Background Whole-genome sequencing (WGS) is the gold standard diagnostic tool to identify and genetically characterise emerging pathogen mutations (variants), but cost, capacity, and timeliness limit its use when large populations need rapidly assessing. We assessed the potential of genotyping assays to provide accurate and timely variant information at scale by retrospectively examining surveillance for SARS-CoV-2 variants in England between March and September, 2021, when genotyping assays were used widely for variant detection. Methods We chose a panel of four RT-PCR genotyping assays to detect circulating variants of SARS-COV-2 in England and developed a decision algorithm to assign a probable SARS-CoV-2 variant to samples using the assay results. We extracted surveillance data from the UK Health Security Agency databases for 115 934 SARS-CoV-2-positive samples (March 1-Sept 6, 2021) when variant information was available from both genotyping and WGS. By comparing the genotyping and WGS variant result, we calculated accuracy metrics (ie, sensitivity, specificity, and positive predictive value [PPV]) and the time difference between the sample collection date and the availability of variant information. We assessed the number of samples with a variant assigned from genotyping or WGS, or both, over time. Findings Genotyping and an initial decision algorithm (April 10-May 11, 2021 data) were accurate for key variant assignment: sensitivities and PPVs were 0.99 (95% CI 0.99-0.99) for the alpha, 1.00 (1.00-1.00) for the beta, and 0.91 (0.80-1.00) for the gamma variants; specificities were 0.97 (0.96-0.98), 1.00 (1.00-1.00), and 1.00 (1.00-1.00), respectively. A subsequent decision algorithm over a longer time period (May 27-Sept 6, 2021 data) remained accurate for key variant assignment: sensitivities were 0.91 (95% CI 0.74-1.00) for the beta, 0.98 (0.98-0.99) for the delta, and 0.93 (0.81-1.00) for the gamma variants; specificities were 1.00 (1.00-1.00), 0.96 (0.96-0.97), and 1.00 (1.00-1.00), respectively; and PPVs were 0.83 (0.62-1.00), 1.00 (1.00-1.00), and 0.78 (0.59-0.97), respectively. Genotyping produced variant information a median of 3 days (IQR 2-4) after the sample collection date, which was faster than with WGS (9 days [8-11]). The flexibility of genotyping enabled a nine-times increase in the quantity of samples tested for variants by this method (from 5000 to 45 000). Interpretation RT-PCR genotyping assays are suitable for high-throughput variant surveillance and could complement WGS, enabling larger scale testing for known variants and timelier results, with important implications for effective public health responses and disease control globally, especially in settings with low WGS capacity. However, the choice of panels of RT-PCR assays is highly dependent on database information on circulating variants generated by WGS, which could limit the use of genotyping assays when new variants are emerging and spreading rapidly.

Objectives The Wirral Assistive Technology Programme (WAT) has operated across the whole population of the Borough for 3 years. It includes the installation of telecare technologies such as falls alerts and movement sensors to prolong users’ independence and reduce use of secondary care. Qualitative evaluation of user and carer perspectives indicated a reduction in admissions as a result of the technology and we sought to demonstrate this at a population level. Methods Secondary care episodes for A&E, admissions and outpatients were temporally analysed to identify changed trend in secondary care usage as a result of installation for 400 users. Primary diagnoses at point of secondary care engagement were categorised to discern those that might have been mediated by WAT (e.g. falls and fractures) from those likely to be incidental (e.g. infection). The nature of the WAT service made the identification of a control group challenging and it was necessary to try and establish the counterfactual of secondary care usage in an equivalent group of patients not engaged with WAT. We used Patients at Risk of Re-Hospitalisation (PARR) scores which are routinely assigned to every patient discharge in Wirral to identify an equivalent group of patients not engaged with WAT and compared trends of secondary care usage as above. Controls were selected on the basis of an equivalent PARR score to an AT user on the same date as that user’s final discharge before installation of AT. Results A&E and inpatient episodes showed regression to the mean around the point of AT installation, both for AT-related and unrelated diagnoses (between 660 days pre-installation and 240 days post-). Outpatient episodes showed a stable trend. We found no evidence that AT installation reduced the average number of secondary care episodes per patient, reduced the average PARR score or reduced the average length of hospital stay in comparison to controls. Conclusions Although conceptually and qualitatively WAT should be impacting secondary care episodes, we could find no evidence of this. This has important implications for the way the programme is currently integrated with other local re-ablement schemes, how it is monitored and what incentives there are in the discharge system to promote its use. This paper will outline actions taken to embed the programme since the evaluation was completed (September 2011).

