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Soybean (Glycine max) is one of the most important cultivated plants worldwide as a source of protein‐rich foods and animal feeds. Anthracnose, caused by different lineages of the hemibiotrophic fungus Colletotrichum, is one of the main limiting factors to soybean production. Losses due to anthracnose have been neglected, but their impact may threaten up to 50% of the grain production. Taxonomy While C. truncatum is considered the main species associated with soybean anthracnose, recently other species have been reported as pathogenic on this host. Until now, it has not been clear whether the association of new Colletotrichum species with the disease is related to emerging species or whether it is due to the undergoing changes in the taxonomy of the genus. Disease symptoms Typical anthracnose symptoms are pre‐ and postemergence damping‐off; dark, depressed, and irregular spots on cotyledons, stems, petioles, and pods; and necrotic laminar veins on leaves that can result in premature defoliation. Symptoms may evolve to pod rot, immature opening of pods, and premature germination of grains. Challenges As accurate species identification of the causal agent is decisive for disease control and prevention, in this work we review the taxonomic designation of Colletotrichum isolated from soybean to understand which lineages are pathogenic on this host. We also present a comprehensive literature review of soybean anthracnose, focusing on distribution, symptomatology, epidemiology, disease management, identification, and diagnosis. We consider the knowledge emerging from population studies and comparative genomics of Colletotrichum spp. associated with soybean providing future perspectives in the identification of molecular factors involved in the pathogenicity process. Useful website Updates on Colletotrichum can be found at http://www.colletotrichum.org/. All available Colletotrichum genomes on GenBank can be viewed at http://www.colletotrichum.org/genomics/., A revision of soybean anthracnose revealed that along with Colletotrichum truncatum, several other species of Colletotrichum are associated with soybean worldwide, revealing a knowledge gap in what we know about this disease so far.

A study on the occurrence of Dirofilaria immitis and its vectors was carried out in order to assess the prevalence of the disease in dogs in previously non-endemic areas of southern Italy. Blood samples (n = 385) and mosquitoes (n = 1540) were collected in two dog shelters and analysed by Knott’s test and duplex real-time PCR, respectively. Dirofilaria immitis was the most prevalent filarioid (44.2%), while Culex pipiens was the most prevalent mosquito species (68.8%). This high prevalence of D. immitis infection confirms this location as one of the most hyperendemic foci of dirofilariosis in Europe.

Understanding the interactions of ecosystems, humans and pathogens is important for disease risk estimation. This is particularly true for neglected and newly emerging diseases where modes and efficiencies of transmission leading to epidemics are not well understood. Using a model for other emerging diseases, the neglected tropical skin disease Buruli ulcer (BU), we systematically review the literature on transmission of the etiologic agent, Mycobacterium ulcerans (MU), within a One Health/EcoHealth framework and against Hill's nine criteria and Koch's postulates for making strong inference in disease systems. Using this strong inference approach, we advocate a null hypothesis for MU transmission and other understudied disease systems. The null should be tested against alternative vector or host roles in pathogen transmission to better inform disease management. We propose a re-evaluation of what is necessary to identify and confirm hosts, reservoirs and vectors associated with environmental pathogen replication, dispersal and transmission; critically review alternative environmental sources of MU that may be important for transmission, including invertebrate and vertebrate species, plants and biofilms on aquatic substrates; and conclude with placing BU within the context of other neglected and emerging infectious diseases with intricate ecological relationships that lead to disease in humans, wildlife and domestic animals.

Over the last decades the vitality and productivity of European ash trees in Slovenia has been seriously impacted by the onset of canker and dieback disease symptoms on young and old trees, primarily identified as ash dieback caused by Hymenoscyphus fraxineus. Given the limited information available about the aetiology of this emerging disease, a study was carried out to isolate, identify and characterize the fungal species involved in the observed ash symptoms. Field surveys were conducted in five forest sites where 50 symptomatic branch samples were collected. All samples were inspected and used for fungal isolation. Based on morphology, colony appearance and DNA sequence data of the internal transcribed spacer region (ITS), 125 fungal colonies belonging to five species were isolated and identified. Only a few symptomatic ash samples yielded colonies of H. fraxineus, whereas Botryosphaeriaceae species were isolated with a high frequency, with Diplodia fraxini as the dominant species. A pathogenicity test proved that all isolated species were pathogenic on European ash, causing bark lesions and wood discoloration. All Botryosphaeriaceae species isolated in this study are reported for the first time on European ash in Slovenia. Avtorji iz Slov.: Ana Brglez, Barbara Piškur, Nikica Ogris. Bibliografija: str. 27-28.

Important lessons have been learned by the Israeli veterinary community regarding Simbu serogroup viruses infections. This serogroup of viruses might cause the births of neonatal malformation in susceptible ruminant’s populations. Until 2012, only Akabane virus was connected with the births of malformed ruminants in Israel. However, serological and genomic detection tests, coupled with viral isolations, revealed that more than a single Simbu serogroup serotype could be present concurrently in the same farm or even in the same animal. From 2012 to date, Aino, Shuni, Shamunda, Satuperi, Peaton, Schmallenberg, and Sango viruses have been found in Israel either by serological or genomic investigation. Israel is located in the Eastern Mediterranean Basin, a terrestrial and climatic bridge between the three old continents. The Eastern Mediterranean shores benefit from both the tropical/subtropical and the continental climatic conditions. Therefore, the Eastern Mediterranean basin might serve as an optimal investigatory compound for several arboviral diseases, acting as a sentinel. This review summarizes updated information related to the presence of Simbu serogroup viruses in Israel.

Household habitat conditions matter for diseases transmission and control, especially in the case of the novel coronavirus (COVID-19). These conditions include availability and adequacy of sanitation facilities, and number of persons per room. Despite this, little attention is being paid to these conditions as a pathway to understanding the transmission and prevention of COVID-19, especially in Africa, where household habitat conditions are largely suboptimal. This study assesses household sanitation and isolation capacities to understand the COVID-19 transmission risk at household level across Africa. We conducted a secondary analysis of the Demographic and Health Surveys of 16 African countries implemented between 2015 and 2018 to understand the status of households for prevention of COVID-19 transmission in home. We assessed handwashing capacity and self-isolation capacity using multiple parameters, and identified households with elderly persons, who are most at risk of the disease. We fitted two-level random intercept logit models to explore independent relationships among the three indicators, while controlling for the selected explanatory variables. Handwashing capacity was highest in Tanzania (48.2%), and lowest in Chad (4.2%), varying by household location (urban or rural), as well as household wealth. Isolation capacity was highest in South Africa (77.4%), and lowest in Ethiopia (30.9%). Senegal had the largest proportion of households with an elderly person (42.1%), while Angola (16.4%) had the lowest. There were strong, independent relationships between handwashing and isolation capacities in a majority of countries. Also, strong associations were found between isolation capacity and presence of older persons in households. Household capacity for COVID-19 prevention varied significantly across countries, with those having elderly household members not necessarily having the best handwashing or isolation capacity. In view of the age risk factors of COVID-19 transmission, and its dependence on handwashing and isolation capacities of households, each country needs to use the extant information on its risk status to shape communication and intervention strategies that will help limit the impact of the disease in its population across Africa. Supplementary Information The online version contains supplementary material available at 10.1186/s41118-021-00130-w.

Species in the Ceratocystis manginecans complex are important fungal pathogens of plantation trees globally. The most important hosts include species of Eucalyptus, Acacia, Mangifera, and Punica. Despite their relevance and widespread occurrence, little is known regarding their population genetics and how this might relate to their host associations or geographic regions in which they occur. A global collection of 491 isolates representing the C. manginecans complex, from four different plant hosts and nine countries, were genotyped using microsatellite markers. Population genetic analyses using numerous tools were conducted to interrogate how their genetic diversity and structure might be affected by host or areas of occurrence. Results of genetic diversity studies showed that when grouping isolates into populations based on their host associations, the population on Eucalyptus was most diverse, and it also has a broad global distribution. When considering countries of origin as a basis for defining populations, the gene and genotypic diversity were highest in populations from China, Indonesia, and Brazil. In contrast, populations from Oman and Pakistan collected from Mangifera had the lowest genetic diversity and were clonal. Molecular variance, population differentiation, and network and structure analyses showed that the genetic structure of isolates in the C. manginecans complex is influenced by both host association as well as geographical isolation. Furthermore, the results reflected the movement of genotypes between plant hosts and geographic regions that have implications regarding the broad global distribution of this pathogen.

