Outcomes of point-of-care testing for influenza in the emergency department of a tertiary referral hospital in Ireland

Background: Seasonal influenza causes significant morbidity and mortality, and represents a recurring financial burden for community- and hospital-based treatment. Nosocomial outbreaks exacerbate the impact of influenza. Rapid diagnosis of influenza has been shown to reduce transmission. However, point-of-care testing (POCT) in emergency departments and prudent direction of patients with the virus to reduce hospital-acquired infection (HAI) have not been evaluated widely. Aim: To assess performance characteristics of the Abbott ID NOW Influenza A & B 2 system, impact on incidence of hospital-acquired influenza, and admission rate ratio for patients who have POCT compared with laboratory testing. POCT was introduced in the 2018e2019 influenza season. Data from then were compared with preceding and subsequent seasons. Methods: Records of POCT and laboratory testing for the 2017e2018, 2018e2019, and 2019e2020 influenza seasons were analysed. Sensitivity and specificity of POCT were compared pairwise with Xpert Flu A/B/RSV. Patient admission rates and time of waiting for admission were compared. Findings: Compared to laboratory assay, POCT demonstrated sensitivity of 90.6% (95% confidence interval (CI): 78.6e96.5) and specificity of 99.2% (95.2e100) for influenza A, with 51.4% and 41.9% reductions in numbers of HAIs observed in the two seasons when POCT was available, respectively. The admission rate ratio for influenza cases diagnosed by POCT compared with laboratory diagnosis was 0.72 (95% CI: 0.53e0.97; P ¼ 0.031). Conclusion: POCT for influenza appears a feasible strategy for testing of patients during peak influenza virus season, with potential to reduce HAI. The relatively rapid turnaround time may also benefit clinical management of patients presenting at emergency departments with suspected influenza

Repeated transmission of SARS-CoV-2 in an overcrowded Irish emergency department elucidated by whole-genome sequencing

Aim: To provide a detailed genomic-epidemiological description of a complex multi-ward SARS-CoV-2 outbreak, which originated in the crowded emergency department (ED) in our hospital during the third wave of the COVID-19 pandemic, and was elucidated promptly by local whole-genome sequencing (WGS).Methods: SARS-CoV-2 was detected by reverse transcriptase real-time polymerase chain reaction on viral RNA extracted from nasopharyngeal swabs. WGS was performed using an Oxford MinION Mk1C instrument following the ARTIC v3 sequencing protocol. High-quality consensus genomes were assembled with the artic-ncov2019 bioinformatics pipeline and viral phylogenetic trees were built, inferred by maximum-likelihood. Clusters were defined using a threshold of 0e1 single nucleotide polymorphisms (SNPs) between epidemiologically linked sequences.Results: In April 2021, outbreaks of COVID-19 were declared on two wards at University Hospital Limerick after 4 healthcare-associated SARS-CoV-2 infections were detected by post-admission surveillance testing. Contact tracing identified 12 further connected cases; all with direct or indirect links to the ED ‘COVID Zone’. All sequences were assigned to the Pangolin B.1.1.7 lineage by WGS, and SNP-level analysis revealed two distinct but simul?taneous clusters of infections. Repeated transmission in the ED was demonstrated, involving patients accommodated on trolleys in crowded areas, resulting in multiple generations of infections across three inpatient hospital wards and subsequently to the local community. These findings informed mitigation efforts to prevent cross-transmission in the ED.Conclusion: Cross-transmission of SARS-CoV-2 occurred repeatedly in an overcrowded emergency department. Viral WGS elucidated complex viral transmission networks in our hospital and informed infection, prevention and control practice.</p