Comparative genomics of Nocardia seriolae reveals recent importation and subsequent widespread dissemination in mariculture farms in South Central Coast, Vietnam

Between 2010 and 2015, nocardiosis outbreaks caused by Nocardia seriolae affected many permit farms throughout Vietnam, causing mass fish mortalities. To understand the biology, origin, and epidemiology of these outbreaks, 20 N. seriolae strains collected from farms in four provinces in the South-Central Coast of Vietnam, along with two Taiwanese strains, were analysed using genetics and genomics. Pulsed-field gel electrophoresis identified a single cluster amongst all Vietnamese strains that was distinct from the Taiwanese strains. Like the PFGE findings, phylogenomic and single-nucleotide polymorphism (SNP) genotyping analyses revealed that all Vietnamese N. seriolae strains belonged to a single, unique clade. Strains fell into two subclades that differed by 103 SNPs, with almost no diversity within clades (0-2 SNPs). There was no association between geographic origin and subclade placement, suggesting frequent N. seriolae transmission between Vietnamese mariculture facilities during the outbreaks. Vietnamese strains shared a common ancestor with strains from Japan and China, with the closest strain, UTF1 from Japan, differing by just 217 SNPs from the Vietnamese ancestral node. Draft Vietnamese genomes range from 7.55-7.96 Mbp in size, have an average G+C content of 68.2%, and encode 7,602-7,958 predicted genes. Several putative virulence factors were identified, including genes associated with host cell adhesion, invasion, intracellular survival, antibiotic and toxic compound resistance, and haemolysin biosynthesis. Our findings provide important new insights into N. seriolae epidemiology and pathogenicity and will aid future vaccine development and disease management strategies, with the ultimate goal of nocardiosis-free aquaculture.

Contribution to Chaetosphaeriaceae—Kionochaeta setosimplicia sp. nov. from Thailand

Species of Kionochaeta are saprobes commonly associated with decaying plant materials. As a part of surveys on freshwater microfungi, Kionochaeta-like taxon was found on a submerged decaying twig at a rivulet in the protected forest area of Khao Kheow Open Zoo (KKOZ), eastern Thailand. This taxon is microscopically similar to Kionochaeta, but clearly differs by its accessory lateral setiform branches and sterile setae arising beside the conidiophores. Multi-locus phylogenies inferred from four combined loci (SSU, ITS, LSU and RPB2) demonstrated that this taxon clustered as a unique clade with Kionochaeta species (Chaetosphaeriaceae, Chaetosphaeriales). Therefore, we introduce this taxon as K. setosimplicia, and it is phylogenetically close to K. castaneae, K. ramifera and K. pughii. Kionochaeta setosimplicia is separated from K. microspora and K. spissa. In Kionochaeta clade 1, K. nanophora forms a basal taxon. Kionochaeta ivoriensis forms a distinct Kionochaeta clade 2 distant from other Kionochaeta.

New species in Aciculosporium, Shimizuomyces and a new genus Morakotia associated with plants in Clavicipitaceae from Thailand

Three new fungal species in the Clavicipitaceae (Hypocreales, Ascomycota) associated with plants were collected in Thailand. Morphological characterisation and phylogenetic analyses based on multi-locus sequences of LSU, RPB1 and TEF1 showed that two species belong to Aciculosporium and Shimizuomyces. Morakotia occupies a unique clade and is proposed as a novel genus in Clavicipitaceae. Shimizuomyces cinereus and Morakotia fusca share the morphological characteristic of having cylindrical to clavate stromata arising from seeds. Aciculosporium siamense produces perithecial plates and occurs on a leaf sheath of an unknown panicoid grass.

