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BackgroundTraditional laboratory-based surveillance of gastrointestinal pathogens is time-consuming, which can impact successful outbreak detection. The INTEGRATE study investigated the utility of metagenomic and metatranscriptomic sequencing for the rapid diagnosis of community-associated gastrointestinal infections.MethodsWe performed an observational study using stool samples from 1,407 patients with acute gastroenteritis, recruited via general practitioners in the UK. 1,067 stool samples were processed using i) routine clinical methods, ii) a molecular multiplex real-time polymerase chain reaction (PCR) assay, and iii) DNA and RNA sequencing. The relationship between assigned taxonomy, routine clinical diagnostics, and PCR was determined with multivariable linear regression models.FindingsThere is a strong, positive relationship between the identification of pathogens in metatranscriptomic reads, and positive results from traditional diagnostics for five out of fifteen pathogens:Campylobacter(pCryptosporidium(pSalmonella(pRotavirus(pSapovirus(pCampylobacter(pSalmonella(pStrong positive relationships between metatranscriptomic reads and positive PCR results were observed for six out of fourteen pathogens: Adenovirus,Campylobacter, Cryptosporidium, Norovirus, RotavirusandSapovirus(pCampylobacter(pSalmonella(pShigella(pA comprehensive transcriptomic profile ofSalmonellaEnteritidis was recovered from the stool of a patient with a subsequently confirmedSalmonellainfection.InterpretationThe metatranscriptomic strategy successfully detected a variety of gastrointestinal pathogens and provided viral and bacterial gene expression profiling directly from stool. We propose that metatranscriptomics could be considered for the future surveillance of gastrointestinal pathogens.FundingThis publication presents independent research supported by the Health Innovation Challenge Fund (WT096200, HICF-T5-354), a parallel funding partnership between the Department of Health and Wellcome Trust. The views expressed in this publication are those of the author(s) and not necessarily those of the Department of Health or Wellcome Trust.

BACKGROUND: Staff actions to prevent infection introduction and transmission in long-term care facilities (LTCFs) were key to reducing morbidity and mortality from COVID-19. Implementing infection control measures (ICMs) requires training, adherence and complex decision making while trying to deliver high quality care. We surveyed LTCF staff in England about their preparedness and morale at three timepoints during the COVID-19 epidemic. METHODS: Online structured survey targeted at LTCF workers (any role) administered at three timepoints (November 2020-January 2021; August-November 2021; March-May 2022). Narrative summary of answers, narrative and statistical summary (proportionality with Pearson’s chi-square or Fisher’s Exact Test) of possible differences in answers between waves. RESULTS: Across all three survey waves, 387 responses were received. Morale, attitudes towards working environment and perception about colleague collaboration were mostly positive at all survey points. Infection control training was perceived as adequate. Staff felt mostly positive emotions at work. The working environment remained challenging. Masks were the single form of PPE most consistently used; eye protection the least used. Mask-wearing was linked to poorer communication and resident discomfort as well as mild negative health impacts on many staff, such as dehydration and adverse skin reactions. Hand sanitiser caused skin irritation. CONCUSIONS: Staff morale and working practices were generally good even though the working environment provided many new challenges that did not exist pre-pandemic.

BackgroundSyndromic surveillance systems are an essential component of public health surveillance and can provide timely detection of infectious disease cases and outbreaks. Whilst surveillance systems are generally embedded within healthcare, there is increasing interest in novel data sources for monitoring trends in illness, such as over-the-counter purchases, internet-based health searches and worker absenteeism. This systematic review considers the utility of school attendance registers in the surveillance of infectious disease outbreaks and occurrences amongst children.MethodsWe searched eight databases using key words related to school absence, infectious disease and syndromic surveillance. Studies were limited to those published after 1st January 1995. Studies based in nursery schools or higher education settings were excluded. Article screening was undertaken by two independent reviewers using agreed eligibility criteria. Data extraction was performed using a standardised data extraction form. Outcomes included estimates of absenteeism, correlation with existing surveillance systems and associated lead or lag times.ResultsFifteen studies met the inclusion criteria, all of which were concerned with the surveillance of influenza. The specificity of absence data varied between all-cause absence, illness absence and syndrome-specific absence. Systems differed in terms of the frequency of data submissions from schools and the level of aggregation of the data. Baseline rates of illness absence varied between 2.3–3.7%, with peak absences ranging between 4.1–9.8%. Syndrome-specific absenteeism had the strongest correlation with other surveillance systems (r = 0.92), with illness absenteeism generating mixed results and all-cause absenteeism performing the least well. A similar pattern of results emerged in terms of lead and lag times, with influenza-like illness (ILI)-specific absence providing a 1–2 week lead time, compared to lag times reported for all-cause absence data and inconsistent results for illness absence data.ConclusionSyndrome-specific school absences have potential utility in the syndromic surveillance of influenza, demonstrating good correlation with healthcare surveillance data and a lead time of 1–2 weeks ahead of existing surveillance measures. Further research should consider the utility of school attendance registers for conditions other than influenza, to broaden our understanding of the potential application of this data for infectious disease surveillance in children.Systematic review registrationPROSPERO 2019 CRD42019119737.

