Diverse Host Species Research Articles

Phylogenomic insights and geographic distribution of the New World genus Amphibolips Reinhard (Hymenoptera: Cynipidae, Cynipini) using ultraconserved elements

AbstractIn recent years, new wasp species and genera of Cynipidae have been described, and their species delimitation and evolutionary relationships have been supported using molecular markers. However, few studies have included comprehensive and extensive sampling of specimens across the complete distribution of a single genus. In this study, we analysed the phylogenetic relationships of the genus Amphibolips throughout its range using ultraconserved elements (UCEs). We collected 520 adult wasps from 401 sites in various geographic locations, predominantly in Mexico, and used 78 wasps for UCE analysis. Our results demonstrate that Amphibolips forms a monophyletic clade. Amphibolips can be further subdivided into four genetically well‐differentiated clades. Each clade had morphological traits that could be collectively characterised. Species delimitation using molecular sequencing highlights the taxonomic complexity involved in separating and assigning species using exclusively morphological criteria. This approach offers an opportunity to refine current morphological taxonomic criteria or propose new criteria to establish more accurate classifications. The rich diversity of host species and geographic regions in Mexico represents a biodiversity hotspot for Amphibolips. The number of undescribed species remains high. This study facilitates the determination of appropriate boundaries for putative new Amphibolips species.

Effectiveness of Diachasmimorpha longicaudata in Killing Ceratitis capitata Larvae Infesting Commercial Fruits in Dryland Agroecosystems of Western Argentina

Ceratitis capitata (Wiedemann) (medfly) strongly affects Argentinean fruit production and export. Augmentative biological control using the exotic parasitoid Diachasmimorpha longicaudata (Ashmead) is currently applied to this problem. The ability to find and parasitize medfly larvae on a wide diversity of fruit host species is a key issue that needs to be analyzed. This research assessed the effect of the physical features of fruit on the preference of foraging D. longicaudata females and the influence of varying release density on parasitoid performance as a pest mortality factor in three fruit species. Trials were performed inside field cages under semi-arid environmental conditions in Argentina’s central-western fruit-growing region. Sweet orange, peach, and fig were tested. The fruits were inoculated with third-instar larvae of the Vienna-8 temperature-sensitive lethal medfly strain. Naïve, 5 d-old mated D. longicaudata females were released in cages at 20, 40, 80, and 160 parasitoid densities. The highest levels of medfly mortality and parasitoid emergence were recorded in fig and peach, although D. longicaudata also induced mortality in orange, a fruit with few physical features favorable to parasitism. The medfly mortality in all fruit host species significantly increased with an increased number of parasitoid females released into the field cages. Diachsmimorpha longicaudata has high potential as a medfly biocontrol agent.

First Report of Haemaphysalis longicornis (Neumann) in Oklahoma, USA.

Haemaphysalis longicornis (Neumann), the Asian longhorned tick, is a species native to East Asia, but invasive to Australia, New Zealand, and most recently, the United States. It has spread rapidly across the eastern United States after being established in New Jersey in 2017. Aiding this rapid expansion is the ability of this tick to reproduce parthenogenically and feed on diverse host species. In cattle, this tick can cause heavy burdens and act as a vector for the pathogenic hemoprotozoan parasite Theileria orientalis, genotype Ikeda, creating economic losses that impact the cattle industry. Here, we report Asian longhorned ticks, collected from cattle, a dog, and pastures and morphologically identified at the Oklahoma Animal Disease Diagnostic Laboratory as H. longicornis before molecular confirmation through PCR amplification of the cox1 gene. Blood samples from infested cattle were collected and assessed molecularly for the presence of T. orientalis, with no pathogenic DNA detected. This report describes the first record of H. longicornis in Oklahoma and the farthest westward detection of this tick in the United States to date.