Polyphasic reassessment of a yellow rice fungus, Penicillium toxicarium

From historical strain records, Penicillium citreonigrum NBRC 4692 was originally isolated as the toxigenic fungus responsible for the yellow rice incident in Japan in 1937. The fungus was named Penicillium toxicarium by I. Miyake, which was considered invalid due to the lack of a Latin diagnosis. Initially, it was named Penicillium sp. by Miyake et al. in 1940. Subsequently, P. toxicarium, which was erroneously cited as synonym of P. citreo-viride, was validated by C. Ramírez in 1982 with a Latin diagnosis and type designation (CBS 351.51). Later, CBS 351.51 was assigned to Penicillium trzebinskii by Houbraken et al. in 2014. In 2016, P. toxicarium was treated as a synonym of Penicillium citreosulfuratum based on a conclusion of molecular phylogenetic analysis. Recently, we discovered the taxonomic and nomenclatural short communication (in Japanese) by I. Miyake in 1947 on P. toxicarium sp. nov. with its Latin description and four illustrations but lacking the type designation. In this paper, we re-examined strain NBRC 4692 for its current taxonomic position based on morphological characteristics and molecular phylogenetic analysis. NBRC 4692 (received from I. Miyake in 1951) has been found to have the same morphological characteristics as P. toxicarium, as was shown in Miyake's diagnosis in 1947. Phylogenetic analysis revealed that the NBRC strain belongs to a unique clade, different from the clade comprising P. citreosulfuratum strains. As a conclusion, herein, P. toxicarium I. Miyake (1947) is reinstated as a correct name with the lectotype designation.

A unique clade of light-driven proton-pumping rhodopsins evolved in the cyanobacterial lineage

Microbial rhodopsin is a photoreceptor protein found in various bacteria and archaea, and it is considered to be a light-utilization device unique to heterotrophs. Recent studies have shown that several cyanobacterial genomes also include genes that encode rhodopsins, indicating that these auxiliary light-utilizing proteins may have evolved within photoautotroph lineages. To explore this possibility, we performed a large-scale genomic survey to clarify the distribution of rhodopsin and its phylogeny. Our surveys revealed a novel rhodopsin clade, cyanorhodopsin (CyR), that is unique to cyanobacteria. Genomic analysis revealed that rhodopsin genes show a habitat-biased distribution in cyanobacterial taxa, and that the CyR clade is composed exclusively of non-marine cyanobacterial strains. Functional analysis using a heterologous expression system revealed that CyRs function as light-driven outward H+ pumps. Examination of the photochemical properties and crystal structure (2.65 Å resolution) of a representative CyR protein, N2098R from Calothrix sp. NIES-2098, revealed that the structure of the protein is very similar to that of other rhodopsins such as bacteriorhodopsin, but that its retinal configuration and spectroscopic characteristics (absorption maximum and photocycle) are distinct from those of bacteriorhodopsin. These results suggest that the CyR clade proteins evolved together with chlorophyll-based photosynthesis systems and may have been optimized for the cyanobacterial environment.

Scent of Jasmine Attracts Alien Invaders and Records on Citizen Science Platforms: Multiple Introductions of the Invasive Lacebug Corythauma ayyari (Drake, 1933) (Heteroptera: Tingidae) in Italy and the Mediterranean Basin

The jasmine lacebug Corythauma ayyari is a pest of cultivated and ornamental plants mainly associated to Jasminum spp. This invasive insect is native to Asia, and it has been recently introduced in several countries, mainly within the Mediterranean basin. Here, we updated the known distribution of this species, including five new Italian regions (Liguria, Tuscany, Latium, Apulia, and Calabria); Salamis Island in Greece, and the Occitanie region in France. Citizen-science data have significantly contributed to the knowledge on species distribution, and the online platform for sharing biodiversity information can represent an effective tool for the early detection. Molecular analyses revealed that the specimens collected in Peninsular Italy and Sicily belong to a unique clade, suggesting the possibility of a single introduction, whereas those from Menton (France) and Calabria (Southern Italy) are separated from the others and probably originate from separated introductions.

Hospital outbreak of carbapenem-resistant Enterobacteriales associated with an OXA-48 plasmid carried mostly by Escherichia coli ST399

A hospital outbreak of carbapenem-resistant Enterobacteriales was detected by routine surveillance. Whole genome sequencing and subsequent analysis revealed a conserved promiscuous OXA-48 carrying plasmid as the defining factor within this outbreak. Four different species of Enterobacteriales were involved in the outbreak. Escherichia coli ST399 accounted for 20/55 of all the isolates. Comparative genomics with publicly available E. coli ST399 sequence data showed that the outbreak isolates formed a unique clade. The OXA-48 plasmid identified in the outbreak differed from other known plasmids by an estimated five homologous recombination events. We estimated a lower bound to the plasmid conjugation rate to be 0.23 conjugation events per lineage per year. Our analysis suggests co-evolution between the plasmid and its main bacterial host to be a key driver of the outbreak. This is the first study to report carbapenem-resistant E. coli ST399 carrying OXA48 as the main cause of a plasmid-borne outbreak within a hospital setting. This study supports complementary roles for both plasmid conjugation and clonal expansion in the emergence of this outbreak.

