\u3ci\u3eEx Uno Plures\u3c/i\u3e: Clonal Reinforcement Drives Evolution of a Simple Microbial Community

A major goal of genetics is to define the relationship between phenotype and genotype, while a major goal of ecology is to identify the rules that govern community assembly. Achieving these goals by analyzing natural systems can be difficult, as selective pressures create dynamic fitness landscapes that vary in both space and time. Laboratory experimental evolution offers the benefit of controlling variables that shape fitness landscapes, helping to achieve both goals. We previously showed that a clonal population of E. coli experimentally evolved under continuous glucose limitation gives rise to a genetically diverse community consisting of one clone, CV103, that best scavenges but incompletely utilizes the limiting resource, and others, CV101 and CV116, that consume its overflow metabolites. Because this community can be disassembled and reassembled, and involves cooperative interactions that are stable over time, its genetic diversity is sustained by clonal reinforcement rather than by clonal interference. To understand the genetic factors that produce this outcome, and to illuminate the community’s underlying physiology, we sequenced the genomes of ancestral and evolved clones. We identified ancestral mutations in intermediary metabolism that may have predisposed the evolution of metabolic interdependence. Phylogenetic reconstruction indicates that the lineages that gave rise to this community diverged early, as CV103 shares only one Single Nucleotide Polymorphism with the other evolved clones. Underlying CV103’s phenotype we identified a set of mutations that likely enhance glucose scavenging and maintain redox balance, but may do so at the expense of carbon excreted in overflow metabolites. Because these overflow metabolites serve as growth substrates that are differentially accessible to the other community members, and because the scavenging lineage shares only one SNP with these other clones, we conclude that this lineage likely served as an ‘‘engine’’ generating diversity by creating new metabolic niches, but not the occupants themselves

Adverse Events of Interest Following Influenza Vaccination in the First Season of Adjuvanted Trivalent Immunization:Retrospective Cohort Study

BACKGROUND: Vaccination is the most effective form of prevention of seasonal influenza; the United Kingdom has a national influenza vaccination program to cover targeted population groups. Influenza vaccines are known to be associated with some common minor adverse events of interest (AEIs), but it is not known if the adjuvanted trivalent influenza vaccine (aTIV), first offered in the 2018/2019 season, would be associated with more AEIs than other types of vaccines. OBJECTIVE: We aim to compare the incidence of AEIs associated with different types of seasonal influenza vaccines offered in the 2018/2019 season. METHODS: We carried out a retrospective cohort study using computerized medical record data from the Royal College of General Practitioners Research and Surveillance Centre sentinel network database. We extracted data on vaccine exposure and consultations for European Medicines Agency–specified AEIs for the 2018/2019 influenza season. We used a self-controlled case series design; computed relative incidence (RI) of AEIs following vaccination; and compared the incidence of AEIs associated with aTIV, the quadrivalent influenza vaccine, and the live attenuated influenza vaccine. We also compared the incidence of AEIs for vaccinations that took place in a practice with those that took place elsewhere. RESULTS: A total of 1,024,160 individuals received a seasonal influenza vaccine, of which 165,723 individuals reported a total of 283,355 compatible symptoms in the 2018/2019 season. Most AEIs occurred within 7 days following vaccination, with a seasonal effect observed. Using aTIV as the reference group, the quadrivalent influenza vaccine was associated with a higher incidence of AEIs (RI 1.46, 95% CI 1.41-1.52), whereas the live attenuated influenza vaccine was associated with a lower incidence of AEIs (RI 0.79, 95% CI 0.73-0.83). No effect of vaccination setting on the incidence of AEIs was observed. CONCLUSIONS: Routine sentinel network data offer an opportunity to make comparisons between safety profiles of different vaccines. Evidence that supports the safety of newer types of vaccines may be reassuring for patients and could help improve uptake in the future

