MICROBIOLOGY
Sequencing was performed using the Oxford Nanopore system for a 30-minute run-time. Metagenomic analysis was performed using an in-house developed bioinformatic pipeline, the cost per sample being very low at only around £10 and took only six hours from sample collection to issuing a report. The air microbiome turned out to be very complex. Although there was distinct overlap with microbial communities on the surface, there were also crucial differences between the two. Detailed analysis showed that some resistance genes were shared between different species and sites. This is a whole new area of study, and the implications of these findings in the context of the spread of AMR and hospital-acquired infection are not really clear at this stage.
Colonies of Clostridioides difficile, just one of the human pathogens detected on dust particles on the air microbiome high in the atmosphere.
represent a paradigm shift in sepsis care within the NHS, offering safe, effective and cost-efficient antimicrobial stewardship. As new research unfolds, these advances will increasingly support clinicians in delivering optimal, more precise patient care and preserving antibiotic efficacy for future generations.
Novel technologies against antimicrobial resistance Professor Hermine Mkrtchyan, Centre for Innovation in Genomics and Microbiome Sciences, University of West London, gave a comprehensive overview of her work on the use of novel technologies in the fight against antimicrobial resistance (AMR). One of the most interesting topics she touched on was the study of the air microbiome, a subject new to most of the audience, but which has been of increasing interest since a pioneering study in 2024 from the University of Barcelona in which dust samples were collected in the air 0.6 to 1.9 miles up in the atmosphere between China and Japan (
https://www.pnas.org/ doi/10.1073/pnas.2404191121). Analysis of the long-range air currents on the days the samples were collected, combined with chemical analysis, showed the dust particles had travelled 1,243 miles from fields in North East China. Microbes were embedded in the particles, which protected them from ultraviolet light and dehydration, allowing some to remain viable. The human pathogen species included bacteria such as Escherichia coli, Staphylococcus saprophyticus and Clostridioides difficile.
Coming back down to earth, since the COVID-19 epidemic there has been increased interest in the possibility of
16
other pathogens being spread by the air. We breathe an average of 14 m3
of
air per day and we know that the indoor environment of the hospital provides a common source of exposure to a range of microbes. It is well known that C. difficile, Klebsiella spp. and others can survive on dry, inanimate surfaces for up to several months; however, the unstated assumption has generally been that it is surfaces that are the main worry and that the airborne microbiome is not really a factor. Indoor public places are often crowded, making social distancing difficult. Such contained spaces – especially if they have inappropriate levels and methods of air handling and hygiene practices – may become incubators of pathogens. Professor Mkrtchyan described solutions they have devised to unlock low-biomass air microbiomes for public health pathogen and AMR surveillance using metagenomics. She and her team have devised a novel unbiased untargeted metagenomic methodology for air sampling in the hospital. The actual procedure took 10–20 minutes per sample, with air collected at a rate of 300 litres per minute. Obviously, the biomass is very low, so special methods were devised for low biomass DNA extraction and amplification.
Accessible clinical bacteriology at the district level Diagnostic microbiology in rural and remote regions is often difficult to access and poorly resourced. This has an impact in delivering healthcare to local populations but also leaves these areas without any disease surveillance or AMR monitoring capacity. The next speaker, Dr Allesandra Natale, MSF Paris, introduced one potential solution to this, known as the Mini-Lab. Historically mobile laboratory solutions have focused on outbreak response and have been able to rely upon experienced microbiologists and technically sophisticated equipment. However, such approaches are rarely sustainable in the medium- to long-term. The Mini-Lab system was developed alongside the international humanitarian organisation Medicins Sans Frontières as a compact and sustainable, all-in- one solution which is intended to have significant and lasting impact. Dr Natale began her talk by providing some background to the challenges that are faced in developing a microbiology service in resource-limited regions. District-level laboratories have the potential to undertake roles in prevention, treatment and disease surveillance. Issues include weak infrastructure, a limited capacity to train and support staff, erratic supply chains, and unavailability of consumables at the local level. The Mini-Lab system is compact
Dr Daniel Carter, UKHSA, Porton Down, gave a fascinating talk on the UK Public Health Rapid Support Team Rapid Response Mobile Laboratory as a critical tool for global outbreak response
AUGUST 2025
WWW.PATHOLOGYINPRACTICE.COM
CDC/Dr. Holdeman Public domain Wikimedia Commons
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