Penicillium diversity in Canadian bat caves, including a new species, P. speluncae

Penicillium species were commonly isolated during a fungal survey of bat hibernacula in New Brunswick and Quebec, Canada. Strains were isolated from arthropods, bats, rodents (i.e. the deer mouse Peromyscus maniculatus), their dung, and cave walls. Hundreds of fungal strains were recovered, of which Penicillium represented a major component of the community. Penicillium strains were grouped by colony characters on Blakeslee's malt extract agar. DNA sequencing of the secondary identification marker, beta-tubulin, was done for representative strains from each group. In some cases, ITS and calmodulin were sequenced to confirm identifications. In total, 13 species were identified, while eight strains consistently resolved into a unique clade with P. discolor, P. echinulatum and P. solitum as its closest relatives. Penicillium speluncae is described using macroand micromorphological characters, multigene phylogenies (including ITS, beta-tubulin, calmodulin and RNA polymerase II second largest subunit) and extrolite profiles. Major extrolites produced by the new species include cyclopenins, viridicatins, chaetoglobosins, and a microheterogenous series of cyclic and linear tetrapeptides.

Summer Outbreak of Severe RSV-B Disease, Minnesota, 2017 Associated with Emergence of a Genetically Distinct Viral Lineage

Background Respiratory syncytial virus (RSV) typically causes winter outbreaks in temperate climates. During summer 2017, the Minnesota Department of Health received a report of increased cases of severe RSV-B infection. Methods We compared characteristics of summer 2017 cases with those of 2014–2018 summers. To understand the genetic relatedness among viruses, we performed high-throughput sequencing of RSV from patients with a spectrum of illness from sites in Minnesota and Wisconsin. Results From May to September 2017, 58 RSV cases (43 RSV-B) were reported compared to 20–29 cases (3–7 RSV-B) during these months in other years. Median age and frequency of comorbidities were similar, but 55% (24/43) were admitted to the ICU in 2017 compared to 12% in preceding 3 years (odds ratio, 4.84, P < .01). Sequencing was performed on 137 specimens from March 2016 to March 2018. Outbreak cases formed a unique clade sharing a single conserved nonsynonymous change in the SH gene. We observed increased cases during the following winter season, when the new lineage was the predominant strain. Conclusions We identified an outbreak of severe RSV-B disease associated with a new genetic lineage among urban Minnesota children during a time of expected low RSV circulation.

A new genus and species of pinworm (Nematoda, Oxyuridae) from the gray mouse opossum, Tlacuatzin canescens

Tlacuatzoxyuris simpsoni n. gen. n. sp. is described from the cecum of the gray opossum, Tlacuatzin canescens, a species endemic to the deciduous dry forest of Mexico. The digestive tracts of four specimens were examined for parasites; three of these were archived in the American Museum of Natural History and one was a live capture. Relative to the other four monotypic genera of pinworms known to infect opossums, the new genus is diagnosed on the basis of a round cephalic plate with a semicircular stoma surrounded by a rim. In addition, males feature a prominent cephalic vesicle not fully developed in females, accounting for sexual dimorphism. The new species includes small worms that feature a conspicuous, not reticulated cephalic vesicle and semicircular stoma and lateral alae with two crests. In addition, the postcloacal cuticle of males features a small area with ornamentation between cloaca and submedial papillae. Finally, both spicule and gubernaculum are relatively short. Although the eggs of Tlacuatzoxyuris n. gen. are unknown, the conspicuous differences in traits used in the diagnosis of genera prompted us to propose a new genus for the new species. This is the first species of Oxyuridae reported in mouse opossums outside South America, and the fifth species of the family occurring in didelphimorph marsupials. This is an example of the usefulness of documenting the diversity of parasites associated with this unique clade of mammals through the examination of preserved tissues.