Collections

Over the last two decades, genome sequencing has become an important tool for understanding and tracking the spread of pathogens. Genomic epidemiology is now a preferred method of surveillance and recent years have seen pathogen sequencing at an unprecedented scale, pushing the underlying technologies to the limit. This has brought major innovations and opportunities to public attention, as well as identifying new research areas. However, major challenges remain in public health settings. These include: incorporating new sequencing technologies and data types for real-time surveillance; developing platforms and nomenclatures for genome-based typing and epidemiology; understanding pathogen evolution and the emergence of virulence and antimicrobial resistance; contextualizing knowledge of clinical microbiology with One Health ecological genomics. In this collection, we bring together recent studies that are establishing pathogen genomics as a major part of contemporary disease control efforts.

The skin is our biggest organ and a primary protective barrier from pathogens. The microbiome of this highly varied environment is now being described in unprecedented detail, revealing complex multispecies communities that play important roles in skin health, the development of the immune system and in wound healing. This collection aims to bring together knowledge of what these microbes are, how they colonise this often nutrient poor and challenging niche, and how they work together to suppress the growth of pathogens, while in themselves also being potential accidental pathogens if the skin barrier is broken.

Fungi are a major global health concern, responsible for over a billion infections annually and an estimated 1.5 million deaths each year. Despite their substantial impact on human health and healthcare systems, fungal pathogens have long been underrepresented in research and public health initiatives. In response to this critical gap, the WHO recently published a fungal priority pathogens list, emphasising the urgent need to address both local and global threats posed by fungal infections.

Advancing our understanding of the molecular and cellular mechanisms underlying fungal pathogenesis is pivotal for the development of innovative therapeutics and treatment strategies, offering the potential to reduce mortality and mitigate the burden on healthcare systems worldwide. To capture the current state of play and provide a platform for progress in this field, this collection welcomes submissions across (but not limited to) the following themes:

Fungal Pathogenesis and Virulence

• Mechanisms of fungal pathogenicity (virulence factors)
• Mechanisms of antifungal resistance e.g. efflux, enzymes, tolerance
• Emergence of new strains and their biology

Host Immune Responses to Fungal Infections

• Innate (e.g., macrophages, dendritic cells, peripheral blood mononuclear cells, neutrophils), adaptive (e.g., T-cell, B-cell, antibody), mucosal, skin, organ specific and systemic responses
• Fungal strategies to evade the human host
• Fungal infection in immunocompromised or co-morbid patients

Antifungal Resistance and clinical challenges

• Mechanisms of antifungal resistance
• Challenges and advances in diagnostics

Fungal Interactions

• Influence of microbiome and dysbiosis on fungal colonisation and infection
• Interactions of fungi with other fungi, bacteria, viruses, protozoa or helminths influencing infection

Emerging threats and innovations

• Impact of climate change, zoonoses and globalisation on fungal transmission
• Advances in vaccines, immunomodulatory therapies and disruption strategies

This collection welcomes Research Articles, Reviews, short communication and Technical Resource article types. Please indicate upon submission that you would like your paper to be considered for the collection.

Editors: Lysangela Alves, Seána Duggan, Campbell Gourlay

Status: Open for submissions

Journals submission links:

Journal of Medical Microbiology

Image credit: iStock/Jannicke Wiik-Nielsen

The Campylobacterales are typically microaerophilic species that are often host adapted with the potential for zoonotic infections. The order includes Campylobacter which is the most common bacterial source of gastroenteritis worldwide; Helicobacter which have been associated with peptic ulcers, chronic gastritis, duodenitis, and stomach cancer; the veterinary and clinical pathogen Arcobacter and other related organisms. In conjunction with recent conferences, we present a collection of contemporary studies investigating the genomics of these organisms, guest-edited by members of the conference organising committees: Dr Beile Gao (CHRO-2022; Chinese Academy of Sciences); Dr Ben Pascoe (CampyUK-2021; University of Oxford) and Professor Sam Sheppard (Ineos Oxford Institute, University of Oxford). The Genomics, epidemiology and evolution of Campylobacter, Helicobacter and Related Organisms collection will bring together recent advances that use genomic data to advance understanding in the field. Wide-ranging contributions include findings from active national surveillance programs, comparisons of local and global variations in population structure, studies of antimicrobial resistance emergence and spread, core and accessory genome evolutionary analyses, pathogenicity studies, investigations of plasmids and mobile elements, and genome rearrangement, editing and/or methylation studies.

Journal of General Virology ICTV Virus Taxonomy Profiles are a freely available series of concise, review-type articles that provide overviews of the classification, structure and properties of individual virus orders, families and genera.

ICTV Virus Taxonomy Profiles are written by the International Committee on Taxonomy of Viruses (ICTV) study groups, comprised of leading experts in the field. The profiles summarise the individual chapters from the ICTV’s online 10th Report on Virus Taxonomy, and provide the latest taxonomic information on viruses.

The Microbiology Society is publishing these citable profiles online, while the full chapters are available to all through the ICTV website, thanks to a five-year Biomedical Resources grant from the Wellcome Trust.

US Food and Drug Administration (FDA), the UK International Coronavirus Network (UK-ICN) - Biotechnology and Biological Research Council (BBSRC) and the Department of Environment, Food and Rural Affairs (DEFRA), the Biosafety Level 4 Zoonotic Laboratory Network (BSL4ZNet), the Commonwealth Scientific and Industrial Research Organisation (CSIRO) collective bring together findings and lessons learnt for science foresight perspectives on Coronaviruses into our future.  

The Microbial Genomics Methods and Software collection will bring together articles describing novel experimental, bioinformatics, modelling, and statistical approaches to the analysis of microbial genomics data, including databases or the integration of genomics with other data streams; as well as systematic comparisons or benchmarking of existing methodologies used in the field of microbial genomics. Guest-edited by Dr Zamin Iqbal (European Bioinformatics Institute) and Dr Caroline Colijn (Simon Fraser University), the collection aims to provide the microbial genomics community with new and systematically validated tools to advance their research. 

The cover image for this collection brings together figures from two of retrospective articles in the collection: a phylogeny richly annotated with insertion sequence sites from the article on ISseeker by Adams et al. 2016 (bottom left); and a genome assembly graph from the article on completing bacterial genomes by Wick et al. 2017 (top right).

This collection is now open for submissions. Submit your article here, stating that your manuscript is part of the Methods and Software collection.

Microbiology is now publishing ‘Microbe Profiles’ – concise, review-type articles that provide overviews of the classification, structure and properties of microbes, written by leading microbiologists. These profiles will provide insights into key microbes within the field.