Clinical microbiology laboratories and COVID-19: an interview with Joseph Blondeau.

This interview was conducted by Atiya Henry, Commissioning Editor of Future Microbiology. Joseph M Blondeau, MSc, PhD, RSM(CCM), SM(AAM), SM(ASCP), FCCP is a Clinical Microbiologist and Head of Clinical Microbiology at Royal University Hospital (Saskatoon Health Region) and the University of Saskatchewan in Saskatoon, Canada. He is also the Provincial Clinical Lead for Microbiology in Saskatchewan, Canada. He holds a Masters of Sciences in Microbiology from Dalhousie University (1985) and a Doctor of Philosophy in Medical Microbiology from the University of Manitoba (1989). Following completion of his PhD, he completed an 1-month post-doctoral training in an infectious diseases research laboratory at Dalhousie University and following which he completed a 2-year post-doctoral residency training program in Clinical Microbiology, also at Dalhousie University. He holds appointments as a Clinical Associate Professor of Pathology, Adjunct Professor of Microbiology and Immunology and Clinical Associate Professor of Ophthalmology. He teaches to undergraduate and graduate students in the areas of microbiology, infectious diseases, antimicrobial agents and pharmacology. Dr Blondeau's main research interests are in the area of antimicrobial agents and antimicrobial resistance, clinical microbiology and clinical outcomes associated with antimicrobial therapy in both human and veterinary medicine.

Next-generation microbiology: from comparative genomics to gene function.

Microbiology is at a turning point in its 120-year history. Widespread next-generation sequencing has revealed genetic complexity among bacteria that could hardly have been imagined by pioneers such as Pasteur, Escherich and Koch. This data cascade brings enormous potential to improve our understanding of individual bacterial cells and the genetic basis of phenotype variation. However, this revolution in data science cannot replace established microbiology practices, presenting the challenge of how to integrate these new techniques. Contrasting comparative and functional genomic approaches, we evoke molecular microbiology theory and established practice to present a conceptual framework and practical roadmap for next-generation microbiology.

Going virtual: a report from the sixth Young Microbiologists Symposium on 'Microbe Signalling, Organisation and Pathogenesis'.

The sixth Young Microbiologists Symposium on 'Microbe Signalling, Organisation and Pathogenesis' was scheduled to be held at the University of Southampton, UK, in late August 2020. However, due to the health and safety guidelines and travel restrictions as a response to the COVID-19 pandemic, the symposium was transitioned to a virtual format, a change embraced enthusiastically as the meeting attracted over 200 microbiologists from 40 countries. The event allowed junior scientists to present their work to a broad audience and was supported by the European Molecular Biology Organization, the Federation of European Microbiological Societies, the Society of Applied Microbiology, the Biochemical Society, the Microbiology Society and the National Biofilms Innovation Centre. Sessions covered recent advances in all areas of microbiology including: Secretion and transport across membranes, Gene regulation and signalling, Host-microbe interactions, and Microbial communities and biofilm formation. This report focuses on several of the highlights and exciting developments communicated during the talks and poster presentations.

Searching for principles of microbial physiology.

Why do evolutionarily distinct microorganisms display similar physiological behaviours? Why are transitions from high-ATP yield to low(er)-ATP yield metabolisms so widespread across species? Why is fast growth generally accompanied with low stress tolerance? Do these regularities occur because most microbial species are subject to the same selective pressures and physicochemical constraints? If so, a broadly-applicable theory might be developed that predicts common microbiological behaviours. Microbial systems biologists have been working out the contours of this theory for the last two decades, guided by experimental data. At its foundations lie basic principles from evolutionary biology, enzyme biochemistry, metabolism, cell composition and steady-state growth. The theory makes predictions about fitness costs and benefits of protein expression, physicochemical constraints on cell growth and characteristics of optimal metabolisms that maximise growth rate. Comparisons of the theory with experimental data indicates that microorganisms often aim for maximisation of growth rate, also in the presence of stresses; they often express optimal metabolisms and metabolic proteins at optimal concentrations. This review explains the current status of the theory for microbiologists; its roots, predictions, experimental evidence and future directions.

The new microbiology: cultivating the future of microbiome-directed medicine.

