Extending the R number by applying hyperparameters of Log Gaussian Cox process models in an epidemiological context to provide insights into COVID-19 positivity in the City of Edinburgh and in students residing at Edinburgh University.

The impact of the COVID-19 pandemic on University students has been a topic of fiery debate and of public health research. This study demonstrates the use of a combination of spatiotemporal epidemiological models to describe the trends in COVID-19 positive cases on spatial, temporal and spatiotemporal scales. In addition, this study proposes new epidemiological metrics to describe the connectivity between observed positivity; an analogous metric to the R number in conventional epidemiology. The proposed indices, Rspatial, Rspatiotemporal and Rscaling will aim to improve the characterisation of the spread of infectious disease beyond that of the COVID-19 framework and as a result inform relevant public health policy. Apart from demonstrating the application of the novel epidemiological indices, the key findings in this study are: firstly, there were some Intermediate Zones in Edinburgh with noticeably high levels of COVID-19 positivity, and that the first outbreak during the study period was observed in Dalry and Fountainbridge. Secondly, the estimation of the distance over which the COVID-19 counts at the halls of residence are spatially correlated (or related to each other) was found to be 0.19km (0.13km to 0.27km) and is denoted by the index, Rspatial. This estimate is useful for public health policy in this setting, especially with contact tracing. Thirdly, the study indicates that the association between the surrounding community level of COVID-19 positivity (Intermediate Zones in Edinburgh) and that of the University of Edinburgh's halls of residence was not statistically significant. Fourthly, this study reveals that relatively high levels of COVID-19 positivity were observed for halls for which higher COVID-19 fines were issued (Spearman's correlation coefficient = 0.34), and separately, for halls which were non-ensuite relatively to those which were not (Spearman's correlation coefficient = 0.16). Finally, Intermediate Zones with the highest positivity were associated with student residences that experienced relatively high COVID-19 positivity (Spearman's correlation coefficient = 0.27).

Evolution and effects of COVID-19 outbreaks in care homes: a population analysis in 189 care homes in one geographical region of the UK.

BACKGROUND: COVID-19 has affected care home residents internationally, but detailed information on outbreaks is scarce. We aimed to describe the evolution of outbreaks of COVID-19 in all care homes in one large health region in Scotland. METHODS: We did a population analysis of testing, cases, and deaths in care homes in the National Health Service (NHS) Lothian health region of the UK. We obtained data for COVID-19 testing (PCR testing of nasopharyngeal swabs for severe acute respiratory syndrome coronavirus 2 [SARS-CoV-2]) and deaths (COVID-19-related and non-COVID-19-related), and we analysed data by several variables including type of care home, number of beds, and locality. Outcome measures were timing of outbreaks, number of confirmed cases of COVID-19 in care home residents, care home characteristics associated with the presence of an outbreak, and deaths of residents in both care homes and hospitals. We calculated excess deaths (both COVID-19-related and non-COVID-19-related), which we defined as the sum of deaths over and above the historical average in the same period over the past 5 years. FINDINGS: Between March 10 and Aug 2, 2020, residents at 189 care homes (5843 beds) were tested for COVID-19 when symptomatic. A COVID-19 outbreak was confirmed at 69 (37%) care homes, of which 66 (96%) were care homes for older people. The size of care homes for older people was strongly associated with a COVID-19 outbreak (odds ratio per 20-bed increase 3·35, 95% CI 1·99-5·63). 907 confirmed cases of SARS-CoV-2 infection were recorded during the study period, and 432 COVID-19-related deaths. 229 (25%) COVID-19-related cases and 99 (24%) COVID-related deaths occurred in five (3%) of 189 care homes, and 441 (49%) cases and 207 (50%) deaths were in 13 (7%) care homes. 411 (95%) COVID-19-related deaths occurred in the 69 care homes with a confirmed COVID-19 outbreak, 19 (4%) deaths were in hospital, and two (<1%) were in one of the 120 care homes without a confirmed COVID-19 outbreak. At the 69 care homes with a confirmed COVID-19 outbreak, 74 excess non-COVID-19-related deaths were reported, whereas ten non-COVID-19-related excess deaths were observed in the 120 care homes without a confirmed COVID-19 outbreak. 32 fewer non-COVID-19-related deaths than expected were reported among care home residents in hospital. INTERPRETATION: The effect of COVID-19 on care homes has been substantial but concentrated in care homes with known outbreaks. A key implication from our findings is that, if community incidence of COVID-19 increases again, many care home residents will be susceptible. Shielding care home residents from potential sources of SARS-CoV-2 infection, and ensuring rapid action to minimise outbreak size if infection is introduced, will be important for any second wave. FUNDING: None.

