Search

In June 2020, a large-scale food poisoning outbreak involving about 3000 elementary and junior high school students occurred in Yashio, Saitama, Japan. A school lunch was the only food stuff ingested by all of the patients. Escherichia coli serotype O7:H4 carrying the astA gene for enteroaggregative E. coli (EAggEC) heat-stable enterotoxin 1 (EAST1) was detected in faecal specimens from the patients, and sample inspection revealed its presence in a seaweed salad and red seaweed (Gigartina tenella) as one of the raw materials. Analysis of the antibiotic sensitivity of the isolates revealed resistance to ampicillin and cefotaxime. All isolates were confirmed to be of the same origin by pulsed-field gel electrophoresis after digestion with the restriction enzyme XbaI, and single nucleotide polymorphism analysis using whole genome sequencing. To our knowledge, this is the first report of a large-scale food poisoning caused by E. coli O7:H4, which lacks well-characterized virulence genes other than astA.

Poultry contact is a risk factor for zoonotic transmission of non-typhoidal Salmonella spp. Salmonella illness outbreaks in the United States are identified by PulseNet, the national laboratory network for enteric disease surveillance. During 2020, PulseNet observed a 25% decline in the number of Salmonella clinical isolates uploaded by state and local health departments. However, 1722 outbreak-associated Salmonella illnesses resulting from 12 Salmonella serotypes were linked to contact with privately owned poultry, an increase from all previous years. This report highlights the need for continued efforts to prevent backyard poultry-associated outbreaks of Salmonella as ownership increases in the United States.

Cyclosporiasis is an illness characterised by watery diarrhoea caused by the food-borne parasite Cyclospora cayetanensis. The increase in annual US cyclosporiasis cases led public health agencies to develop genotyping tools that aid outbreak investigations. A team at the Centers for Disease Control and Prevention (CDC) developed a system based on deep amplicon sequencing and machine learning, for detecting genetically-related clusters of cyclosporiasis to aid epidemiologic investigations. An evaluation of this system during 2018 supported its robustness, indicating that it possessed sufficient utility to warrant further evaluation. However, the earliest version of CDC's system had some limitations from a bioinformatics standpoint. Namely, reliance on proprietary software, the inability to detect novel haplotypes and absence of a strategy to select an appropriate number of discrete genetic clusters would limit the system's future deployment potential. We recently introduced several improvements that address these limitations and the aim of this study was to reassess the system's performance to ensure that the changes introduced had no observable negative impacts. Comparison of epidemiologically-defined cyclosporiasis clusters from 2019 to analogous genetic clusters detected using CDC's improved system reaffirmed its excellent sensitivity (90%) and specificity (99%), and confirmed its high discriminatory power. This C. cayetanensis genotyping system is robust and with ongoing improvement will form the basis of a US-wide C. cayetanensis genotyping network for clinical specimens.

Experience gained from responding to major outbreaks may have influenced the early coronavirus disease-2019 (COVID-19) pandemic response in several countries across Africa. We retrospectively assessed whether Guinea, Liberia and Sierra Leone, the three West African countries at the epicentre of the 2014–2016 Ebola virus disease outbreak, leveraged the lessons learned in responding to COVID-19 following the World Health Organization's (WHO) declaration of a public health emergency of international concern (PHEIC). We found relatively lower incidence rates across the three countries compared to many parts of the globe. Time to case reporting and laboratory confirmation also varied, with Guinea and Liberia reporting significant delays compared to Sierra Leone. Most of the selected readiness measures were instituted before confirmation of the first case and response measures were initiated rapidly after the outbreak confirmation. We conclude that the rapid readiness and response measures instituted by the three countries can be attributed to their lessons learned from the devastating Ebola outbreak, although persistent health systems weaknesses and the unique nature of COVID-19 continue to challenge control efforts.

Nosocomial severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) outbreaks among health care workers have been scarcely reported so far. This report presents the results of an epidemiologic and molecular investigation of a SARS-CoV-2 outbreak among laundromat facility workers in a large tertiary centre in Israel. Following the first three reported cases of SARS-CoV-2 among laundromat workers, all 49 laundromat personnel were screened by qRT-PCR tests using naso- and oropharingeal swabs. Epidemiologic investigations included questionnaires, interviews and observations of the laundromat facility. Eleven viral RNA samples were then sequenced, and a phylogenetic analysis was performed using MEGAX. The integrated investigation defined three genetic clusters and helped identify the index cases and the assumed routes of transmission. It was then deduced that shared commute and public showers played a role in SARS-CoV-2 transmission in this outbreak, in addition to improper PPE use and social gatherings (such as social eating and drinking). In this study, we present an integrated epidemiologic and molecular investigation may help detect the routes of SARS-CoV-2 transmission, emphasising such routes that are less frequently discussed. Our work reinforces the notion that person-to-person transmission is more likely to cause infections than environmental contamination (e.g. from handling dirty laundry).

