A first insight into the genome of Prototheca wickerhamii, a major causative agent of human protothecosis

The synthetic future of algal genomes

Algae are diverse organisms with significant biotechnological potential for resource circularity. Taking inspiration from fermentative microbes, engineering algal genomes holds promise to broadly expand their application ranges. Advances in genome sequencing with improvements in DNA synthesis and delivery techniques are enabling customized molecular tool development to confer advanced traits to algae. Efforts to redesign and rebuild entire genomes to create fit-for-purpose organisms currently being explored in heterotrophic prokaryotes and eukaryotic microbes could also be applied to photosynthetic algae. Future algal genome engineering will enhance yields of native products and permit the expression of complex biochemical pathways to produce novel metabolites from sustainable inputs. We present a historical perspective on advances in engineering algae, discuss the requisite genetic traits to enable algal genome optimization, take inspiration from whole-genome engineering efforts in other microbes for algal systems, and present candidate algal species in the context of these engineering goals.

Integration of transcriptomics, proteomics, and metabolomics data for the detection of the human pathogenic Prototheca wickerhamii from a One Health perspective

Prototheca species are the only microalgae known to cause opportunistic infections in vertebrates and humans. Most cases of protothecosis in humans are caused by Prototheca wickerhamii, but knowledge of the pathogenicity and biology of Prototheca is limited. Globally, the diagnostic rate of Prototheca species infection is much lower than the actual rate of P. wickerhamii. The precise mechanisms underlying the pathogenesis of Prototheca infections remain unclear. In this study, we identified a strain of P. wickerhamii with atypical colony morphology. To reveal the morphological differences between P. wickerhamii S1 (mucous) and the molecular basis of its pathogenicity, the transcriptomics, proteomics, and metabolomics of two pathogenic P. wickerhamii strains and one environmental strain were analysed. Interestingly, mannan endo-1,4-β-mannosidase was significantly downregulated in P. wickerhamii S1, which contributes to a thinner cell wall in S1 compared to strains with typical colony morphology, and the toxicity of macrophages is reduced. Metabolite analysis revealed that the mucoid appearance of P. wickerhamii S1 may have been caused by an increase in linoleic acid, glycerol, and other metabolites. There is still a need to better understand the ecology, aetiology, and pathogenesis of P. wickerhamii, and in particular, its transmission between humans, animals, and the environment, from a One Health perspective.

Drug Susceptibility Profiling of Prototheca Species Isolated from Cases of Human Protothecosis

Prototheca are unicellular, achlorophyllous, yeast-like microalgae that occur in a wide range of natural habitats. At least five species have been implicated as the causative agents of opportunistic infections of men. Human protothecosis typically manifests as cutaneous, articular, or systemic disease. Treatment is largely empirical with poorly predictable and often unsuccessful outcomes. This is largely due to the frequently observed resistance of Prototheca species to conventional antimicrobial agents. This work is the first to perform drug susceptibility profiling exclusively on isolates from human cases of protothecosis. A total of 23 such isolates were tested against amphotericin B and 9 azoles, including efinaconazole and luliconazole, whose activities against Prototheca have never been studied before. Efinaconazole was the most active, with median minimum inhibitory concentration (MIC) and minimum algicidal concentration (MAC) values of 0.031 mg/L and 0.063 mg/L, respectively. Fluconazole and luliconazole had the lowest activity, with median MIC and MAC values of 128 mg/L. To conclude, amphotericin B and most of the azoles showed in vitro activity, with an algicidal rather than algistatic effect, against Prototheca. Still, the activity of individual drugs differed significantly between the species and even between strains of the same species. These differences can be attributed to a species-specific potential for acquiring drug resistance, which, in turn, might be linked to the treatment history of the patient from whom the strain was recovered. The results of this study underscore the potential clinical utility of efinaconazole as a promising therapeutic agent for the treatment of human protothecosis.

The origin and early evolution of plants

Plant (archaeplastid) evolution has transformed the biosphere, but we are only now beginning to learn how this took place through comparative genomics, phylogenetics, and the fossil record. This has illuminated the phylogeny of Archaeplastida, Viridiplantae, and Streptophyta, and has resolved the evolution of key characters, genes, and genomes - revealing that many key innovations evolved long before the clades with which they have been casually associated. Molecular clock analyses estimate that Streptophyta and Viridiplantae emerged in the late Mesoproterozoic to late Neoproterozoic, whereas Archaeplastida emerged in the late-mid Palaeoproterozoic. Together, these insights inform on the coevolution of plants and the Earth system that transformed ecology and global biogeochemical cycles, increased weathering, and precipitated snowball Earth events, during which they would have been key to oxygen production and net primary productivity (NPP).

Indurated Plaque With Ulceration on the Dorsum of the Left Hand

A man in his 70s presented with a 6-month history of a rash on the left forearm, which gradually increased in severity. What is your diagnosis?