A case of cutaneous toxigenic Corynebacterium ulcerans likely acquired from a domestic dog.

INTRODUCTION: Corynebacterium ulcerans can produce diphtheria toxin and although still rare, is now the predominant cause of toxigenic diphtheria infection in the UK, making this organism of great clinical and public health importance. Here we describe a cutaneous case, likely secondary to domestic animal contact. CASE PRESENTATION: A 60-year-old female presented with a slow-healing finger-burn wound. A skin swab cultured Corynebacterium ulcerans, which was confirmed to be toxin producing. She resided with her partner and two dogs, one of which had a chronic skin lesion. Her most recent diphtheria vaccine was in 2009. Four close contacts were identified, two of whom were healthcare professionals, and nose and throat swabs were obtained. The patient was treated with clarithromycin (14 day course), diphtheria vaccine and excluded from work until completion of antibiotics and negative clearance swabs. Contacts were given erythromycin (7 day course), vaccinated and healthcare worker contacts excluded from work until swab negative. A veterinary practitioner swabbed the throats and a skin lesion of their dogs. One contact (partner of patient) and all dog swabs were positive. Partial allelic profiles from MLST supported an epidemiological link. The dogs were treated with antibiotics and antimicrobial skin wash. Repeat swabs for the index case, contact and both dogs were negative following treatment. CONCLUSION: This was a rare case of cutaneous diphtheria secondary to Corynebacterium ulcerans with domestic animals the most likely source, although human-to-human contact could not be excluded, with important human and animal public health implications.

Home versus in-patient treatment for deep vein thrombosis.

