COVID-19 Prognostic Models: A Pro-con Debate for Machine Learning vs. Traditional Statistics.

The SARS-CoV-2 virus, which causes the COVID-19 pandemic, has had an unprecedented impact on healthcare requiring multidisciplinary innovation and novel thinking to minimize impact and improve outcomes. Wide-ranging disciplines have collaborated including diverse clinicians (radiology, microbiology, and critical care), who are working increasingly closely with data-science. This has been leveraged through the democratization of data-science with the increasing availability of easy to access open datasets, tutorials, programming languages, and hardware which makes it significantly easier to create mathematical models. To address the COVID-19 pandemic, such data-science has enabled modeling of the impact of the virus on the population and individuals for diagnostic, prognostic, and epidemiological ends. This has led to two large systematic reviews on this topic that have highlighted the two different ways in which this feat has been attempted: one using classical statistics and the other using more novel machine learning techniques. In this review, we debate the relative strengths and weaknesses of each method toward the specific task of predicting COVID-19 outcomes

Operating Room Fomites as Potential Sources for Microbial Transmission in Burns Theatres.

BACKGROUND: Burn patients are susceptible to healthcare-associated infections. Contaminated surfaces play a role in microbial transmission. This study aimed to quantify the degree of contamination of burns theatre fomites during routine clinical use. METHODS: The Patslide Patient Transfer Board (PAT slide) and operating table were investigated using two methods—bacterial swabs to culture viable organisms and adenosine triphosphate (ATP) swabs to measure biological material. Both items were sampled four times a day: before the first case, immediately after a case, immediately before the next case after cleaning and after the terminal clean. RESULTS: Among 82 bacterial samples, four organisms were isolated, including Staphylococcus aureus, Enterobacter cloacae (E. cloacae) x2 and Pseudomonas aeruginosa (P. aeruginosa), all from the PAT slide. The E. cloacae persisted after cleaning. In 9/82 swabs, the ATP count was >10 relative light units (RLU). In all cases where an organism was identified, the ATP count was >10 RLU. Hence the sensitivity and specificity of ATP > 10 RLU in detecting an organism were 100% and 94% respectively. CONCLUSIONS: Within burns theatres, there are instances of bacterial contamination on surfaces that persist despite cleaning. ATP luminometers as a point-of-care device may have a role in determining the cleanliness of surfaces, potentially minimizing onwards-bacterial transmission

Bacteraemia variation during the COVID-19 pandemic; a multi-centre UK secondary care ecological analysis

BackgroundWe investigated for change in blood stream infections (BSI) with Enterobacterales, coagulase negative staphylococci (CoNS), Streptococcus pneumoniae, and Staphylococcus aureus during the first UK wave of SARS-CoV-2 across five London hospitals.MethodsA retrospective multicentre ecological analysis was undertaken evaluating all blood cultures taken from adults from 01 April 2017 to 30 April 2020 across five acute hospitals in London. Linear trend analysis and ARIMA models allowing for seasonality were used to look for significant variation.ResultsOne hundred nineteen thousand five hundred eighty-four blood cultures were included. At the height of the UK SARS-CoV-2 first wave in April 2020, Enterobacterales bacteraemias were at an historic low across two London trusts (63/3814, 1.65%), whilst all CoNS BSI were at an historic high (173/3814, 4.25%). This differed significantly for both Enterobacterales (p = 0.013), CoNS central line associated BSIs (CLABSI) (p ConclusionsSignificantly fewer than expected Enterobacterales BSI occurred during the UK peak of the COVID-19 pandemic; identifying potential causes, including potential unintended consequences of national self-isolation public health messaging, is essential. High rates of CoNS BSI, with evidence of increased CLABSI, but also likely contamination associated with increased use of personal protective equipment, may result in inappropriate antimicrobial use and indicates a clear area for intervention during further waves

Safety, immunogenicity, and reactogenicity of BNT162b2 and mRNA-1273 COVID-19 vaccines given as fourth-dose boosters following two doses of ChAdOx1 nCoV-19 or BNT162b2 and a third dose of BNT162b2 (COV-BOOST): a multicentre, blinded, phase 2, randomised trial