The pre and postharvest disease named ‘aqueous spot’ is an emerging risk for sweet cherries growing in Jerte Valley (Cáceres, Spain). Early stages of the disease appear in the tree, but it is usually detected after harvesting, during the postharvest period. Symptoms include the appearance of skin discolouration and translucency in the shoulder areas. At the most advanced stages, a mycelium of white colour partially or completely covers the fruit. This manuscript provides a detailed description of the microbes involved in this disease, such as bacteria, yeasts, and moulds. Microbes of different cherry cultivars were studied during two consecutive seasons (2019 and 2020). The counts of bacteria and yeast in damaged tissues were higher (7.05 and 6.38 log10 CFU/g for total aerobic mesophilic microbes and yeasts, respectively) than sound tissues (6.08 and 5.19 log10 CFU/g, respectively). The Enterobacterales order dominated the bacteria population. Among yeasts, Yarrowia lipolytica, in 2019, and Metschnikowia pulcherrima and Metschnikowia viticola, in 2020, were consistently isolated from all samples. The presence of moulds was inconsistently detected at the early stage of this disease by plate counts. However, microscopic observations revealed the presence of hyphae in cherry flesh. Different pathogenic moulds were identified, although white mycelium, identified as Botrytis cinerea by molecular methods, was consistently isolated at later stages. Inoculation tests confirmed the involvement of white-mycelium B. cinerea in the development of this new postharvest disease in the Jerte Valley. Its combination with Enterobacterales enhanced the evolution of rotting, whereas the combination with yeasts decreased and delayed the symptoms. This work presents the first report of a consortia of microorganisms implicated in the development of ‘aqueous spot’, an emerging disease in sweet cherry cultivars in the Jerte Valley.

In order to evaluate the pathogenicity of Senecavirus A (SVA) to weaned piglets preliminarily, 28-day-old weaned piglets were challenged with SVA by intramuscular injection. The clinical manifestations, antibody levels, and tissue viral load of infected piglets were detected. The results indicated that the piglets challenged with SVA CH/FuJ/2017 showed drowsiness, lameness, oral blisters, diarrhea, and other clinical signs. Lesions on the hooves were observed. Red spots or plaques were initially observed on the hoof and then developed into blisters that cracked and gradually formed scab. The symptoms and signs were relieved after 8 days post-infection (dpi). The sentinel piglet, feeding together with the challenged piglets, showed similar clinical signs with the challenged piglets after 3 dpi. Monitoring of antibody levels showed that anti-SVA antibody could be detected at 5 dpi by competition enzyme-linked immunosorbent assay (cELISA) method, and neutralizing antibody could be detected after 7 dpi. Analysis of viral tissue distribution and viral load indicated that SVA could replicate in the liver, spleen, lung, kidney, and lymph node. In all, Senecavirus disease was successfully replicated by SVA CH/FuJ/2017 isolate, which verified the clinical manifestations of SVA infection in weaned piglets, and provided a foundation for further SVA pathogenesis and vaccine development.

Many fungi in the Ophiostomatales are vectored by bark beetles that introduce these fungi directly into their tree hosts. Most of these fungal associates have little effect on their hosts, but some can cause serious diseases. One such fungus, Leptographium wageneri, causes an economically and ecologically important tree disease known as black stain root disease (BSRD). For this study, 159 full genome sequences of L. wageneri were analyzed using a population genomics approach to investigate the epidemiology, dispersal capabilities, and reproductive biology of this fungus. Analyses were performed with SNP haplotypes from 155 isolates of L. wageneri var. pseudotsugae collected in 16 Douglas-fir stands in Oregon and 4 isolates of L. wageneri var. wageneri collected in pinyon pine stands in southern California. These two host-specific varieties appear to be evolutionarily divergent, likely due a combination of factors such as host differentiation and geographic isolation. We analyzed gene flow and population structure within and among Douglas-fir plantations in western Oregon to infer the relative importance of local vs. long distance dispersal in structuring populations of L. wageneri var. pseudotsugae. Long-distance gene flow has occurred between Douglas-fir plantations, contributing to diversity and population structure within stands, and likely reflecting the behavior of an important insect vector. Genetic clustering analyses revealed the presence of unique local clusters within stands and plantations in addition to those common among multiple stands or plantations. Although populations of L. wageneri var. pseudotsugae are primarily asexual, two mating types were present in many stands, suggesting that recombination is at least possible and may contribute to genetic diversity.

Ovine anaplasmosis is a vector-borne disease caused by Anaplasma ovis and mainly transmitted through tick bites. In Spain, the first outbreak of ovine anaplasmosis occurred in 2014. An epidemiological study in fifty-one farms was carried out associated with this outbreak in the affected geographical area. An epidemiological questionnaire was performed. In addition, whole blood samples were taken for molecular analysis in 47 of these farms to determine the prevalence of infection of Anaplasma ovis. A. ovis was present in 44 out of 47 PCR-analysed farms (93.6%). However, only 40.4% of the studied farms showed severe clinical signs. The clinical signs affected mainly young animals, which showed severe anaemia, weakness, anorexia, cachexia and epiphora. The early culling of young animals was more frequently reported by severely affected farms than the analysed farms without clinical signs (71.4% vs. 12.5%, p &lt, 0.001). The geographical area where the farm is located seems to be relevant for the presence of clinical signs of the disease. Ovine anaplasmosis is an emerging disease in Europe that spreads rapidly through tick bites and is capable of causing significant economic losses when it spreads in a naive area and causes an epidemic.

Many members of the Saprolegniales (Oomycete) cause mycoses and disorders of fishes, of which Achlya and Saprolegnia are most ubiquitous genera worldwide. During a survey of the diversity of freshwater oomycetes in Korea, we collected seven isolates of Achlya, for which morphological and molecular phylogenetic analyses enabled them to identify as Achlya americana and Achlya bisexualis. In Korea, only a species of Achlya, A. prolifera, has been previously found to cause seedling rot on rice (Oryza sativa), but none of the two species have been reported yet. Importantly, A. bisexualis was isolated from a live fish, namely rice fish (Oryzias sinensis), as well as freshwater, and this is the first report of Achlya-causing mycoses on freshwater fishes in Korea. The presence of A. americana and A. bisexualis on live fish in Korea should be closely monitored, as considering the well-known broad infectivity of these species it has the potential to cause an important emerging disease on aquaculture industry.

Review. et al., Many infectious diseases originating from, or carried by, wildlife affect wildlife conservation and biodiversity, livestock health, or human health. We provide an update on changes in the epidemiology of 25 selected infectious, wildlife-related diseases in Europe (from 2010–16) that had an impact, or may have a future impact, on the health of wildlife, livestock, and humans. These pathogens were selected based on their: 1) identification in recent Europe-wide projects as important surveillance targets, 2) inclusion in European Union legislation as pathogens requiring obligatory surveillance, 3) presence in recent literature on wildlife-related diseases in Europe since 2010, 4) inclusion in key pathogen lists released by the Office International des Epizooties, 5) identification in conference presentations and informal discussions on a group email list by a European network of wildlife disease scientists from the European Wildlife Disease Association, or 6) identification as pathogens with changes in their epidemiology during 2010–16. The wildlife pathogens or diseases included in this review are: avian influenza virus, seal influenza virus, lagoviruses, rabies virus, bat lyssaviruses, filoviruses, canine distemper virus, morbilliviruses in aquatic mammals, bluetongue virus, West Nile virus, hantaviruses, Schmallenberg virus, Crimean-Congo hemorrhagic fever virus, African swine fever virus, amphibian ranavirus, hepatitis E virus, bovine tuberculosis (Mycobacterium bovis), tularemia (Francisella tularensis), brucellosis (Brucella spp.), salmonellosis (Salmonella spp.), Coxiella burnetii, chytridiomycosis, Echinococcus multilocularis, Leishmania infantum, and chronic wasting disease. Further work is needed to identify all of the key drivers of disease change and emergence, as they appear to be influencing the incidence and spread of these pathogens in Europe. We present a summary of these recent changes during 2010–16 to discuss possible commonalities and drivers of disease change and to identify directions for future work on wildlife-related diseases in Europe. Many of the pathogens are entering Europe from other continents while others are expanding their ranges inside and beyond Europe. Surveillance for these wildlife-related diseases at a continental scale is therefore important for planet-wide assessment, awareness of, and preparedness for the risks they may pose to wildlife, domestic animal, and human health., F.R.F. was funded by the Spanish Ministry for the Economy, Industry and Competitiveness (MINECO) through the ‘Ramon y Cajal program.