Automated software bots infiltrate online surveys and corrupt data integrity, not to mention waste researcher time and budgets. Although resources exist to help keep bots out and identify bots when they do evade survey barriers, bot attacks may be a persistent problem for online surveys for a long time to come. Bots are evolving -- even as survey designers try ever more sophisticated methods to fend them off and weed their answers out. Vigilance needs to be high and the bot generators should not be under-estimated. We recount here some bot features we encountered after our own survey was attacked that helped to identify them, and that have not been detailed elsewhere. We also discuss reasons why commonly recommended strategies for how to keep bots out may not be feasible for many scientific researchers.

Transmission of Cryptosporidium can occur via contaminated food or water, contact with animals or other people. Exposures are often identified from outbreak investigations, but sources for sporadic disease and pathways to infection are still unclear. The aim of this review is to consolidate the literature to describe exposures associated with human cryptosporidiosis in industrialised countries.Methods followed the recommendations made in the Cochrane Handbook for Systematic Reviews of Interventions. Three steps were used to identify the literature including electronic database searching using PubMed, Scopus and Web Of Science; reference list trawling; and an exploration of the grey literature. Quality was assessed using the Newcastle-Ottawa Scale. Screening of results was undertaken by two reviewers and data extracted using a standardised form. A narrative summary presented. Papers were included if they reported on sporadic cases and were published between 2008 and 2018. Exposures were grouped into pathways.After full-text screening, eight articles (comprising 11 studies) were included, and seven (comprising 10 studies) were suitable for further synthesis. None of the identified grey literature was included. Four studies described case-control methods, two were case-case studies and one cross-sectional. Study year ranged from 1999 to 2017 and the studies were conducted in five, large countries in three continents: Europe (UK and the Netherlands), North America (USA, Canada), and Australia.Included papers investigated water and animal exposures most frequently. Recreational water was not a major source of sporadic illness in this review. The person-to-person pathway represented the most consistent finding, with all three studies reporting on contact with a symptomatic individual demonstrating correlations between exposure and disease. This applied particularly to the home environment, which is increasingly understood to be a significant setting for spread of Cryptosporidium infection. Further work on this would help support public health messaging on preventing spread of disease at home.Systematic review registration: PROSPERO number CRD42017056589.

Background Acute gastroenteritis (AGE) is a highly transmissible condition spreading rapidly between individuals and within households. Rotavirus vaccination was introduced in the UK in 2013. The study objectives were to investigate how acute gastroenteritis incidence changed over 25 years and household incidence of AGE since 2013. Methods Repeated cross-sectional study of Royal College of General Practitioners Research and Surveillance Centre network. We used a negative binomial model to report incidence rate ratio (IRR) using the last 5 years data. We also conducted a retrospective cohort analysis, using a shared gamma frailty model (2013–2017). We explored the impact of child under 5- years, household size, socioeconomic status quintile, and rurality. Results In the cross-sectional analysis, the IRR of AGE in households with a child of under 5 years was 12.20 (95%CI 11.08–13.45-, p p The cohort study revealed that the presence of an under 5 in the household was associated with a higher risk of household presentation (HR = 6.29, 95% CI 5.61–7.06, p Conclusions The incidence of AGE has changed over time: pre-school children, larger households, and living in London were associated with higher rates, and male gender and higher economic status associated with lower rates.

BACKGROUND:Clostridium difficile is capable of causing severe enterocolitis in adults. The significance of toxin-producing C. difficile in children with diarrhea is unclear and practice differs on whether to institute treatment. We aimed to characterize the microbiome in relation to the presence of C. difficile and co-infection with other pathogens and to describe host response to infection. METHODS:Participants were children with acute diarrhea, 0-16 years of age, from whom stool samples had been submitted to the hospital laboratory for routine microbiology/virology. Convenience sampling was used for 50 prospective and 150 retrospective samples. No participants were treated for C. difficile. Rates of culture positivity for C. difficile, presence of toxin and PCR-ribotype were compared between age groups. Presence of other potential pathogens, comorbidities and complications were recorded. Microbiotal diversity was measured by 16S profiling. RESULTS:Nineteen of 77 (25%) children 2 years of age were C. difficile positive, of whom 10 (53%) and 9 (69%), respectively, carried toxigenic strains. Increased Shannon diversity was seen in children carrying C. difficile, with altered milieu. Presence of C. difficile was not associated with adverse clinical outcomes. In stools containing both Norovirus and C. difficile, there was increased relative abundance of verrucomicrobia. CONCLUSIONS:Children with diarrhea regularly carried toxigenic and non-toxigenic strains of C. difficile, demonstrating enhanced microbiotal diversity, and change in milieu, without apparent morbidity. This unexpected finding is contrary to that seen in adults with C. difficile disease.

