Outbreak Control Team Research Articles

Feta safe than sorry - gastroenteritis outbreak associated with contaminated cheese

Abstract A gastroenteritis outbreak among attendees at a catered HSE event was notified. No faecal samples were obtained - all cases had recovered. An outbreak control team was convened. A retrospective cohort study hypothesised that “people who attended the HSE event and subsequently became unwell did so as a result of consuming food at the event”. Epidemiological, environmental, and microbiological investigations commenced. An outbreak-specific food questionnaire was distributed. The food business was inspected, obtaining food samples. Survey responses were analysed.The attack rate was 25%. Associations were identified between illness and specific foods. Multivariable regression highlighted: feta salad (OR = 36.22 [95% CI 2.24-585.52] p = 0.01), and turkey (OR = 12.57 [95% CI 1.12-140.58] p = 0.04). Most (93%) turkey consumers had consumed feta salad. Microbiology of unopened feta cheese, sourced by the caterer from a supermarket, was positive for E coli at 1.7 x 105. The Food Safety Authority of Ireland corroborated separate illness complaints from a family consuming the product. The supermarket voluntarily withdrew the product internationally.This outbreak prompted a cross-sectoral food safety investigation. Despite no pathogen detection in a faecal samples, epidemiological evidence led to the withdrawal of contaminated feta by the supermarket, removing over 1000 units from the market, emphasising the importance of epidemiology in protecting public health. Key messages • Epidemiological investigation resulted in mass contaminated cheese withdrawal internationally. • Cross-sectoral work is important to safeguard public health.

A prolonged outbreak of tuberculosis associated with an intellectual disability daycentre in Ireland

Abstract One of the factors impeding tuberculosis elimination in low burden countries is its persistence and concentration in vulnerable populations. This is a complex, prolonged Tuberculosis (TB) outbreak in a daycentre for adults with intellectual disability in Ireland. This is a particularly vulnerable population with special considerations for Public Health (PH) management. There are eight cases of active TB, 46 cases of Latent TB Infection (LTBI) and a cumulative total of 116 contacts associated with this outbreak, with diagnosis spanning 15 years. The last three cases were identical on Whole Genome Sequencing. The index case was an Irish-born, Caucasian, social care worker, with smear positive pulmonary TB, who was symptomatic in the facility for three months prior to diagnosis. Case 2 was a household contact of the index case and the other 6 cases were Service Users (SUs) at the facility. At least five of the subsequent seven cases are secondary cases of the index case. Significant to this outbreak was the change in Irish guidance, 2010, relating to the management of contacts of cases. Following the notification of the most recent case, July 2023, the Outbreak Control Team decided a retrospective review be conducted of all SU contacts of the seven cases associated with the facility. The contacts were stratified according to hierarchical risk. A total of six contacts met the criteria for review and offered screening, re-screening or treatment as appropriate. In this outbreak 21.8% of the total contacts and 16.1% of SU contacts completed treatment for LTBI. The significance of this outbreak lies in its duration, infectivity of the index case and particular vulnerabilities of the SUs. There were issues with overcrowding and difficulties in relation to symptom recognition, diagnosis and treatment. The PH team tailored their approach to meet the SU needs, demonstrating the importance of person-centred contact tracing in the disruption of transmission. Key messages • A factor impeding tuberculosis elimination in low burden countries is it’s persistence and concentration in vulnerable populations. • Adapting a patient-centred approach to contact tracing can lead to higher participation rate and the disruption of infection transmission.

Implementation of the infection control estimate: A case study on the use of a newly developed digital tool for outbreak management in the acute setting.