Consumption of pork and pork products can be associated with outbreaks of human salmonellosis. Salmonella infection is usually subclinical in pigs, and farm-based control measures are challenging to implement. To obtain data on Salmonella prevalence, samples can be collected from pigs during the slaughter process. Here we report the results of a Great Britain (GB) based abattoir survey conducted by sampling caecal contents from pigs in nine British pig abattoirs during 2019. Samples were collected according to a randomised stratified scheme, and pigs originating from 286 GB farms were included in this survey. Salmonella was isolated from 112 pig caecal samples; a prevalence of 32.2% [95% confidence interval (CI) 27.4–37.4]. Twelve different Salmonella serovars were isolated, with the most common serovars being S. 4,[5],12:i:-, a monophasic variant of Salmonella Typhimurium (36.6% of Salmonella-positive samples), followed by S. Derby (25.9% of Salmonella-positive samples). There was no significant difference compared to the estimate of overall prevalence (30.5% (95% CI 26.5–34.6)) obtained in the last abattoir survey conducted in the UK (2013). Abattoir-based control measures are often effective in the reduction of Salmonella contamination of carcasses entering the food chain. In this study, the effect of abattoir hygiene practices on the prevalence of Salmonella on carcasses was not assessed. Continuing Salmonella surveillance at slaughter is recommended to assess effect of farm-based and abattoir-based interventions and to monitor potential public health risk associated with consumption of Salmonella-contaminated pork products.

On 16–17 January 2020, four suspected mumps cases were reported to the local Public Health Authorities with an epidemiological link to a local school and football club. Of 18 suspected cases identified, 14 were included in this study. Laboratory results confirmed mumps virus as the cause and further sequencing identified genotype G. Our findings highlight that even with a high MMR vaccine coverage, mumps outbreaks in children and young adults can occur. Since most of the cases had documented immunity for mumps, we hypothesise that waning immunity or discordant mumps virus strains are likely explanations for this outbreak.

Monitoring the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) community-wide transmission with a suitable and effective sampling method would be of great support for public health response to the spreading due to asymptomatic subjects in the community. Here, we describe how using saliva samples for SARS-CoV-2 detection has allowed for a weekly surveillance of a small business company and the early detection of coronavirus disease 2019 cases. As on 23rd March, two cases were detected and investigated, and control measures were rapidly applied.

In August 2017, a cluster of four persons infected with genetically related strains of Shiga toxin-producing Escherichia coli (STEC) O157:H7 was identified. These strains possessed the Shiga toxin (stx) subtype stx2a, a toxin type known to be associated with severe clinical outcome. One person died after developing haemolytic uraemic syndrome. Interviews with cases revealed that three of the cases had been exposed to dogs fed on a raw meat-based diet (RMBD), specifically tripe. In two cases, the tripe had been purchased from the same supplier. Sampling and microbiological screening of raw pet food was undertaken and indicated the presence of STEC in the products. STEC was isolated from one sample of raw tripe but was different from the strain causing illness in humans. Nevertheless, the detection of STEC in the tripe provided evidence that raw pet food was a potential source of human STEC infection during this outbreak. This adds to the evidence of raw pet food as a risk factor for zoonotic transmission of gastrointestinal pathogens, which is widely accepted for Salmonella, Listeria and Campylobacter spp. Feeding RMBD to companion animals has recently increased in popularity due to the belief that they provide health benefits to animals. Although still rare, an increase in STEC cases reporting exposure to RMBDs was detected in 2017. There has also been an increased frequency of raw pet food incidents in 2017, suggesting an increasing trend in potential risk to humans from raw pet food. Recommendations to reduce the risk of infection included improved awareness of risk and promotion of good hygiene practices among the public when handling raw pet food.