Background: \ud The SARS-CoV-2 delta (B.1.617.2) variant was first detected in England in March, 2021. It has since rapidly become the predominant lineage, owing to high transmissibility. It is suspected that the delta variant is associated with more severe disease than the previously dominant alpha (B.1.1.7) variant. We aimed to characterise the severity of the delta variant compared with the alpha variant by determining the relative risk of hospital attendance outcomes.\ud \ud Methods: \ud This cohort study was done among all patients with COVID-19 in England between March 29 and May 23, 2021, who were identified as being infected with either the alpha or delta SARS-CoV-2 variant through whole-genome sequencing. Individual-level data on these patients were linked to routine health-care datasets on vaccination, emergency care attendance, hospital admission, and mortality (data from Public Health England's Second Generation Surveillance System and COVID-19-associated deaths dataset; the National Immunisation Management System; and NHS Digital Secondary Uses Services and Emergency Care Data Set). The risk for hospital admission and emergency care attendance were compared between patients with sequencing-confirmed delta and alpha variants for the whole cohort and by vaccination status subgroups. Stratified Cox regression was used to adjust for age, sex, ethnicity, deprivation, recent international travel, area of residence, calendar week, and vaccination status.\ud \ud Findings: \ud Individual-level data on 43 338 COVID-19-positive patients (8682 with the delta variant, 34 656 with the alpha variant; median age 31 years [IQR 17–43]) were included in our analysis. 196 (2·3%) patients with the delta variant versus 764 (2·2%) patients with the alpha variant were admitted to hospital within 14 days after the specimen was taken (adjusted hazard ratio [HR] 2·26 [95% CI 1·32–3·89]). 498 (5·7%) patients with the delta variant versus 1448 (4·2%) patients with the alpha variant were admitted to hospital or attended emergency care within 14 days (adjusted HR 1·45 [1·08–1·95]). Most patients were unvaccinated (32 078 [74·0%] across both groups). The HRs for vaccinated patients with the delta variant versus the alpha variant (adjusted HR for hospital admission 1·94 [95% CI 0·47–8·05] and for hospital admission or emergency care attendance 1·58 [0·69–3·61]) were similar to the HRs for unvaccinated patients (2·32 [1·29–4·16] and 1·43 [1·04–1·97]; p=0·82 for both) but the precision for the vaccinated subgroup was low.\ud \ud Interpretation: \ud This large national study found a higher hospital admission or emergency care attendance risk for patients with COVID-19 infected with the delta variant compared with the alpha variant. Results suggest that outbreaks of the delta variant in unvaccinated populations might lead to a greater burden on health-care services than the alpha variant.\ud \ud Funding: \ud Medical Research Council; UK Research and Innovation; Department of Health and Social Care; and National Institute for Health Research.

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections were rising during early summer 2021 in many countries as a result of the Delta variant. We assessed reverse transcription polymerase chain reaction swab positivity in the Real-time Assessment of Community Transmission–1 (REACT-1) study in England. During June and July 2021, we observed sustained exponential growth with an average doubling time of 25 days, driven by complete replacement of the Alpha variant by Delta and by high prevalence at younger, less-vaccinated ages. Prevalence among unvaccinated people [1.21% (95% credible interval 1.03%, 1.41%)] was three times that among double-vaccinated people [0.40% (95% credible interval 0.34%, 0.48%)]. However, after adjusting for age and other variables, vaccine effectiveness for double-vaccinated people was estimated at between ~50% and ~60% during this period in England. Increased social mixing in the presence of Delta had the potential to generate sustained growth in infections, even at high levels of vaccination.

Background Infection with the Cryptosporidium parasite causes over 4000 cases of diagnosed illness (cryptosporidiosis) in England and Wales each year. The incidence of sporadic disease has not been sufficiently established, and how frequently this arises from contact with other infected people is not well documented. This project aimed to explore potential transmission in the home and attempt to identify asymptomatic infections, which might play a role in transmission. Risk factors and characteristics associated with spread of infection in the home were described including any differences between Cryptosporidium species. Methods The study identified cryptosporidiosis cases from North West England and Wales over a year and invited them and their household to take part. Each household was sent a study pack containing study information and a questionnaire, and stool sample kits to provide samples from consenting household members. Cryptosporidium-positive stool samples, identified by immunofluorescence microscopy, were characterised using molecular methods to help describe any patterns of transmission. Characteristics of households with and without additional cases were described, and compared using odds ratios (OR) and a multivariable logistic regression identified independent risk factors for household transmission. Data collection ran for one year, beginning in September 2018 with an initial pilot phase. Results We enrolled 128 index cases and their households. Additional illness occurred in over a quarter of homes, each reporting an average of two additional cases. The majority of these were undiagnosed and unreported to surveillance. This burden was even greater in households where the index case was infected with C. hominis versus C. parvum, or the index case was under five years old, with mums and siblings most at risk of secondary infection. Only having an index case of C. hominis was independently associated with transmission in the multivariable model (OR 4.46; p = 0.01). Conclusions Cryptosporidium was a considerable burden in the home. At-risk homes were those where the index was less than five years old and/or infected with C. hominis. Of particular risk were female caregivers and siblings. Hygiene advice should be specifically directed here. This work provides evidence for humans as sources of C. hominis infection and that person-person is a key pathway. We recommend that all stools submitted for the investigation of gastrointestinal pathogens are tested for Cryptosporidium to better capture cases, inclusion of speciation data in routine surveillance, and the consideration of specific clinical advice on prevention for high-risk homes.