Objective: Managing an outbreak of gastroenteritis (GI) on board a cruise ship while minimising disruption to passengers' on board and shore visit activities is difficult. For this reason it is important to understand the complex patterns of transmission in a closed community. We describe the epidemiological investigation of an outbreak of norovirus during an international cruise.Methods: A retrospective cohort study was conducted using information from lists routinely maintained by the travel company, including the passenger manifest, and organised coach tour lists. Information on air-conditioning (AC) systems was used to assess the possible sources of exposures.Findings: Of the 1194 passengers 191 (16%) and 5 crew (<1%) became ill with GI symptoms. The attack rate was higher amongst passengers whose cabin was on the main deck (RR 3.41, 95% CI 1.47-7.94) that houses both passengers' cabins and leisure facilities including shops. Passengers who went on one of the organised coach tours where there were symptomatic passengers were at an increased risk of infection (RR 2.14, CI 1.51-3.03). Analysis of the 56 AC sections on the ship and did not detect an association with infection.Conclusions: Patterns of transmission of norovirus on a cruise ship are complex. Our study suggests infections are more likely among those passengers staying in areas of the ship that are highly transited or used for communal activities and more difficult to clean. Emphasis on the importance of early reporting of symptoms can help minimise transmission. Internationally agreed guidelines on the management of outbreaks on cruise ships are needed. Crown Copyright (C) 2010 Published by Elsevier Ltd on behalf of The British Infection Society. All rights reserved.

Viruses are the major pathogens of community-acquired (CA) acute gastroenteritis (AGE) in children, but their role in healthcare-associated (HA) AGE is poorly understood. Children with AGE hospitalized at Alder Hey Children's Hospital, Liverpool, UK, were enrolled over a 2-year period. AGE was classified as HA if diarrhea developed >= 48 hours after admission. Rotavirus, norovirus, adenovirus 40/41, astrovirus, and sapovirus were detected by PCR. A total of 225 children with HA-AGE and 351 with CA-AGE were enrolled in the study. HA viral gastroenteritis constituted one fifth of the diarrheal diseases among hospitalized children and commonly occurred in critical care areas. We detected >= 1 virus in 120 (53%) of HA-AGE cases; rotavirus (31%), norovirus (16%), and adenovirus 40/41 (15%) were the predominant viruses identified. Molecular evidence indicated rotaviruses and noroviruses were frequently introduced into the hospital from the community. Rotavirus vaccines could substantially reduce the incidence of HA-AGE in children.

SUMMARYA national outbreak of verotoxin-producingEscherichia coliO157 infection affected five English regions and Wales. Twelve cases were associated with lemon-and-coriander chicken wrap from a single supermarket chain consumed over a 5-day period. An outbreak investigation aimed to identify the source of infection. Descriptive epidemiology and phenotypic and genotypic tests on human isolates indicated a point-source outbreak; a case-control study showed a very strong association between consumption of lemon-and-coriander chicken wrap from the single supermarket chain and being a case (OR 46·40, 95% CI 5·39–∞,P=0·0002). Testing of raw ingredients, products and faecal samples from staff in the food production unit did not yield any positive results. The outbreak was probably caused by one contaminated batch of an ingredient in the chicken wrap. Even when current best practice is in place, ready-to-eat foods can still be a risk for widespread infection.

ABSTRACT This study uses multilocus sequence typing (MLST) to investigate the epidemiology of Campylobacter coli in a continuous study of a population in Northwest England. All cases of Campylobacter identified in four Local Authorities (government administrative boundaries) between 2003 and 2006 were identified to species level and then typed, using MLST. Epidemiological information was collected for each of these cases, including food and recreational exposure variables, and the epidemiologies of C. jejuni and C. coli were compared using case-case methodology. Samples of surface water thought to represent possible points of exposure to the populations under study were also sampled, and campylobacters were typed with multilocus sequence typing. Patients with C. coli were more likely to be older and female than patients with C. jejuni . In logistic regression, C. coli infection was positively associated with patients eating undercooked eggs, eating out, and reporting problems with their water supply prior to illness. C. coli was less associated with consuming pork products. Most of the cases of C. coli yielded sequence types described elsewhere in both livestock and poultry, but several new sequence types were also identified in human cases and water samples. There was no overlap between types identified in humans and surface waters, and genetic analysis suggested three distinct clades but with several “intermediate” types from water that were convergent with the human clade. There is little evidence to suggest that epidemiological differences between human cases of C. coli and C. jejuni are a result of different food or behavioral exposures alone.