Population-based seroprevalence studies on coronavirus disease 2019 (COVID-19) in low- and middle-income countries are lacking. We investigated the seroprevalence of severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2) antibodies in Sergipe state, Northeast Brazil, using rapid IgM−IgG antibody test and fluorescence immunoassay. The seroprevalence was 9.3% (95% CI 8.5–10.1), 10.2% (95% CI 9.2–11.3) for women and 7.9% (IC 95% 6.8–9.1) for men (P = 0.004). We found a decline in the prevalence of SARS-CoV-2 antibodies according to age, but the differences were not statistically significant: 0–19 years (9.9%; 95% CI 7.8–12.5), 20–59 years (9.3%; 95% CI 8.4–10.3) and ≥60 years (9.0%; 95% CI 7.5–10.8) (P = 0.517). The metropolitan area had a higher seroprevalence (11.7%, 95% CI 10.3–13.2) than outside municipalities (8.0%, 95% CI 7.2–8.9) (P < 0.001). These findings highlight the importance of serosurveillance to estimate the real impact of the COVID-19 outbreak and thereby provide data to better understand the spread of the virus, as well as providing information to guide stay-at-home measures and other policies. In addition, these results may be useful as basic data to follow the progress of COVID-19 outbreak as social restriction initiatives start to be relaxed in Brazil.

Control of the novel COronaVIrus Disease-2019 (COVID-19) in a hospital setting is a priority. A COVID-19-infected surgeon performed surgical activities before being tested. An exposure risk classification was applied to the identified exposed subjects and high- and medium-risk contacts underwent active symptom monitoring for 14 days at home. All healthcare professionals (HCPs) were tested for severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2) at the end of the quarantine and serological tests were performed. Three household contacts and 20 HCPs were identified as high- or medium-risk contacts and underwent a 14-day quarantine. Fourteen HCPs and 19 patients were instead classified as low risk. All the contacts remained asymptomatic and all HCPs tested negative for SARS-CoV-2. About 25–28 days after their last exposure, HCPs underwent serological testing and two of them had positive IgM but negative confirmatory swabs. In a low COVID-19 burden area, the in-hospital transmission of SARS-CoV-2 from an infectious doctor did not occur and, despite multiple and frequent contacts, a hospital outbreak was avoided. This may be linked to the adoption of specific recommendations and to the use of standard personal protective equipment by HCPs.

Severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2) led to a significant disease burden and disruptions in health systems. We describe the epidemiology and transmission characteristics of early coronavirus disease 2019 (COVID-19) cases in Bavaria, Germany. Cases were reverse transcription polymerase chain reaction (RT-PCR)-confirmed SARS-CoV-2 infections, reported from 20 January−19 March 2020. The incubation period was estimated using travel history and date of symptom onset. To estimate the serial interval, we identified pairs of index and secondary cases. By 19 March, 3546 cases were reported. A large proportion was exposed abroad (38%), causing further local transmission. Median incubation period of 256 cases with exposure abroad was 3.8 days (95%CI: 3.5–4.2). For 95% of infected individuals, symptom onset occurred within 10.3 days (95%CI: 9.1–11.8) after exposure. The median serial interval, using 53 pairs, was 3.5 days (95%CI: 3.0–4.2; mean: 3.9, s.d.: 2.2). Travellers returning to Germany had an important influence on the spread of SARS-CoV-2 infections in Bavaria in early 2020. Especially in times of low incidence, public health agencies should identify holiday destinations, and areas with ongoing local transmission, to monitor potential importation of SARS-CoV-2 infections. Travellers returning from areas with ongoing community transmission should be advised to quarantine to prevent re-introductions of COVID-19.

In April 2018, Public Health England was notified of cases of Shigella sonnei who had eaten food from three different catering outlets in England. The outbreaks were initially investigated as separate events, but whole-genome sequencing (WGS) showed they were caused by the same strain. The investigation included analyses of epidemiological data, the food chain and microbiological examination of food samples. WGS was used to determine the phylogenetic relatedness and antimicrobial resistance profile of the outbreak strain. Ultimately, 33 cases were linked to this outbreak; the majority had eaten food from seven outlets specialising in Indian or Middle Eastern cuisine. Five outlets were linked to two or more cases, all of which used fresh coriander although a shared supplier was not identified. An investigation at one of the venues recorded that 86% of cases reported eating dishes with coriander as an ingredient or garnish. Four cases were admitted to hospital and one had evidence of treatment failure with ciprofloxacin. Phylogenetic analysis showed that the outbreak strain was part of a wider multidrug-resistant clade associated with travel to Pakistan. Poor hygiene practices during cultivation, distribution or preparation of fresh produce are likely contributing factors.