Symptom profiles have previously been identified for infectious intestinal disease (IID) which distinguish bacterial from viral organisms. However, there is evidence that the seasonality, severity, and duration of IID may differ between children, adults and elderly. A secondary data analysis was undertaken to explore whether symptom profiles for bacterial and viral IID vary across different age groups. Data from 844 cases of IID were divided into three age categories: 65 years. Multivariable logistic regression modelling was used to compare the significance of different symptoms across the three age groups. The odds of bacterial IID in children were increased by onset in the summer, diarrhoea in the absence of vomiting and fever. These symptoms were also associated with lower odds of a viral pathogen. In adults, diarrhoea but no vomiting, bloody diarrhoea and diarrhoea lasting more than 3 days were associated with increased odds of a bacterial organism, whilst onset in the winter or spring and a loss of appetite were associated with viral IID. In the elderly, diarrhoea in the absence of vomiting and diarrhoea lasting more than 3 days were associated with higher odds of bacterial IID and lower odds of a viral cause. Only diarrhoea in the absence of vomiting emerged as a key symptom across all three age groups. Variation in symptom profiles by age has implications for clinicians, public health specialists and epidemiologists who use symptoms to guide presumptive diagnoses in the absence of microbiological confirmation.

Foodborne outbreaks associated with transmission of norovirus are increasingly becoming a public health concern. Foods can be contaminated with faecal material at the point of production or during food preparation, in both the home and in commercial premises. Transmission of norovirus occurs through the faecal-oral route, either via person-to-person contact or through faecal-contamination of food, water, or environmental surfaces. Understanding the role and pathways of norovirus transmission - either via food handlers' hands, contaminated foods or the environment - remains a key public health priority to reduce the burden of norovirus-associated gastroenteritis. However the proportion of norovirus that is typically transferred remains unknown. Understanding this is necessary to estimate the risk of infection and the burden of gastroenteritis caused by norovirus. In this paper we present a novel method of capture, concentration and molecular detection of norovirus from a wider range of complex food matrices than those demonstrated in existing published methods. We demonstrate that this method can be used as a tool to detect and quantify norovirus from naturally contaminated food, and for monitoring norovirus transfer between food handlers' gloved hands, food or the environment. We measure the effect of introducing contamination at different food production process stages, to the final food product, to determine whether this could cause infection and disease. Between 5.9 and 6.3 Log10 cDNA copies/μl of norovirus GII were inoculated onto food handlers' gloved hands, food or the environment and 1.1-7.4% of norovirus contamination was recovered from all samples tested. When interpreted quantitatively, this percentage equates to levels predicted to be sufficient to cause infection and disease through consumption of the final food product, demonstrating a public health risk. Overall detection and quantification of norovirus from foods, food handlers' gloved hands and the environment, when suspected to be implicated in foodborne transmissions, is paramount for appropriate outbreak investigation.

Purpose of review The purpose of the review is to provide an update on control measures for norovirus (NoV), which is the most commonly implicated pathogen in acute gastroenteritis and outbreaks, causing major disruption in nurseries, schools, hospitals and care homes. Recent findings Important developments include the discovery that virus particles, previously considered to be the infectious unit, also occur in clusters, which appear to be more virulent than individual virus particles; a working culture system using human stem-cell derived enteroids; promising results from early phase clinical trials of candidate NoV vaccines, which appear to be safe and immunogenic; chronic NoV affects patients with primary and secondary immune deficiencies. Although several treatments have been used none are supported by well designed clinical trials; infection control procedures are effective if properly implemented. Summary NoV remains an important cause of morbidity and mortality. Although there are exciting developments on the vaccine front, the mainstay of control remains good hand hygiene, adherence to infection control procedures and limiting contamination of food, water and the wider environment. Once vaccines are available there will be important decisions to be made about how best to implement them.

BACKGROUND Infectious intestinal disease (IID) is common, and children are more likely than adults both to have IID and to transmit infection onto others. Before the introduction of the vaccine, rotavirus was the leading cause of severe childhood diarrhea, with norovirus and Campylobacter predominate pathogens. Public health surveillance of IID is primarily based on health care data, and as such, illness that is managed within the community will often go undetected. School attendance registers offer a novel data set that has the potential to identify community cases and outbreaks of IID that would otherwise be missed by current health surveillance systems. Although studies have explored the role of school attendance registers in the monitoring of influenza among children, no studies have been identified that consider this approach in the surveillance of IID. OBJECTIVE The aim of this study is to explore the role and utility of school attendance registers in the detection and surveillance of IID in children. The secondary aims are to estimate the burden of IID on school absenteeism and to assess the impact of the rotavirus vaccine on illness absence among school-aged children. METHODS This study is a retrospective analysis of school attendance registers to investigate whether school absences due to illness can be used to capture seasonal trends and outbreaks of infectious intestinal disease among school-aged children. School absences in Merseyside, United Kingdom will be compared and combined with routine health surveillance data from primary care, laboratories, and telehealth services. These data will be used to model spatial and temporal variations in the incidence of IID and to apportion likely causes to changes in school absenteeism trends. This will be used to assess the potential utility of school attendance data in the surveillance of IID and to estimate the burden of IID absenteeism in schools. It will also inform an analysis of the impact of the rotavirus vaccine on disease within this age group. RESULTS This study has received ethical approval from the University of Liverpool Research Ethics Committee (reference number 1819). Use of general practice data has been approved for the evaluation of rotavirus vaccination in Merseyside by NHS Research Ethics Committee, South Central-Berkshire REC Reference 14/SC/1140. CONCLUSIONS This study is unique in considering whether school attendance registers could be used to enhance the surveillance of IID. Such data have multiple potential applications and could improve the identification of outbreaks within schools, allowing early intervention to reduce transmission both within and outside of school settings. These data have the potential to act as an early warning system, identifying infections circulating within the community before they enter health care settings. School attendance data could also inform the evaluation of vaccination programs, such as rotavirus and, in time, norovirus. INTERNATIONAL REGISTERED REPORT DERR1-10.2196/30078