Safety of routine childhood vaccine coadministration versus separate vaccination

Introduction: As new vaccines are developed more vaccine coadministrations vaccines are being offered to make delivery more practical for health systems and patients. We compared the safety of coadministered vaccines with separate vaccination for 20 coadministrations by considering nine types of adverse events following immunisation (AEFI). Methods: Real-life immunisation and adverse event data for this observational cohort study were extracted from the Oxford-Royal College of General Practitioners Research and Surveillance Centre for children registered in the database between 2008 and 2018. We applied the self-controlled case series method to calculate relative incidence ratios (RIR) for AEFI. These RIRs compare the RI of AEFI following coadministration with the RI following separate administration of the same vaccines. Results: We assessed 3 518 047 adverse events and included 5 993 290 vaccine doses given to 958 591 children. 17% of AEFI occurred less and 11% more frequently following coadministration than would have been expected based on the RIs following separate vaccinations, while there was no significant difference for 72% of AEFI. We found amplifying interaction effects for AEFI after five coadministrations comprising three vaccines: for fever (RIR 1.93 (95% CI 1.63 to 2.29)), rash (RIR 1.49 (95% CI 1.29 to 1.74)), gastrointestinal events (RIR 1.31 (95% CI 1.14 to 1.49)) and respiratory events (RIR 1.27 (1.17–1.38)) following DTaP/IPV/Hib+MenC+ PCV; gastrointestinal events (RIR 1.65 (95% CI 1.35 to 2.02)) following DTaP/IPV/Hib+MenC+ RV; fever (RIR 1.44 (95% CI 1.09 to 1.90)) and respiratory events (RIR 1.40 (95% CI 1.25 to 1.57)) following DTaP/IPV/Hib+PCV+ RV; gastrointestinal (RIR 1.48 (95% CI 1.20 to 1.82)) and respiratory events (RIR 1.43 (95% CI 1.26 to 1.63)) following MMR+Hib/MenC+PCV; gastrointestinal events (RIR 1.68 (95% CI 1.07 to 2.64)) and general symptoms (RIR 11.83 (95% CI 1.28 to 109.01)) following MMR+MenC+PCV. Coadministration of MMR+PCV led to more fever (RIR 1.91 (95% CI 1.83 to 1.99)), neurological events (RIR 2.04 (95% CI 1.67 to 2.49)) and rash (RIR 1.06 (95% CI 1.01 to 1.11)) compared with separate administration, DTaP/IPV/Hib+MMR to more musculoskeletal events (RIR 3.56 (95% CI 1.21 to 10.50)) and MMR+MenC to more fever (RIR 1.58 (95% CI 1.37 to 1.82)). There was no indication that unscheduled coadministrations are less safe than scheduled coadministrations. Conclusion: Real-life RIRs of AEFI justify coadministering routine childhood vaccines according to the immunisation schedule. Further research into the severity of AEFI following coadministration is required for a complete understanding of the burden of these AEFI

Over-use of thyroid testing in Canadian and UK primary care in frequent attenders : a cross-sectional study

Dr Greiver is supported through the Gordon F. Cheesbrough Research Chair in Family and Community Medicine from North York General Hospital.Background Thyroid stimulating hormone (TSH) is a common test used to detect and monitor clinically significant hypo- and hyperthyroidism. Population based screening of asymptomatic adults for thyroid disorders is not recommended. Objective The research objectives were to determine patterns of TSH testing in Canadian and English primary care practices, as well as patient and physician practice characteristics associated with testing TSH for primary care patients with no identifiable indication. Methods In this two-year cross-sectional observational study, Canadian and English electronic medical record databases were used to identify patients and physician practices. Cohorts of patients aged 18 years or older, without identifiable indications for TSH testing, were generated from these databases. Analyses were performed using a random-effects logistic regression to determine patient and physician practice characteristics associated with increased testing. We determined the proportion of TSH tests done concurrently with at least one common screening blood test (lipid profile or hemoglobin A1c). Standardized proportions of TSH test per family practice were used to examine the heterogeneity in the populations. Results At least one TSH test was done in 35.97 % (N=489,663) of Canadian patients and 29.36% (N=1,030,489) of English patients. Almost all TSH tests in Canada and England (95.69% and 99.23% respectively) were within the normal range (0.40-5.00 mU/L). A greater number of patient-physician encounters was the strongest predictor of TSH testing. 51.40% of TSH tests in Canada and 76.55% in England were done on the same day as at least one other screening blood test. There was no association between practice size and proportion of asymptomatic patients tested. Conclusions This comparative binational study found TSH patterns suggestive of over-testing and potentially thyroid disorder screening in both countries. There may be significant opportunities to improve appropriateness of TSH ordering in Canada and England and therefore improve allocation of limited system resources.PostprintPeer reviewe

Development of a modified Cambridge Multimorbidity Score for use with SNOMED CT:an observational English primary care sentinel network study