Eradication of small ruminant morbillivirus (PPRV) is targeted for 2030. PPRV lineage IV is found in much of Asia and Africa. We used PPRV lineage IV strain Kurdistan/2011 in transmission trials to investigate the role of pigs, wild boar, and small ruminants as PPRV reservoirs. Suids were a possible source of infection.

Angiostrongylus cantonensis is an emerging zoonotic nematode recognized as the leading cause of eosinophilic meningitis in the word. After its discovery in China, it was recorded in 30 countries worldwide. Recently, it has expanded to new areas such as South America and it has been recently found in the Atlantic island of Tenerife (Canary Islands). In order to characterize the distribution of A. cantonensis in the Canary Islands, the lungs of 1462 rodents were sampled in eight islands of the archipelago over 13 years and were then analyzed for A. cantonensis. Remarkably, the parasite was detected only in Tenerife, in Rattus rattus (19.7%) and Rattus norvegicus (7.14%). They were concretely in the northern part of the island, which had a warmer and more humid climate than the south and main cities. The absence of this nematode in other islands with similar environmental conditions could be explained by an isolation effect or by a recent introduction of the parasite in the islands. Besides, the presence in Tenerife of the most invasive lineage of A. cantonensis reinforced the hypothesis of a recent introduction on this island. This study highlights the need to implement control measures to prevent the expansion to other areas in order to avoid the transmission to humans and other animals.

Phytoplasmas (Mollicutes, Acholeplasmataceae), vector‐borne obligate bacterial plant parasites, infect nearly 1,000 plant species and unknown numbers of insects, mainly leafhoppers (Hemiptera, Deltocephalinae), which play a key role in transmission and epidemiology. Although the plant–phytoplasma–insect association has been evolving for >300 million years, nearly all known phytoplasmas have been discovered as a result of the damage inflicted by phytoplasma diseases on crops. Few efforts have been made to study phytoplasmas occurring in noneconomically important plants in natural habitats. In this study, a subsample of leafhopper specimens preserved in a large museum biorepository was analyzed to unveil potential new associations. PCR screening for phytoplasmas performed on 227 phloem‐feeding leafhoppers collected worldwide from natural habitats revealed the presence of 6 different previously unknown phytoplasma strains. This indicates that museum collections of herbivorous insects represent a rich and largely untapped resource for discovery of new plant pathogens, that natural areas worldwide harbor a diverse but largely undiscovered diversity of phytoplasmas and potential insect vectors, and that independent epidemiological cycles occur in such habitats, posing a potential threat of disease spillover into agricultural systems. Larger‐scale future investigations will contribute to a better understanding of phytoplasma genetic diversity, insect host range, and insect‐borne phytoplasma transmission and provide an early warning for the emergence of new phytoplasma diseases across global agroecosystems., Phytoplasmas are a diverse group of obligate intracellular bacterial parasites, and diseases associated with these bacteria are among the most important problems affecting agriculture worldwide. However, most knowledge of the diversity and ecology of phytoplasmas and their hosts has been accumulated through studies of phytoplasma disease epidemiology in agroecosystems. In light of recent attention to the importance of wildlife as reservoirs of emergent diseases, we screened potential insect vectors collected in natural areas and preserved in museum biorepositories, 6 of them were positive for the presence of phytoplasmas.

Background: Recently, an emerging flavivirus, Usutu virus (USUV), has caused an epidemic among birds in Europe, resulting in a massive die-off in Eurasian blackbirds. Currently found only in Europe and Africa, it can be envisioned that Usutu virus will follow the path of other flaviviruses, like West Nile virus and Zika virus, and will spread via its mosquito vectors and bird hosts to other parts of the world. Several cases of human infections by Usutu virus have already been published. Anticipating this spread, development of an efficacious vaccine would be highly desirable. Method: This study describes the production in E. coli, purification, and refolding of a partial USUV envelope protein. Prior to immunization, the protein was characterized using size exclusion chromatography, transmission electron microscopy and dynamic light scattering, showing the limited presence of virus-like structures, indicating that the protein solution is probably a mixture of mono and multimeric envelope proteins. Results: Immunizations of two rabbits with the refolded E-protein fraction, mixed with a strong adjuvant, resulted in the generation of neutralizing antibodies, as evidenced in an in vitro assay. Discussion: The way forward towards a subunit vaccine against Usutu virus infection is discussed.

Within the landscape of globally distributed pathogens, populations differentiate via both adaptive and nonadaptive forces. Individual populations are likely to show unique trends of genetic diversity, host-pathogen interaction, and ecological adaptation. In plant pathogens, allopatric divergence may occur particularly rapidly within simplified agricultural monoculture landscapes. As such, the study of plant pathogen populations in monocultures can highlight the distinct evolutionary mechanisms that lead to local genetic differentiation. Xylella fastidiosa is a plant pathogen known to infect and damage multiple monocultures worldwide. One subspecies, Xylella fastidiosa subsp. fastidiosa, was first introduced to the United States ∼150 years ago, where it was found to infect and cause disease in grapevines (Pierce’s disease of grapevines, or PD). Here, we studied PD-causing subsp. fastidiosa populations, with an emphasis on those found in the United States. Our study shows that following their establishment in the United States, PD-causing strains likely split into populations on the East and West Coasts. This diversification has occurred via both changes in gene content (gene gain/loss events) and variations in nucleotide sequence (mutation and recombination). In addition, we reinforce the notion that PD-causing populations within the United States acted as the source for subsequent subsp. fastidiosa outbreaks in Europe and Asia. IMPORTANCE Compared to natural environments, the reduced diversity of monoculture agricultural landscapes can lead bacterial plant pathogens to quickly adapt to local biological and ecological conditions. Because of this, accidental introductions of microbial pathogens into naive regions represents a significant economic and environmental threat. Xylella fastidiosa is a plant pathogen with an expanding host and geographic range due to multiple intra- and intercontinental introductions. X. fastidiosa subsp. fastidiosa infects and causes disease in grapevines (Pierce’s disease of grapevines [PD]). This study focused on PD-causing X. fastidiosa populations, particularly those found in the United States but also invasions into Taiwan and Spain. The analysis shows that PD-causing X. fastidiosa has diversified via multiple cooccurring evolutionary forces acting at an intra- and interpopulation level. This analysis enables a better understanding of the mechanisms leading to the local adaptation of X. fastidiosa and how a plant pathogen diverges allopatrically after multiple and sequential introduction events.

In Italy, after the first report in Friuli-Venezia Giulia along the border with Slovenia in 2009, ash dieback has successively been reported in Veneto, Tuscany and Trentino-Alto Adige. Given its alarming expansion in European ash formations along the sub-montane belt of north-eastern Italy and the limited information about the associated fungal microorganisms, since 2017, a study has been conducted in order to isolate and characterize the fungal species involved in the aetiology of the disease. The surveys were conducted in six ash&ndash, maple forests distributed along the Veneto and Friuli-Venezia Giulia pre-Alpine regions (Italy). In each site, the health status of ash trees was assessed and a sample (shoot or branch) with the typical symptoms of the disease was taken from ten trees to isolate the associated pathogens. The fungal colonies developed were identified using morphological features and DNA sequences. The 60 samples processed yielded a total of 109 fungal isolates belonging to 9 families including: Botryosphaeriaceae (62 isolates), Diaporthaceae (18), Nectriaceae (10), Didymellaceae (9), Helotiaceae (5), Diatrypaceae (2), Didymosphaeriaceae (1), Phaeosphaeriaceae (1) and Valsaceae (1). In particular, three species&mdash, Diplodia subglobosa, Diplodia fraxini and Diaporthe eres&mdash, were isolated with high frequency, while Hymenoscyphus fraxineus was isolated from only five plants distributed in four sites. The pathogenicity tests, conducted on 3-year-old seedlings, detached branches (3&ndash, 4 cm diameter), and leaves of Fraxinus excelsior, showed that Diplodia fraxini is the most virulent species and the only one able to reproduce the symptoms observed in nature. Overall, the results obtained emphasize that several fungal pathogens are involved in the aetiology of the disease, many of which belong to the Botryosphaeriaceae family.