BackgroundSyndromic surveillance provides public health intelligence to aid in early warning and monitoring of public health impacts (e.g. seasonal influenza), or reassurance when an impact has not occurred. Using information collected during routine patient care, syndromic surveillance can be based on signs/symptoms/preliminary diagnoses. This approach makes syndromic surveillance much timelier than surveillance requiring laboratory confirmed diagnoses.The provision of healthcare services and patient access to them varies globally. However, emergency departments (EDs) exist worldwide, providing unscheduled urgent care to people in acute need. This provision of care makes ED syndromic surveillance (EDSyS) a potentially valuable tool for public health surveillance internationally.The objective of this study was to identify and describe the key characteristics of EDSyS systems that have been established and used globally.MethodsWe systematically reviewed studies published in peer review journals and presented at International Society of Infectious Disease Surveillance conferences (up to and including 2017) to identify EDSyS systems which have been created and used for public health purposes. Search criteria developed to identify “emergency department” and “syndromic surveillance” were applied toNICE healthcare, Global HealthandScopusdatabases.ResultsIn total, 559 studies were identified as eligible for inclusion in the review, comprising 136 journal articles and 423 conference abstracts/papers. From these studies we identified 115 EDSyS systems in 15 different countries/territories across North America, Europe, Asia and Australasia. Systems ranged from local surveillance based on a single ED, to comprehensive national systems. National EDSyS systems were identified in 8 countries/territories: 2 reported inclusion of ≥85% of ED visits nationally (France and Taiwan).ConclusionsEDSyS provides a valuable tool for the identification and monitoring of trends in severe illness. Technological advances, particularly in the emergency care patient record, have enabled the evolution of EDSyS over time. EDSyS reporting has become closer to ‘real-time’, with automated, secure electronic extraction and analysis possible on a daily, or more frequent basis.The dissemination of methods employed and evidence of successful application to public health practice should be encouraged to support learning from best practice, enabling future improvement, harmonisation and collaboration between systems in future.Prospero numberCRD42017069150.

Highlights • We examined trends in infectious intestinal disease (IID) hospitalisations in England. • Overall IID admission rates for children and older adults declined between 2012 & 2017. • Increasing unemployment was associated with increasing IID admission rates. • Healthcare access, underlying morbidity and ethnicity were also associated with IID rates. • Policies should address inequalities in emergency IID hospitalisations., Summary Background Previous studies have observed that infectious intestinal disease (IID) related hospital admissions are higher in more deprived neighbourhoods. These studies have mainly focused on paediatric populations and are cross-sectional in nature. This study examines recent trends in emergency IID admission rates, and uses longitudinal methods to investigate the effects of unemployment (as a time varying measure of neighbourhood deprivation) and other socio-demographic characteristics on IID admissions for adults and children in England. Methods A longitudinal ecological analysis was performed using Hospital Episode Statistics on emergency hospitalisations for IID, collected over the time period 2012–17 across England. Analysis was conducted at the neighbourhood (Lower-layer Super Output Area) level for three age groups (0–14; 15–64; 65+ years). Mixed-effect Poisson regression models were used to assess the relationship between trends in neighbourhood unemployment and emergency IID admission rates, whilst controlling for measures of primary and secondary care access, underlying morbidity and the ethnic composition of each neighbourhood. Results From 2012–17, declining trends in emergency IID admission rates were observed for children and older adults overall, while rates increased for some sub-groups in the population. Each 1 percentage point increase in unemployment was associated with a 6.3, 2.4 and 4% increase in the rate of IID admissions per year for children [IRR=1.06, 95%CI 1.06–1.07], adults [IRR=1.02, 95%CI 1.02–1.03] and older adults [IRR=1.04, 95%CI 1.036–1.043], respectively. Increases in poor primary care access, the percentage of people from a Pakistani ethnic background, and the prevalence of long-term health problems, in a neighbourhood, were also associated with increases in IID admission rates. Conclusions Increasing trends in neighbourhood deprivation, as measured by unemployment, were associated with increases in emergency IID admission rates for children and adults in England, despite controlling for measures of healthcare access, underlying morbidity and ethnicity. Research is needed to improve understanding of the mechanisms that explain these inequalities, so that effective policies can be developed to reduce the higher emergency IID admission rates experienced by more disadvantaged communities.

