKGROUND

Translocation of native species and introduction of non-native species are potentially harmful to the existing biota by introducing e.g. diseases, parasites and organisms that may negatively affect the native species. The enemy release hypothesis states that parasite species will be lost from host populations when the host is introduced into new environments.

METHODS

We tested the enemy release hypothesis by comparing 14 native and 29 introduced minnow (Phoxinus phoxinus) populations in Norway with regard to the ectoparasitic Gyrodactylus species community and load (on caudal fin). Here, we used a nominal logistic regression on presence/absence of Gyrodactylus spp. and a generalized linear model on the summed number of Gyrodactylus spp. on infected populations, with individual minnow heterozygosity (based on 11 microsatellites) as a covariate. In addition, a sample-based rarefaction analysis was used to test if the Gyrodactylus-species specific load differed between native and introduced minnow populations. An analysis of molecular variance was performed to test for hierarchical population structure between the two groups and to test for signals of population bottlenecks the two-phase model in the Wilcoxon signed-rank test was used. To test for demographic population expansion events in the introduced minnow population, we used the kg-test under a stepwise mutation model.

RESULTS

The native and introduced minnow populations had similar species compositions of Gyrodactylus, lending no support to the enemy release hypothesis. The two minnow groups did not differ in the likelihood of being infected with Gyrodactylus spp. Considering only infected minnow populations it was evident that native populations had a significantly higher mean abundance of Gyrodactylus spp. than introduced populations. The results showed that homozygotic minnows had a higher Gyrodactylus spp. infection than more heterozygotic hosts. Using only infected individuals, the two minnow groups did not differ in their mean number of Gyrodactylus spp. However, a similar negative association between heterozygosity and abundance was observed in the native and introduced group. There was no evidence for demographic bottlenecks in the minnow populations, implying that introduced populations retained a high degree of genetic variation, indicating that the number of introduced minnows may have been large or that introductions have been happening repeatedly. This could partly explain the similar species composition of Gyrodactylus in the native and introduced minnow populations.

CONCLUSIONS

In this study it was observed that native and introduced minnow populations did not differ in their species community of Gyrodactylus spp., lending no support to the enemy release hypothesis. A negative association between individual minnow host heterozygosity and the number of Gyrodactylus spp. was detected. Our results suggest that the enemy release hypothesis does not necessarily limit fish parasite dispersal, further emphasizing the importance of invasive fish species dispersal control.

Disentangling host, pathogen, and environmental determinants of a recently emerged wildlife disease: lessons from the first 15 years of amphibian chytridiomycosis research

The amphibian fungal disease chytridiomycosis, which affects species across all continents, recently emerged as one of the greatest threats to biodiversity. Yet, many aspects of the basic biology and epidemiology of the pathogen, Batrachochytrium dendrobatidis (Bd), are still unknown, such as when and from where did Bd emerge and what is its true ecological niche? Here, we review the ecology and evolution of Bd in the Americas and highlight controversies that make this disease so enigmatic. We explore factors associated with variance in severity of epizootics focusing on the disease triangle of host susceptibility, pathogen virulence, and environment. Reevaluating the causes of the panzootic is timely given the wealth of data on Bd prevalence across hosts and communities and the recent discoveries suggesting co-evolutionary potential of hosts and Bd. We generate a new species distribution model for Bd in the Americas based on over 30,000 records and suggest a novel future research agenda. Instead of focusing on pathogen "hot spots," we need to identify pathogen "cold spots" so that we can better understand what limits the pathogen's distribution. Finally, we introduce the concept of "the Ghost of Epizootics Past" to discuss expected patterns in postepizootic host communities.