Parasite Abundance‐Occupancy Relationships Across Biogeographic Regions: Joint Effects of Niche Breadth, Host Availability and Climate

ABSTRACTAimChanging biodiversity and environmental conditions may allow multi‐host pathogens to spread among host species and affect prevalence. There are several widely acknowledged theories about mechanisms that may influence variation in pathogen prevalence, including the controversially debated dilution effect and abundance‐occupancy relationship hypotheses. Here, we explore such abundance‐occupancy relationships for unique lineages of three vector‐borne avian blood parasite genera (the avian malaria parasite Plasmodium and the related haemosporidian parasites Parahaemoproteus and Leucocytozoon) across biogeographical regions.LocationNearctic‐Neotropical and Palearctic‐Afrotropical regions.MethodsWe compiled a cross‐continental dataset of 17,116 bird individuals surveyed from 46 bird assemblages across the Nearctic‐Neotropical and Palearctic‐Afrotropical regions and explored relationships between local parasite lineage prevalence and host assemblage metrics in a Bayesian random regression framework.ResultsMost lineages from these three genera infected ≥ 5 host species and exhibited clear phylogenetic or functional host specificity. Lineage prevalence from all three genera increased with host range, but also with higher degrees of specialisation to phylogenetically or functionally related host species. Local avian community features were also found to be important drivers of prevalence. For example, bird species richness was positively correlated with lineage prevalence for Plasmodium and Leucocytozoon, whereas higher relative abundances of the main host species were associated with lower prevalence for Plasmodium and Parahaemoproteus but higher prevalence for Leucocytozoon.ConclusionsOur results broadly support several of the leading hypotheses about mechanisms that influence pathogen prevalence, including the niche breadth hypothesis in that higher avian host species diversity and broader host range amplify prevalence through increasing ecological opportunities and the trade‐off hypotheses in that specialisation among subsets of available host species may increase prevalence. Furthermore, the three studied avian haemosporidian genera exhibited different abundance‐occupancy relationships across the major global climate gradients and in relation to host availability, emphasising that these relationships do not strictly follow common rules for vector‐borne parasites with different life histories.

Diversity of Host Species and Optimized Cultivation Practices for Enhanced Bioactive Compound Production in Cordyceps militaris

Cordyceps militaris, recognized for its diverse and potent medicinal properties, plays a critical role in herbal medicine. This study investigates the genus Cordyceps, particularly focusing on C. militaris, a species widely utilized in East Asian traditional medicine for its therapeutic properties. C. militaris is rich in bioactive compounds, including cordycepin, adenosine, polysaccharides, ergosterol, and mannitol, which contribute to its broad physiological activities. The research aims to explore the diversity of host species in the cultivation of C. militaris and assess their impact on the biological activity and chemical composition of the fungus. The study highlights the variability in the efficacy of bioactive compounds due to different cultivation conditions and host species, emphasizing the need for standardized cultivation practices. Advances in genetic engineering and fermentation technology have significantly enhanced the production of these metabolites, supporting the sustainable scale-up of C. militaris cultivation. Future research should continue to explore the molecular mechanisms of its bioactive compounds, identify new clinical applications, and improve production efficiency and environmental sustainability. This comprehensive review provides insights for researchers, healthcare professionals, and cultivators on optimizing C. militaris for medicinal and commercial applications.

Climate influences the gut eukaryome of wild rodents in the Great Rift Valley of Jordan

BackgroundThe mammalian gut microbiome includes a community of eukaryotes with significant taxonomic and functional diversity termed the eukaryome. The molecular analysis of eukaryotic diversity in microbiomes of wild mammals is still in its early stages due to the recent emergence of interest in this field. This study aimed to fill this knowledge gap by collecting data on eukaryotic species found in the intestines of wild rodents. Because little is known about the influence of climate on the gut eukaryome, we compared the composition of the gut eukaryotes in two rodent species, Mus musculus domesticus and Acomys cahirinus, which inhabit a transect crossing a temperate and tropical zone on the Jordanian side of the Great Rift Valley (GRV).MethodsWe used high-throughput amplicon sequencing targeting the 18S rRNA gene in fecal samples from rodents to identify eukaryotic organisms, their relative abundance, and their potential for pathogenicity.ResultsNematodes and protozoa were the most prevalent species in the eukaryome communities, whereas fungi made up 6.5% of the total. Sixty percent of the eukaryotic ASVs belonged to taxa that included known pathogens. Eighty percent of the rodents were infected with pinworms, specifically Syphacia obvelata. Eukaryotic species diversity differed significantly between bioclimatic zones (p = 0.001). Nippostrongylus brasiliensis and Aspiculuris tetraptera were found to be present exclusively in the Sudanian zone rodents. This area has not reported any cases of Trichuris infections. Yet, Capillaria infestations were unique to the Mediterranean region, while Trichuris vulpis infestations were also prevalent in the Mediterranean and Irano-Turanian regions.ConclusionsThis study highlights the importance of considering host species diversity and environmental factors when studying eukaryome composition in wild mammals. These data will be valuable as a reference to eukaryome study.Graphical

