Update on Biosafety and Emerging Infections for the Clinical Microbiology Laboratory.

Biosafety risks are prevalent in all areas of the clinical laboratories. Clinical laboratorians have become accustomed to accepting these risks. When an emerging pathogen appears, the concerns become elevated. Since the appearance of Ebola virus in the United States in 2014, biosafety practices have made progress. A recent Association of Public Health Laboratories survey shows that clinical laboratories are unprepared for current and emerging biosafety challenges. This article focuses on the biosafety program that clinical laboratory leaders should build to meet the needs of clinical laboratories; biosafety challenges of automated laboratory systems, facilities, personnel, and practices; and the relationship with occupational health.

A toddler SHIME® model to study microbiota of young children.

The 'first 1000 days of life' determine the gut microbiota composition and can have long-term health consequences. In this study, the simulator of the human intestinal microbial ecosystem (SHIME®) model, which represents the main functional sections of the digestive tract, was chosen to study the microbiota of young children. The aim of this study was to reproduce the digestive process of toddlers and their specific colonic environment. The ascending, transverse and descending colons of SHIME® model were inoculated with feces from three donors aged between 1 and 2 years-old, in three separate runs. For each run, samples from colon vessels were collected at days 14, 21 and 28 after microbiota stabilization period. Short chain fatty acid concentrations determined by HPLC showed that microbiota obtained in SHIME® model shared characteristics between adults and infants. In addition, microbial diversity and bacterial populations determined by 16S rRNA amplicon sequencing were specific to each colon vessel. In conclusion, the SHIME® model developed in this study seemed well adapted to evaluate prebiotic and probiotic impact on the specific microbiota of toddlers, or medicine and endocrine disruptor metabolism. Moreover, this study is the first to highlight some biofilm development in in vitro gastrointestinal modelling systems.

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.

Analysis of the results of the SEIMC External Quality Control Programme. Year 2017. / Análisis de resultados del Programa de Control de Calidad Externo SEIMC. AÑO 2017.

This article provides an analysis of the results obtained in 2017 by the participants inscribed in the External Quality Control Programme of the Spanish Society of Infectious Diseases and Clinical Microbiology (SEIMC), which includes controls for bacteriology, serology, mycology, parasitology, mycobacteria, virology, molecular microbiology, and genotypic bacterial resistance. The results obtained in 2017 confirm the excellent skill and good technical standards found in previous editions. However, the programme again showed that erroneous results can be obtained in any laboratory and even in clinically relevant determinations. Once again, the results of this program highlight the need to implement both internal and external controls, as in the SEIMC programme.

Analysis of the results of the SEIMC External Quality Control Programme. Year 2018. / Análisis de resultados del Programa de Control de Calidad Externo SEIMC. Año 2018.

This article provides an analysis of the results obtained in 2018 by the participants inscribed in the External Quality Control Programme of the Spanish Society of Infectious Diseases and Clinical Microbiology (SEIMC), which includes controls for bacteriology, serology, mycology, parasitology, mycobacteria, virology, molecular microbiology, and genotypic bacterial resistance. The results obtained in 2018 confirm the excellent skill and good technical standards found in the vast majority of Spanish clinical microbiology laboratories, as shown in previous editions. However, the programme again shows that erroneous results can be obtained in any laboratory and even in clinically relevant determinations. Once again, the results of this programme highlight the need to implement both internal and external controls, as in the SEIMC programme.

Shift in the paradigm towards next-generation microbiology.

In this work, the position of contemporary microbiology is considered from the perspective of scientific success, and a list of historical points and lessons learned from the fields of medical microbiology, microbial ecology and systems biology is presented. In addition, patterns in the development of top-down research topics that emerged over time as well as overlapping ideas and personnel, which are the first signs of trans-domain research activities in the fields of metagenomics, metaproteomics, metatranscriptomics and metabolomics, are explored through analysis of the publication networks of 28 654 papers using the computer programme Pajek. The current state of affairs is defined, and the need for meta-analyses to leverage publication biases in the field of microbiology is put forward as a very important emerging field of microbiology, especially since microbiology is progressively dealing with multi-scale systems. Consequently, the need for cross-fertilisation with other fields/disciplines instead of 'more microbiology' is needed to advance the field of microbiology as such. The reader is directed to consider how novel technologies, the introduction of big data approaches and artificial intelligence have transformed microbiology into a multi-scale field and initiated a shift away from its history of mostly manual work and towards a largely technology-, data- and statistics-driven discipline that is often coupled with automation and modelling.

[Evaluation of the environmental contamination in microbiology Which strategy to adopt?] / Évaluation de la contamination environnementale en microbiologie Quelle stratégie adopter ?