Children are important transmitters of infection. Within schools they encounter large numbers of contacts and infections can spread easily causing outbreaks. However, not all schools are affected equally. We conducted a retrospective analysis of school outbreaks to identify factors associated with the risk of gastroenteritis, influenza, rash or other outbreaks. Data on reported school outbreaks in England were obtained from Public Health England and linked with data from the Department for Education and the Office for Standards in Education, Children's Services and Skills (Ofsted). Primary and all-through schools were found to be at increased risk of outbreaks, compared with secondary schools (odds ratio (OR) 5.82, 95% confidence interval (CI) 4.50–7.58 and OR 4.66, 95% CI 3.27–6.61, respectively). School size was also significantly associated with the risk of outbreaks, with higher odds associated with larger schools. Attack rates were higher in gastroenteritis and influenza outbreaks, with lower attack rates associated with rashes (relative risk 0.17, 95% CI 0.15–0.20). Deprivation and Ofsted rating were not associated with either outbreak occurrence or the subsequent attack rate. This study identifies primary and all-through schools as key settings for health protection interventions. Public health teams need to work closely with these schools to encourage early identification and reporting of outbreaks.

Shiga toxin-producing Escherichia coli is carried in the intestine of ruminant animals, and outbreaks have occurred after contact with ruminant animals or their environment. The presence of STEC virulence genes in the environment was investigated along recreational walking paths in the North West and East Anglia regions of England. In all, 720 boot sock samples from walkers' shoes were collected between April 2013 and July 2014. Multiplex PCR was used to detect E. coli based on the amplification of the uidA gene and investigate STEC-associated virulence genes eaeA, stx1 and stx2. The eaeA virulence gene was detected in 45·5% of the samples, where stx1 and/or stx2 was detected in 12·4% of samples. There was a difference between the two regions sampled, with the North West exhibiting a higher proportion of positive boot socks for stx compared to East Anglia. In univariate analysis, ground conditions, river flow and temperature were associated with positive boot socks. The detection of stx genes in the soil samples suggests that STEC is present in the English countryside and individuals may be at risk for infection after outdoor activities even if there is no direct contact with animals. SIGNIFICANCE AND IMPACT OF THE STUDY: Several outbreaks within the UK have highlighted the danger of contracting Shiga toxin-producing Escherichia coli from contact with areas recently vacated by livestock. This is more likely to occur for STEC infections compared to other zoonotic bacteria given the low infectious dose required. While studies have determined the prevalence of STEC within farms and petting zoos, determining the risk to individuals enjoying recreational outdoor activities that occur near where livestock may be present is less researched. This study describes the prevalence with which stx genes, indicative of STEC bacteria, were found in the environment in the English countryside.

Background:\ud Campylobacter jejuni is the most common bacterial cause of human infectious intestinal disease.\ud \ud Methods:\ud We genome sequenced 601 human C. jejuni isolates, obtained from two large prospective studies of infectious intestinal disease (IID1 [isolates from 1993–1996; n = 293] and IID2 [isolates from 2008–2009; n = 93]), the INTEGRATE project [isolates from 2016–2017; n = 52] and the ENIGMA project [isolates from 2017; n = 163].\ud \ud Results:\ud There was a significant increase in the prevalence of the T86I mutation conferring resistance to fluoroquinolone between each of the three later studies (IID2, INTEGRATE and ENIGMA) and IID1. Although the distribution of major multilocus sequence types (STs) was similar between the studies, there were changes in both the abundance of minority STs associated with the T86I mutation, and the abundance of clones within single STs associated with the T86I mutation.\ud \ud Discussion:\ud Four population-based studies of community diarrhoea over a 25 year period revealed an increase over time in the prevalence of the T86I amongst isolates of C. jejuni associated with human gastrointestinal disease in the UK. Although associated with many STs, much of the increase is due to the expansion of clones associated with the resistance mutation.

Background Infectious intestinal disease (IID) is common, and children are more likely than adults both to have IID and to transmit infection onto others. Before the introduction of the vaccine, rotavirus was the leading cause of severe childhood diarrhea, with norovirus and Campylobacter predominate pathogens. Public health surveillance of IID is primarily based on health care data, and as such, illness that is managed within the community will often go undetected. School attendance registers offer a novel data set that has the potential to identify community cases and outbreaks of IID that would otherwise be missed by current health surveillance systems. Although studies have explored the role of school attendance registers in the monitoring of influenza among children, no studies have been identified that consider this approach in the surveillance of IID. Objective The aim of this study is to explore the role and utility of school attendance registers in the detection and surveillance of IID in children. The secondary aims are to estimate the burden of IID on school absenteeism and to assess the impact of the rotavirus vaccine on illness absence among school-aged children. Methods This study is a retrospective analysis of school attendance registers to investigate whether school absences due to illness can be used to capture seasonal trends and outbreaks of infectious intestinal disease among school-aged children. School absences in Merseyside, United Kingdom will be compared and combined with routine health surveillance data from primary care, laboratories, and telehealth services. These data will be used to model spatial and temporal variations in the incidence of IID and to apportion likely causes to changes in school absenteeism trends. This will be used to assess the potential utility of school attendance data in the surveillance of IID and to estimate the burden of IID absenteeism in schools. It will also inform an analysis of the impact of the rotavirus vaccine on disease within this age group. Results This study has received ethical approval from the University of Liverpool Research Ethics Committee (reference number 1819). Use of general practice data has been approved for the evaluation of rotavirus vaccination in Merseyside by NHS Research Ethics Committee, South Central-Berkshire REC Reference 14/SC/1140. Conclusions This study is unique in considering whether school attendance registers could be used to enhance the surveillance of IID. Such data have multiple potential applications and could improve the identification of outbreaks within schools, allowing early intervention to reduce transmission both within and outside of school settings. These data have the potential to act as an early warning system, identifying infections circulating within the community before they enter health care settings. School attendance data could also inform the evaluation of vaccination programs, such as rotavirus and, in time, norovirus. International Registered Report Identifier (IRRID) DERR1-10.2196/30078

