Using routinely collected hospital data to investigate healthcare worker mobility and patient contacts within a UK hospital during the COVID-19 pandemic

Movement and contacts are central to the transmission of infectious diseases and, within the hospital setting, healthcare worker (HCW) mobility and their contact with patients play an important role in the spread of nosocomial disease. Yet data relating to HCW behaviours associated with mobility and contacts in the healthcare environment are often limited. This paper proposes a framework for integrating several electronic data sources routinely-collected by modern hospitals, to enable the measurement of HCW behaviours relevant to the transmission of infections. Using data from a London teaching hospital during the COVID-19 pandemic, we demonstrate how, at an aggregate level, electronic medical records (EMRs) and door access logs can be used to establish changes in HCW mobility and patient contacts. In addition, to show the utility of these data sources in supporting infection prevention and control (IPC), we investigate changes in the indirect connectivity of patients (resulting from shared contacts with HCWs) and spatial connectivity of floors (owing to the movements of HCWs). Average daily rates of patient contacts are computed and found to be higher throughout the pandemic compared to that pre-pandemic, while the average daily rates of HCW mobility remained stable until the second wave, where they surpassed pre-pandemic levels. The response of HCW behaviour to the pandemic was not equal between floors, whereby the highest increases in patient contacts and mobility were on floors handling the majority of COVID-19 patients. The first wave of COVID-19 patients resulted in changes to the flow of HCWs between floors, but the interconnectivity between COVID-19 and non COVID-19 wards was evident throughout the pandemic. Daily rates of indirect contact between patients provided evidence for reactive staff cohorting, whereby indirect contact rates between COVID-19 positive and negative patients were lowest during peaks in COVID-19 hospital admissions. We propose that IPC practitioners use these routinely collected data on HCW behaviour to support infection control activities and to help better protect hospital staff and patients from nosocomial outbreaks of communicable diseases.

Systematic evaluation and external validation of 22 prognostic models among hospitalised adults with COVID-19: An observational cohort study

BackgroundThe number of proposed prognostic models for COVID-19, which aim to predict disease outcomes, is growing rapidly. It is not known whether any are suitable for widespread clinical implementation. We addressed this question by independent and systematic evaluation of their performance among hospitalised COVID-19 cases. MethodsWe conducted an observational cohort study to assess candidate prognostic models, identified through a living systematic review. We included consecutive adults admitted to a secondary care hospital with PCR-confirmed or clinically diagnosed community-acquired COVID-19 (1st February to 30th April 2020). We reconstructed candidate models as per their original descriptions and evaluated performance for their original intended outcomes (clinical deterioration or mortality) and time horizons. We assessed discrimination using the area under the receiver operating characteristic curve (AUROC), and calibration using calibration plots, slopes and calibration-in-the-large. We calculated net benefit compared to the default strategies of treating all and no patients, and against the most discriminating predictor in univariable analyses, based on a limited subset of a priori candidates. ResultsWe tested 22 candidate prognostic models among a cohort of 411 participants, of whom 180 (43.8%) and 115 (28.0%) met the endpoints of clinical deterioration and mortality, respectively. The highest AUROCs were achieved by the NEWS2 score for prediction of deterioration over 24 hours (0.78; 95% CI 0.73-0.83), and a novel model for prediction of deterioration <14 days from admission (0.78; 0.74-0.82). Calibration appeared generally poor for models that used probability outcomes. In univariable analyses, admission oxygen saturation on room air was the strongest predictor of in-hospital deterioration (AUROC 0.76; 0.71-0.81), while age was the strongest predictor of in-hospital mortality (AUROC 0.76; 0.71-0.81). No prognostic model demonstrated consistently higher net benefit than using the most discriminating univariable predictors to stratify treatment, across a range of threshold probabilities. ConclusionsOxygen saturation on room air and patient age are strong predictors of deterioration and mortality among hospitalised adults with COVID-19, respectively. None of the prognostic models evaluated offer incremental value for patient stratification to these univariable predictors.

Excess deaths in people with cardiovascular diseases during the COVID-19 pandemic.

