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Ranid herpesvirus 3 (RaHV3) is a recently discovered virus associated with skin disease in frogs. We detected RaHV3 DNA in free-ranging common frog (Rana temporaria) tadpoles, consistent with premetamorphic infection. Our finding reveals a critical aspect of RaHV3 pathogenesis, relevant for amphibian ecology and conservation and, potentially, for human health.

Health monitoring based on post-mortem examination is essential for the management of endangered animal species. This is especially true for reintroduced species living in small populations with low genetic diversity, such as the Eurasian lynx ( Lynx lynx ) in Switzerland. Thanks to systematic post-mortem examinations, the Institute for Fish and Wildlife Health (FIWI), University of Bern, has acquired a comprehensive view of the lynx health in Switzerland. This study provides an updated overview of the causes of morbidity and mortality in the Eurasian lynx in Switzerland from 2000 to 2022. A total of 346 necropsied lynx (found dead, euthanized, or culled) were included in this study, and a cause of death (COD) was identified in 318 of them (91.9%). Overall, the main COD was blunt trauma (n = 183, 52.9% - largely vehicular collision). Starvation, resulting from the separation of dependent juveniles from their mother, was the second most frequent COD (n = 63, 18.2%). Fatal infectious diseases were relatively low (n = 32, 9.2%). However, we documented some significant pathogens such as canine distemper virus (CDV) and metastrongyloid nematodes. Illegal killing was confirmed in 23 cases (6.6%). Of note, illegal killing is likely underestimated in this study, given that radio-collared lynx were found to be proportionally more often illegally killed than the unmonitored ones found by chance. Furthermore, most individuals were found to be affected at least by one non-specific, mild to moderate inflammatory process of unknown origin, such as interstitial pneumonia (n = 59) or interstitial nephritis (n = 25). Additionally, cardiac changes of variable severity were observed in 125 lynx, and severe soft tissue mineralization was detected in 10 individuals. The frequency of these findings warrants further investigation. Thus, this study confirms the importance of systemic post-mortem examination and general health surveillance of free-ranging Eurasian lynx in Switzerland, in support of translocation projects, conservation of the species, and to provide a better understanding of their pathologies.

Amphibians are undergoing a dramatic global decline. This massive biodiversity loss, which is critically impacting public and planetary health, has been attributed to multiple causes including infectious diseases. Of the known pathogens associated with obvious diseases in amphibians, herpesviruses have recently raised attention secondary to the discovery of two new species, both associated with skin diseases. Here, we provide the detection and characterization of a novel amphibian herpesvirus associated with a proliferative skin disease, closely resembling that previously described in association with Batravirus ranidallo3 (previously Ranid herpesvirus 3-RaHV3) and Bufonid herpesvirus 1 (BfHV1). The novel virus, tentatively named candidate Batravirus ranidallo5 is genetically related, but distinct from the previously described Batraviruses and it is the first amphibian herpesvirus described in Spain. The full-length genome obtained for this novel herpesvirus is approximately 220 kb and it contains the homologues of herpesvirus hallmark genes, which allows us to propose its unambiguous classification as a herpesvirus. Interestingly, a number of predicted ORFs showed to match closer to fish Alloherpesviruses homologues than Batraviruses. The discovery within a limited time span of three distinct herpesviruses, all associated with obvious skin diseases in Europe is alarming and may have significant implication for amphibian conservation.

The fungus Ophiodimyces ophiodiicola is the etiologic agent of snake fungal disease. Recent findings date US occurrence at least as far back as 1945. We analyzed 22 free-ranging snakes with gross lesions consistent with snake fungal disease from museum collections from Europe. We found 5 positive samples, the oldest collected in 1959.The fungus Ophiodimyces ophiodiicola is the etiologic agent of snake fungal disease. Recent findings date US occurrence at least as far back as 1945. We analyzed 22 free-ranging snakes with gross lesions consistent with snake fungal disease from museum collections from Europe. We found 5 positive samples, the oldest collected in 1959.