BACKGROUND: Deep vein thrombosis (DVT) occurs when a blood clot blocks blood flow through a vein, which can occur after surgery, after trauma, or when a person has been immobile for a long time. Clots can dislodge and block blood flow to the lungs (pulmonary embolism (PE)), causing death. DVT and PE are known by the term venous thromboembolism (VTE). Heparin (in the form of unfractionated heparin (UFH)) is a blood-thinning drug used during the first three to five days of DVT treatment. Low molecular weight heparins (LMWHs) allow people with DVT to receive their initial treatment at home instead of in hospital. This is an update of a review first published in 2001 and updated in 2007. OBJECTIVES: To compare the incidence and complications of venous thromboembolism (VTE) in patients treated at home versus patients treated with standard in-patient hospital regimens. Secondary objectives included assessment of patient satisfaction and cost-effectiveness of treatment. SEARCH METHODS: For this update, the Cochrane Vascular Information Specialist searched the Cochrane Vascular Specialised Register (last searched 16 March 2017), the Cochrane Central Register of Controlled Trials (CENTRAL; 2017, Issue 2), and trials registries. We also checked the reference lists of relevant publications. SELECTION CRITERIA: Randomised controlled trials (RCTs) examining home versus hospital treatment for DVT, in which DVT was clinically confirmed and was treated with LMWHs or UFH. DATA COLLECTION AND ANALYSIS: One review author selected material for inclusion, and another reviewed the selection of trials. Two review authors independently extracted data and assessed included studies for risk of bias. Primary outcomes included combined VTE events (PE and recurrent DVT), gangrene, heparin complications, and death. Secondary outcomes were patient satisfaction and cost implications. We performed meta-analysis using fixed-effect models with risk ratios (RRs) and 95% confidence intervals (CIs) for dichotomous data. MAIN RESULTS: We included in this review seven RCTs involving 1839 randomised participants with comparable treatment arms. All seven had fundamental problems including high exclusion rates, partial hospital treatment of many in the home treatment arms, and comparison of UFH in hospital versus LMWH at home. These trials showed that patients treated at home with LMWH were less likely to have recurrence of VTE events than those given hospital treatment with UFH or LMWH (fixed-effect risk ratio (RR) 0.58, 95% confidence interval (CI) 0.39 to 0.86; 6 studies; 1708 participants; P = 0.007; low-quality evidence). No clear difference was seen between groups for major bleeding (RR 0.67, 95% CI 0.33 to 1.36; 6 studies; 1708 participants; P = 0.27; low-quality evidence), minor bleeding (RR 1.29, 95% CI 0.94 to 1.78; 6 studies; 1708 participants; P = 0.11; low-quality evidence), or mortality (RR 0.69, 95% CI 0.44 to 1.09; 6 studies; 1708 participants; P = 0.11; low-quality evidence). The included studies reported no cases of venous gangrene. We could not combine patient satisfaction and quality of life outcomes in meta-analysis owing to heterogeneity of reporting, but two of three studies found evidence that home treatment led to greater improvement in quality of life compared with in-patient treatment at some point during follow-up, and the third study reported that a large number of participants chose to switch from in-patient care to home-based care for social and personal reasons, suggesting it is the patient's preferred option (very low-quality evidence). None of the studies included in this review carried out a full cost-effectiveness analysis. However, a small randomised economic evaluation of the two alternative treatment settings involving 131 participants found that direct costs were higher for those in the in-patient group. These findings were supported by three other studies that reported on their costs (very low-quality evidence).Quality of evidence for data from meta-analyses was low to very low. This was due to risk of bias, as many of the included studies used unclear randomisation techniques, and blinding was a concern for many. Also, indirectness was a concern, as most studies included a large number of participants randomised to the home (LMWH) treatment group who were treated in hospital for some or all of the treatment period. A further issue for some outcomes was heterogeneity that was evident in measurement and reporting of outcomes. AUTHORS' CONCLUSIONS: Low-quality evidence suggests that patients treated at home with LMWH are less likely to have recurrence of VTE than those treated in hospital. However, data show no clear differences in major or minor bleeding, nor in mortality (low-quality evidence), indicating that home treatment is no worse than in-patient treatment for these outcomes. Because most healthcare systems are moving towards more LMWH usage in the home setting it is unlikely that additional large trials will be undertaken to compare these treatments. Therefore, home treatment is likely to become the norm, and further research will be directed towards resolving practical issues by devising local guidelines that include clinical prediction rules, developing biomarkers and imaging that can be used to tailor therapy to disease severity, and providing training for community healthcare workers who administer treatment and monitor treatment progress.

Epidemiology and clinical characteristics of parainfluenza virus 3 outbreak in a Haemato-oncology unit.

OBJECTIVES: We describe molecular investigations of a large hospital outbreak of parainfluenza virus type 3 (PIV3), in which 32 patients became infected. We outline infection control measures that successfully limited further spread of PIV3 in a Haemato-oncology unit. METHODS: Clinical retrospective review of infected haemato-oncology patients was undertaken. PIV3 haemagglutinin sequences from each case (n = 32) and local epidemiologically unlinked controls (n = 53) were compared to identify potential linkage. RESULTS: PIV3-infected patients presented with upper (n = 18) and lower (n = 11) respiratory tract infections, 3 showed pyrexia only and one was asymptomatic. All symptomatic patients received antibiotics; bacterial co-infection was confirmed in eleven patients. PIV3 infections were associated with lower mortality than documented previously; three of the PIV3-infected patients died (3/32; 9%). All deaths were associated with relapsed malignancies, and PIV3 was not believed to be the primary cause of death in any of these patients. Sequences from 27 cases clustered closely together, consistent with nosocomial infections from PIV3 circulating within the ward. Factors favouring transmission were high patient turnaround between the day treatment unit and in-patient ward, and limited isolation facilities for immunocompromised and infected patients, especially within the day treatment unit. New infections reduced to baseline levels three days after enhanced infection control interventions were introduced. CONCLUSIONS: Molecular epidemiological analysis provided evidence for nosocomial transmission of PIV3 infection that facilitated effective implementation of infection control measures. These were instrumental in restricting further spread of the virus among high-risk patients.