BackgroundCardiovascular diseases(CVD) increase mortality risk from coronavirus infection(COVID-19), but there are concerns that the pandemic has affected supply and demand of acute cardiovascular care. We estimated excess mortality in specific CVDs, both "direct", through infection, and "indirect", through changes in healthcare. MethodsWe used population-based electronic health records from 3,862,012 individuals in England to estimate pre- and post-COVID-19 mortality risk("direct" effect) for people with incident and prevalent CVD. We incorporated: (i)pre-COVID-19 risk by age, sex and comorbidities, (ii)estimated population COVID-19 prevalence, and (iii)estimated relative impact of COVID-19 on mortality(relative risk, RR: 1.5, 2.0 and 3.0). For "indirect" effects, we analysed weekly mortality and emergency department data for England/Wales and monthly hospital data from England(n=2), China(n=5) and Italy(n=1) for CVD referral, diagnosis and treatment until 1 May 2020. FindingsCVD service activity decreased by 60-100% compared with pre-pandemic levels in eight hospitals across China, Italy and England during the pandemic. In China, activity remained below pre-COVID-19 levels for 2-3 months even after easing lockdown, and is still reduced in Italy and England. Mortality data suggest indirect effects on CVD will be delayed rather than contemporaneous(peak RR 1.4). For total CVD(incident and prevalent), at 10% population COVID-19 rate, we estimated direct impact of 31,205 and 62,410 excess deaths in England at RR 1.5 and 2.0 respectively, and indirect effect of 49932 to 99865 excess deaths. InterpretationSupply and demand for CVD services have dramatically reduced across countries with potential for substantial, but avoidable, excess mortality during and after the COVID-19 pandemic. FundingNIHR, HDR UK, Astra Zeneca

Scalable and Resilient SARS-CoV2 testing in an Academic Centre

The emergence of the novel coronavirus SARS-CoV-2 has led to a pandemic infecting more than two million people worldwide in less than four months, posing a major threat to healthcare systems. This is compounded by the shortage of available tests causing numerous healthcare workers to unnecessarily self-isolate. We provide a roadmap instructing how a research institute can be repurposed in the midst of this crisis, in collaboration with partner hospitals and an established diagnostic laboratory, harnessing existing expertise in virus handling, robotics, PCR, and data science to derive a rapid, high throughput diagnostic testing pipeline for detecting SARS-CoV-2 in patients with suspected COVID-19. The pipeline is used to detect SARS-CoV-2 from combined nose-throat swabs and endotracheal secretions/ bronchoalveolar lavage fluid. Notably, it relies on a series of in-house buffers for virus inactivation and the extraction of viral RNA, thereby reducing the dependency on commercial suppliers at times of global shortage. We use a commercial RT-PCR assay, from BGI, and results are reported with a bespoke online web application that integrates with the healthcare digital system. This strategy facilitates the remote reporting of thousands of samples a day with a turnaround time of under 24 hours, universally applicable to laboratories worldwide.

Estimating excess 1- year mortality from COVID-19 according to underlying conditions and age in England: a rapid analysis using NHS health records in 3.8 million adults

BackgroundThe medical, health service, societal and economic impact of the COVID-19 emergency has unknown effects on overall population mortality. Previous models of population mortality are based on death over days among infected people, nearly all of whom (to date at least) have underlying conditions. Models have not incorporated information on high risk conditions or their longer term background (pre-COVID-19) mortality. We estimated the excess number of deaths over 1 year under different COVID-19 incidence rates and differing mortality impacts. MethodsUsing population based linked primary and secondary care electronic health records in England (HDR UK - CALIBER), we report the prevalence of underlying conditions defined by UK Public Health England COVID-19 guidelines (16 March 2020) in 3,862,012 individuals aged [≥]30 years from 1997-2017. We used previously validated phenotypes, openly available (https://caliberresearch.org/portal), for each condition using ICD-10 diagnosis, Read, procedure and medication codes. We estimated the 1-year mortality in each condition, and developed simple models of excess COVID-19-related deaths assuming relative risk (RR) of the impact of the emergency (compared to background mortality) of 1.2, 1.5 and 2.0. Findings20.0% of the population are at risk according to current PHE guidelines, of which; 13.7% were age>70 years and 6.3% aged [≤]70 years with [≥]1 underlying condition (cardiovascular disease (2.3%), diabetes (2.2%), steroid therapy (1.9%), severe obesity (0.9%), chronic kidney disease (0.6%) and chronic obstructive pulmonary disease, COPD (0.5%). Multimorbidity (co-occurrence of [≥]2 conditions in an individual) was common (10.1%). The 1-year mortality in the at-risk population was 4.46%, and age and underlying conditions combine to influence background risk, varying markedly across conditions (5.9% in age>70 years, 8.6% for COPD and 13.1% in those with [≥]3 or more conditions). In a suppression scenario (at SARS CoV2 rates of 0.001% of the UK population), there would be minimal excess deaths (3 and 7 excess deaths at relative risk, RR, 1.5 and 2.0 respectively). At SARS CoV2 rates of 10% of the UK population (mitigation) the model estimates the numbers of excess deaths as: 13791, 34479 and 68957 (at RR 1.2, 1.5 and 2.0 respectively). At SARS CoV2 rates of 80% in the UK population ("do-nothing"), the model estimates the number of excess deaths as 110332, 275,830 and 551,659 (at RR 1.2, 1.5 and 2.0) respectively. InterpretationWe provide the public, researchers and policy makers a simple model to estimate the excess mortality over 1 year from COVID-19, based on underlying conditions at different ages. If the relative mortality impact of COVID-19 were to be about 20% (similar magnitude as the established winter vs summer mortality excess), then the excess deaths would be 0 when 1 in 100 000 (suppression), 13791 when 1 in 10 (mitigation) and 110332 when 8 in 10 are infected ("do nothing") scenario. However, the relative impact of COVID-19 is unknown. If the emergency were to double the mortality risk, then we estimate 7, 68957 and 551,659 excess deaths in the same scenarios. These results may inform the need for more stringent suppression measures as well as efforts to target those at highest risk for a range of preventive interventions.