The culture of micro-organisms exposes to the risk of microbiological contamination at all stages of the analysis: inoculation on culture media, incubation, and observation of cultures. During our accreditation renewal audit, a surveillance point was notified, regarding the lack of consideration of the risk of microbiological contamination. Its mastery mainly relies on cleaning/disinfection operations and their traceability. In addition, several strategies based on environmental sampling or indicators can be performed. We propose a risk analysis in order to present these strategies.

Use and reliability of multiplex bead-based assays (Luminex) at Containment Level 4.

In the UK, research on hazard group 4 (HG4) pathogens requires specialised Containment Level 4 (CL4) facilities. These differ from Biosafety Level 4 (BSL4) conditions in that work is conducted in class III microbiological safety cabinets for primary containment instead of using positive pressure suits. This presents unique challenges associated with the physical restrictions of working in a limited space, and prohibits the use of many techniques and specialist equipment. In consequence, detailed studies on the biology of HG4 pathogens and in particular their immunological relationships with the host are understudied in the UK; for example, the majority of immunological assays with which the immune system is interrogated require specialist equipment that is unsuitable for CL4. Multiplexing to simultaneously measure multiple analytes is increasingly being used in immunological studies. This assay is attractive for CL4 work because it reduces the time spent in the laboratory whilst maximising the use of valuable sample volume. The Luminex microsphere approach allows for the determination of many cytokines and chemokines, however, the detection system uses fixed aligned lasers and integrated computer systems which are unsuitable for use at CL4. Therefore, we have developed an approach in which the Luminex assay is conducted within the CL4 laboratory and a formalin-fixation stage is introduced to allow for analysis to be undertaken outside of containment. Quality control preparations allow the assay characteristics to be monitored and analysis of assay performance to be evaluated. Our data demonstrate that Luminex is an applicable tool for use at CL4 and that assays can be run reliably to generate reproducible standardised data across different plates and individual experiments.

Methodological approach towards a Gap Assessment of the Serbian microbiology system in the function of surveillance in line with EU standards and acquis.

INTRODUCTION: Italian and Serbian Health authorities performed an in-depth Gap Assessment of the Serbian microbiology system in the function of communicable disease surveillance using a methodology adapted to context and information needs. METHODS: There were two study phases: a capacity based survey and an equipment mapping survey. Invited participants included national health authorities, heads of national reference laboratories and of public/private diagnostic laboratories in Serbia. Findings were analysed preliminarily and identified gaps were discussed, prioritized and validated through two ad hoc workshops involving all concerned institutions. RESULTS: The Gap Assessment was performed between September and December 2017. The overall response rate was 69% for phase one and 74% for phase two. Identified gaps were assessed as highly relevant during the project workshops. DISCUSSION: Gaps and priorities were highlighted, validated, and studied with a suitable level of detail to develop a concrete action-plan. The same methodological approach could be used to monitor progress in Serbia as well as in other EU candidate countries.

Identifying and Overcoming Threats to Reproducibility, Replicability, Robustness, and Generalizability in Microbiome Research.

The "reproducibility crisis" in science affects microbiology as much as any other area of inquiry, and microbiologists have long struggled to make their research reproducible. We need to respect that ensuring that our methods and results are sufficiently transparent is difficult. This difficulty is compounded in interdisciplinary fields such as microbiome research. There are many reasons why a researcher is unable to reproduce a previous result, and even if a result is reproducible, it may not be correct. Furthermore, failures to reproduce previous results have much to teach us about the scientific process and microbial life itself. This Perspective delineates a framework for identifying and overcoming threats to reproducibility, replicability, robustness, and generalizability of microbiome research. Instead of seeing signs of a crisis in others' work, we need to appreciate the technical and social difficulties that limit reproducibility in the work of others as well as our own.

Practical Guidance for Clinical Microbiology Laboratories: Implementing a Quality Management System in the Medical Microbiology Laboratory

This document outlines a comprehensive practical approach to a laboratory quality management system (QMS) by describing how to operationalize the management and technical requirements described in the ISO 15189 international standard. It provides a crosswalk of the ISO requirements for quality and competence for medical laboratories to the 12 quality system essentials delineated by the Clinical and Laboratory Standards Institute. The quality principles are organized under three main categories: quality infrastructure, laboratory operations, and quality assurance and continual improvement. The roles and responsibilities to establish and sustain a QMS are outlined for microbiology laboratory staff, laboratory management personnel, and the institution's leadership. Examples and forms are included to assist in the real-world implementation of this system and to allow the adaptation of the system for each laboratory's unique environment. Errors and nonconforming events are acknowledged and embraced as an opportunity to improve the quality of the laboratory, a culture shift from blaming individuals. An effective QMS encourages "systems thinking" by providing a process to think globally of the effects of any type of change. Ultimately, a successful QMS is achieved when its principles are adopted as part of daily practice throughout the total testing process continuum.