The discovery of human-associated microscopic life forms has captivated the scientific community since their first documentation in the 17th century. Subsequent isolation and cultivation of microorganisms have spurred great leaps in medicine, including the discovery of antibiotics, identifying pathogens that cause infectious diseases, and vaccine development. The realization that there is a vast discrepancy between the number of microscopic cell counts and how many could thrive in the laboratory motivated the advent of sequencing-based approaches to characterize the uncultured fraction of the microbiota, leading to an unprecedented view into their composition and putative function on all bodily surfaces. It soon became apparent that specific members of the microbiota can be our commensal partners with new implications on various aspects of health, as well as a rich source of therapeutic compounds and tools for biotechnology. Harnessing the immense repertoire of microbial properties, however, inadvertently requires pure cultures for validation and manipulation of candidate genes, proteins, or metabolic pathways, just as mammalian cell culture has become an indispensable tool for mechanistic understanding of host biology. Yet, this renewed interest in growing microorganisms, individually or as a consortium, is stalled by the laborious nature of conventional cultivation methods. Addressing this unmet need through implementation of improved media design and new cultivation techniques is arguably instrumental to future milestones in translational microbiome research.

Present and future of Spanish Military Telemedicine / Presente y futuro de la Telemedicina Militar Española. 25 años de la Unidad de Telemedicina en el Hospital Central de la Defensa «Gómez Ulla»

Telemedicine consists of the exchange of health information between healthcare professionals, and between healthcare professionals and patients, through the use of information and communications technologies (ICT). It is already considered an emerging technology in what is commonly called the «Productivity Plateau». It is also probably an exponential growth technology, in which the «trigger» for such growth will be a mixture of new technologies such as portable sensors/ wearables that detect multiple patient data (Blood Pressure, Heart Rate, Respiratory Rate, Glycaemia, Temperature, etc.), better communications (5G), augmented and mixed reality (augmented and virtual), artificial intelligence systems to improve diagnosis, etc. In Spain, Military Telemedicine is a pioneer in the field. The main mission is to provide remote health support to health professionals or military personnel deployed in Operations and remote or difficult-to-access locations. In 2021 the Spanish Telemedicine Unit at Central Defense Hospital «Gómez Ulla» will celebrate its 25Th anniversary. This article discusses the aforementioned aspects of telemedicine as an emerging technology and describes the current mission, organization and capabilities of Spanish military telemedicine, as well as its future

La Telemedicina consiste en el intercambio de información sanitaria entre profesionales sanitarios, o entre profesional sanitario y paciente, mediante el uso de las tecnologías de la información y comunicaciones (TIC). Se considera ya una tecnología emergente en el denominado «Plateau de productividad». Probablemente se trate de una tecnología de crecimiento exponencial, en la cual el «gatillo» para dicho crecimiento será una mezcla de diferentes tecnologías, como nuevos sensores portátiles que detecten múltiples datos de los pacientes (Tensión Arterial, Frecuencia cardiaca, Frecuencia respiratoria, Glucemia, Temperatura, etc), mejores comunicaciones (5G), realidad aumentada y mixta (aumentada y virtual), sistemas de inteligencia artificial para ayuda al diagnóstico, etc. En España, la Telemedicina Militar es pionera en este campo. Su misión fundamental es el apoyo y asesoramiento sanitario a distancia a personal sanitario y también no sanitario, tanto en Zona de Operaciones (ZO) como en situación de aislamiento y/o localización remota. En 2021 el Servicio de Telemedicina del Hospital Central de la Defensa «Gomez Ulla» celebrará su 25 aniversario. En el artículo se tratan los mencionados aspectos acerca de la Telemedicina como tecnología emergente y se describe la misión, organización y capacidades actuales de la Telemedicina Militar Española, así como sus perspectivas de futuro

Trends in Microbiology publications: are classic scientific journals condemned to extinction?

Scientific journals have played an essential role in the diffusion of research breakthroughs. For many years there was no competition between journals, but, in recent decades they have become categorized by a careful assessment of their published contents based on several metric parameters. Of greater note, the 'prestige index' has become an essential tool used by public and private institutions to develop their scientific policy. Thus, the evaluation of research staffs, the concession of grants or fellowships and even the scholarly reputation and academic positions are mainly founded on a given journal's 'quality'. As a consequence, the prestige of some journals has gone up, based on the assumption that they publish cutting-edge science, while the reputation of others has gone down. Within the field of Microbiology, we have carried out a direct analysis by monitoring several representative classic journals according to customary metric parameters over 20 years. This analysis also covers another set of journals of recent appearance (novel journals). Although a direct comparison between both groups is not possible, this approach serves to perceive the trends of publication among microbiologists. Our preliminary conclusion is that the continued existence of many so-termed classic journals devoted to Microbiology is seriously threatened.