Background People with multiple health conditions are more likely to have poorer health outcomes and greater care and service needs; a reliable measure of multimorbidity would inform management strategies and resource allocation. Aim To develop and validate a modified version of the Cambridge Multimorbidity Score in an extended age range, using clinical terms that are routinely used in electronic health records across the world (Systematized Nomenclature of Medicine — Clinical Terms, SNOMED CT). Design and setting Observational study using diagnosis and prescriptions data from an English primary care sentinel surveillance network between 2014 and 2019. Method In this study new variables describing 37 health conditions were curated and the associations modelled between these and 1-year mortality risk using the Cox proportional hazard model in a development dataset (n = 300 000). Two simplified models were then developed — a 20-condition model as per the original Cambridge Multimorbidity Score and a variable reduction model using backward elimination with Akaike information criterion as the stopping criterion. The results were compared and validated for 1-year mortality in a synchronous validation dataset (n = 150 000), and for 1-year and 5-year mortality in an asynchronous validation dataset (n = 150 000). Results The final variable reduction model retained 21 conditions, and the conditions mostly overlapped with those in the 20-condition model. The model performed similarly to the 37- and 20-condition models, showing high discrimination and good calibration following recalibration. Conclusion This modified version of the Cambridge Multimorbidity Score allows reliable estimation using clinical terms that can be applied internationally across multiple healthcare settings

Incidence of household transmission of acute gastroenteritis (AGE) in a primary care sentinel network (1992-2017): cross-sectional and retrospective cohort study protocol

INTRODUCTION: Acute gastroenteritis (AGE) is a highly transmissible condition. Determining characteristics of household transmission will facilitate development of prevention strategies and reduce the burden of this disease. We are carrying out this study to describe household transmission of medically attended AGE, and explore whether there is an increased incidence in households with young children. METHODS AND ANALYSIS: This study used the Royal College of General Practitioners (RCGP) Research and Surveillance Centre (RSC) primary care sentinel network, comprising data from 1 750 167 registered patients (August 2017 database). We conducted a novel analysis using a ’household key', to identify patients within the same household (n=811 027, mean 2.16 people). A 25-year repeated cross-sectional study will explore the incidence of medically attended AGE overall and then a 5-year retrospective cohort study will describe household transmission of AGE. The cross-sectional study will include clinical data for a 25-year period—1 January 1992 until the 31 December 2017. We will describe the incidence of AGE by age-band and gender, and trends in incidence. The 5-year study will use Poisson and quasi-Poisson regression to identify characteristics of individuals and households to predict medically attended AGE transmitted in the household. This will include whether the household contained a child under 5 years and the age category of the first index case (whether adult or child under 5 years). If there is overdispersion and zero-inflation we will compare results with negative binomial to handle these issues

Middle and Late Pleistocene environmental history of the Marsworth area, south-central England

To elucidate the Middle and Late Pleistocene environmental history of south-central England, we report the stratigraphy, sedimentology, palaeoecology and geochronology of some deposits near the foot of the Chiltern Hills scarp at Marsworth, Buckinghamshire. The Marsworth site is important because its sedimentary sequences contain a rich record of warm stages and cold stages, and it lies close to the Anglian glacial limit. Critical to its history are the origin and age of a brown pebbly silty clay (diamicton) previously interpreted as weathered till. The deposits described infill a river channel incised into chalk bedrock. They comprise clayey, silty and gravelly sediments, many containing locally derived chalk and some with molluscan, ostracod and vertebrate remains. Most of the deposits are readily attributed to periglacial and fluvial processes, and some are dated by optically stimulated luminescence to Marine Isotope Stage (MIS) 6. Although our sedimentological data do not discriminate between a glacial or periglacial interpretation of the diamicton, amino-acid dating of three molluscan taxa from beneath it indicates that it is younger than MIS 9 and older than MIS 5e. This makes a glacial interpretation unlikely, and we interpret the diamicton as a periglacial slope deposit. The Pleistocene history reconstructed for Marsworth identifies four key elements: (1) Anglian glaciation during MIS 12 closely approached Marsworth, introducing far-travelled pebbles such as Rhaxella chert and possibly some fine sand minerals into the area. (2) Interglacial environments inferred from fluvial sediments during MIS 7 varied from fully interglacial conditions during sub-stages 7e and 7c, cool temperate conditions during sub-stage 7b or 7a, temperate conditions similar to those today in central England towards the end of the interglacial, and cool temperate conditions during sub-stage 7a. (3) Periglacial activity during MIS 6 involved thermal contraction cracking, permafrost development, fracturing of chalk bedrock, fluvial activity, slopewash, mass movement and deposition of loess and coversand. (4) Fully interglacial conditions during sub-stage 5e led to renewed fluvial activity, soil formation and acidic weathering