An Infection Control Estimate (ICE) Tool was developed based on a previously published concept of applying military planning techniques to Infection Prevention and Control (IPC) management strategies in the acute healthcare setting. Initial testing of the outbreak management tool was undertaken in a large acute hospital in the North-West of England during a localised outbreak of COVID-19. The tool, developed using Microsoft Excel, was completed by trained IPC practitioners in real-time to log outbreak details, assign and manage meeting actions and to generate surveillance data. The ICE tool was utilised across five outbreak control meetings to identify and allocate tasks to members of the outbreak control team and to monitor progress. Within the meetings, the tool was used primarily by the trained IPC Specialist Nurses who were guided by and entered data into the relevant sections. Feedback indicated that the tool was easy to use and useful as the sole repository of outbreak information and data. Suggested improvements following the testing period were made and additional functionality was added. Utilisation of the ICE tool has the potential to improve our understanding of the efficacy of currently employed outbreak management interventions and provides a cognitive support and targeted education for teams responsible for the management of outbreaks. It is hoped that by guiding teams through an outbreak with prompts and guidance, as well as facilitating collection and presentation of surveillance data, outbreaks will be resolved sooner and risks to patients will be reduced.

SARS-CoV-2 in a long-term care facility: lessons learnt and importance of repeated mass testing

Abstract The COVID-19 pandemic has had a devastating impact on long-term care facilities worldwide. Reflecting on public health management of COVID-19 outbreaks in these settings is crucial to identify lessons learnt and improve outbreak control strategies for the future. A confirmed case of COVID-19 in a private nursing home facility was notified to the Department of Public Health West on December 30th 2020. Immediate actions included case investigation, contact tracing, implementation of infection prevention and control (IPC) measures and mass testing of all residents and staff. On December 31st 2 more confirmed cases were notified. A multidisciplinary outbreak control team was convened. Testing of SARS-CoV-2 samples was via reverse transcription polymerase chain reaction. IPC site visits were made. Seven further mass testing rounds were completed at 5-7-day intervals. Data collation and descriptive analyses were performed using Microsoft Excel. There were 56 laboratory-confirmed COVID-19 cases associated with the outbreak (28 residents, 28 staff). Overall attack rate was 52.8% (66.7% for residents, 44.0% for staff). Over half of all cases (51.7%) were detected from the first and second mass testing rounds (positivity rates 34.2% and 27.8% respectively) in the first week of the outbreak. Mean age of resident cases was 81.5 years. The majority (96.4%) were symptomatic (diarrhoea 64.3%, fever 57.1% and anorexia 25%). Hospitalisation and case fatality rates for residents were 21.4% and 41.4% respectively. Mean age of staff cases was 35.5 years. One-quarter were asymptomatic, with no hospitalisations or deaths. The outbreak was declared over on February 16th 2021. Residents of long-term care facilities are extremely vulnerable to COVID-19. Mass testing is a critically important outbreak control strategy which can facilitate rapid case finding and contact tracing in these settings, minimising the potential for further spread of infection and harm to residents and staff. Key messages Residents of long-term care facilities are extremely vulnerable to COVID-19, and may present with atypical clinical symptoms and signs of this disease. A low threshold for testing is required. Mass testing is a crucial COVID-19 outbreak control strategy in long-term care facilities to enable rapid case finding and contact tracing, minimising the potential for further spread of infection.

Investigation and management of an outbreak of COVID-19 infection in an acute admission unit in a District General Hospital: lessons learnt

SummaryBackgroundSARS-CoV-2 outbreaks are difficult to recognise and control due to its high infectivity and the wide range of clinical manifestations of the infection. An outbreak at Watford general hospital provided an opportunity to recognise the complexity involved in a COVID-19 outbreak investigation.MethodsAn outbreak control team (OCT) was convened. The terms outbreak, a case and a significant exposure were defined as per Public Health England (PHE) Guidance and in the context of the local outbreak. Root cause analyses (RCAs) were carried out on cases to identify possible causes, possible route of transmission and any learning points. All contact patients and staff were screened with RT PCR and genomic sequencing was performed on a set of positive specimens.In addition to active contact tracing, screening and cohorting of patients and staff, standard and transmission-based precautions were reinforced to control the outbreak.FindingsFifteen patients and four staff members were identified in this outbreak investigation. With contact tracing, screening and through strict infection control measures the outbreak was brought under control.ConclusionWe could successfully contain the spread of this outbreak following PHE outbreak control guidelines and our local guidelines. We recognised several challenges in investigating a COVID-19 outbreak in a hospital setting. Problems arising from variable sensitivity of the tests, difficulty in differentiating COVID-19 related symptoms from underlying diseases, problems related to establishing the route of transmission, issues with contact tracing are discussed. Additionally, the importance and limitations of genomic studies in COVID-19 are discussed.