Emerging strains of Bacillus cereus, traditionally considered a self-limiting foodborne pathogen, have been associated with anthrax-like disease in mammals, including humans. The strains have emerged by divergent evolution and, as exchange of genetic material in the Bacillus genus occurs naturally, it is possible that further isolates will be identified in the future. The strains vary in their genotypes and phenotypes, combining traits of both B. cereus and B. anthracis species. Cases of anthrax-like disease associated with these strains result in similar symptoms and mortality rates as those caused by B. anthracis. The strains are susceptible to frontline antibiotics used in the treatment of anthrax and existing vaccines provide protection in animal models. The emergence of these strains has reignited the debate surrounding classification of the B. cereus sensu lato group and serves as a reminder that the field of medical microbiology is constantly changing and remains an important and ongoing area of research.

Made available in DSpace on 2020-12-12T01:35:34Z (GMT). No. of bitstreams: 0 Previous issue date: 2020-01-01 Mycoplasma suis and Mycoplasma parvum bind strongly to erythrocytes and may cause clinical hemoplasmosis in swine, affecting several age groups. Mycoplasma spp. infected animals may be asymptomatic carriers and/or show nonspecific clinical signs. In Brazil, information on genetic diversity associated with porcine hemoplasmas (PH) has not been described yet. Therefore, this study has aimed to detect, quantify and characterize the genetic diversity of PH in finishing pigs from technified farms in the state of Goiás, central-western Brazil. Ethylenediaminetetraacetic acid-blood samples from 450 swine belonging to 30 different farms from Goiás state were collected at the slaughterhouse. Quantitative real-time PCR (qPCR) assays were performed for the molecular detection and quantification of PH 16S rRNA gene fragments. Cloning and sequencing of 16S and 23S rRNA amplicons were performed to evaluate the genetic diversity. Moreover, a questionnaire was applied to each farm manager to obtain epidemiological information about the herd. The results on qPCR showed herd occurrence of 68.89% for PH. Quantification values (starting quantity [SQ]) ranged from 8.43 × 10−1 to 4.69 × 106 copies/µl, and 52.71% of the samples presented SQ values equal or lower than 1 × 103 copies/µl. Risk factors were not evaluated once all farms had at least one positive animal. However, Spearman's coefficient test revealed that the occurrence of PH was inversely associated with the number of farrows per week, weaned piglets per week, and weight at slaughter. Phylogenetic analysis based on maximum likelihood and Bayesian methods showed that the 16S rRNA and 23S rRNA gene sequences obtained from five samples formed a single cluster closely related to M. parvum. Genotype analysis using DNASP software confirmed seven and four different 16S and 23S rRNA genotypes among the cloned amplicons, indicating that there are several genotypes of M. parvum circulating in individual pigs and among pig farms in central-western Brazil. School of Agricultural and Veterinarian Sciences São Paulo State University (Unesp) Ourofino Animal Health COMIGO Cooperative Vector-Borne Diseases Laboratory Departament of Veterinary Medicine Universidade Federal do Paraná (UFPR) Global One Health initiative (GOHi) The Ohio State University School of Agricultural and Veterinarian Sciences São Paulo State University (Unesp)

Mycobacterium pseudoshottsii, a slow-growing mycobacterium closely related to M. marinum, has been isolated only in wild fish in the United States and in Japanese fish farms to date. Here, we report cases of mortality in three farmed fish species (Dicentrarchus labrax, Sparus aurata, and Sciaenops ocellatus) caused by M. pseudoshottsii in Italy. Samples underwent necropsy, histology, and culture with pathogen identification based on PCR and sequencing of housekeeping genes (16S rRNA, hsp65, rpoB). Multifocal to coalescing granulomatous and necrotizing inflammation with acid-fast bacilli were observed in the parenchymatous organs, from which M. pseudoshottsii was isolated and identified. Phylogenetic analysis confirmed the results of gene sequencing and allowed subdivision of the isolates into three distinct groups. M. pseudoshottsii poses a potential threat for Mediterranean aquaculture. Its origin in the area under study needs to be clarified, as well as the threat to the farmed fish species.

In a large-scale survey in the UK, recruited veterinary practices were asked to inspect client-owned cats and dogs, selected at random between April and June 2018, following a standardised flea inspection protocol. A total of 326 veterinary practices participated and 812 cats and 662 dogs were examined during the 3-month period. Fleas were collected, identified to species level and fleas of the same species collected from a single animal were pooled together and treated as a single sample. A total of 470 pooled flea samples were screened by PCR and DNA sequence analysis for a subset of Rickettsia species including R. felis and R. typhi. On analysis, 27 (5.7%) of the pooled flea samples were positive for R. felis DNA; these were predominantly in the cat flea, Ctenocephalides felis, but one dog flea, Ctenocephalides canis was also positive for this pathogen.

Introduction. The white spot syndrome virus (WSSV) causes systemic destruction of ectodermal and mesodermal tissues in shrimp and can cause 100 % mortality. Enterocytozoon hepatopenaei (EHP) is an intracellular microsporidian that causes lysis of epithelial cells in hepatopancreatic tubules in shrimp. Objective. Detect the presence of WSSV and EHP in fifteen shrimp farms in the Gulf of Nicoya and the Central Pacific from Costa Rica. Materials and methods. Between January 2017 and July 2018 water during the filling process of the pond, postlarvae, and juvenile shrimp of Penaeus vannamei was collected, during a production cycle in each one of the fifteen farms. Samples were analyzed through polymerase chain reaction (PCR) using primers and protocols to detect the VP41B gene in WSSV, and the small subunit ribosomal RNA gene of EHP. Results. The presence of WSSV was detected in one farm, while EHP was not detected in any of the fifteen farms. The sequencing of the amplified segments of the VP41B gene showed 100 % identity with isolated shrimp sequences in Taiwan and Mexico. Conclusion. WSSV was detected at a very low frequency and EHP was not detected in this study. It is necessary to continue monitoring these agents in the country’s shrimp farms. Introducción. El virus del síndrome de la mancha blanca (WSSV) causa la destrucción sistémica de los tejidos ectodérmicos y mesodérmicos en los camarones y puede causar una mortalidad del 100 %. El Enterocytozoon hepatopenaei (EHP) es un microsporidio intracelular que ocasiona lisis de las células epiteliales en los túbulos hepatopancreáticos del camarón. Objetivo. Detectar la presencia de WSSV y EHP en camarones de quince granjas ubicadas en el Golfo de Nicoya y el Pacífico Central de Costa Rica. Materiales y métodos. Entre enero 2017 y julio 2018 se recolectó agua durante el proceso de llenado del estanque, postlarvas y camarones juveniles de Penaeus vannamei, durante un ciclo productivo en cada una de las quince fincas. Las muestras se analizaron a través de reacción en cadena de la polimerasa (PCR), utilizando cebadores y protocolos para detectar el gen VP41B de WSSV y el gen de ARN ribosomal de la subunidad pequeña del EHP. Resultados. Se detectó la presencia de WSSV en una finca, mientras que no se detectó EHP en ninguna de las quince fincas. Las secuencias de los segmentos amplificados del gen VP41B mostraron una identidad del 100 % con secuencias aisladas de camarón en Taiwán y en México. Conclusión. Hubo baja frecuencia de WSSV, mientras que el EHP no fue detectado en este estudio. Es necesario continuar monitoreando estos agentes en las granjas camaroneras del país. Universidad Nacional, Costa Rica Escuela de Medicina Veterinaria

Senecavirus A (SVA), an emerging infectious disease, is associated with the porcine idiopathic vesicular disease. Here, the pathogenesis of different strains of SVA was investigated in growing-finishing pigs. We aimed to evaluate the replication characteristics, virus particle morphology, clinical signs, and vesicular lesions in comparison with two different strains of SVA. The animals were infected with SVA HB-CH-2016 or CH/AH-02/2017 by intranasal routes (3 mL, 109TCID50/mL) and monitored daily for 14 days post-inoculation (dpi) for clinical signs and vesicular lesions. Viremia or viral shedding was detected in the blood, fecal swab, and nasal swab samples. Results showed no distinct differences in plaque size, replication ability, and characteristic virions between SVA HB-CH-2016 and CH/AH-02/2017 strains. Animal experimental results showed that both SVA CH/AH-02/2017 and SVA HB-CH-2016 could infect pigs. However, an obvious difference in the pathogenicity and dynamics of infection was observed between SVA HB-CH-2016 and CH/AH-02/2017 strains. The pathogenesis of SVA CH/AH-02/2017 was similar to that of published results of USA strains, whereas the SVA HB-CH-2016 strain had low pathogenicity to pigs. Clinical signs and vesicular lesions were observed in SVA CH/AH-02/2017-infected pigs. Additionally, the different branches of SVA should be capable of inducing broad cross-reactive neutralizing antibodies, which play an important role in clearing the SVA virus. This study of animal models for SVA infection will be beneficial to develop vaccines and antivirals.