Epidemic forecasting provides an opportunity to predict geographic disease spread and counts when an outbreak occurs and plays a key role in preventing or controlling their adverse impact. However, conventional prediction models based on complex mathematical modeling rely on the estimation of model parameters, which yields unreliable and unsustainable results. Herein, we proposed a simple model for predicting the epidemic transmission dynamics based on nonlinear regression of the epidemic growth rate and iterative methods, which is applicable to the progression of the COVID-19 outbreak under the strict control measures of the Chinese government. Our model yields reliable and accurate results as confirmed by the available data: we predicted that the total number of infections in mainland China would be 91,253, and the maximum number of beds required for hospitalized patients would be 62,794. We inferred that the inflection point (when the growth rate turns from positive to negative) of the epidemic across China would be mid-February, and the end of the epidemic would be in late March. This model is expected to contribute to resourceallocation and planning in the health sector while providing a theoretical basis forgovernments to respond to future global health crises or epidemics.

During a disease outbreak, healthcare workers (HCWs) are essential to treat infected individuals. However, these HCWs are themselves susceptible to contracting the disease. As more HCWs get infected, fewer are available to provide care for others, and the overall quality of care available to infected individuals declines. This depletion of HCWs may contribute to the epidemic's severity. To examine this issue, we explicitly model declining quality of care in four differential equation-based susceptible, infected and recovered-type models with vaccination. We assume that vaccination, recovery and survival rates are affected by quality of care delivered. We show that explicitly modelling HCWs and accounting for declining quality of care significantly alters model-predicted disease outcomes, specifically case counts and mortality. Models neglecting the decline of quality of care resulting from infection of HCWs may significantly under-estimate cases and mortality. These models may be useful to inform health policy that may differ for HCWs and the general population. Models accounting for declining quality of care may therefore improve the management interventions considered to mitigate the effects of a future outbreak.

From 24 January 2020 to 18 May 2020, Chaoshan took measures to limit the spread of coronavirus disease 2019 (COVID-19), such as restricting public gatherings, wearing masks and suspending classes. We explored the effects of these measures on the pathogen spectrum of paediatric respiratory tract infections in Chaoshan. Pharyngeal swab samples were collected from 4075 children hospitalised for respiratory tract infection before (May–December 2019) and after (January–August 2020) the COVID-19 outbreak. We used liquid chip technology to analyse 14 respiratory pathogens. The data were used to explore between-group differences, age-related differences and seasonal variations in respiratory pathogens. The number of cases in the outbreak group (1222) was 42.8% of that in the pre-outbreak group (2853). Virus-detection rates were similar in the outbreak (48.3%, 590/1222) and pre-outbreak groups (51.5%, 1468/2853; χ2 = 3.446, P = 0.065), while the bacteria-detection rate was significantly lower in the outbreak group (26.2%, 320/1222) than in the pre-outbreak group (44.1%, 1258/2853; χ2 = 115.621, P < 0.05). With increasing age, the proportions of respiratory syncytial virus (RSV) and cytomegalovirus (CMV) infections decreased, while those of Mycoplasma pneumoniae and adenovirus infections increased. Streptococcus pneumoniae, CMV and rhinovirus infections peaked in autumn and winter, while RSV infections peaked in summer and winter. We found that the proportion of virus-only detection decreased with age, while the proportion of bacteria-only detection increased with age (Table 2). Anti-COVID-19 measures significantly reduced the number of paediatric hospitalisations for respiratory tract infections, significantly altered the pathogen spectrum of such infections and decreased the overall detection rates of 14 common respiratory pathogens. The proportion of bacterial, but not viral, infections decreased.

In August 2019, public health surveillance systems in Scotland and England identified seven, geographically dispersed cases infected with the same strain (defined as isolates that fell within the same five single nucleotide polymorphism single linage cluster) of Shiga toxin-producing Escherichia coli O157:H7. Epidemiological analysis of enhanced surveillance questionnaire data identified handling raw beef and shopping from the same national retailer (retailer A) as the common exposure. Concurrently, a microbiological survey of minced beef at retail identified the same strain in a sample of minced beef sold by retailer A, providing microbiological evidence of the link. Between September and November 2019, a further four primary and two secondary cases infected with the same strain were identified; two cases developed haemolytic uraemic syndrome. None of the four primary cases reported consumption of beef from retailer A and the transmission route of these subsequent cases was not identified, although all four primary cases visited the same petting farm. Generally, outbreaks of STEC O157:H7 in the UK appear to be distinct, short-lived events; however, on-going transmission linked to contaminated food, animals or environmental exposures and person-to-person contact do occur. Although outbreaks of STEC caused by contaminated fresh produce are increasingly common, undercooked meat products remain a risk of infection.