Genome Sequences of Two Strains of Prototheca wickerhamii Provide Insight Into the Protothecosis Evolution

The Prototheca alga is the only chlorophyte known to be involved in a series of clinically relevant opportunistic infections in humans and animals, namely, protothecosis. Most pathogenic cases in humans are caused by Prototheca wickerhamii. In order to investigate the evolution of Prototheca and the genetic basis for its pathogenicity, the genomes of two P. wickerhamii strains S1 and S931 were sequenced using Nanopore long-read and Illumina short-read technologies. The mitochondrial, plastid, and nuclear genomes were assembled and annotated including a transcriptomic data set. The assembled nuclear genome size was 17.57 Mb with 19 contigs and 17.45 Mb with 26 contigs for strains S1 and S931, respectively. The number of predicted protein-coding genes was approximately 5,700, and more than 96% of the genes could be annotated with a gene function. A total of 2,798 gene families were shared between the five currently available Prototheca genomes. According to the phylogenetic analysis, the genus of Prototheca was classified in the same clade with A. protothecoides and diverged from Chlorella ~500 million years ago (Mya). A total of 134 expanded genes were enriched in several pathways, mostly in metabolic pathways, followed by biosynthesis of secondary metabolites and RNA transport. Comparative analysis demonstrated more than 96% consistency between the two herein sequenced strains. At present, due to the lack of sufficient understanding of the Prototheca biology and pathogenicity, the diagnosis rate of protothecosis is much lower than the actual infection rate. This study provides an in-depth insight into the genome sequences of two strains of P. wickerhamii isolated from the clinic to contribute to the basic understanding of this alga and explore future prevention and treatment strategies.

Prototheca-ID: a web-based application for molecular identification of Prototheca species

The genus Prototheca houses unicellular, achlorophyllous, yeast-like algae, widely distributed in the environment. Protothecae are the only known plants that have repeatedly been reported to infect vertebrates, including humans. Although rare, protothecosis can be clinically demanding, with an unpredictable and treatment-resistant behavior. Accurate identification of Prototheca species relies upon DNA sequence-based typing of the mitochondrially encoded CYTB gene. However, no bioinformatic tool for the processing and analyzing of protothecal sequence data exists. Moreover, currently available sequence databases suffer from a limited number of records and lack of or flawed sequence annotations, making Prototheca identification challenging and often inconclusive. This report introduces the Prototheca-ID, a user-friendly, web-based application providing fast and reliable speciation of Prototheca isolates. In addition, the application offers the users the possibility of depositing their sequences and associated metadata in a fully open Prototheca-ID database, developed to enhance research integrity and quality in the field of Protothecae and protothecosis. Database URL: The Prototheca-ID application is available at https://prototheca-id.org.

Survey on the Presence of Bacterial, Fungal and Helminthic Agents in Off-Leash Dog Parks Located in Urban Areas in Central-Italy

Simple Summary

Off-leash dog parks are designated, generally fenced, public spaces where dogs can move freely under the supervision of their owners. These areas, allowing animals to socialize and run free, play a fundamental role in dogs’ welfare. However, such environments may be a source of different pathogens, even zoonotic, excreted by the attending animals. The present study evaluated the occurrence of bacterial, fungal, and parasitic pathogens in off-leash dog parks located in Florence (central Italy). Yersinia spp., Listeria innocua, Toxocara canis eggs and Ancylostoma caninum/Uncinaria stenocephala eggs were found in canine feces. Keratinophilic geophilic fungi (mostly Microsporum gypseum/A. incurvatum, Microsporum canis in a single case) were recovered from soil. Trichosporon sp. and Geotrichum candidum were isolated from two water samples. The obtained results suggest that, despite the not negligible canine fecal contamination of selected areas (feces were found in 88.5% of the parks), attending dogs did not act as important carriers for the investigated pathogens, although examined off-leash dog parks may represent a risk for the spreading of some dermatophytoses to both pets and their owners. Thus, in a One-Health perspective, periodical examinations to detect the main bacteriological, parasitological and mycological pathogens in different samples collected in off-leash dog parks are recommended.

Abstract

Off-leash dog parks are designated public spaces where dogs can move freely, under their owners’ supervision. These areas, allowing animals to socialize and move freely, are fundamental for dogs’ welfare. However, different pathogens, even zoonotic, may be excreted by the attending animals and contaminate the environment. The aim of the present study was to verify the occurrence of bacterial, fungal and parasitic pathogens in off-leash dog parks located in Florence (central Italy). Between March and May 2019, 83 fecal samples, 43 soil samples and 23 water samples (from fountains and puddles) collected from 26 off-leash fenced areas were examined. Fecal samples scored positive for Yersinia spp. (n = 7), Listeria innocua (n = 4), Toxocara canis eggs (n = 2) and Ancylostoma caninum/Uncinaria stenocephala eggs (n = 1). Keratinophilic geophilic fungi (mostly Microsporum gypseum /A. incurvatum) were recovered from 43 soil samples belonging to 23 out of 26 parks, along with Microsporum canis in a single case. Prototheca spp. was never isolated from water samples, while Trichosporon sp. was cultured in two cases, alone and in association with Geotrichum candidum. These results show that dogs did not act as important carriers for the investigated bacterial and parasitic pathogens, although examined areas may represent a risk for the spreading of some dermatophytoses to both pets and their owners. Periodical examinations to assess the main bacteriological, parasitological and mycological pathogens in different samples collected in off-leash dog parks should be carried out in a One-Health perspective.