Investigation and management of Klebsiella Pneumoniae Outbreak in Intensive Care Unit of Tanta University Emergency Hospital

Background: Klebsiella pneumoniae infection is responsible for a wide range of infections including pneumonia, bacteremia, wound infections, and urinary tract infections. Objective: To investigate and manage the occurrence of multi-drug resistant Klebsiella pneumoniae outbreak in Intensive Care Unit of Tanta University Emergency Hospital. Methodology: The investigation of the outbreak included isolates identification and typing while management included implementation of infection prevention and control precautions; establishment of an Outbreak Control Team; epidemiological investigations; and decontamination of environment. Results: During September 2020, five patients in the Intensive Care Unit in Emergency Hospital of Tanta University had multi drug-resistant Klebsiella pneumoniae identified in samples obtained from a variety of specimens. The fifth case was identified 10 days following confirmation of the first case. The Microbiology laboratory confirmed the five cases had identical Klebsiella pneumoniae strains. This suggests that there was a patient-to- patient spread of multidrug resistant Klebsiella pneumoniae. Conclusion: This investigation revealed the importance of proactive recognition of a possible outbreak, screening of patients transferred from other hospitals, early identification of any unusual microorganisms and implementation of early infection control interventions.

Investigation of a foodborne outbreak of Shigella sonnei in Ireland and Northern Ireland, December 2016: the benefits of cross-border collaboration and commercial sales data

ObjectivesTo describe a cross-border foodborne outbreak of Shigella sonnei that occurred in Ireland and Northern Ireland (NI) in December 2016 whilst also highlighting the valuable roles of sales data and international collaboration in the investigation and control of this outbreak. Study designA cross-border outbreak control team was established to investigate the outbreak. MethodsEpidemiological, microbiological, and environmental investigations were undertaken. Traditional analytical epidemiological studies were not feasible in this investigation. The restaurant chain provided sales data, which allowed assessment of a possible increased risk of illness associated with exposure to a particular type of heated food product (product A). ResultsConfirmed cases demonstrated sole trimethoprim resistance: an atypical antibiogram for Shigella isolates in Ireland. Early communication and the sharing of information within the outbreak control team facilitated the early detection of the international dimension of this outbreak. A joint international alert using the European Centre for Disease Control's confidential Epidemic Intelligence Information System for Food- and Waterborne Diseases and Zoonoses (EPIS-FWD) did not reveal further cases outside of the island of Ireland. The outbreak investigation identified that nine of thirteen primary case individuals had consumed product A from one of multiple branches of a restaurant chain located throughout the island of Ireland. Product A was made specifically for this chain in a food production facility in NI. S. sonnei was not detected in food samples from the food production facility. Strong statistical associations were observed between visiting a branch of this restaurant chain between 5 and 9 December 2016 and eating product A and developing shigellosis. ConclusionsThis outbreak investigation highlights the importance of international collaboration in the efficient identification of cross-border foodborne outbreaks and the value of using sales data as the analytical component of such studies.

Applying probability-weighted incubation period distributions to traditional wind rose methodology to improve public health investigations of Legionnaires' disease outbreaks.