North American crayfish harbour diverse members of the Nudiviridae

Three novel crayfish-infecting nudiviruses from crayfish in North America represent the first genomic confirmation of nudiviruses in crayfish: Faxonius propinquus nudivirus (FpNV), Faxonius rusticus nudivirus (FrNV), and Faxonius virilis nudivirus (FvNV). Histopathology and electron microscopy revealed nuclear infections, including nuclear hypertrophy in hepatopancreatic epithelial cells and the presence of membrane-bound bacilliform virions. Metagenomic sequencing resulted in complete circular genome assembly, and phylogenetic analyses (based on nudivirus core genes) placed these viruses within the unofficial Epsilonnudivirus genus. One of the nudiviruses was detected in the antennal gland of its host, and another is correlated with invasive crayfish decline in one infected lake ecosystem - suggesting a potential route for viral transmission through water, and possible population level impact. This study highlights the importance of genomic and ecological data in elucidating the diversity and evolutionary relationships of the Nudiviridae, while expanding their known diversity and range of host species.

Identifying life-history patterns along the fast-slow continuum of mammalian viral carriers.

Life-history traits have been identified as major indicators of mammals' susceptibility and exposure to viruses due to evolutionary constraints that link life-history speed with species' ecology and immunity. Nonetheless, it is unclear where along the fast-slow continuum of mammalian life-history lies the greatest diversity of host species. Consequently, life-history patterns that govern host-virus associations remain largely unknown. Here we analyse the virome of 1350 wild mammals and detect the characteristics that drive species' compatibility with different groups of viruses. We highlight that mammals with larger body size and either very rapid or very slow life histories are more likely to carry different groups of viruses, particularly zoonotic ones. While some common life-history patterns emerge across carriers, eco-evolutionary characteristics of viral groups appear to determine association with certain carrier species. Our findings underline the importance of incorporating both mammals' life-history information and viruses' ecological diversity into surveillance strategies to identify potential zoonotic carriers in wildlife.

A metagenomic investigation of the faecal RNA virome structure of asymptomatic chickens obtained from a commercial farm in Durban, KwaZulu-Natal province, South Africa

BackgroundVirome studies on birds, including chickens are relatively scarce, particularly from the African continent. Despite the continuous evolution of RNA viruses and severe losses recorded in poultry from seasonal viral outbreaks, the information on RNA virome composition is even scantier as a result of their highly unstable nature, genetic diversity, and difficulties associated with characterization. Also, information on factors that may modulate the occurrence of some viruses in birds is limited, particularly for domesticated birds. Viral metagenomics through advancements in sequencing technologies, has enabled the characterization of the entire virome of diverse host species using various samples.MethodsThe complex RNA viral constituents present in 27 faecal samples of asymptomatic chickens from a South African farm collected at 3-time points from two independent seasons were determined, and the impact of the chicken’s age and collection season on viral abundance and diversity was further investigated. The study utilized the non-invasive faecal sampling method, mRNA viral targeted enrichment steps, a whole transcriptome amplification strategy, Illumina sequencing, and bioinformatics tools.ResultsThe results obtained revealed a total of 48 viral species spanning across 11 orders, 15 families and 21 genera. Viral RNA families such as Coronaviridae, Picornaviridae, Reoviridae, Astroviridae, Caliciviridae, Picorbirnaviridae and Retroviridae were abundant, among which picornaviruses, demonstrated a 100% prevalence across the three age groups (2, 4 and 7 weeks) and two seasons (summer and winter) of the 27 faecal samples investigated. A further probe into the extent of variation between the different chicken groups investigated indicated that viral diversity and abundance were significantly influenced by age (P = 0.01099) and season (P = 0.00099) between chicken groups, while there was no effect on viral shedding within samples in a group (alpha diversity) for age (P = 0.146) and season (P = 0.242).ConclusionThe presence of an exceedingly varied chicken RNA virome, encompassing avian, mammalian, fungal, and dietary-associated viruses, underscores the complexities inherent in comprehending the causation, dynamics, and interspecies transmission of RNA viruses within the investigated chicken population. Hence, chickens, even in the absence of discernible symptoms, can harbour viruses that may exhibit opportunistic, commensal, or pathogenic characteristics.