In a study of Campylobacter infection in northwestern England, 2003–2006, C. jejuni multilocus sequence type (ST)–45 was associated with early summer onset and was the most prevalent C. jejuni type in surface waters. ST-45 is likely more adapted to survival outside a host, making it a key driver of transmission between livestock, environmental, and human settings.

Rotavirus is a major cause of acute, community-acquired gastroenteritis in infants and young children but its importance in healthcare-associated paediatric gastroenteritis is much less well understood. A prospective study was undertaken at the Royal Liverpool Children's NHS Trust, Liverpool, UK. We enrolled 243 children with acute gastroenteritis (AGE) who were hospitalised between January and May 2006. Rotavirus was detected in faecal specimens by enzyme immunoassay. This virus was responsible for 17/91 cases (19%) of healthcare-associated AGE and 54/152 cases (36%) of community-acquired AGE. Sixteen children with healthcare-associated acute rotavirus gastroenteritis required source isolation and eight received intravenous rehydration. We conclude that rotavirus is an important cause of healthcare-associated AGE in a large paediatric hospital. Rotavirus vaccines represent a public health tool that could prevent the majority of symptomatic rotavirus infections within this healthcare setting.

Detailed understanding of the epidemiology of Campylobacter is increasingly facilitated through use of universal and reproducible techniques for accurate strain differentiation and subtyping. Multilocus sequence typing (MLST) enables discriminatory subtyping and grouping of isolate types into genetically related clonal complexes; it also has the advantage of ease of application and repeatability. Recent studies suggest that a measure of host association may be distinguishable with this system. We describe the first continuous population-based survey to investigate the potential of MLST to resolve questions of campylobacteriosis epidemiology. We demonstrate the ability of MLST to identify variations in the epidemiology of campylobacteriosis between distinct populations and describe the distribution of key subtypes of interest.

Between 1996 and 2000, rates of cryptosporidiosis in North West England were significantly higher than overall in England and Wales, particularly during the first half of each year. In addition, during the second quarter of each year in this period, up to 40% of all cases recorded in England and Wales were from the North West Region. In 2001, cryptosporidiosis dramatically decreased throughout the United Kingdom and the springtime excess of cases formerly seen in the North West was no longer apparent. This changed epidemiology was due to a decline in cases of Cryptosporidium parvum (formerly genotype 2), associated with zoonotic transmission. Although the initial loss of a spring peak of infection corresponded with the outbreak of foot-and-mouth disease throughout the United Kingdom, its continued absence relates to major structural changes in the North West public water supply. This study highlights the far-reaching public health benefit of local working relationships in addressing re-occurring disease issues.

The creation of the new Health Protection Agency in England and Wales has brought both the challenge and the opportunity for broadening current surveillance systems to incorporate the full range of agents likely to cause harm to human health. The new surveillance system must be capable of measuring, recording and reporting the effects of infectious disease, chemical, and radiological hazards on human health. The pathways resulting in adverse human health are complex and infection control efforts are often hampered as a result. We describe an approach to health protection surveillance that draws on models of hazard/exposure/ outcome and the use of Hazard Analysis Critical Control Points to identify points at which the application of surveillance and intervention would have the maximum impact on final health outcome. This approach facilitates the identification of key surveillance partnerships and proposes the integration of existing surveillance networks. Illustrations of the application of this approach to common problems of infection control are given in the regional surveillance of Legionnaires' disease and Campylobacter in north-west England. We propose that the principles of this approach should be adopted in England and Wales to ensure that the new health protection function achieves its goals.

EDITOR—We support Jefferson's recommendation to strengthen surveillance capability for influenza, especially the identification of circulating virus amidst non-specific respiratory illness.1 In north west England the Health Protection Agency has been developing influenza surveillance to increase the coverage of the national consultation system for general practitioners (run by the Royal College of General Practitioners),2 after a successful pilot scheme in 1999 that detected a …