In the event of a Legionnaires' disease outbreak, rapid location and control of the source of bacteria are crucial for outbreak management and regulation. In this paper, we describe an enhancement of the traditional wind rose for epidemiological use; shifting the focus of measurement from relative frequency of the winds speeds and directions to the relative volume of air carried, whilst also incorporating probability distributions of disease incubation periods to refine identification of the important wind directions during a cases window of exposure, i.e. from which direction contaminated aerosols most likely originated. The probability-weighted wind rose offers a potential improvement over the traditional wind rose by weighting the importance of wind measurements through incorporation of probability of exposure given an individual's time of symptom onset (obtained through knowledge of the incubation period), and by instead focusing on the volume of carrying air which offers better insight into the most probable direction of the source. This then provides a probabilistic distribution of which direction the wind was blowing around the time of infection. We discuss how the probability-weighted wind rose can be implemented during a Legionnaires' disease outbreak, and how outbreak control teams might use it as supportive evidence to identify the most likely direction of the contaminated source from the presumed site of exposure. In addition, this paper discusses how minor adjustments can be made to the method allowing the probability-weighted wind rose to be applied to other non-communicable airborne diseases, providing the disease's probability distribution for the incubation period distribution is well known.

Outbreak of Shiga toxin-producing Escherichia coli O157:H7 linked to raw drinking milk resolved by rapid application of advanced pathogen characterisation methods, England, August to October 2017.

An outbreak of Shiga toxin-producing Escherichia coli (STEC) O157:H7 occurred on the Isle of Wight between August and October 2017. Of the seven cases linked to the outbreak, five were identified through the statutory notification process and two were identified through national surveillance of whole genome sequencing data. Enhanced surveillance questionnaires established a common link to a farm, and link to the likely food vehicle, raw drinking milk (RDM). Microbiological investigations, including PCR, identified the presence of STEC O157:H7 in samples of RDM. Analysis of core genome single nucleotide polymorphism (SNP) data of STEC O157:H7 from human stool specimens, animal faecal samples and RDM demonstrated a one SNP difference between isolates, and therefore close genetic relatedness. Control measures that were put in place included suspension of sales and recall of RDM, as well as restrictions on public access to parts of the farm. Successful integration of traditional epidemiological surveillance and advanced laboratory methods for the detection and characterisation of STEC O157:H7 from human, animal and environmental samples enabled prompt identification of the outbreak vehicle and provided evidence to support the outbreak control team’s decision-making, leading to implementation of effective control measures in a timely manner.

A cross-sectional study to describe and explore factors associated with measles immunisation and recording among cases linked to an outbreak, South West England, 2016

Following an outbreak of measles across South West England in 2016, the multi-agency outbreak control team suggested that immunisation history records collected for the health protection response may not be reliable. We undertook a cross-sectional study to compare measles immunisation records collected from outbreak cases on the case management system HPZone by the Health Protection Team with the full primary care record. A total of 122 cases were reported. We identified 86.9% cases were not fully immunised and 5.7% had an unknown immunisation status. There were 14 cases whose primary care records did not match HPZone and 18 cases where primary care records were available and immunisation status was not documented in HPZone. Complex, non-linear associations were found between age and socioeconomic deprivation status of each case and having an incorrect HPZone record. Cases who resided in postcode areas of greater socioeconomic deprivation had statistically significantly higher odds of having been fully immunised. Only 13.3% of partially or unimmunised cases received an MMR immunisation following their onset of measles infection. Collecting immunisation status from the full primary care record during acute management of measles cases may support improvements in control and prevention of further cases.

Vaccination strategies for control of community outbreaks of hepatitis A: A comparison of two outbreaks in England

In August 2015 two community outbreaks of hepatitis A virus (HAV) occurred in sub-urban communities in Northern England. Each was managed by an independent outbreak control team. In outbreak one, mass vaccination was deployed targeting a residential area and two schools, while in outbreak two, vaccination was reserved for household-type contacts of cases. The highest vaccination uptake was achieved in the school settings (82% and 95%). These case studies illustrate the range of approaches that can be used and the factors that influence decision-making in response to a hepatitis A community outbreak. Both outbreaks likely started from importation(s) of HAV by returning travellers and spread through extended social networks and the local community. Vaccination strategies were selected based on hypotheses about transmission pathways, which were informed by evidence from oral fluid (OF) testing of asymptomatic contacts. More evidence about the effectiveness of mass vaccination in community outbreaks of hepatitis A in low endemicity settings is needed. Hepatitis A guidelines should include recommendations for the use of mass vaccination and OF testing in outbreaks.

