Biology subjects

Lebre, P. H.

Publications and source records attributed to Lebre, P. H..

3 recordsLinked to original sources

bioRxiv2026

Comprehensive analysis of air and surface hospital microbiomes uncovers potential hotspots and avenues for transmission of diverse pathogens linked to hospital-acquired infections

Fomite-mediated and airborne transmission pathways play a significant role in the dissemination of healthcare associated pathogens, contributing to the burden of hospital-acquired infections (HAIs). Effective infection prevention and control therefore require robust surveillance approaches capable of capturing the complexity of air and surface microbial communities present in healthcare settings. However, to date such approaches are not widely employed. In this study we used a rapid and low-biomass optimized metagenomic workflow to detect clinically relevant pathogens, characterise genetic signatures such as antimicrobial resistance and virulence determinants, and profile the wider airborne microbiome, including unculturable taxa) essential for HAI surveillance. Air samples were collected from multiple clinical and non-clinical areas across three multi-storey healthcare units within a UK hospital, alongside to surface samples from a haematology/oncology ward with a documented history of outbreaks. Following DNA extraction and enrichment optimised for low-biomass samples, sequencing was performed using the Oxford Nanopore Technologies MinIon long-read platform. Metagenomics data were analysed using an in-house developed bioinformatics pipeline. Metagenomic profiling revealed high bacterial taxonomic diversity across sampled environments, with limited overlap between the airborne and surface communities. Approximately 0.3% of bacterial reads harboured a large variety of antimicrobial resistance genes (ARGs), virulence factors (VFs) and mobile genetics elements (MGEs) across different hospital sample groups. Notably, critical and emerging pathogens were detected across ten wards and were associated with clinically significant resistance determinants, including multiple blaOXA subtypes, vanA gene clusters, and multidrug efflux pumps conferring resistance to eight important classes of antibiotics, including carbapenems, cephalosporins, penams, and vancomycin. In addition, several plasmid replicons implemented in horizontal gene transfer (HGT) were identified within these pathogens, indicating an increased potential for the emergence and dissemination of multi-drug resistance within hospital associated microbial communities. Our findings highlight the importance of using rapid metagenomics-based methodologies for environmental surveillance in healthcare settings. Correspondingly, this study revealed that hospital air and surface microbiomes comprise complex and dynamic microbial communities that harbour diverse of ARGs and VFs with the potential for rapid transmission across the surface-air interface, particularly in high-risk/vulnerable patient areas where outbreaks are more likely to occur.

microbiology↗

bioRxiv2026

Trace gas oxidation supports sub-surface microbial communities across Namib Desert fog and aridity gradients

Widely accepted climate predictions indicate that drylands will expand to cover more than half of the Earths terrestrial surface by the end of the 21st century. In these environments, harsh conditions including nutrient and water limitations restrict plant and animal life, thereby increasing the importance of soil microbial communities in nutrient cycling and ecosystem functioning. The Namib Desert is a distinctive dryland ecosystem characterised by a steep natural aridity gradient, transitioning from a coastal hyperarid zone influenced by frequent fog deposition to an inland arid region receiving seasonal rainfall. This study investigates the impact of water availability and moisture regime on microbial trace gas oxidation and community composition across this aridity gradient. Quantitative analyses revealed that total microbial abundance and activity indicators, including ATP concentrations and respiration rates, were significantly (p < 0.005) reduced in hyperarid soils compared to their arid counterparts. In contrast, hyperarid fog-dominated soils exhibited significantly (p < 0.0005) elevated rates of atmospheric hydrogen oxidation, even in the absence of water inputs. We propose that sustained high-affinity hydrogen oxidation, coupled with rapid microbial resuscitation following wetting events, supports shallow sub-surface microbial communities in the Namib Desert, particularly in the coastal hyperarid zone. Together, these findings challenge current understanding of the lower limits of microbial activity and reveal alternate metabolic pathways that enable microbial persistence in hyperarid hot desert soils. ImportanceDrylands are expanding globally, yet the mechanisms that allow microbial life to persist under extreme and sustained water limitation remain poorly understood. This study demonstrates that atmospheric trace gas oxidation, particularly high-affinity hydrogen oxidation, supports active and resilient microbial communities in hyperarid soils of the Namib Desert, even in the absence of liquid water inputs. By revealing how microbes may couple trace gas metabolism to energy and water generation, our findings provide new insight into the lower limits of microbial activity in dry hot desert soils and highlight the need to investigate how microbes persist and sustain soil ecosystem functioning.

microbiology↗

bioRxiv2020

Phages actively challenge niche communities in the Antarctic soils

By modulating the structure, diversity and trophic outputs of microbial communities, phages play crucial roles in many biomes. In oligotrophic polar deserts, the effects of katabatic winds, constrained nutrients and low water availability are known to limit microbial activity. Although phages may substantially govern trophic interactions in cold deserts, relatively little is known regarding the precise ecological mechanisms. Here, we provide the first evidence of widespread antiphage innate immunity in Antarctic environments using metagenomic sequence data from hypolith communities as model systems. In particular, immunity systems such as DISARM and BREX are shown to be dominant systems in these communities. Additionally, we show a direct correlation between the CRISPR-cas adaptive immunity and the metavirome of hypolith communities, suggesting the existence of dynamic hostphage interactions. In addition to providing the first exploration of immune systems in cold deserts, our results suggest that phages actively challenge niche communities in Antarctic polar deserts. We provide evidence suggesting that the regulatory role played by phages in this system is an important determinant of bacterial host interactions in this environment. ImportanceIn Antarctic environments, the combination of both abiotic and biotic stressors results in simple trophic levels dominated by microbiomes. Although the past two decades have revealed substantial insights regarding the diversity and structure of microbiomes, we lack mechanistic insights regarding community interactions and how phages may affect these. By providing the first evidence of widespread antiphage innate immunity, we shed light on phage-host dynamics in Antarctic niche communities. Our analyses reveal several antiphage defense systems including DISARM and BREX, which appear to dominate in cold desert niche communities. In contrast, our analyses revealed that genes, which encode antiphage adaptive immunity were under-represented in these communities suggesting lower infection frequencies in cold edaphic environments. We propose that by actively challenging niche communities, phages play crucial roles in the diversification of Antarctic communities.

microbiology↗