Background Outbreaks of infectious gastroenteritis are common in care homes for the elderly. Norovirus can cause these outbreaks, but diagnosis is frequently based solely on clinical characteristics. Our objective in this study was to describe the epidemiology of norovirus and other gastrointestinal pathogens in these settings. Methods We analysed surveillance data from gastroenteritis outbreaks reported in North East England between 04 July 2016 to 01 July 2018. Stool samples taken during these outbreaks were tested for a range of viral and bacterial pathogens. We described the epidemiology of these outbreaks and explored the characteristics of norovirus outbreaks versus from other viral causes using multivariable logistic regression. Results From the 566 care home gastroenteritis outbreaks in this study, we found that norovirus was the pathogen most frequently isolated. Norovirus was detected in 64% of outbreaks with a pathogen identified. Sapovirus was found in 13%; rotavirus in 11%. We found that norovirus outbreaks were associated with higher attack rates (aOR 1.03, 95% CI 1.01–1.05) and fewer cases sampled (aOR 0.74, 95% CI 0.60–0.91), compared to outbreaks caused by other viral pathogens. Conclusions These results are important as they quantify the contribution of norovirus to gastroenteritis outbreaks in care homes. Given this evidence, we emphasize the importance of non-specific outbreak interventions that can affect the impact of all such outbreaks. We further recommend that these findings are used to inform the implementation strategies of any norovirus-specific interventions such as a norovirus vaccine.

ObjectivesHaemolytic uraemic syndrome (HUS) following Shiga toxin-producingEscherichia coli(STEC) infection is the the most common cause of acute renal failure among children in the UK. This study explored differential progression from STEC to HUS by social, demographic and clinical risk factors.MethodsWe undertook a retrospective cohort study linking two datasets. We extracted data on paediatric STEC and HUS cases identified in the Public Health England National Enhanced Surveillance System for STEC and British Paediatric Surveillance Unit HUS surveillance from 1 October 2011 to 31 October 2014. Using logistic regression, we estimated the odds of HUS progression by risk factors.Results1059 paediatric STEC cases were included in the study, of which 207 (19.55%, 95% CI 17% to 22%) developed HUS. In the fully adjusted model, the odds of progression to HUS were highest in those aged 1–4 years (OR 4.93, 95% CI 2.30 to 10.56, compared with 10–15 years), were infected with an Shiga toxin (stx)2-only strain (OR 5.92, 95% CI 2.49 to 14.10), were prescribed antibiotics (OR 8.46, 95% CI 4.71 to 15.18) and had bloody diarrhoea (OR 3.56, 95% CI 2.04 to 6.24) or vomiting (OR 4.47, 95% CI 2.62 to 7.63), but there was no association with progression to HUS by socioeconomic circumstances or rurality.ConclusionCombining data from an active clinical surveillance system for HUS with the national enhanced STEC surveillance system suggests that 20% of diagnosed paediatric STEC infections in England resulted in HUS. No relationship was found with socioeconomic status or rurality of cases, but differences were demonstrated by age,stxtype and presenting symptoms.

Contamination of bivalve shellfish, particularly oysters, with norovirus is recognised as a food safety risk and a potential contributor to the overall burden of gastroenteritis in the community. The United Kingdom (UK) has comprehensive national baseline data on the prevalence, levels, and seasonality of norovirus in oysters in production areas resulting from a previous two-year study (2009–2011). However, previously, data on final product as sold to the consumer have been lacking. As part of a wider project to establish the overall burden of foodborne norovirus in the UK, this study aimed to address this data gap. A one-year survey of oysters collected from the point-of-sale to the consumer was carried out from March 2015 to March 2016. A total of 630 samples, originating in five different European Union Member States, were collected from 21 regions across the UK using a randomised sampling plan, and tested for norovirus using a method compliant with ISO 15216-1, in addition to Escherichia coli as the statutory indicator of hygiene status. As in the previous production area study, norovirus RNA was detected in a high proportion of samples (68.7%), with a strong winter seasonality noted. Some statistically significant differences in prevalences and levels in oysters from different countries were noted, with samples originating in the Netherlands showing lower prevalences and levels than those from either the UK or Ireland. Overall, levels detected in positive samples were considerably lower than seen previously. Investigation of potential contributing factors to this pattern of results was carried out. Application of normalisation factors to the data from the two studies based on both the numbers of norovirus illness reports received by national surveillance systems, and the national average environmental temperatures during the two study periods resulted in a much closer agreement between the two data sets, with the notably different numbers of illness reports making the major contribution to the differences observed in norovirus levels in oysters. The large majority of samples (76.5%) contained no detectable E. coli; however, in a small number of samples (2.4%) levels above the statutory end product standard (230 MPN/100 g) were detected. This study both revealed the high prevalence of norovirus RNA in oysters directly available to the UK consumer, despite the high level of compliance with the existing E. coli-based health standards, while also highlighting the difficulty in comparing the results of surveys carried out in different time periods, due to variability in risk factors. Electronic supplementary material The online version of this article (10.1007/s12560-018-9338-4) contains supplementary material, which is available to authorized users.