International audience; Rapid detection is key to managing emerging diseases because it allows their spread around the world to be monitored and limited. The first major wheat blast epidemics were reported in 1985 in the Brazilian state of Paraná. Following this outbreak, the disease quickly spread to neighboring regions and countries and, in 2016, the first report of wheat blast disease outside South America was released. This Asian outbreak was due to the trade of infected South American seed, demonstrating the importance of detection tests in order to avoid importing contaminated biological material into regions free from the pathogen. Genomic analysis has revealed that one particular lineage within the fungal species Pyricularia oryzae is associated with this disease: the Triticum lineage. A comparison of 81 Pyricularia genomes highlighted polymorphisms specific to the Triticum lineage, and this study developed a real-time PCR test targeting one of these polymorphisms. The test's performance was then evaluated in order to measure its analytical specificity, analytical sensitivity, and robustness. The C17 quantitative PCR test detected isolates belonging to the Triticum lineage with high sensitivity, down to 13 plasmid copies or 1 pg of genomic DNA per reaction tube. The blast-based approach developed here to study P. oryzae can be transposed to other emerging diseases. © 2020 The American Phytopathological Society

Senecavirus A (SVA), an emerging swine picornavirus of swine, is one of the causative agents of vesicular disease which is clinically indistinguishable from foot-and-mouth disease in pigs. Here, 3 cases of vesicular disease were reported which was caused by SVA in November 2018 in Henan, China. Three new SVA strains were identified and conducted a genetically evolutionary analysis. The isolates shared 98.1–99.0% genomic pairwise identity to each other and had the highest similarity, of 98.3–98.7%, with the American strain KS15-01, respectively. Phylogenetic analysis indicated that the Chinese prevalent strains could be clearly divided into cluster 1, cluster 2, and cluster 3. Furthermore, one isolate (HeNNY-1/2018) and two previously reported strains (HB-CH-2016 and SVA/CHN/10/2017) were identified as recombinants using several algorithms. It revealed that the recombination among SVA strains has occurred in China since 2016 or earlier. The findings of studies updated the prevalent status of SVA in China. Besides, the genetic evolution and recombinant events of SVA should be attracted more attentions in the future.

Pathogen introductions have led to numerous disease outbreaks in naive regions of the globe. The plant pathogen Xylella fastidiosa has been associated with various recent epidemics in Europe affecting agricultural crops, such as almond, grapevine, and olive, but also endemic species occurring in natural forest landscapes and ornamental plants. We compared whole-genome sequences of X. fastidiosa subspecies multiplex from America and strains associated with recent outbreaks in southern Europe to infer their likely origins and paths of introduction within and between the two continents. Phylogenetic analyses indicated multiple introductions of X. fastidiosa subspecies multiplex into Italy, Spain, and France, most of which emerged from a clade with limited genetic diversity with a likely origin in California, USA. The limited genetic diversity observed in X. fastidiosa subspecies multiplex strains originating from California is likely due to the clade itself being an introduction from X. fastidiosa subspecies multiplex populations in the southeastern United States, where this subspecies is most likely endemic. Despite the genetic diversity found in some areas in Europe, there was no clear evidence of recombination occurring among introduced X. fastidiosa strains in Europe. Sequence type taxonomy, based on multilocus sequence typing (MLST), was shown, at least in one case, to not lead to monophyletic clades of this pathogen; whole-genome sequence data were more informative in resolving the history of introductions than MLST data. Although additional data are necessary to carefully tease out the paths of these recent dispersal events, our results indicate that whole-genome sequence data should be considered when developing management strategies for X. fastidiosa outbreaks., This work was funded by the following awards: XF-ACTORS (Xylella fastidiosa Active Containment Through a Multidisciplinary-Oriented Research Strategy, grant 727987 from the European Union’s Horizon 2020 Framework Research Programme), E-RTA2017-00004-C02 (Desarrollo de estrategias de erradicación, contención y control de X. fastidiosa en España from “Programa Estatal de I+D+I Orientada a los Retos de la Sociedad of the Spanish Government” and FEDER), the Spanish Olive Oil Interprofessional, and the California Department of Food and Agriculture Pierce’ Disease Research Program.

Most of the human pandemics reported to date can be classified as zoonoses. Among these, there is a long history of infectious diseases that have spread from non-human primates (NHP) to humans. For millennia, indigenous groups that depend on wildlife for their survival were exposed to the risk of NHP pathogens' transmission through animal hunting and wild meat consumption. Usually, exposure is of no consequence or is limited to mild infections. In rare situations, it can be more severe or even become a real public health concern. Since the emergence of acquired immune deficiency syndrome (AIDS), nobody can ignore that an emerging infectious diseases (EID) might spread from NHP into the human population. In large parts of the Central Africa and Asia, wildlife still remains the primary source of meat and income for millions of people living in rural areas. However, in the past decades the risk of exposure to an NHP pathogen has taken a new dimension. Unprecedented breaking down of natural barriers between NHP and humans has increased exposure to health risks for a much larger population including people living in urban areas. There are several reasons to this: (i) due to road development and massive destruction of ecosystems for agricultural needs, wildlife and humans come more frequently into contact; (ii) due to the ecological awareness, many long distance travelers are in search of wildlife discovery, with a particular fascination for African great apes; (iii) due to attraction for ancient temples and mystical practices, others travelers visit Asian places colonized by NHP. In each case, there is a risk of pathogen transmission through bite or another route of infection. Beside the individual risk to contracting a pathogen, there is also a possibility of starting a new pandemic. This article reviews the known cases of NHP pathogens' transmission to humans whether they are hunters, travelers, ecotourists, veterinarians or scientists working on NHP. Although pathogen transmission is supposed to be a rare outcome, some pathogens including Rabies virus, Herpes B virus, Monkeypox virus, Ebola virus, or Yellow fever virus are of greater concern and require quick countermeasures from healthcare professionals.

International audience; A multilocus sequence analysis (MLSA) was performed on five housekeeping genes (fusA, gapA, gltA, lacF and lepA) of 22 Xanthomonas euvesicatoria strains recently isolated from alfalfa, pepper and tomato plants in Iran. In addition, 161 strains isolated worldwide from pepper, poinsettia, rose and tomato plants were included in the analysis. All X.euvesicatoria pv. perforans isolates from tomato plants in Iran clustered in a monophyletic group, although five MLSA haplotypes were detected among them. The Iranian tomato strains presented 10 nucleotide differences in the lepA gene sequences compared to the known worldwide population of X.euvesicatoria pv. perforans. Statistical analyses revealed a recombination event that had occurred in the lepA gene of the strains isolated from tomato in Iran. BOX-PCR analysis confirmed the inclusion of Iranian tomato strains within X.euvesicatoria pv. perforans. Furthermore, X.euvesicatoria pv. euvesicatoria strains isolated from pepper in Iran differed in one nucleotide in the lepA gene sequence from the known worldwide population of the pathovar, and clustered in a group containing strains isolated in Nigeria. The strains isolated from alfalfa in Iran clustered with the type strain of X.euvesicatoria pv. alfalfae. Altogether, the results reveal the existence of a phylogenetically novel population of X.euvesicatoria pv. perforans in Iran which needs further in-depth analysis to pinpoint the epidemiological impact of these strains.

