Emerging Fungal Infections: New Species, New Names, and Antifungal Resistance.

BACKGROUND: Infections caused by fungi can be important causes of morbidity and mortality in certain patient populations, including those who are highly immunocompromised or critically ill. Invasive mycoses can be caused by well-known species, as well as emerging pathogens, including those that are resistant to clinically available antifungals. CONTENT: This review highlights emerging fungal infections, including newly described species, such as Candida auris, and those that having undergone taxonomic classification and were previously known by other names, including Blastomyces and Emergomyces species, members of the Rasamsonia argillacea species complex, Sporothrix brasiliensis, and Trichophyton indotinae. Antifungal resistance also is highlighted in several of these emerging species, as well as in the well-known opportunistic pathogen Aspergillus fumigatus. Finally, the increased recognition and importance of fungal co-infections with respiratory pathogens, including severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is discussed. SUMMARY: Both clinicians and clinical microbiology laboratories should remain vigilant regarding emerging fungal infections. These may be difficult both to diagnose and treat due to the lack of experience of clinicians and laboratory personnel with these organisms and the infections they may cause. Many of these fungal infections have been associated with poor clinical outcomes, either due to inappropriate therapy or the development of antifungal resistance.

Fully automated fast-flow synthesis of antisense phosphorodiamidate morpholino oligomers.

Rapid development of antisense therapies can enable on-demand responses to new viral pathogens and make personalized medicine for genetic diseases practical. Antisense phosphorodiamidate morpholino oligomers (PMOs) are promising candidates to fill such a role, but their challenging synthesis limits their widespread application. To rapidly prototype potential PMO drug candidates, we report a fully automated flow-based oligonucleotide synthesizer. Our optimized synthesis platform reduces coupling times by up to 22-fold compared to previously reported methods. We demonstrate the power of our automated technology with the synthesis of milligram quantities of three candidate therapeutic PMO sequences for an unserved class of Duchenne muscular dystrophy (DMD). To further test our platform, we synthesize a PMO that targets the genomic mRNA of SARS-CoV-2 and demonstrate its antiviral effects. This platform could find broad application not only in designing new SARS-CoV-2 and DMD antisense therapeutics, but also for rapid development of PMO candidates to treat new and emerging diseases.

Leveraging natural history biorepositories as a global, decentralized, pathogen surveillance network.

The Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) pandemic reveals a major gap in global biosecurity infrastructure: a lack of publicly available biological samples representative across space, time, and taxonomic diversity. The shortfall, in this case for vertebrates, prevents accurate and rapid identification and monitoring of emerging pathogens and their reservoir host(s) and precludes extended investigation of ecological, evolutionary, and environmental associations that lead to human infection or spillover. Natural history museum biorepositories form the backbone of a critically needed, decentralized, global network for zoonotic pathogen surveillance, yet this infrastructure remains marginally developed, underutilized, underfunded, and disconnected from public health initiatives. Proactive detection and mitigation for emerging infectious diseases (EIDs) requires expanded biodiversity infrastructure and training (particularly in biodiverse and lower income countries) and new communication pipelines that connect biorepositories and biomedical communities. To this end, we highlight a novel adaptation of Project ECHO's virtual community of practice model: Museums and Emerging Pathogens in the Americas (MEPA). MEPA is a virtual network aimed at fostering communication, coordination, and collaborative problem-solving among pathogen researchers, public health officials, and biorepositories in the Americas. MEPA now acts as a model of effective international, interdisciplinary collaboration that can and should be replicated in other biodiversity hotspots. We encourage deposition of wildlife specimens and associated data with public biorepositories, regardless of original collection purpose, and urge biorepositories to embrace new specimen sources, types, and uses to maximize strategic growth and utility for EID research. Taxonomically, geographically, and temporally deep biorepository archives serve as the foundation of a proactive and increasingly predictive approach to zoonotic spillover, risk assessment, and threat mitigation.

Not just a pathogen: The importance of recognizing genetic variability to mitigate a wildlife pandemic.