Rapid host switching of Wolbachia and even more rapid turnover of their phages and incompatibility-causing loci.

About half of all insect species carry maternally inherited Wolbachia alphaproteobacteria, making Wolbachia the most common endosymbionts known in nature. Often Wolbachia spread to high frequencies within populations due to cytoplasmic incompatibility (CI), a Wolbachia-induced sperm modification caused by prophage-associated genes (cifs) that kill embryos without Wolbachia. Several Wolbachia variants also block viruses, including wMel from Drosophila melanogaster when transinfected into the mosquito Aedes aegypti. CI enables the establishment and stable maintenance of pathogen-blocking wMel in natural Ae. aegypti populations. These transinfections are reducing dengue disease incidence on multiple continents. While it has long been known that closely related Wolbachia occupy distantly related hosts, the timing of Wolbachia host switching and molecular evolution has not been widely quantified. We provide a new, conservative calibration for Wolbachia chronograms based on examples of co-divergence of Wolbachia and their insect hosts. Synthesizing publicly available and new genomic data, we use our calibration to demonstrate that wMel-like variants separated by only about 370,000 years have naturally colonized holometabolous dipteran and hymenopteran insects that diverged approximately 350 million years ago. Data from Wolbachia variants closely related to those currently dominant in D. melanogaster and D. simulans illustrate that cifs are rapidly acquired and lost among Wolbachia genomes, on a time scale of 104-105 years. This turnover occurs with and without the Wovirus prophages that contain them, with closely related cifs found in distantly related phages and distantly related cifs found in closely related phages. We present evidence for purifying selection on CI rescue function and on particular Cif protein domains. Our results quantify the tempo and mode of rapid host switching and horizontal gene transfer that underlie the spread and diversity of Wolbachia sampled from diverse host species. The wMel variants we highlight from hosts in different climates may offer new options for broadening Wolbachia-based biocontrol of diseases and pests.

"Isolation by Gentes with Asymmetric Migration" shapes the genetic structure of the common cuckoo in China.

Amid coevolutionary arms races between brood parasitic birds and their diverse host species, the formation of host-specific races, or gentes, has drawn significant research focus. Nevertheless, numerous questions about gentes evolutionary patterns persist. Here, we investigated the potential for gentes evolution across multiple common cuckoo (Cuculus canorus) populations parasitizing diverse host species in China. Using maternal (mitochondrial and W-linked DNA) and biparental (autosomal and Z-linked DNA) markers, we found consistent clustering of cuckoo gentes (rather than geographical populations) into distinct clades in matrilineal gene trees, indicating robust differentiation. In contrast, biparental markers indicated intermixing of all gentes, suggesting asymmetric gene flow regardless of geography. Unlike the mitonuclear discordance commonly resulting from incomplete lineage sorting, adaptive introgression, or demographic disparities, the observed pattern in brood parasitic cuckoos might reflect biased host preferences between sexes. We hereby present the "Isolation by Gentes with Asymmetric Migration" model. According to this model, the maternal line differentiation of the common cuckoo in China is potentially driven by host preferences in females, whereas males maintained the integrity of the cuckoo species through random mating. To achieve this, cuckoo males could perform flexible migration among gentes or engage in early copulation with females before reaching the breeding sites, allowing female cuckoos to store sperm from various gentes. Future studies collecting additional samples from diverse cuckoo gentes with overlapping distribution and investigating the migratory and copulation patterns of each sex would enhance our understanding of sex-biased differentiation among cuckoo populations in China.

Epidemiological update of cystic echinococcosis in livestock and assessment of practices related to its control in the Mediterranean area

Cystic echinococcosis (CE), caused by the tapeworm Echinococcus granulosus, is a zoonotic parasitic disease that still represents a serious threat to human and animal health worldwide. The Mediterranean basin is recognized as one of the major hotspots of CE due to several factors, including the presence of diverse intermediate host species as well as socio-economic and cultural conditions of local communities. This study aims to take a closer look at epidemiological data on CE in the Mediterranean area and assess the knowledge attitudes and practices of shepherds towards this disease in four countries (Algeria, Greece, Italy and Tunisia), highly endemic for CE, with the final goal of identifying highly endemic risk areas and practices in use which might potentially allow the persistence of E. granulosus infection in these areas. To update the epidemiological scenario of CE in Mediterranean areas, a comprehensive review of peer-reviewed literature on CE prevalence data published during the 2017–2023 period was carried out and, through a geographical information system (GIS), a map displaying the current CE distribution in the Mediterranean area was generated. In addition, a questionnaire survey was conducted through in-depth interviews of the farmers to collect information on their management system as well as knowledge attitudes and practices towards CE. From the farmer-participatory survey some risky practices emerged including the non-regular deworming of dogs or the use of ineffective drugs or dosing, as well as the provision of uncooked animal viscera to dogs. Finally, lower levels of knowledge and awareness of the disease was observed among farmers from North Africa compared with those of European countries. In conclusion, the results obtained highlight that CE is still a very serious problem in Mediterranean areas and increased efforts are needed to promote awareness among farmers and to turn research results into policy in order to reduce the spread of this disease, according to the One Health perspective.