In the Abruzzi village of Cocullo (Italy), each year, on May 1st, local snake hunters (known as Serpari) display colubrids, captured in the wild, to commemorate the ancient ritual of San Domenico. The ascomycete Ophidiomyces ophidiicola (Oo) is the causative agent of ophidiomycosis, an emerging disease with sublethal effects. Skin lesions, such as dysecdysis, edematous, crusty or necrotic scales, swellings, nodules, and ulcers, are the most common clinical manifestation of the disease. The pathogen and its associated disease are well characterized in wild snakes in North America, whereas broad screenings of free ranging wild ophidians in Europe are rare. In 2019, as part of a multi-year snake health monitoring project, all the Cocullo ophidians were carefully examined for integumentary affections and those showing signs consistent with ophidiomycosis were dry swabbed on the skin and on any visible cutaneous lesions with a single applicator. The extracted DNA underwent a broad-range panfungal PCR targeting the D1-D2 region, as well as two conventional PCRs specific to the ITS2 and IGS regions of Oo DNA. Twenty-three out of 129 snakes (13/82 Elaphe quatuorlineata; 7/31 Hierophis viridiflavus; 3/15 Zamenis longissumus; 0/1 Natrix helvetica) resulted clinically affected, but no specific Oo genomic DNA was detected by PCR. The Cocullo ritual celebration provided a unique opportunity for the first systematic testing of a large sample size of a local snake community for the monitoring of this pathogen in Italy.

Aeromonas salmonicida subsp. salmonicida is an important pathogen in salmonid aquaculture and is responsible for furunculosis, a common infectious disease in salmon, trout and char. The type-three secretion system (T3SS) is considered as the major virulence attribute of A. salmonicida. It is used by the bacterium to secrete and translocate a large number of toxins and effector proteins into the host cell. Some of these factors such as the bi-functional ADP ribosylating – GTPase activating protein AexT have been shown to have a detrimental impact on the integrity of the cell cytoskeleton, and hence contribute to impair phagocytosis. Other effector proteins that are injected to the host cell such as AopP act by inhibiting the NF-κB signalling pathway blocking the translocation of NF-κB (p65) into the nucleus, thus influencing the host’s inflammatory response. Several additional effectors that are secreted and translocated via the T3SS including Ati2, AopN and ExsE have been suggested to modulate the host’s immune response in particular by down regulating the inflammatory reaction. The analysis of the immune response in rainbow trout (Oncorhynchus mykiss) infected with virulent, T3SS harbouring A. salmonicida subsp. salmonicida revealed that the infection leads to a rapid and strong downregulation of several immune-relevant markers affecting both the innate and the adaptive immune response, leading to mortality of the infected fish. In contrast, infection with a T3SS deficient mutant causes a normal immune reaction and clearing of the pathogen. These findings show that T3SS-delivered effector molecules and toxins of A. salmonicida do not only impair the host’s cytoskeleton thus damaging cell physiology and phagocytosis, but also affect the transcription of critical immune markers including the shut-down of important warning signals to recognize infection and induce immune defense.

Francisella tularensis subsp. holarctica is a select agent causing life-threatening tularemia. It has been isolated from humans and animals, mainly lagomorphs and rodents, rarely other wild carnivore species. Increasing numbers of human tularemia cases have been reported during the last 5 years in Switzerland. Here we report the first isolation of Francisella tularensis subsp. holarctica from a domestic cat in Europe and compare its genome sequence with other Swiss isolates. The cat isolate shows a close phylogenetic relationship with a contemporary hare isolate from close geographic proximity, indicating a possible epidemiological link.

Bovine tuberculosis (bTB) caused by Mycobacterium bovis or M. caprae has recently (re-) emerged in livestock and wildlife in all countries bordering Switzerland (CH) and the Principality of Liechtenstein (FL). Comprehensive data for Swiss and Liechtenstein wildlife are not available so far, although two native species, wild boar (Sus scrofa) and red deer (Cervus elaphus elaphus), act as bTB reservoirs elsewhere in continental Europe. Our aims were (1) to assess the occurrence of bTB in these wild ungulates in CH/FL and to reinforce scanning surveillance in all wild mammals; (2) to evaluate the risk of a future bTB reservoir formation in wild boar and red deer in CH/FL. Tissue samples collected from 2009 to 2011 from 434 hunted red deer and wild boar and from eight diseased ungulates with tuberculosis-like lesions were tested by direct real-time PCR and culture to detect mycobacteria of the Mycobacterium tuberculosis complex (MTBC). Identification of suspicious colonies was attempted by real-time PCR, genotyping and spoligotyping. Information on risk factors for bTB maintenance within wildlife populations was retrieved from the literature and the situation regarding identified factors was assessed for our study areas. Mycobacteria of the MTBC were detected in six out of 165 wild boar (3.6%; 95% CI: 1.4-7.8) but none of the 269 red deer (0%; 0-1.4). M. microti was identified in two MTBC-positive wild boar, while species identification remained unsuccessful in four cases. Main risk factors for bTB maintenance worldwide, including different causes of aggregation often resulting from intensive wildlife management, are largely absent in CH and FL. In conclusion, M. bovis and M. caprae were not detected but we report for the first time MTBC mycobacteria in Swiss wild boar. Present conditions seem unfavorable for a reservoir emergence, nevertheless increasing population numbers of wild ungulates and offal consumption may represent a risk.

