Culture-based methods remain standard practice for pathogenic bacterial detection in routine diagnostic laboratories but frequently fail to identify pathogens, particularly in low bacterial burden or antibiotic-exposed samples. While full-length 16S rRNA sequencing improves detection and taxonomic resolution, its adoption is hindered by bioinformatic complexity and operational feasibility. We developed an in-house Oxford Nanopore Technologies (ONT)-based full-length 16S assay coupled with an open-access, automated analysis pipeline designed for non-specialist staff. In this pilot study, 116 culture-negative clinical samples underwent sequencing, with 86 tested in parallel against outsourced standard-of-care 16S or species-specific PCR. Medical microbiologists, blinded to comparative results, independently assessed clinical relevance. Turnaround time, workflow integration, and cost requirements were also evaluated. Compared to outsourced 16S testing, the in-house workflow demonstrated a 100% positive percent agreement (12/12; 95% CI: 75.7%-100.0%). It significantly expanded clinical diagnostic yield from 14.0% (12/86) to 37.2% (32/86) (p<0.0001), identifying clinically relevant organisms in an additional 20 samples reported as negative by outsourced testing. It enhanced species-level resolution and identified polymicrobial infections (n=8). The NanoPATH pipeline generated clinically interpretable outputs via a single-command workflow and implementation modelling demonstrated that twice-weekly runs would achieve comparable turnaround times to outsourced testing, with cost-neutrality reached at 9 samples per run. An open-access ONT-based 16S workflow which is feasible for routine diagnostic laboratory implementation and operated without specialist bioinformaticians significantly improves pathogen detection from clinical samples. By overcoming analytical and operational barriers, this approach provides a practical framework for integrating sequencing-based diagnostics into standard clinical workflows and improving patient care.

Neisseria meningitidis is the causative agent of invasive meningococcal disease. Although third-generation cephalosporins remain the recommended empirical therapy, there has been a growing number of globally reported isolates with resistance. This study aims to elucidate the genetic and evolutionary mechanisms underlying third-generation cephalosporin resistance in N. meningitidis. Whole-genome sequencing and phenotypic antibiotic susceptibility testing were performed, and the potential resistance determinants, genomic features, and evolutionary trajectories of resistant strains were comprehensively characterized. Seven PBP2 mutation sites potentially associated with resistance were identified, including A311V, R468K, E469K, D/N472E, L/P480A, T483S, and G545S. Genomic analysis revealed that strains possessing these seven potential resistance determinant mutations emerged within the past two decades and exhibited an increasing trend. The majority of these strains were isolated from northern regions of China. The predominant mutation strains were located in mainly epidemic strains, like cc4821, cc23, serogroup B and serogroup Y, respectively. Systematic phylogenetic analysis revealed that there has been a phenomenon of cross-regional transmission. Three potential cross-regional transmission third-generation cephalosporin-resistant strain types were identified, namely cc4821-ST-8920-NEIS1753_3923-penA795, ST-14760-NEIS1753_3652-penA1357, and cc23-ST-18108-NEIS1753_5058-penA1258. This study systematically analyzed the phenotypic and genetic characteristics of third-generation cephalosporin-resistant N. meningitidis strains. It not only deepened the understanding of the resistance mechanism but also provided a scientific basis and practical guidance for rapid clinical detection, laboratory monitoring, as well as the prevention and control of cross-regional transmission risks.

A strong 2026-27 El Niño is developing, with potentially important consequences for infectious-disease epidemiology worldwide. For UK infection services, the principal effect is likely to arise indirectly through changes in the incidence and geographical distribution of infections among returning travellers, particularly vector-borne and enteric infections, rather than through substantial increases in infections acquired within the UK. Changes in rainfall, temperature, flooding and drought may alter transmission patterns internationally, while invasive mosquito detections, changing vector ecology and extreme weather provide smaller and less predictable potential routes to domestic effects. However, associations between El Niño and infectiousdisease outbreaks are complex, and should not be interpreted deterministically. For UK infection specialists, the appropriate response is proportionate vigilance; this includes obtaining detailed travel and exposure histories, using contemporary outbreak surveillance to inform differential diagnoses, and recognising and acting on unusual epidemiological signals promptly. El Niño should be viewed as a temporary modifier of infectious-disease risk rather than a predictor of individual outbreaks.

Encephalitis, characterised by inflammation of the brain parenchyma, is a neurological emergency with diverse infectious, autoimmune and inflammatory causes. Delays in recognition and treatment carry significant risks of morbidity and mortality. Since the first UK guideline for management of suspected viral encephalitis in adults was published in 2012, there have been substantial developments in this field. Advances in molecular diagnostics, antibody testing, alongside improved access to neuroimaging and electrophysiology have broadened the capacity to identify underlying aetiologies. The recognised spectrum of infectious and immune-mediated causes has expanded, and clinical experience with immunomodulatory therapies has grown considerably. A multidisciplinary national working group, representing neurology, infectious diseases, microbiology, virology, neuroimmunology and acute medicine, alongside national professional and third-sector organisations, was convened in Liverpool in 2023 to develop updated UK Joint Societies guidelines for the management of suspected infectious and autoimmune encephalitis in adults. This guideline provides pragmatic, evidence-informed recommendations on clinical recognition, investigation, diagnosis, acute management and rehabilitation. It emphasises early identification and parallel consideration of infectious and immune-mediated causes, with particular attention to decision-making during the critical first 24-72hours of presentation. Standardised diagnostic and therapeutic pathways are presented to support consistent care across healthcare settings. Where the evidence base remains limited, the need for multidisciplinary input is highlighted. These recommendations aim to reduce mortality, limit long-term neurological morbidity and improve outcomes for adults with encephalitis across the UK.