International audience; In the past decade, the spread of emerging zoonotic flaviviruses (genus Flavivirus, family Flaviviridae) has been reported in many regions worldwide, representing a threat to both human and animal health. A serosurvey was carried out to assess exposure and risk factors associated with antigenically related flaviviruses, particularly West Nile virus (WNV), Usutu virus (USUV) and tick-borne encephalitis virus (TBEV), in dogs in Spain. Flavivirus antibodies were detected in 39 of 815 dogs (4.8%; 95% CI: 3.3-6.3) by bELISA. Significantly higher seropositivity was observed in hunting dogs compared to pet dogs. Virus neutralization tests confirmed WNV-specific and TBEV-specific antibodies in 11 and 14 bELISA-positive dogs, respectively. This is the first serosurvey of WNV and TBEV in dogs in Spain and the first report of TBEV circulation in this country. The seropositivity obtained indicates widespread, but not homogeneous, distribution of WNV and TBEV in dogs in Spain. In 2013 and 2015, WNV-seropositive dogs were detected in those areas of Andalusia where the highest number of WNV outbreaks were reported in both horses and humans. Antibodies against TBEV have been found in dogs sampled in two different periods and regions in Spain. Serosurveillance in dogs could be a complementary way of monitoring the activity of emerging flaviviruses in Spain.

Crimean-Congo hemorrhagic fever (CCHF) is a severe tick-borne viral zoonotic disease caused by Crimean-Congo hemorrhagic fever virus (CCHFV). The disease is usually asymptomatic in domestic and wild animals, both of which may act as reservoirs of the virus. CCHF is endemic in parts of Africa, Asia, the Middle East and Eastern Europe. During the last decade, the emergence or re-emergence of CCHF was described in several countries in the Eastern Mediterranean Region, with an increasing risk of extension into new areas. Given the public health importance, this study undertakes a semi-quantitative risk assessment to analyse the likelihood of entry and exposure of CCHFV into 9 CCHF-free countries in Southern and Western Europe. Based on a framework outlining the probability of the virus entry and exposure, the risk estimates were assessed for each individual country. The risk assessment was performed using information from public databases and the available scientific literature. The likelihood of entry was conducted considering 3 main pathways: infected tick vectors, wildlife and livestock. The likelihood of exposure was assessed considering the probability of survival of the infected ticks once introduced in CCHF-free countries (depending on abiotic and biotic factors), and the exposure of resident uninfected susceptible ticks to infected imported wildlife and livestock. The risk estimates (combined CCHFV introduction and exposure) were low for the majority of the countries (Austria, Belgium, Germany, Luxembourg, Netherlands, Slovenia and Switzerland) and medium for France and Italy, if accounting only for animal health consequences. Considering the public health consequences only, the risks were rated low for all the countries, except for Italy where it was assessed to be medium.

Lyssaviruses are neurotropic rhabdoviruses thought to be restricted to mammalian hosts, and to originate from bats. The identification of lyssavirus sequences from amphibians and reptiles by metatranscriptomics thus comes as a surprise and challenges the mammalian origin of lyssaviruses. The novel sequences of the proposed American tree frog lyssavirus (ATFLV) and anole lizard lyssavirus (ALLV) reveal substantial phylogenetic distances from each other and from bat lyssaviruses, with ATFLV being the most distant. As virus isolation has not been successful yet, we have here studied the functionality of the authentic ATFLV- and ALLV-encoded glycoproteins in the context of rabies virus pseudotype particles. Cryogenic electron microscopy uncovered the incorporation of the plasmid-encoded G proteins in viral envelopes. Infection experiments revealed the infectivity of ATFLV and ALLV G-coated RABV pp for a broad spectrum of cell lines from humans, bats, and reptiles, demonstrating membrane fusion activities. As presumed, ATFLV and ALLV G RABV pp escaped neutralization by human rabies immune sera. The present findings support the existence of contagious lyssaviruses in poikilothermic animals, and reveal a broad cell tropism in vitro, similar to that of the rabies virus.

The genus Hyaloperonospora (Peronosporaceae; Oomycota) is an obligate biotrophic group that causes downy mildew disease on the Brassicaceae and allied families of Brassicales, including many economically relevant crops, such as broccoli, cabbage, radish, rape, and wasabi. To investigate the diversity of Hyaloperonospora species in northeast Asia, we performed a morphological analysis for the dried herbarium specimens collected in Korea, along with molecular phylogenetic inferences based on internal transcribed spacer rDNA and cox2 mtDNA sequences. It was confirmed that 14 species of Hyaloperonospora exist in Korea. Of these, three species, previously classified under the genus Peronospora, were combined to Hyaloperonospora: H. arabidis-glabrae comb. nov. (ex Arabis glabra), H. nasturtii-montani comb. nov. (ex Rorippa indica), and H. nasturtii-palustris comb. nov. (ex Rorippa palustris). In addition, finding two potentially new species specific to northeast Asian plants is noteworthy in support of the view that the species abundance of Hyaloperonospora has been underestimated hitherto.

The media and public health generally focus on the biological and physical ramifications of epidemics. Mental health issues that coincide with emerging diseases and epidemics are rarely examined and sometimes, even eschewed due to cultural considerations. Psychiatric manifestations of various infectious diseases, especially with a focus on Ebola Virus disease (EVD) and Zika Virus, are discussed in this commentary to illustrate the continued need of care after the resolution of the actual illness. Various infectious diseases have associations with mental illness, such as an increased risk of obsessive-compulsive disorders and Tourette syndrome in children with Group B streptococcal infection. Current EVD literature does not demonstrate a strong association of mental illness symptoms or diseases but there is a necessity of care that extends beyond the illness. Patients and their families experience depression, anxiety, trauma, suicidal ideation, panic and other manifestations. Zika virus has been associated neuronal injury, genetic alteration that affects fetal development and detrimental maternal mental health symptoms are being documented. While funding calls from the international community are present, there are no specific epidemiological data or fiscal estimates solely for mental health during or after infectious diseases epidemics or disasters that support health care providers and strengthen policies and procedures for responding to such situations. Therefore, those on the frontlines of epidemics including emergency physicians, primary care providers and infectious disease specialists should serve communicate this need and advocate for sustained and increased funding for mental health programs to heighten public awareness regarding acute psychiatric events during infectious diseases outbreaks and offer treatment and support when necessary.

RNA viruses are a major source of emerging and re-emerging infectious diseases around the world. We developed a method to identify RNA viruses that is based on the fact that RNA viruses produce double-stranded RNA (dsRNA) while replicating. Purifying and sequencing dsRNA from the total RNA isolated from infected tissue allowed us to recover dsRNA virus sequences and replicated sequences from single-stranded RNA (ssRNA) viruses. We refer to this approach as dsRNA-Seq. By assembling dsRNA sequences into contigs we identified full length or partial RNA viral genomes of varying genome types infecting mammalian culture samples, identified a known viral disease agent in laboratory infected mice, and successfully detected naturally occurring RNA viral infections in reptiles. Here, we show that dsRNA-Seq is a preferable method for identifying viruses in organisms that don&rsquo, t have sequenced genomes and/or commercially available rRNA depletion reagents. In addition, a significant advantage of this method is the ability to identify replicated viral sequences of ssRNA viruses, which is useful for distinguishing infectious viral agents from potential noninfectious viral particles or contaminants.

International audience; Bacteria of the Vibrio genus are the most predominant infectious agents threatening marine wildlife and aquaculture. Due to the large genetic diversity of these pathogens, the molecular determinants of Vibrio virulence are only poorly understood. Furthermore, studies tend to ignore co-evolutionary interactions between different host populations and their locally encountered Vibrio communities. Here, we explore the molecular targets of such co-evolutionary interactions by analyzing the genomes of nine Vibrio strains from the Splendidus-clade showing opposite virulence patterns towards two populations of Pacific oysters introduced into European Wadden Sea. By contrasting Vibrio phylogeny to their host specific virulence patterns, we could identify two core genome genes (OG1907 and OG 3159) that determine the genotype by genotype (G × G) interactions between oyster larvae and their sympatric Vibrio communities. Both genes show positive selection between locations targeting only few amino acid positions. Deletion of each gene led to a loss of the host specific virulence patterns while complementation with OG3159 alleles from both locations could recreate the wild type phenotypes matching the origin of the allele. This indicates that both genes can act as a genetic switch for Vibrio-oyster coevolution demonstrating that local adaptation in distinct Vibrio lineages can rely on only few genes independent of larger pathogenicity islands or plasmids.