Incredible Host Diversity and Regional Potential Distribution of an Oriental Parasitic Plant (Taxillus yadoriki)

This study investigates the host diversity and characteristics of the rare parasitic plant Silverberry-like taxillus (Taxillus yadoriki). Seogwipo, Jeju Island, where T. yadoriki grows naturally, was examined to clarify the diversity of host species, their location, and the part of the tree where T. yadoriki is attached. A total of 687 host trees were found. Taxillus yadoriki was intensively distributed in the lowlands below 200 m a.s.l. The host trees belonged to 40 species, four varieties, three cultivars, and two hybrids from 32 genera and 21 families, of which 23 taxa were identified as host plants for the first time in this study. Incredibly, this plant was found to be able to parasitize a variety of plants from 12 orders. Taxillus yadoriki was found to be parasitic in three orders of Gymnosperms, Ginkgoales, Cupressales, and Pinales, as well as nine orders of Angiosperms, including Magnoliales, Rosales, and Ericales. Rosaceae was the most diverse at 18.0%, and most species were broad-leaved and arboreal. Among them, Cryptomeria japonica and Litsea japonica had the highest frequency of parasitization and T. yadoriki was mainly attached to the upper part of the main tree and the main branch; as a result, T. yadoriki was distributed and showed specificity in the position of disturbance on the host. T. yadoriki’s specific distribution model was built as a Maxent program. The area under the curve of the receiver operation characteristic was 0.948 ± 0.026 (mean ± standard deviation), and the performance of the constructed model was excellent. Of the total eight environmental factors, density of artistic forest and meant temperature of coldest quarter accounted for 75.3% of the total importance, which was the main distribution determinant of species. In the average distribution probability map of T. yadoriki, the critical probability for determining distribution was calculated to be 0.2898 ± 0.1018. Accordingly, the distribution of species is predicted to expand from Jeju Island to the entire southern and southeastern coasts.

Host Plant Modulated Physio-Biochemical Process Enhances Adaptive Response of Sandalwood (Santalum album L.) under Salinity Stress.

Salinity is one of the most significant abiotic stress that affects the growth and development of high-value tree species, including sandalwood, which can also be managed effectively on saline soils with the help of suitable host species. Therefore, the current investigation was conducted to understand the physiological processes and antioxidant mechanisms in sandalwood along the different salinity gradients to explore the host species that could support sandalwood growth in salt-affected agro-ecosystems. Sandalwood seedlings were grown with ten diverse host species with saline water irrigation gradients (ECiw~3, 6, and 9 dS m-1) and control (ECiw~0.82 dS m-1). Experimental findings indicate a decline in the chlorophyll content (13-33%), relative water content (3-23%), photosynthetic (27-61%) and transpiration rate (23-66%), water and osmotic potential (up to 137%), and ion dynamics (up to 61%) with increasing salinity levels. Conversely, the carotenoid content (23-43%), antioxidant activity (up to 285%), and membrane injury (82-205%) were enhanced with increasing salinity stress. Specifically, among the hosts, Dalbergia sissoo and Melia dubia showed a minimum reduction in chlorophyll content, relative water content, and plant water relation and gas exchange parameters of sandalwood plants. Surprisingly, most of the host tree species maintained K+/Na+ of sandalwood up to moderate water salinity of ECiw~6 dS m-1; however, a further increase in water salinity decreased the K+/Na+ ratio of sandalwood by many-fold. Salinity stress also enhanced the antioxidative enzyme activity, although the maximum increase was noted with host plants M. dubia, followed by D. sissoo and Azadirachta indica. Overall, the investigation concluded that sandalwood with the host D. sissoo can be successfully grown in nurseries using saline irrigation water and, with the host M. dubia, it can be grown using good quality irrigation water.

