Changing patterns of bloodstream infections in the community and in acute care across two COVID-19 epidemic waves: a retrospective analysis (preprint)

Introduction We examined the epidemiology of community- and hospital-acquired bloodstream infections (BSIs) in COVID-19 and non-COVID-19 patients across two epidemic waves. Methods We analysed blood cultures, SARS-CoV-2 tests, and hospital episodes of patients presenting and admitted to a London hospital group between January 2020 and February 2021. We reported BSI incidence, as well as changes in sampling, case mix, bed and staff capacity, and COVID-19 variants. Results 34,044 blood cultures were taken. We identified 1,047 BSIs; 653 (62.4%) defined epidemiologically as community-acquired and 394 (37.6%) as hospital-acquired. BSI rates and community / hospital ratio were similar to those pre-pandemic. However, important changes in patterns were seen. Among community-acquired BSIs, Escherichia coli BSIs remained lower than pre-pandemic level during the two COVID-19 waves, however peaked following lockdown easing in May 2020, deviating from the historical trend of peaking in August. The hospital-acquired BSI rate was 100.4 per 100,000 patient-days across the pandemic, increasing to 132.3 during the first COVID-19 wave and 190.9 during the second, with significant increase seen in elective non-COVID-19 inpatients. Patients who developed a hospital-acquired BSI, including those without COVID-19, experienced 20.2 excess days of hospital stay and 26.7% higher mortality, higher than reported in pre-pandemic literature. In intensive care units (ICUs), the overall BSI rate was 311.8 per 100,000 patient-ICU days, increasing to 421.0 during the second wave, compared to 101.3 pre-COVID. The BSI incidence in those infected with the SARS-CoV-2 Alpha variant was similar to that seen with earlier variants. Conclusion The pandemic and national responses have had an impact on patterns of community- and hospital-acquired BSIs, in both COVID-19 and non-COVID-19 patients. Factors driving the observed BSI patterns are complex, including changed patient mix, deferred access to health care, and sub-optimal practice. Infection surveillance needs to consider key aspects of pandemic response and changes in healthcare access and practice.

Investigating SARS-CoV-2 surface and air contamination in an acute healthcare setting during the peak of the COVID-19 pandemic in London (preprint)

Objectives: To evaluate SARS-CoV-2 surface and air contamination during the peak of the COVID-19 pandemic in London. Design: Prospective cross-sectional observational study. Setting: An acute NHS healthcare provider. Participants: All inpatient wards were fully occupied by patients with COVID-19 at the time of sampling. Interventions: Air and surface samples were collected from a range of clinical areas and a public area of the hospital. An active air sampler was used to collect three or four 1.0 m3 air samples in each area. Surface samples were collected by swabbing approximately 25 cm2 of items in the immediate vicinity of each air sample. SARS-CoV-2 was detected by RT-qPCR and viral culture using Vero E6 and Caco2 cells; additionally the limit of detection for culturing SARS-CoV-2 dried onto surfaces was determined. Main outcome measures: SARS-CoV-2 detected by PCR or culture. Results: Viral RNA was detected on 114/218 (52.3%) of surface and 14/31 (38.7%) air samples but no virus was cultured. The proportion of surface samples contaminated with viral RNA varied by item sampled and by clinical area. Viral RNA was detected on surfaces and in air in public areas of the hospital but was more likely to be found in areas immediately occupied by COVID-19 patients (67/105 (63.8%) in areas immediately occupied by COVID-19 patients vs. 29/64 (45.3%) in other areas (odds ratio 0.5, 95% confidence interval 0.2-0.9, p=0.025, Fishers exact test). The PCR Ct value for all surface and air samples (>30) indicated a viral load that would not be culturable. Conclusions: Our findings of extensive viral RNA contamination of surfaces and air across a range of acute healthcare settings in the absence of cultured virus underlines the potential risk from surface and air contamination in managing COVID-19, and the need for effective use of PPE, social distancing, and hand/surface hygiene.

Analysis of national and international guidelines on respiratory protection equipment for COVID-19 in healthcare settings. (preprint)

Introduction Consistent guidelines on respiratory protection for healthcare professionals combined with improved global supply chains are critical to protect staff and patients from COVID-19. We summarized and compared the guidelines published by national and international societies/organizations on facemasks and respirators to prevent COVID-19 in healthcare settings. Methods From the 1st January to the 2nd April 2020, guidelines published in four countries (France, Germany, United States, United Kingdom), and two international organizations (US and European Center for Diseases Control, and World Health Organization) were reviewed to analyze the mask and respirators recommended as PPE for the care of patients during the COVID-19 outbreak. Guidelines were eligible for analysis if they (1) included specific guidelines, (2) were written for HCP protection, (3) targeting healthcare settings. The strategy recommended for optimizing supplies and overcoming shortages was collected. Observations The guidelines publication process on respiratory protections varied greatly across countries. Some referred to a unique guide whereas others saw the issue of multiple recommendations by various societies and organization. In term of chronology, most guidelines were published in March with either downgraded (US and European CDC), relatively stable (WHO, Germany, and UK), or a mixing of high and low level equipment (France). The recommendation of respirators was universally recommended for aerosol generating procedures (AGP) across countries, although the type of respirators and what constituted an AGP was variable. Some guidance maintained the use of N95/99 for all contact with confirmed COVID-19 cases (i.e. Germany) whereas others, recommended a surgical mask (i.e. WHO, UK, France). The strategies to overcome shortage of respiratory protection equipment were based on minimizing the need and rationalizing the use, but also prolonging their use, reusing them after cleaning/sterilization, or using cloth masks. Conclusions Stable and consistent guidelines inside and across countries, clearly detailing the respiratory protection type, and the circumstances in which they need to be used may prevent the confusion among frontline staff, and avoid shortage.