OBJECTIVES:To identify sources and routes of infection for sporadic cases of campylobacter infection in the North West of England.METHODS:Standard, structured questionnaires were used to gather epidemiological information from cases of campylobacter infection in the North West Region of England between 1997 and 1999. The strains of campylobacter isolated from these cases were identified and typed using serotyping and phage typing methods. Analysis of combined serotype and epidemiological data is presented.RESULTS AND CONCLUSIONS:Human campylobacter infection in the North West is seasonal and a new observation was a peak in cases in March each year. Drinking bird-pecked milk was a highly seasonal exposure that might be an indicator of environmental contamination with campylobacter. A possible environmental basis for seasonality of infection is discussed. Frequencies of risk exposures related to serotypes of cases are described and a potential association was demonstrated between Campylobacter jejuni HS6 and consumption of bird-pecked milk. Also, Campylobacter coli infections were more commonly associated with travel abroad than C. jejuni and a decreased proportion of C. jejuni HS2 and C. jejuni HS11 reported consumption of meat and unpasteurised milk (respectively). Contact with a sick animal may be a significant risk exposure in younger age groups and in those who do not consume poultry or meat. It is clear from this and other studies that the sources and vehicles of human campylobacter infection are numerous and interventions that target a single risk factor are unlikely to impact significantly on the overall burden of disease.

Background: In the past few years, increased diagnoses of syphilis have been reported in cities around Britain and Europe. Enhanced surveillance of cases began in 1999 to identify the epidemiology of this increase in Greater Manchester.Methods: Information was collected on all cases of syphilis newly diagnosed in genitourinary medicine (GUM) clinics in Greater Manchester between January 1999 and November 2002. The data collected included demographic information and information about other sexually transmitted infections, sexual behaviour, perception of risk of infection, and awareness of syphilis transmission.Results: The majority of cases identified were white homosexual men resident in Greater Manchester. Of the 414 cases diagnosed, 74% had either a primary or secondary stage of syphilis infection and 37% of cases were HIV positive. High numbers of individuals practised unprotected oral sex despite good awareness of the risk of infection with syphilis. There is evidence that the way people are meeting sexual contacts is changing, with increasing numbers meeting most of their partners through the internet.Conclusions: These findings have implications for targeting interventions. The provision of rapid diagnostic and treatment services is likely to be key for the control of syphilis and potentially of subsequent increases in HIV in the region.

SARS has been called the first global epidemic of the 21st century and has been the cause of a massive and varied public health response in many countries of the world. This report describes observations made by two authors on a journey from Manchester in the United Kingdom to Chiang Mai in Thailand during the peak of global transmission. The public response to SARS, particularly characterised by the wearing of face masks, seemed to outstrip official guidance. Though of uncertain protective benefit, the wearing of masks may have contributed to the awareness of the collective and personal responsibility in combating infectious disease. Active and empowered involvement of the general public in implementing and cooperating with public health control measures supported by national and international authorities has clearly helped to bring SARS under control. The public health significance of such potent symbols as the face mask may be considered in strategies to tackle other emerging infections.

Influenza has serious implications among residents, but the tools available to control it are improving. The authors look at the best approaches to managing the infection.

Background: In 2000, the World Health Organization ( WHO) had eight sets of conflicting recommendations for decontaminating medical equipment. We conducted a systematic review of observational studies to assist WHO in reconciling the various guidelines. This paper summarises the methods developed and illustrates the results for three procedures alcohol, bleach and povidone iodine.Methods: We developed a Medline search strategy and applied inclusion criteria specifying the decontamination procedures of interest and an outcome of microbial destruction for a set of marker organisms. We developed protocols to assess the quality of studies and categorised them according to the reliability of the methods used. Through an iterative process we identified best practice for the decontamination methods and key additional factors required to ensure their effectiveness. We identified 88 published papers for inclusion, describing 135 separate studies of decontamination.Results: For disinfection with alcohol, best practice was identified from 23 studies as an exposure to 70-80% ethanol or isopropanol for at least 5 minutes. Bleach was effective for sterilization at a concentration of 5000 ppm for 5 minutes and for disinfection at 1000 ppm for 10 minutes ( 33 studies). Povidone iodine was only partially effective for disinfection at a concentration of 1% for 15 minutes ( 15 studies).Conclusions: Our findings provide an evidence base for WHO guidelines on decontaminating medical equipment. The results support the recommended use of bleach and show that alcohol could be used more widely than current guidelines suggest, provided best practice is followed. The effectiveness of povidone iodine is uncertain.

En la region noroeste de Inglaterra se ha creado una red centinela local de medicos generales para la vigilancia de la gripe. En el invierno 2001-02, las tasas de consultas por sindromes gripales (influenza-like-illness; ILI) fueron bajas, pero la red de vigilancia pudo demostrar variaciones subregionales en el momento de aparicion de los picos de actividad gripal, asi como la infeccion de distintos grupos de edad. Ello sugiere que la red puede ayudar a planificar mejor las necesidades invernales en el servicio de salud de la region noroeste.