Background The burden of infectious intestinal disease (IID) in the UK is substantial. Negative consequences including sickness absence are common, but little is known about the social patterning of these outcomes, or the extent to which they relate to disease severity. Methods We performed a cross-sectional analysis using IID cases identified from a large population-based survey, to explore the association between socioeconomic status (SES) and symptom severity and sickness absence; and to assess the role of symptom severity on the relationship between SES and absence. Regression modelling was used to investigate these associations, whilst controlling for potential confounders such as age, sex and ethnicity. Results Among 1164 cases, those of lower SES versus high had twice the odds of experiencing severe symptoms (OR 2.2, 95%CI;1.66–2.87). Lower SES was associated with higher odds of sickness absence (OR 1.8, 95%CI;1.26–2.69), however this association was attenuated after adjusting for symptom severity (OR 1.4, 95%CI;0.92–2.07). Conclusions In a large sample of IID cases, those of low SES versus high were more likely to report severe symptoms, and sickness absence; with greater severity largely explaining the higher absence. Public health interventions are needed to address the unequal consequences of IID identified. Electronic supplementary material The online version of this article (doi:10.1186/s12879-017-2551-1) contains supplementary material, which is available to authorized users.

Lack of disease surveillance in small companion animals worldwide has contributed to a deficit in our ability to detect and respond to outbreaks. In this paper we describe the first real-time syndromic surveillance system that conducts integrated spatio-temporal analysis of data from a national network of veterinary premises for the early detection of disease outbreaks in small animals. We illustrate the system’s performance using data relating to gastrointestinal disease in dogs and cats. The data consist of approximately one million electronic health records for dogs and cats, collected from 458 UK veterinary premises between March 2014 and 2016. For this illustration, the system predicts the relative reporting rate of gastrointestinal disease amongst all presentations, and updates its predictions as new data accrue. The system was able to detect simulated outbreaks of varying spatial geometry, extent and severity. The system is flexible: it generates outcomes that are easily interpretable; the user can set their own outbreak detection thresholds. The system provides the foundation for prompt detection and control of health threats in companion animals.

Within the European Union (EU), microbiological criteria (MC) sampling for Salmonella in poultry was introduced in 2005. In particular, processors had to meet a target of fewer than seven positive samples out of 50. However, processors producing small amounts of poultry meat did not have to sample if national authorities determined this was an acceptable risk. The U.K. Food Standards Agency (FSA) thus has a sampling regime based on throughput that allows smaller processors not to sample. In 2011, the limit of 7/50 was reduced to 5/50. Given the current uncertainty regarding U.K. trade relations with the EU, the U.K. FSA decided to conduct a new risk assessment of the risks of Salmonella produced by smaller processors, to determine whether sampling was now necessary. Current evidence suggests that an MC sampling regime in smaller slaughterhouses is not warranted from a national public health perspective. Because of the insensitivities of the MC sampling scheme, the introduction of MC sampling into smaller slaughterhouses would only be necessary if the suspected carcass prevalence was 15% or more. While our analysis is prone to uncertainty, we estimated that the carcass prevalence in smaller processors is below this. Thus, we recommended that the current sampling framework, allowing smaller processors not to sample, was still applicable.

Shiga toxin-producing Escherichia coli (STEC) infection can cause serious illness including haemolytic uraemic syndrome. The role of socio-economic status (SES) in differential clinical presentation and exposure to potential risk factors amongst STEC cases has not previously been reported in England. We conducted an observational study using a dataset of all STEC cases identified in England, 2010–2015. Odds ratios for clinical characteristics of cases and foodborne, waterborne and environmental risk factors were estimated using logistic regression, stratified by SES, adjusting for baseline demographic factors. Incidence was higher in the highest SES group compared to the lowest (RR 1.54, 95% CI 1.19–2.00). Odds of Accident and Emergency attendance (OR 1.35, 95% CI 1.10–1.75) and hospitalisation (OR 1.71, 95% CI 1.36–2.15) because of illness were higher in the most disadvantaged compared to the least, suggesting potential lower ascertainment of milder cases or delayed care-seeking behaviour in disadvantaged groups. Advantaged individuals were significantly more likely to report salad/fruit/vegetable/herb consumption (OR 1.59, 95% CI 1.16–2.17), non-UK or UK travel (OR 1.76, 95% CI 1.40–2.27; OR 1.85, 95% CI 1.35–2.56) and environmental exposures (walking in a paddock, OR 1.82, 95% CI 1.22–2.70; soil contact, OR 1.52, 95% CI 2.13–1.09) suggesting other unmeasured risks, such as person-to-person transmission, could be more important in the most disadvantaged group.