Clinical outcome and cost comparison between laparoscopic and open appendicectomy

<p><b>INTRODUCTION</b>Local data comparing laparoscopic appendicectomy (LA) and open appendicectomy (OA) is lacking. We perform a cost and outcome comparison between LA and OA.</p><p><b>MATERIALS AND METHODS</b>A retrospective review of all appendicectomies performed for suspected appendicitis from July 2010 to December 2010 was conducted. Patient demographics, duration of surgery, complication rates, total cost of stay (COS) and length of stay (LOS) were compared between LA and OA.</p><p><b>RESULTS</b>A total of 198 patients underwent appendicectomy during the duration of study; 82 LA and 116 OA. There were 115 males (58.1%) and 83 females (41.9%). Median age was 33 years. Patients who underwent LA were significantly younger (P <0.001) with a greater proportion of females (P <0.0001) and were more likely to be negative appendicectomies (18.3% vs. 6.9%, P = 0.023). Duration of surgery was significantly longer in LA patients (86 min vs. 74 min, P = 0.003). LOS in the LA group was shorter by 1.3 days compared to OA (2.0 days vs. 3.3 days, P <0.0001). The differences in operative duration and LOS between LA and OA remained significant on multivariate analysis (P = 0.001 and P = 0.008, respectively). The COS (P = 0.359), wound infection rates (P = 0.528) and complication rates (P = 0.131) were not significantly different between the 2 groups.</p><p><b>CONCLUSION</b>LA is associated with a shorter LOS while its cost is equivalent to OA. From the perspective of utilisation of healthcare resources, LA appears to be superior.</p>

Infected pancreatic necrosis--an evaluation of the timing and technique of necrosectomy in a Southeast Asian population

<p><b>INTRODUCTION</b>Acute pancreatitis appears to be less prevalent in multi-ethnic Southeast Asia, where the aetiology also appears to be influenced by ethnicity. As with acute pancreatitis elsewhere, however, pancreatic necrosis is a cause of significant mortality and the aim of this study was to review our institutional experience with pancreatic necrosectomy.</p><p><b>MATERIALS AND METHODS</b>The records of all patients who underwent pancreatic necrosectomy from January 2000 to December 2004 were analysed. Indications for surgery were the presence of infected necrosis, unresolving sepsis attributable to ongoing pancreatitis or the presence of gas in the pancreatic bed on imaging. Surgical debridement was achieved by debridement with closure over drains or by debridement with open packing.</p><p><b>RESULTS</b>The cohort comprised 14 of 373 patients admitted for acute pancreatitis (3.8%), with an overall mortality rate of 29%. All patients had infected necrosis with positive bacteriological cultures. Eight patients (57%) underwent debridement with closure over drains and 6 patients (43%) underwent debridement with open packing. All mortalities occurred in patients who underwent open packing, who were also associated with a higher mean Acute Physiology and Chronic Health Evaluation (APACHE) II score. The mortality rate in patients who underwent debridement less than 4 weeks after admission was 33% (2 of 6), compared with 25% (2 of 8) in patients who underwent debridement after 4 weeks. There were no mortalities in patients operated on after 6 weeks.</p><p><b>CONCLUSION</b>Surgical debridement with closure of drains and a policy of performing delayed necrosectomy are viable in our population.</p>