Emerging infectious diseases (EIDs) are increasingly recognized as a threat to both biodiversity and human health (Scheele et al., 2019; Wells et al., 2020). But pathogens cannot been seen as unique entities; their intraspecific genetic variability represented in variants, strains, antigenic types or genetic lineages may cause different impacts at the population level (Nelson and Holmes, 2007; Greenspan et al., 2018). The global spread of pathogens has been largely facilitated by globalization of transport, which particularly intensified during the last century (O'Hanlon et al., 2018). As seen with SARS-CoV-2, air travel can rapidly spread a pathogen globally (Wells et al., 2020). Furthermore, after initial introduction subsequent translocations of a pathogen may cause the contact of different variants facilitating the rise of novel genotypes that may have higher pathogenicity or transmissibility (Nelson and Holmes, 2007; Greenspan et al., 2018). Chytridiomycosis is an EID caused by the fungus Batrachochytrium dendrobatidis (Bd), that infects amphibian skin causing population declines to extinction in susceptible species. Now a wildlife pandemic, Bd has been recognized as the single pathogen causing the greatest loss of biodiversity on Earth (Scheele et al., 2019). Recent advances in genetics have made novel tools for pathogen detection and characterization more accessible and reliable (Boyle et al., 2004; Byrne et al., 2019). In this issue of Molecular Ecology Resources, Ghosh et al. (2021) report the development of a new genotyping qPCR assay targeting mitochondrial DNA (mtDNA) of Bd, and based on noninvasive swab samples (Figure 1), discriminate between the two most globally widespread and pathogenic genetic lineages of Bd. Having a better understanding of how the genetic diversity of a pathogen is distributed is crucial to understand their spread patterns and develop timely mitigation strategies.

The microbiome of bat guano: for what is this knowledge important?

Bats as flying mammals are potent vectors and natural reservoir hosts for many infectious viruses, bacteria, and fungi, also detected in their excreta such as guano. Accelerated deforestation, urbanization, and anthropization hastily lead to overpopulation of the bats in urban areas allowing easy interaction with other animals, expansion, and emergence of new zoonotic disease outbreaks potentially harmful to humans. Therefore, getting new insights in the microbiome of bat guano from different places represents an imperative for the future. Furthermore, the use of novel high-throughput sequencing technologies allows better insight in guano microbiome and potentially indicated that some species could be typical guano-dwelling members. Bats are well known as a natural reservoir of many zoonotic viruses such as Ebola, Nipah, Marburg, lyssaviruses, rabies, henipaviruses, and many coronaviruses which caused a high number of outbreaks including ongoing COVID-19 pandemic. Additionally, many bacterial and fungal pathogens were identified as common guano residents. Thus, the presence of multi-drug-resistant bacteria as environmental reservoirs of extended spectrum ß-lactamases and carbapenemase-producing strains has been confirmed. Bat guano is the most suitable substrate for fungal reproduction and dissemination, including pathogenic yeasts and keratinophilic and dimorphic human pathogenic fungi known as notorious causative agents of severe endemic mycoses like histoplasmosis and fatal cryptococcosis, especially deadly in immunocompromised individuals. This review provides an overview of bat guano microbiota diversity and the significance of autochthonous and pathogenic taxa for humans and the environment, highlighting better understanding in preventing emerging diseases. KEY POINTS: Bat guano as reservoir and source for spreading of autochthonous and pathogenic microbiota Bat guano vs. novel zoonotic disease outbreaks Destruction of bat natural habitats urgently demands increased human awareness.

[Epidemics: lessons from History]. / Épidémies: Leçons d'Histoire.

TITLE: Épidémies: Leçons d'Histoire. ABSTRACT: Jusqu'au milieu du XVIIIe siècle, l'espérance de vie était de 25 ans dans les pays d'Europe, proche alors de celle de la préhistoire. À cette époque, nos ancêtres succombaient, pour la plupart, à une infection bactérienne ou virale, quand la mort n'était pas le résultat d'un épisode critique, comme la guerre ou la famine. Un seul microbe suffisait à terrasser de nombreuses victimes. L'épidémie de SARS-CoV-2 est là pour nous rappeler que ce risque est désormais à nouveau d'actualité. Si son origine zoonotique par la chauve-souris est probable, la contamination interhumaine montre son adaptation rapide à l'homme et permet d'évoquer ainsi la transmission des épidémies, qu'elle soit ou non liée à des vecteurs, ces derniers pouvant représenter dans d'autres occasions un des maillons de la chaîne.

Introduction: microbes, networks, knowledge-disease ecology and emerging infectious diseases in time of COVID-19.

This is an introduction to the topical collection Microbes, Networks, Knowledge: Disease Ecology in the twentieth Century, based on a workshop held at Queen Mary, University London on July 6-7 2016. More than twenty years ago, historian of science and medicine Andrew Mendelsohn asked, "Where did the modern, ecological understanding of epidemic disease come from?" Moving beyond Mendelsohn's answer, this collection of new essays considers the global history of disease ecology in the past century and shows how epidemics and pandemics have made "microbes complex".