We report the first de novo sequence assembly and analysis of the genome of Testudinid herpesvirus 3 (TeHV3), one of the most pathogenic chelonian herpesviruses. The genome of TeHV3 is at least 150,080 nucleotides long, is arranged in a type D configuration and comprises at least 102 open reading frames extensively co-linear with those of Human herpesvirus 1. Consistently, the phylogenetic analysis positions TeHV3 among the Alphaherpesvirinae, closely associated with Chelonid herpesvirus 5, a Scutavirus. To date, there has been limited genetic characterization of TeHVs and a resolution beyond the genotype was not feasible because of the lack of informative DNA sequences. To exemplify the potential benefits of the novel genomic information provided by this first whole genome analysis, we selected the glycoprotein B (gB) gene, for detailed comparison among different TeHV3 isolates. The rationale for selecting gB is that it encodes for a well-conserved protein among herpesviruses but is coupled with a relevant antigenicity and is consequently prone to accumulate single nucleotide polymorphisms. These features were considered critical for an ideal phylogenetic marker to investigate the potential existence of distinct TeHV3 genogroups and their associated pathology. Fifteen captive tortoises presumptively diagnosed to be infected with TeHVs or carrying compatible lesions on the basis of either the presence of intranuclear inclusions (presumptively infected) and/or diphtheronecrotic stomatitis-glossitis or pneumonia (compatible lesions) were selected for the study. Viral isolation, TeHV identification, phylogenetic analysis and pathological characterization of the associated lesions, were performed. Our results revealed 1) the existence of at least two distinct TeHV3 genogroups apparently associated with different pathologies in tortoises and 2) the first evidence for a putative homologous recombination event having occurred in a chelonian herpesvirus. This novel information is not only fundamental for the genetic characterization of this virus but is also critical to lay the groundwork for an improved understanding of host-pathogen interactions in chelonians and contribute to tortoise conservation.

Enzootic pneumonia (EP) caused by Mycoplasma hyopneumoniae has a significant economic impact on domestic pig production. A control program carried out from 1999 to 2003 successfully reduced disease occurrence in domestic pigs in Switzerland, but recurrent outbreaks suggested a potential role of free-ranging wild boar (Sus scrofa) as a source of re-infection. Since little is known on the epidemiology of EP in wild boar populations, our aims were: (1) to estimate the prevalence of M. hyopneumoniae infections in wild boar in Switzerland; (2) to identify risk factors for infection in wild boar; and (3) to assess whether infection in wild boar is associated with the same gross and microscopic lesions typical of EP in domestic pigs. Nasal swabs, bronchial swabs and lung samples were collected from 978 wild boar from five study areas in Switzerland between October 2011 and May 2013. Swabs were analyzed by qualitative real time PCR and a histopathological study was conducted on lung tissues. Risk factor analysis was performed using multivariable logistic regression modeling. Overall prevalence in nasal swabs was 26.2% (95% CI 23.3-29.3%) but significant geographical differences were observed. Wild boar density, occurrence of EP outbreaks in domestic pigs and young age were identified as risk factors for infection. There was a significant association between infection and lesions consistent with EP in domestic pigs. We have concluded that M. hyopneumoniae is widespread in the Swiss wild boar population, that the same risk factors for infection of domestic pigs also act as risk factors for infection of wild boar, and that infected wild boar develop lesions similar to those found in domestic pigs. However, based on our data and the outbreak pattern in domestic pigs, we propose that spillover from domestic pigs to wild boar is more likely than transmission from wild boar to pigs.