A cluster of Legionnaires' disease in Belgium linked to a cooling tower, August-September 2016: practical approach and challenges.

A cluster of Legionnaires' disease (LD) with 10 confirmed, three probable and four possible cases occurred in August and September 2016 in Dendermonde, Belgium. The incidence in the district was 7 cases/100 000 population, exceeding the maximum annual incidence in the previous 5 years of 1.5/100 000. Epidemiological, environmental and geographical investigations identified a cooling tower (CT) as the most likely source. The case risk around the tower decreased with increasing distance and was highest within 5 km. Legionella pneumophila serogroup 1, ST48, was identified in a human respiratory sample but could not be matched with the environmental results. Public health authorities imposed measures to control the contamination of the CT and organised follow-up sampling. We identified obstacles encountered during the cluster investigation and formulated recommendations for improved LD cluster management, including faster coordination of teams through the outbreak control team, improved communication about clinical and environmental sample analysis, more detailed documentation of potential exposures obtained through the case questionnaire and earlier use of a geographical information tool to compare potential sources and for hypothesis generation.

First use of whole-genome sequencing to investigate a cluster of Yersinia enterocolitica, Liverpool, United Kingdom, 2017.

In May 2017 we were notified of a cluster of Yersinia enterocolitica-positive isolates from Liverpool. The purpose of this work was to investigate this cluster of cases and find a possible common source. We combined epidemiological information with whole-genome sequencing (WGS) results, which indicated that these cases were unlikely to be from the same source. This investigation provides evidence that WGS could be used to investigate future clusters of Y. enterocolitica cases. A case was defined as a person with a laboratory-confirmed isolate of Y. enterocolitica, sampled in 2017, who is a resident in Liverpool local authority at the time of sampling. Faecal samples were cultured at the local laboratory and presumptive isolates of Yersinia sp. were identified using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS). Positive isolates were whole-genome sequenced by the reference laboratory. Nine cases were identified, which was significantly greater (P<0.0001) than the average number of cases in this area from the last 10 years. Six cases were female (66.67 %) and the ages of the patients ranged from 20 to 81 (median 54). The sample dates ranged from 29 April to 1 August 2017. The WGS results showed that Y. enterocolitica isolates belonged to different sequence types. This was the first time that WGS was used to investigate a cluster of Y. enterocolitica cases; the cases were clustered in time, person and place, but the WGS results indicate that these cases were not from the same source. This result informed the Outbreak Control Team's decision-making and resulted in the investigation being closed.

National outbreak of Shiga toxin-producing Escherichia coli O157:H7 linked to mixed salad leaves, United Kingdom, 2016.

We investigated a large outbreak of Escherichia coli O157 in the United Kingdom (UK) with 165 cases between 31 May and 29 July 2016. No linked cases were reported in other countries. Cases were predominately female (n = 128) and adult (n = 150), 66 attended hospital and nine had features of haemorrhagic uraemic syndrome. A series of epidemiological studies (case–control, case–case, ingredients-based and venue-based studies) and supply chain investigations implicated mixed salad leaves from Supplier A as the likely outbreak vehicle. Whole genome sequencing (WGS) indicated a link with strains from the Mediterranean and informed the outbreak control team to request that Supplier A cease distributing salad leaves imported from Italy. Microbiological tests of samples of salad leaves from Supplier A were negative. We were unable to confirm the source of contamination or the contaminated constituent leaf although our evidence pointed to red batavia received from Italy as the most likely vehicle. Variations in Shiga toxin-producing E. coli surveillance and diagnosis may have prevented detection of cases outside the UK and highlights a need for greater standardisation. WGS was useful in targeting investigations, but greater coverage across Europe is needed to maximise its potential.