Xylella fastidiosa is an economically important bacterial plant pathogen. With insights gained from 72 genomes, this study investigated differences among the three main subspecies, which have allopatric origins: X. fastidiosa subsp. fastidiosa, multiplex, and pauca. The origin of recombinogenic X. fastidiosa subsp. morus and sandyi was also assessed. The evolutionary rate of the 622 genes of the species core genome was estimated at the scale of an X. fastidiosa subsp. pauca subclade (7.62 × 10−7 substitutions per site per year), which was subsequently used to estimate divergence time for the subspecies and introduction events. The study characterized genes present in the accessory genome of each of the three subspecies and investigated the core genome to detect genes potentially under positive selection. Recombination is recognized to be the major driver of diversity in X. fastidiosa, potentially facilitating shifts to novel plant hosts. The relative effect of recombination in comparison to point mutation was calculated (r/m = 2.259). Evidence of recombination was uncovered in the core genome alignment; X. fastidiosa subsp. fastidiosa in the United States was less prone to recombination, with an average of 3.22 of the 622 core genes identified as recombining regions, whereas a specific clade of X. fastidiosa subsp. multiplex was found to have on average 9.60 recombining genes, 93.2% of which originated from X. fastidiosa subsp. fastidiosa. Interestingly, for X. fastidiosa subsp. morus, which was initially thought to be the outcome of genome-wide recombination between X. fastidiosa subsp. fastidiosa and X. fastidiosa subsp. multiplex, intersubspecies homologous recombination levels reached 15.30% in the core genome. Finally, there is evidence of X. fastidiosa subsp. pauca strains from citrus containing genetic elements acquired from strains infecting coffee plants as well as genetic elements from both X. fastidiosa subsp. fastidiosa and X. fastidiosa subsp. multiplex. In summary, our data provide new insights into the evolution and epidemiology of this plant pathogen. IMPORTANCEXylella fastidiosa is an important vector-borne plant pathogen. We used a set of 72 genomes that constitutes the largest assembled data set for this bacterial species so far to investigate genetic relationships and the impact of recombination on phylogenetic clades and to compare genome content at the subspecies level, and we used a molecular dating approach to infer the evolutionary rate of X. fastidiosa. The results demonstrate that recombination is important in shaping the genomes of X. fastidiosa and that each of the main subspecies is under different selective pressures. We hope insights from this study will improve our understanding of X. fastidiosa evolution and biology.

International audience; Human trypanosomoses are the sleeping sickness in Africa and Chagas disease in Latin America. However, atypical human infections by animal trypanosomes have been described, but poorly investigated. Among them, the supposed rat-specific T. lewisi was shown to be responsible for a few severe cases. In Africa, the scarcity of data and the null awareness about the atypical human trypanosomoses suggest that the number of cases may be higher that currently thought. Furthermore, T. lewisi is resistant to normal human serum and therefore a po-tential human pathogen. In order to document T. lewisi distribution and ecology, a qPCR- and 16DNA sequen-cing-based survey was conducted in 369 rodents from three urban districts of Cotonou city, Benin, during three different periods of the same year. Our study demonstrated very high prevalence (57.2%) even when considering only individuals identified as positive through DNA sequencing (39.2%). Black rats represented the most dominant as well as the most T. lewisi-parasitized species. No diffrence was retrieved neither between seasons nor districts, suggesting a large infestation of rodents by trypanosomes throughout the year and the city. Our results suggest that conditions are gathered for rat to human transmission of T. lewisi in these socio-en-vironmentally degraded urban areas, thus pointing towards the rapidly urbanizing Abidjan-Lagos corridor as a region at particular risk.

International audience; Among the emerging fungal diseases threatening food security, the Pseudocercospora fijiensis fungus causing black leaf streak disease of banana is one of the most marked examples of a recent worldwide pandemic on a major crop. We assessed how this pathogen spread throughout the latest invaded region, i.e. Central America and the Caribbean. We retraced its population history combining detailed monitoring information on disease outbreaks and population genetic analyses based on large-scale sampling of P. fijiensis isolates from 121 locations throughout the region. The results first suggested that sexual reproduction was not lost during the P. fijiensis expansion, even in the insular Caribbean context, and a high level of genotypic diversity was maintained in all the populations studied. The population genetic structure of P. fijiensis and historical data showed that two disease waves swept northward and southward in all banana-producing countries in the study area from an initial entry point in Honduras, probably mainly through gradual stepwise spore dispersal. Serial founder events accompanying the northern and southern waves led to the establishment of two different genetic groups. A different population structure was detected on the latest invaded islands (Martinique, Dominica and Guadeloupe), revealing multiple introductions and admixture events that may have been partly due to human activities. The results of this study highlight the need to step up surveillance to limit the spread of other known emerging diseases of banana spread mainly by humans, but also to curb gene flow between established pathogen populations which could increase their evolutionary potential.

Migratory waterfowl play an important role in the maintenance and spread of zoonotic diseases worldwide. An example is cercarial dermatitis, caused when larval stages of schistosomes that normally develop in birds penetrate human skin. Members of the genus Trichobilharzia (Schistosomatidae), transmitted mainly by ducks, are considered to be major etiological agents of cercarial dermatitis globally. To better understand the diversity and distribution of Trichobilharzia spp., we surveyed ducks from the United States, eastern Canada, Argentina, South Africa and New Zealand. To aid in species identification of the Trichobilharzia worms recovered, regions of the Cox1, ND4 and ITS1 were sequenced. Furthermore, we provide molecular phylogenetic evidence for the cosmopolitan distribution and trans-hemispheric gene flow for one species, Trichobilharzia querquedulae, previously thought to be restricted to North America. These new samples from endemic non-migratory duck species indicate that T. querquedulae transmission occurs within each of the regions we sampled and that it is specific to the blue-winged + silver teal duck clade. Prevalence within this host group is >95% across the known range of T. querquedulae, indicating that transmission is common. Genetic divergence is evenly distributed among continents, and no phylogenetic structure associated with geography was observed. The results provide strong support for the global distribution and transmission of T. querquedulae and represent, to our knowledge, the first report of a cosmopolitan schistosome confirmed by genetic data. These data are the first known to support trans-hemispheric genetic exchange in a species responsible for causing cercarial dermatitis, indicating that the epidemiology of this group of poorly known zoonotic parasites is more complex than previously expected. Fil: Ebbs, Erika T.. University of New Mexico; Estados Unidos Fil: Loker, Eric S.. University of New Mexico; Estados Unidos Fil: Davis, Norm E.. University of Otago; Nueva Zelanda Fil: Flores, Verónica Roxana. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Patagonia Norte. Instituto de Investigaciones en Biodiversidad y Medioambiente. Universidad Nacional del Comahue. Centro Regional Universidad Bariloche. Instituto de Investigaciones en Biodiversidad y Medioambiente; Argentina Fil: Veleizán, Aylén Anabella. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Patagonia Norte. Instituto de Investigaciones en Biodiversidad y Medioambiente. Universidad Nacional del Comahue. Centro Regional Universidad Bariloche. Instituto de Investigaciones en Biodiversidad y Medioambiente; Argentina Fil: Brant, Sara V.. University of New Mexico; Estados Unidos

Chikungunya virus (CHIKV) is an arthritogenic alphavirus that during the last decade has significantly expanded its geographical range and caused large outbreaks of human disease around the world. Although mortality rates associated with CHIKV outbreaks are low, acute and chronic illnesses caused by CHIKV represent a significant burden of disease largely affecting low and middle income countries. This report summarizes the current status of vaccine development for CHIKV.