Identity, Pathogenicity, and Genetic Diversity of Lasiodiplodia Species Associated with Stem-End Rot of Avocado in China.

Stem-end rot (SER) causes brown necrotic lesions in the pulp near the base of the fruit pedicel and is one of the most devastating postharvest diseases of avocados in all avocado-growing regions of the world. China's avocado industry is growing very rapidly, and the planting area is expanding, but little is known about the pathogens and genetic diversity of avocado SER. To determine the causal agents of SER, avocado fruits were sampled from the main avocado-producing areas in China during 2020 and 2021. Fungal isolates were obtained from SER symptomatic avocado fruits and identified by morphology combined with phylogenetic analysis of internal transcribed spacer (ITS), translation elongation factor 1-α (EF1-α), and β-tubulin (TUB2) gene sequences. All 101 isolates belonged to Lasiodiplodia spp.; four Lasiodiplodia species were identified, namely, L. pseudotheobromae (59.41%), L. theobromae (24.75%), L. mahajangana (7.92%), and L. euphorbiaceicola (1.98%); and six others are classified as Lasiodiplodia sp. (5.94%). There were only slight morphological differences in colonies and conidia of these four species of Lasiodiplodia. The pathogenicity tests showed symptoms of SER, and 92.08% of the isolates exhibited a high level of virulence on avocado (disease index >70), related to the disease severity on avocado fruits. All tested isolates grew well under the temperature ranging from 23 to 33°C. There was a significant difference in mycelial growth between the four species of Lasiodiplodia after treatment with high or low temperatures. The growth of L. pseudotheobromae was the fastest at 13 to 18°C but was the lowest at 38°C (P < 0.05). The red pigment could be produced by all tested isolates after culturing for 7 days at 38°C. The mycelial growth rate was the fastest on PDA medium, and the slowest on the OMA medium but promoted spore formation (P < 0.05). In addition, the genetic diversity of pathogenic Lasiodiplodia species associated with SER collected from avocado, mango, guava, and soursop fruits was determined. A total of 74 isolates were clustered into four main ISSR groups by the unweighted pair-group method with arithmetic mean analysis, and the classification of this group was related to the host. Extensive diversity was detected in the Lasiodiplodia populations. The diverse geographical origins and host species significantly influenced the population differentiation, and most of the genetic variation occurred within populations (P < 0.001). This is the first study to identify the major pathogens of avocado SER in China, survey their occurrence and pathogenicity, and include a comparative analysis of genetic diversity with Lasiodiplodia spp. causing SER on other fruit hosts. Collectively, the Lasiodiplodia species complex affecting avocado showed high pathogenicity and diversity, while L. pseudotheobromae was the most frequently isolated species in China. The results of this study provide insights into the aspects of the epidemic of SER disease caused by Lasiodiplodia species, which will help in developing strategies for the management and control of SER in avocado.

Global transmission of extended-spectrum cephalosporin resistance in Escherichia coli driven by epidemic plasmids