Controlling infectious disease outbreaks in low-income and middle-income countries.

When an infectious disease outbreak is detected or suspected, a healthcare facility’s infection control personnel should be notified and an outbreak control team formed that is pertinent to the size and severity of the outbreak and healthcare facility. Management of an infectious disease outbreak in a middle- or low-income country is challenging. Cost-effective recommendations that are easy to carry out and that have been stratified according to the type of infection and prevention and control intervention used are provided in this paper and constitute basic practices.

Online market research panel members as controls in case-control studies to investigate gastrointestinal disease outbreaks: early experiences and lessons learnt from the UK.

Established methods of recruiting population controls for case-control studies to investigate gastrointestinal disease outbreaks can be time consuming, resulting in delays in identifying the source or vehicle of infection. After an initial evaluation of using online market research panel members as controls in a case-control study to investigate a Salmonella outbreak in 2013, this method was applied in four further studies in the UK between 2014 and 2016. We used data from all five studies and interviews with members of each outbreak control team and market research panel provider to review operational issues, evaluate risk of bias in this approach and consider methods to reduce confounding and bias. The investigators of each outbreak reported likely time and cost savings from using market research controls. There were systematic differences between case and control groups in some studies but no evidence that conclusions on the likely source or vehicle of infection were incorrect. Potential selection biases introduced by using this sampling frame and the low response rate are unclear. Methods that might reduce confounding and some bias should be balanced with concerns for overmatching. Further evaluation of this approach using comparisons with traditional methods and population-based exposure survey data is recommended.

Outbreak of Salmonella enteritidis PT14b gastroenteritis at a restaurant in England: the use of molecular typing to achieve a successful prosecution

ObjectivesTo describe an outbreak of Salmonella enteritidis phage type (PT) 14b in people who had eaten at a restaurant, and the investigation and subsequent prosecution of the food business operator (FBO). Study designThe local health protection team and environmental health department formed an outbreak control team to investigate the outbreak. MethodsEpidemiological, microbiological, and environmental investigations were undertaken. Epidemiological investigations involved case finding and interviews. Microbiological investigation: stool samples from the suspected cases and environmental samples from the implicated food business were investigated. Salmonella isolates obtained were subjected to multiple locus variable-number tandem repeat analysis (MLVA) profiling and whole genome sequencing. In addition, adenosine triphosphate (ATP) hygiene swab tests were used to verify the quality of cleaning procedures and data loggers were used to determine the water temperature of the mechanical dishwasher. ResultsFifteen cases of illness where the causative agent was shown to be S. enteritidis PT14b were identified, all of whom had eaten at the same restaurant. S. enteritidis PT14b was also identified from three of the 11 food and environmental samples taken at the restaurant and found to have the same MLVA profile as the cases. A case for prosecution was built and the FBO was successfully prosecuted in July 2015. ConclusionsThis investigation highlighted that the use of molecular typing as part of thorough epidemiological, microbiological, and environmental investigations can present a robust case for prosecution against restaurants which pose a risk to public health.

P207 Outbreak of hep a affecting msm: the london response

Introduction:Outbreaks of hepatitis A virus (HAV) have previously been described in men who have sex with men (MSM). BASHH only recommends HAV vaccination for MSM during outbreaks. A UK cluster of HAV cases was identified and, by 27/2/2017, London had 45 probable and confirmed cases in MSM. London sexual health commissioning is in flux with new arrangements imminent.Methods:For individual notified cases, Health Protection Teams (HPT) routinely assess source, offer infection control advice to the case and organise vaccination of household and sexual contacts. A London outbreak control team (OCT) comprised epidemiologists, commissioners and providers of immunisation and sexual health services, health promotion partners and communications. The OCT scoped possible additional interventions to control the outbreak.Results:The OCT recommended: Awareness raising re risk behaviour:Distribute a nationally commissioned leaflet with safer sex advice to cases and to genitourinary medicine (GUM) clinics, plus relevant content on digital platforms.Liaison with providers, commissioners: Inform GPs. Survey current practice in GUM for HAV immunisation. Vaccinate MSM opportunistically in GUM clinics (if had a new or casual partner in last 3 months).Link with existing health promotion networks: Working with gay venues, to get understanding and cooperation.Set up vaccination clinics near the popular venuesDiscussion:It is challenging to set up an immunisation programme in a large city with complex commissioning relationships at short notice. Consideration should be given to vaccination between outbreaks to reduce the proportion susceptible, or ‘outbreak ready’ plans included in sexual health commissioning arrangements.