[Emerging bacteria in cystic fibrosis and non-cystic fibrosis bronchiectasis from a microbiologist's perspective]. / Bactéries émergentes dans la mucoviscidose et les dilatations des bronches hors mucoviscidose. Le point de vue du microbiologiste.

INTRODUCTION: Common major pathogens like Pseudomonas aeruginosa are identified in the airways of patients with cystic fibrosis (CF) and non-CF bronchiectasis. However, other opportunistic bacterial pathogens like Achromobacter xylosoxidans complex, Stenotrophomonas maltophilia and non-tuberculous mycobacteria are currently emerging in CF and are also reported in non-CF bronchiectasis. BACKGROUND: The emergence of opportunistic bacterial pathogens has been recognized in CF through annual national reports of sputum microbiology data. Despite common factors driving the emergence of bacteria identified in CF and non-CF bronchiectasis patients, bronchiectasis registries have been created more recently and no longitudinal analysis of recorded microbiological data is currently available in the literature, thereby preventing the recognition of emerging bacteria in patients with non-CF bronchiectasis. OUTLOOK: A longitudinal follow-up of microbiological data is still needed in non-CF bronchiectasis to identify emerging opportunistic bacterial pathogens. Homogeneity in practice of sputum microbiological examination is also required to allow comparative analysis of data in CF and non-CF bronchiectasis. CONCLUSION: Bacterial pathogens recognized as emerging in CF have to be more carefully monitored in non-CF bronchiectasis in view of their association with deterioration of the lung disease.

Toward High-Throughput Fungal Electroculturomics and New Omics Methodologies in 21st-Century Microbiology and Ecology.

Modern microbiology and drug development are in a watershed moment with the advent of electroceuticals. In addition to genomics, electrical impulses in an organism are believed to contribute to tissue and cellular plasticity. Hence, electroceuticals or bioelectronics offers the promise to identify innovative approaches to treat human diseases. However, applications toward electromicrobiology are still limited and rare, despite the high potential to innovate the fields of both microbiology and therapeutics. For example, electric modalities for manipulating microbial growth are highly sustainable; can be combined with biopharmaceuticals, probiotics, and pharmacobiotics; and, thus, are well poised for use in medicine, public health, and ecology and diverse industries. We report here the introduction of a new research framework and technology platform for electroculturomics, by coupling standard solid-state mycological cultures with conductive treatment using a conformité Européene (CE-)-certified medical ionophoresis device. We share our experience with a diverse range of fungi that have been treated with the electroculturomics approach reported herein. We suggest that this line of inquiry can be extended to electrotranscriptomics and electrometabolomics by deploying electroculturomics in tandem with multi-omics approaches in the future. This article makes a specific contribution to fungal microbiology, and a broader contribution to advance the theory and practice of the field of electroculturomics emerging in 21st-century microbiology and ecology research.

Prokaryotic names: the bold and the beautiful.

In recent years, names of ∼170 new genera and ∼1020 new species were added annually to the list of prokaryotic names with standing in the nomenclature. These names were formed in accordance with the Rules of the International Code of Nomenclature of Prokaryotes. Most of these names are not very interesting as specific epithets and word elements from existing names are repeatedly recycled. The rules of the Code provide many opportunities to create names in far more original ways. A survey of the lists of names of genera and species of prokaryotes shows that there is no lack of interesting names. The annotated selection presented here proves that at least some authors have exploited the possibilities allowed by the rules of the Code to name novel organisms in ways that are more attractive. I here call upon all colleagues who describe new taxa to devote more thought to the naming of new genera and species. It takes some effort, and it requires proper use of the lexicon of Classical Greek and Latin as well as an understanding of the Code and the guidelines of its orthography appendix. Creation of attractive names will boost the general interest in prokaryotic nomenclature.

The potential for use of non-thermal plasma in microbiology and medicine.

The overview provides basic information on non-thermal plasma, its properties, and methods of its generation. It gives examples of its use in the inactivation of bacteria including biofilms, fungi, and prions. Related applications in human medicine, namely in wound healing, antitumor therapy, dental medicine, and dermatomycosis therapy are also mentioned.