In-pandemic development of an application ontology for COVID-19 surveillance in a primary care sentinel network

Background: Creating an ontology for coronavirus disease 2019 (COVID-19) surveillance should help ensure transparency and consistency. Ontologies formalise conceptualisations at either domain or application level. Application ontologies cross domains and are specified through testable use cases. Our use case was extension of the role of the Oxford Royal College of General Practitioners (RCGP) Research and Surveillance Centre (RSC) to monitor the current pandemic and become an in-pandemic research platform. Objective: To develop an application ontology for COVID-19 which can be deployed across the various use case domains of the Oxford- RCGP RSC research and surveillance activities. Methods: We described our domain-specific use case. The actor was the RCGP RSC sentinel network; the system the course of the COVID-19 pandemic; the outcomes the spread and effect of mitigation measures. We used our established three-step method to develop the ontology, separating ontological concept development from code mapping and data extract validation. We developed a coding system–independent COVID-19 case identification algorithm. As there were no gold standard pandemic surveillance ontologies, we conducted a rapid Delphi consensus exercise through the International Medical Informatics Association (IMIA) Primary Health Care Informatics working group and extended networks. Results: Our use case domains included primary care, public health, virology, clinical research and clinical informatics. Our ontology supported: (1) Case identification, microbiological sampling and health outcomes at both an individual practice and national level; (2) Feedback through a dashboard; (3) A national observatory, (4) Regular updates for Public Health England, and (5) Transformation of the sentinel network to be a trial platform. We have identified a total of 8,627 people with a definite COVID-19 status, 4,240 with probable, and 59,147 people with possible COVID-19, within the RCGP RSC network (N=5,056,075). Conclusions: The underpinning structure of our ontological approach has coped with multiple clinical coding challenges. At a time when there is uncertainty about international comparisons, clarity about the basis on which case definitions and outcomes are made from routine data is essential

Extracting primary care records for prostate cancer patients in the CHHiP multicentre randomised control trial: A healthcare data linkage study

Introduction The aim is to investigate the effect of cardiovascular and diabetes comorbidities on radiotherapy-related side-effects in prostate cancer. Previous research suggests that comorbidities increase the risk of side-effects, but some cardiovascular medications may reduce symptoms by protecting against radiation damage. The evidence is inconclusive and mechanisms are not fully understood. Objective To explore whether routine primary care data can supplement clinical trial data in evaluating the impact of comorbidities and prescription medications on patient outcomes. Approach The CHHiP radiotherapy trial (CRUK/06/16) recruited 3,216 prostate cancer patients from 71 centres in UK, Ireland, Switzerland, and New Zealand between 2002 and 2011. Baseline comorbidity and radiotherapy-related side-effects over time were recorded. This was linked to computerised medical records (CMRs) from the Royal College of General Practitioners (RCGP) Research and Surveillance Centre (RSC) database. RCGP RSC is a network of 192 English general practices with over 2 million patients (2.8% of the population). Results The English population of CHHiP patients (N=2811) was used. 120 CMRs were linked, which exceeded the estimation of 79 linked records. However, six CMRs showed no evidence of regular GP care and a further eight patients were not recruited into the CHHiP trial until after they had de-registered from an RCGP RSC practice. Information on cardiovascular and diabetes comorbidities was extracted for 106 patients. The mean age was 69±7 years, representative of the CHHiP population. From the CMRs, 23 (22%) patients had diabetes and 47 (44%) had hypertension including 37 (35%) who took angiotensin converting enzyme (ACE) inhibitors (medications lowering blood pressure). In addition, 44 (41%) patients took aspirin, 65 (61%) statins (lowering blood lipids) and 14 (13%) took metformin (lowering blood sugar levels).  Conclusion/Implications The small sample limits statistical analysis. However, a clinical trial was successfully linked to GP data to determine comorbidities and medications of patients. This will serve as a pilot for further research. The advantage of data linkage is that it may provide a mechanism for long-term follow-up of radiotherapy-related side-effects