Background Some high-income countries have deployed fourth doses of COVID-19 vaccines, but the clinical need, effectiveness, timing, and dose of a fourth dose remain uncertain. We aimed to investigate the safety, reactogenicity, and immunogenicity of fourth-dose boosters against COVID-19.Methods The COV-BOOST trial is a multicentre, blinded, phase 2, randomised controlled trial of seven COVID-19 vaccines given as third-dose boosters at 18 sites in the UK. This sub-study enrolled participants who had received BNT162b2 (Pfizer-BioNTech) as their third dose in COV-BOOST and randomly assigned them (1:1) to receive a fourth dose of either BNT162b2 (30 µg in 0·30 mL; full dose) or mRNA-1273 (Moderna; 50 µg in 0·25 mL; half dose) via intramuscular injection into the upper arm. The computer-generated randomisation list was created by the study statisticians with random block sizes of two or four. Participants and all study staff not delivering the vaccines were masked to treatment allocation. The coprimary outcomes were safety and reactogenicity, and immunogenicity (antispike protein IgG titres by ELISA and cellular immune response by ELISpot). We compared immunogenicity at 28 days after the third dose versus 14 days after the fourth dose and at day 0 versus day 14 relative to the fourth dose. Safety and reactogenicity were assessed in the per-protocol population, which comprised all participants who received a fourth-dose booster regardless of their SARS-CoV-2 serostatus. Immunogenicity was primarily analysed in a modified intention-to-treat population comprising seronegative participants who had received a fourth-dose booster and had available endpoint data. This trial is registered with ISRCTN, 73765130, and is ongoing.Findings Between Jan 11 and Jan 25, 2022, 166 participants were screened, randomly assigned, and received either full-dose BNT162b2 (n=83) or half-dose mRNA-1273 (n=83) as a fourth dose. The median age of these participants was 70·1 years (IQR 51·6–77·5) and 86 (52%) of 166 participants were female and 80 (48%) were male. The median interval between the third and fourth doses was 208·5 days (IQR 203·3–214·8). Pain was the most common local solicited adverse event and fatigue was the most common systemic solicited adverse event after BNT162b2 or mRNA-1273 booster doses. None of three serious adverse events reported after a fourth dose with BNT162b2 were related to the study vaccine. In the BNT162b2 group, geometric mean anti-spike protein IgG concentration at day 28 after the third dose was 23 325 ELISA laboratory units (ELU)/mL (95% CI 20 030–27 162), which increased to 37 460 ELU/mL (31 996–43 857) at day 14 after the fourth dose, representing a significant fold change (geometric mean 1·59, 95% CI 1·41–1·78). There was a significant increase in geometric mean anti-spike protein IgG concentration from 28 days after the third dose (25 317 ELU/mL, 95% CI 20 996–30 528) to 14 days after a fourth dose of mRNA-1273 (54 936 ELU/mL, 46 826–64 452), with a geometric mean fold change of 2·19 (1·90–2·52). The fold changes in anti-spike protein IgG titres from before (day 0) to after (day 14) the fourth dose were 12·19 (95% CI 10·37–14·32) and 15·90 (12·92–19·58) in the BNT162b2 and mRNA-1273 groups, respectively. T-cell responses were also boosted after the fourth dose (eg, the fold changes for the wild-type variant from before to after the fourth dose were 7·32 [95% CI 3·24–16·54] in the BNT162b2 group and 6·22 [3·90–9·92] in the mRNA-1273 group).Interpretation Fourth-dose COVID-19 mRNA booster vaccines are well tolerated and boost cellular and humoral immunity. Peak responses after the fourth dose were similar to, and possibly better than, peak responses after the third dose

To screen or not to screen?

Introduction Screening for carbapenem resistant organisms (CROs) enables early isolation and prevention of transmission in inpatient healthcare settings. In 2013, the UK Department of Health detailed a national approach to screening for CROs. Implementation of this policy has been variable and the growing numbers of patients who meet screening criteria likely exceeds capacity for isolation. Method We undertook a point prevalence study across two London hospitals to ascertain the frequency of per-policy screening. We assessed the screening of acutely admitted patients in March 2019 at hospital 1 and July 2019 at Hospital 2. We then modelled variations in screening approaches to optimise risk assessments in the context of isolation room availability. Results A total of 199 patients (112 patients at hospital 1 and 87 patients at hospital 2) were included in the analysis. Overall, 27/112 (24%) and 32/87 (37%) met the criteria for CRO screening according to current guidelines. Of these, 0/27 (0%) of patients at hospital 1 and 5/32 (16%) at hospital 2 had a CRO screen performed [p=0.06]. Across both hospitals, the principal risk factors for CRO carriage included: admission to a UK hospital in a high risk area (63/199;32%); admission to a non-UK hospital (3/199/;2%) and previous CRO carriage (1/199;0.5%) albeit with some variation between sites Conclusion Six years after the roll out of the national toolkit, CRO screening is still variable. Reworking of the risk stratification is needed, and we suggest technological approaches with electronic healthcare records may enable more robust screening strategie