Background : Rift Valley fever (RVF) is a fatal arthropod-borne zoonotic disease of livestock and humans. Since the identification of RVF in Kenya in the 1930s, repeated epizootics and epidemics coinciding with El Nino events have occurred in several locations in Africa and Saudi Arabia, causing mass deaths of livestock and humans. RVF is of great interest worldwide because of its negative effect on international livestock trade and its potential to spread globally. The latter is due to the increasing incidence of extreme climatic phenomena caused by global warming, as well as to the increase in global trade and international travel. How RVF is maintained and sustained between epidemics and epizootics is not clearly understood, but it has been speculated that wildlife reservoirs and trans-ovarian transmission in the vector may be important. Several studies have examined the role of wildlife and livestock in isolation or in a limited geographical location within the one country over a short time (usually less than a year). In this study, we examined the seroprevalence of anti-RVF antibodies in cattle and several wildlife species from several locations in Kenya over an inter-epidemic period spanning up to 7 years. Methods : A serological survey of immunoglobulin G (IgG) antibodies to RVF using competitive ELISA was undertaken on 297 serum samples from different wildlife species at various locations in Kenya. The samples were collected between 2008 and 2015. Serum was also collected in 2014 from 177 cattle from Ol Pejeta Conservancy; 113 of the cattle were in close contact with wildlife and the other 64 were kept separate from buffalo and large game by an electric fence. Results : The seroprevalence of RVF virus (RVFV) antibody was 11.6% in wildlife species during the study period. Cattle that could come in contact with wildlife and large game were all negative for RVFV. The seroprevalence was relatively high in elephants, rhinoceros, and buffalo, but there were no antibodies in zebras, baboons, vervet monkeys, or wildebeest. Conclusions : Diverse species in conservation areas are exposed to RVFV. RVFV exposure in buffalo may indicate distribution of the virus over wide geographical areas beyond known RVFV foci in Kenya. This finding calls for thorough studies on the epizootology of RVFV in specific wildlife species and locations. Keywords: inter-epidemic period; zoonosis; emerging disease; trans-boundary disease; cattle; one-health (Published: 15 December 2015) Citation: Infection Ecology and Epidemiology 2015, 5: 30106 - http://dx.doi.org/10.3402/iee.v5.30106

Eastern white pine is a crucial ecological and economic component of forests in the northern USA and eastern Canada, and is now facing an emerging problem in white pine needle damage (WPND). It is still unclear whether WPND results from one, or the combination of several fungal pathogens. Therefore, the first objective of this study was to characterize the fungi associated with WPND in the northeastern United States and document the damage being done to mature eastern white pine as a result of repeated defoliation. To date, 22 species of fungi, either cultured from diseased pine needles or formed fruiting bodies on pine needles were identified based on morphology and sequence data. Lecanosticta acicola and a putative new species of Septorioides were the species most frequently recovered from diseased needles, in addition to needle cast fungi Lophophacidium dooksii and Bifusella linearis, two obligate fungal pathogens that were frequently observed on pine needles in the northeast, but have not been known to cause excessive defoliation of eastern white pine. A second objective was to monitor yearly the health of 63 pairs of healthy and unhealthy trees in eight affected locations throughout New England. Since 2012, affected trees are increasingly and repeatedly chlorotic and defoliated every year. Trees that were initially healthy are now exhibiting symptoms. While L. acicola appears to be the primary pathogen causing WPND, several other common needle pathogens are being more frequently observed and the role of climate change may be important in the disease ecology of WPND. These defoliation events, while once a sporadic occurrence, have now become more frequent as observed in continued crown deterioration of eastern white pine in long-term monitoring plots followed during the course of this three-year study.

Emerging pests and diseases are a major threat to food production worldwide. In a recent survey, Tomato torrado virus (ToTV) was identified on tomato crops in the Limpopo province of South Africa and a first report of the disease was published. In this follow-up study, the full genome sequence of a tomato-infecting isolate of ToTV from South Africa was elucidated. High-throughput sequencing was used to generate the full genome of ToTV infecting tomato crops in South Africa. The longest contig obtained for the RNA-1 and RNA-2 genome of ToTV was comprised of 7420 and 5381 nucleotides (nt), respectively. Blast analysis of the RNA-1 sequence of ToTV from South Africa (ToT-186) matched 99% to a Spanish and Polish isolate, the RNA-2 segment of ToTV from South Africa (ToT-186) matched 99% to ToTV isolates from Italy and Poland, respectively. The information presented in this study will go a long way towards better understanding the emergence and spread of ToTV and devising sustainable management of ToTV diseases.

1AbstractMass mortalities of the larval stage of the giant freshwater prawn, Macrobrachium rosenbergii, have been occurring in Bangladesh since 2011. Mortalities can reach 100% and have resulted in an 80% decline in the number of hatcheries actively producing M. rosenbergii. To investigate a causative agent for the mortalities, a disease challenge was carried out using infected material from a hatchery experiencing mortalities. Moribund larvae from the challenge were prepared for metatranscriptomic sequencing. De novo virus assembly revealed a 29 kb single-stranded positive-sense RNA virus with similarities in key protein motif sequences to yellow head virus (YHV), an RNA virus that causes mass mortalities in marine shrimp aquaculture, and other viruses in the Nidovirales order. Primers were designed against the novel virus and used to screen cDNA from larvae sampled from hatcheries in the South of Bangladesh from two consecutive years. Larvae from all hatcheries screened from both years were positive by PCR for the novel virus, including larvae from a hatchery that at the point of sampling appeared healthy, but later experienced mortalities. These screens suggest that the virus is widespread in M. rosenbergii hatchery culture in southern Bangladesh, and that early detection of the virus can be achieved by PCR. The hypothesised protein motifs of MrGV suggest that it is likely to be a new species within the Nidovirales order. Biosecurity measures should be taken in order to mitigate global spread through the movement of post-larvae within and between countries, which has previously been linked to other virus outbreaks in crustacean aquaculture.

Lactococcosis is a hyperacute hemorrhagic septicemia disease caused by Lactococcus garvieae, which is an emerging pathogen in global fish farming. Between 2016 and 2018, rainbow trout (Oncorhynchus mykiss) from five farms that presented outbreaks were sampled as part of a Mexican surveillance program for the detection of fish diseases. Fourteen L. garvieae isolates were recovered from sampled fish, as confirmed by biochemical tests, 16S rRNA gene sequencing, and clinical and histological insights. The biochemical and protein profiles of the isolates obtained were homogeneous. Repetitive extragenic palindromic&mdash, (REP)&mdash, and enterobacterial repetitive intergenic consensus sequence PCR (ERIC-PCR) analyses established weak genetic heterogeneity. Rainbow trout challenged with two of the isolates used at different bacterial concentrations (10&minus, 2 and 10&minus, 4 CFU/mL) showed melanosis, and hemorrhages were observed in the fins, liver, kidney, and spleen. Isolates were obtained from all of the organs sampled, including from surviving fish, as either pure or mixed cultures. The present study is the first to confirm the presence of L. garvieae as the agent of severe lactococcosis outbreaks in the two primary Mexican states for trout farming.

Diffuse alveolar hemorrhage is a condition with high morbidity and mortality. The majority of cases are caused by pulmonary capillaritis associated with systemic vasculitis. Infection disease has also been associated with this condition. A 62-year-old woman with a history of chronic alcohol abuse presented with shortness of breath, hemoptysis, constipation, and icterus. Chest x-rays on admission showed diffuse patchy opacities concerning for diffuse alveolar hemorrhage. The patient quickly developed acute respiratory failure requiring intubation. PCR identified human metapneumovirus and bronchoalveolar lavage confirmed alveolar hemorrhage. Despite all efforts, the patient ultimately developed multi-organ failure and died. Human metapneumovirus is usually associated with mild upper and lower respiratory tract infections in young children. Nevertheless, clinicians should recognize that this virus has recently emerged as a significant pathogen, particularly in adult patients with underlying conditions and the elderly population.

In a world where climate change, vector expansion, human activity, and pathogen dispersal do not respect boundaries, the human–animal–pathogen interface has become less defined.Consequently, a One Health approach to disease surveillance and control has generated much interest across several disciplines. This systematic review evaluates current global research on the use of domestic dogs as sentinels for human infectious disease, and critically appraises how this may be applied within Canada. Results highlighted a bias in research from highandmiddle-income-economy countries, with 35% of the studies describing data from the Latin America/Caribbean region, 25% from North America, and 11% from the European/Central Asia region. Bacteria were the most studied type of infectious agent, followed by protozoa, viruses,helminths, and fungi. Only six out of 142 studies described disease in Canada: four researched a variety of pathogens within Indigenous communities, one researched Borrelia burgdorferi in British Columbia, and one researched arboviruses in Quebec. Results from this review suggest that dogscould provide excellent sentinels for certain infectious-disease pathogens in Canada, yet are currently overlooked. Further research into the use of dog-sentinel surveillance is specifically recommended forCalifornia serogroup viruses, Chikungunya virus,West Nile virus, Lyme borreliosis, Rickettsia spp., Ehrlichia spp., and Dirofilaria immitis.