Whole genome sequencing of group A Streptococcus: development and evaluation of an automated pipeline for emmgene typing.

Streptococcus pyogenes group A Streptococcus (GAS) is the most common cause of bacterial throat infections, and can cause mild to severe skin and soft tissue infections, including impetigo, erysipelas, necrotizing fasciitis, as well as systemic and fatal infections including septicaemia and meningitis. Estimated annual incidence for invasive group A streptococcal infection (iGAS) in industrialised countries is approximately three per 100,000 per year. Typing is currently used in England and Wales to monitor bacterial strains of S. pyogenes causing invasive infections and those isolated from patients and healthcare/care workers in cluster and outbreak situations. Sequence analysis of the emm gene is the currently accepted gold standard methodology for GAS typing. A comprehensive database of emm types observed from superficial and invasive GAS strains from England and Wales informs outbreak control teams during investigations. Each year the Bacterial Reference Department, Public Health England (PHE) receives approximately 3,000 GAS isolates from England and Wales. In April 2014 the Bacterial Reference Department, PHE began genomic sequencing of referred S. pyogenes isolates and those pertaining to selected elderly/nursing care or maternity clusters from 2010 to inform future reference services and outbreak analysis (n = 3, 047). In line with the modernizing strategy of PHE, we developed a novel bioinformatics pipeline that can predict emmtypes using whole genome sequence (WGS) data. The efficiency of this method was measured by comparing the emmtype assigned by this method against the result from the current gold standard methodology; concordance to emmsubtype level was observed in 93.8% (2,852/3,040) of our cases, whereas in 2.4% (n = 72) of our cases concordance was observed to emm type level. The remaining 3.8% (n = 117) of our cases corresponded to novel types/subtypes, contamination, laboratory sample transcription errors or problems arising from high sequence similarity of the allele sequence or low mapping coverage. De novo assembly analysis was performed in the two latter groups (n = 72 + 117) and was able to diagnose the problem and where possible resolve the discordance (60/72 and 20/117, respectively). Overall, we have demonstrated that our WGS emm-typing pipeline is a reliable and robust system that can be implemented to determine emm type for the routine service.

Waterborne outbreak of cryptosporidiosis in the South East of Ireland: weighing up the evidence.

In late Spring 2012, 12 cases of cryptosporidiosis in a town in the South East of Ireland were notified to the regional Department of Public Health. The purpose of this paper is to describe the outbreak and the investigative process which led to the conclusion that the source was a public drinking water supply. Outbreak and incident control teams were convened to investigate and control the outbreak. Eleven cases were speciated as Cryptosporidium parvum. GP60 analysis demonstrated that 10 were C. parvum IIaA20G3R1, indicating that the cases were linked. The public water supply was the only common risk factor identified. Increased water sampling identified Cryptosporidium muris/andersoni in the treated water at one of two water treatment plants (Water Treatment Plant, WTP A) for the supply, and on the network. C. parvum was subsequently identified in raw water from WTP A. The Health Service Executive (HSE) concluded that this outbreak was "probably associated with water" produced at WTP A based on (1) descriptive epidemiological evidence suggesting water-related illness and excluding other obvious explanations; and (2) water treatment failure at WTP A. WTP A was closed to facilitate an upgrade. No boil water notice was required as a supplementary supply was available. The upgrade was completed and the incident closed in 2013.