Extended-spectrum cephalosporins (ESCs) are third and fourth generation cephalosporin antimicrobials used in humans and animals to treat infections due to multidrug-resistant (MDR) bacteria. Resistance to ESCs (ESC-R) in Enterobacterales is predominantly due to the production of extended-spectrum β-lactamases (ESBLs) and plasmid-mediated AmpC β-lactamases (AmpCs). The dynamics of ESBLs and AmpCs are changing across countries and host species, the result of global transmission of ESC-R genes. Plasmids are known to play a key role in this dissemination, but the relative importance of different types of plasmids is not fully understood. In this study, Escherichia coli with the major ESC-R genes blaCTX-M-1, blaCTX-M-15, blaCTX-M-14 (ESBLs) and blaCMY-2 (AmpC), were selected from diverse host species and other sources across Canada, France and Germany, collected between 2003 and 2017. To examine in detail the vehicles of transmission of the ESC-R genes, long- and short-read sequences were generated to obtain complete contiguous chromosome and plasmid sequences (n=192 ESC-R E.coli). The types, gene composition and genetic relatedness of these plasmids were investigated, along with association with isolate year, source and geographical origin, and put in context with publicly available plasmid sequences. We identified five epidemic resistance plasmid subtypes with distinct genetic properties that are associated with the global dissemination of ESC-R genes across multiple E.coli lineages and host species. The IncI1 pST3 blaCTX-M-1 plasmid subtype was found in more diverse sources than the other main plasmid subtypes, whereas IncI1 pST12 blaCMY-2 was more frequent in Canadian and German human and chicken isolates. Clonal expansion also contributed to the dissemination of the IncI1 pST12 blaCMY-2 plasmid in ST131 and ST117 E.coli harbouring this plasmid. The IncI1 pST2 blaCMY-2 subtype was predominant in isolates from humans in France, while the IncF F31:A4:B1 blaCTX-M-15 and F2:A-:B- blaCTX-M-14 plasmid subtypes were frequent in human and cattle isolates across multiple countries. Beyond their epidemic nature with respect to ESC-R genes, in our collection almost all IncI1 pST3 blaCTX-M-1 and IncF F31:A4:B1 blaCTX-M-15 epidemic plasmids also carried multiple antimicrobial resistance (AMR) genes conferring resistance to other antimicrobial classes. Finally, we found genetic signatures in the regions surrounding specific ESC-R genes, identifying the predominant mechanisms of ESC-R gene movement, and using publicly available databases, we identified these epidemic plasmids from widespread bacterial species, host species, countries and continents. We provide evidence that epidemic resistance plasmid subtypes contribute to the global dissemination of ESC-R genes, and in addition, some of these epidemic plasmids confer resistance to multiple other antimicrobial classes. The success of these plasmids suggests that they may have a fitness advantage over other plasmid types and subtypes. Identification and understanding of the vehicles of AMR transmission are crucial to develop and target strategies and interventions to reduce the spread of AMR. This project was supported by the Joint Programming Initiative on Antimicrobial Resistance (JPIAMR), through the Medical Research Council (MRC, MR/R000948/1), the Canadian Institutes of Health Research (CFC-150770), and the Genomics Research and Development Initiative (Government of Canada), the German Federal Ministry of Education and Research (BMBF) grant no. 01KI1709, the French Agency for food environmental and occupational health & safety (Anses), and the French National Reference Center (CNR) for antimicrobial resistance. Support was also provided by the Biotechnology and Biological Sciences Research Council (BBSRC) through the BBSRC Institute Strategic Programme Microbes in the Food ChainBB/R012504/1 and its constituent project BBS/E/F/000PR10348 (Theme 1, Epidemiology and Evolution of Pathogens in the Food Chain).

Metarhizium dianzhongense sp. nov. and New Record of M. bibionidarum (Clavicipitaceae, Hyocreales) Attacking Insects from China

The genus Metarhizium is one of the most significant entomopathogenic fungi with diverse morphological characteristics and host species. Species of Metarhizium have been widely used for pest control as an environmentally safe alternative to chemical pesticides. This study reports a new species of Metarhizium and a new record of M. bibionidarum from China. The taxonomic positions of the two species within Metarhizium were assessed by morphological and multi-gene phylogenetic data. This assessment confirmed that the new species M. dianzhongense on white grubs (Coleoptera) is a sister to M. ellipsoideum on adult leafhoppers (Hemiptera) and represents a distinctive fungus according to the morphological and phylogenetic evidence. The two species, M. dianzhongense and M. bibionidarum, were described and illustrated. Pathogenicity tests by M. bibionidarum and M. dianzhongense were performed on early instar larvae of the significant agricultural pest Spodoptera frugipera (Lepidoptera). The results demonstrated that both M. bibionidarum and M. dianzhongense exhibit significant insecticidal activity against larvae of S. frugipera, providing new fungal resources for the development of an eco-friendly biocontrol agent against this pest.

Unveiling the impacts of land use on the phylogeography of zoonotic New World Hantaviruses

Billions of genomic sequences and records of species occurrence are available in public repositories (e.g. National Center for Biotechnology Information, NCBI and the Global Biodiversity Information Facility, GBIF). By implementing analytical tools from different scientific disciplines, data mining these databases can aid in the global surveillance of zoonotic pathogens that circulate among wildlife. We illustrate this by investigating the Hantavirus–rodent system in the Americas, i.e. New World Hantaviruses (NWH). First, we considered the circulation of pathogenic NWH among Cricetidae rodents, by inferring the phylogenetic links among 277 genomic samples of the S segment (N protein) of NWH found in 55 species. Second, we used machine learning to assess the impact of land use on the probability of presence of the rodent species linked with reservoirs of pathogenic Hantaviruses. Our results show that hosts are widely present across the Americas. Some hosts are present in the primary forest and agricultural land, but not in the secondary forest, whereas other hosts are present in secondary forest and agricultural land. The diversity of host species allows Hantavirus to circulate in a wide spectrum of habitats, in particular rural rather than urban. We highlight that public repositories of genomic data and species occurrence are very useful resources for monitoring potential enzootic transmission and spillover of zoonotic viruses in relation with the changes that humans produce in the biosphere.