Characteristics of Surgical Site Infection Following Colorectal Surgery in a Tertiary Center: Extended-spectrum β-Lactamase-producing Bacteria Culprits in Disease

INTRODUCTION: Surgical site infection (SSI) is a well-known complication of colorectal surgery associated with increased morbidity and hospital stay. Antimicrobial prophylaxis can reduce the risk of SSI by as much as 75%. Extended-spectrum β-lactamase (ESBL)-producing pathogens make the successful use of such prophylaxis a challenge and are a real threat to patient care following colorectal surgery. OBJECTIVE: The aim of this study is to report the common characteristics of SSIs after colorectal surgery and to highlight the prevalence, risk factors, and clinical relevance of ESBL infections among these patients in a tertiary center. MATERIALS AND METHODS: All patients who underwent bowel resection operation (ie, laparoscopy, laparotomy, or laparoscopic-assisted colectomy) for benign or malignant colorectal disease were identified retrospectively from the prospective database of the colorectal department in the authors' tertiary center from March 2015 to March 2016. RESULTS: There were 123 patients included in this study, of which 21% (n = 26) had a SSI. The microorganisms isolated in the surgical sites included Escherichia coli, Pseudomonas aeruginosa, Klebsiella pneumoniae, methicillin-resistant Staphylococcus aureus, Proteus mirabilis, Morganella morganii, and Enterobacter cloacae. Thirty-eight percent of the wound infections grew ESBL-producing pathogens in their wound cultures and 62% grew non-ESBL microbes. CONCLUSIONS: More than one-third of the wound infections were due to ESBL-producing pathogens, which were resistant to the antibiotic prophylaxis given. Inappropriate antibiotic usage can delay postoperative recovery. High-risk patients for ESBL colonization may benefit from preoperative screening based on an established protocol. The cost effectiveness of an ESBL screening program needs to be further studied

Evaluating the long-term impact of an antimicrobial stewardship programme in a central London mixed medical and surgical intensive care unit

BACKGROUND: Antimicrobial overuse causes increased antimicrobial resistance in ICUs; antimicrobial stewardship programmes (ASPs) aim to optimize usage. Following an MDR Acinetobacter baumannii (MRAb) outbreak in 2008, an ASP was implemented at a London ICU, and then continued as a long-term programme. This study aimed to determine long-term changes in antimicrobial prescribing 9 years on. METHODS: Data were collected from ICU patients in 2008 immediately before ASP implementation, and thereafter for 6 month cohort periods in 2010–2011, 2012 and 2017. Antimicrobial usage in DDD per 1000 occupied bed days (OBD) were compared. Multivariate linear regression models for antimicrobial days were fitted, adjusting for APACHE II score and patient days. Antimicrobial resistance in Pseudomonas aeruginosa (as an indicator organism) was compared across cohort periods. FINDINGS: Across 400 patients over 9 years, antimicrobial use changed significantly (P < 0.011) and remained lower in all post-ASP cohorts compared with pre-ASP [(2008; 1827 DDD/1000 OBD), (2010; 1264 DDD/1000 OBD), (2012; 1270 DDD/1000 OBD) and (2017; 1566 DDD/1000 OBD)]. There was reduction in usage of all antimicrobial classes except β-lactams (where there was no significant increase nor decrease, P = 0.178) and aminoglycosides (where there was a significant increase in usage, P < 0.0001). The latter was temporally associated with restrictions on specific carbapenems. There was an increase in carbapenem-resistant P. aeruginosa in 2012 only (P = 0.028) but not subsequently. CONCLUSIONS: Following ASP implementation after an outbreak of MRAb, reduced antimicrobial prescribing was maintained 9 years on. We identify several factors influencing successful long-term maintenance of ASPs in ICUs