Morphological and molecular characterisation of Cymothoa eremita (Brunnich, 1783) (Isopoda: Cymothoidae) from the South China Sea

A morphological description and molecular characterisation of the parasitic isopod Cymothoa eremita Brünnich, 1783, collected off the fish host Nemipterus furcosus (Valenciennes, 1830) from the South China Sea, is presented here. Since most cymothoid descriptions are primarily based on females, this paper highlights the morphological characteristics from 20 ovigerous female and 20 male C. eremita cymothoids, isolated from 300 fish individuals. Furthermore, our findings indicated significant variations in the morphological features of C. eremita, including: 1) average length and width dimensions, 2) the presence or absence of eyes, 3) the length of pleotelson, 4) the configuration of its posterior and lateral margins, and 5) the structure of the cephalon. These characteristics were compared among diverse fish host species reported in different geographical regions. Twenty one of 300 N. furcosus were infested with C. eremita, with a prevalence of 7%, and mean intensity of 1.9 (two cymothoids per individual fish) respectively. A total of 687 base pairs (bp) from the mitochondrial cytochrome oxidase subunit I (COI) gene were sequenced for C. eremita as a complementary measure to the morphological analysis undertaken in this study. These sequences were utilized to reconstruct a phylogenetic tree, incorporating our sequenced specimens and relevant sequences sourced from the GenBank database. The Maximum Likelihood (ML) phylogenetic tree comprised 45 cymothoid species, with partial COI gene sequences showing monophyletic clustering of most species within the same genus, which is in congruence with their morphological divergence. Continued efforts to conduct studies on the biology, taxonomy, ecology and genetics of both cymothoid and fish host are crucial to better understand the patterns of host-parasite specificity and co-evolutionary changes, which may indirectly contribute towards cymothoid speciation and diversification.

Phylogenetically evolutionary analysis provides insights into the genetic diversity and adaptive evolution of porcine deltacoronavirus

BackgroundPorcine deltacoronavirus (PDCoV) is one of the emerging swine enteric coronaviruses (SECoVs), which has been widely prevalent in the North America and Asia. In addition to causing severe diarrhea in piglets, PDCoV also shows the potential to infect diverse host species, including calves, chickens, turkey poults, and humans. However, the clinical pathogenicity and genetic evolution of PDCoV is still not fully understood.ResultsHere, we recorded an outbreak of a novel recombinant PDCoV strain (CHN-HeN06-2022) in a large nursery fattening pig farm. Genomic analysis showed that the CHN-HeN06-2022 strain shared 98.3-98.7% sequence identities with the Chinese and American reference strains. To clarify the evolutionary relationships, phylogenetic analysis was performed using the PDCoV genome sequences available in the GenBank database. Based on genetic distance and geographical distribution, the phylogenetic tree clearly showed that all the PDCoV sequences could be divided into lineage 1 and lineage 2, which were further classified into sublineage 1.1 (Chinese strains), 1.2 (the North American strains), 2.1 (the Southeast Asian strains), and 2.2 (Chinese strains). Corresponding to the evolutionary tree, we found that, compared to lineage 1, lineage 2 strains usually contain a continuous 6-nt deletion in Nsp2 and a 9-nt deletion in Nsp3, respectively. Furthermore, recombination analysis suggested that the CHN-HeN06-2022 occurred segments exchange crossed Nsp2 and Nsp3 region between sublineage 1.1 and sublineage 2.1. Combined with previously reported recombinant strains, the highest recombination frequency occurred in Nsp2, Nsp3, and S gene. Additionally, we identified a total of 14 amino acid sites under positive selection in spike protein, most of which are located in the regions related with the viral attachment, receptor binding, and membrane fusion.ConclusionsTaken together, our studies provide novel insights into the genetic diversity and adaptive evolution of PDCoV. It would be helpful to the development of vaccine and potential antiviral agent.