In October 2019, public health surveillance systems in Scotland identified an increase in the number of reported infections of Shiga toxin-producing Escherichia coli (STEC) O26:H11 involving bloody diarrhoea. Ultimately, across the United Kingdom (UK) 32 cases of STEC O26:H11 stx1a were identified, with the median age of 27 years and 64% were male; six cases were hospitalised. Among food exposures there was an association with consuming pre-packed sandwiches purchased at outlets belonging to a national food chain franchise (food outlet A) [odds ratio (OR) = 183.89, P < 0.001]. The common ingredient identified as a component of the majority of the sandwiches sold at food outlet A was a mixed salad of Apollo and Iceberg lettuce and spinach leaves. Microbiological testing of food and environmental samples were negative for STEC O26:H11, although STEC O36:H19 was isolated from a mixed salad sample taken from premises owned by food outlet A. Contamination of fresh produce is often due to a transient event and detection of the aetiological agent in food that has a short-shelf life is challenging. Robust, statistically significant epidemiological analysis should be sufficient evidence to direct timely and targeted on-farm investigations. A shift in focus from testing the microbiological quality of the produce to investigating the processes and practices through the supply chain and sampling the farm environment is recommended.

Recurrent outbreaks of haemolytic uraemic syndrome (HUS) caused by Shiga toxin-producingEscherichia coli(STEC) serotype O55:H7 occurred in England between 2014 and 2018. We reviewed the epidemiological evidence to identify potential source(s) and transmission routes of the pathogen, and to assess the on-going risk to public health. Over the 5-year period, there were 43 confirmed and three probable cases of STEC O55:H7. The median age of cases was 4 years old (range 6 months to 69 years old) and over half of all cases were female (28/46, 61%). There were 36/46 (78.3%) symptomatic cases, and over half of all cases developed HUS (25/46, 54%), including two fatal cases. No common food or environmental exposures were identified, although the majority of cases lived in rural or semi-rural environments and reported contact with both wild and domestic animals. This investigation informed policy on the clinical and public health management of HUS caused by STEC other than serotype O157:H7 (non-O157 STEC) in England, including comprehensive testing of all household contacts and household pets and more widespread use of polymerase chain reaction assays for the rapid diagnosis of STEC-HUS.

Estimating the case fatality ratio (CFR) for COVID-19 is an important aspect of public health. However, calculating CFR accurately is problematic early in a novel disease outbreak, due to uncertainties regarding the time course of disease and difficulties in diagnosis and reporting of cases. In this work, we present a simple method for calculating the case fatality ratio using only public case and death data over time by exploiting the correspondence between the time distributions of cases and deaths. The time-shifted distribution (TSD) analysis generates two parameters of interest: the delay time between reporting of cases and deaths and the case fatality ratio. These parameters converge reliably over time once the exponential growth phase has finished. Analysis is performed for early COVID-19 outbreaks in many countries, and we discuss corrections to CFR values using excess-death and seroprevalence data to estimate the infection fatality ratio (IFR). While CFR values range from 0.2-20% in different countries, estimates for IFR are mostly around 0.5-0.8% for countries that experienced moderate outbreaks and 1-3% for severe outbreaks. The simplicity and transparency of TSD analysis enhance its usefulness in characterizing a new disease as well as the state of the health and reporting systems.

In November 2017, eight confirmed measles cases were reported to Public Health England from a hospital in the West Midlands. A multidisciplinary Incident Management Team (IMT) was established to determine the extent of the problem and coordinate an outbreak response. Between 1 November 2017 and 4 June 2018, a total of 116 confirmed and 21 likely measles cases were linked to this outbreak; just under half (43%) were aged over 15 years of age. Fifty-five of the confirmed cases were hospitalised (48%) and no deaths were reported. At the start of the outbreak, cases were mostly individuals of Romanian origin; the outbreak subsequently spread to the wider population. Over the 8-month response, the IMT conducted the following control measures: extensive contact tracing, immediate provision of post-exposure prophylaxis, community engagement amongst specific high-risk groups, MMR awareness raising including catch-up campaigns and enhanced vaccination services at selected GP surgeries. Key challenges to the effective control measures included language difficulties limiting community engagement; delays in diagnosis, notification and appropriate isolation of cases; limited resources for contact tracing across multiple high-risk settings (including GPs and hospitals) and lack of timely data on vaccine coverage in sub-groups of the population to guide public health action.

Two general practitioners (GPs) with SARS-CoV-2 infection provided in-person patient care to patients of their joint medical practice before and after symptom onset, up until SARS-CoV-2 laboratory confirmation. Through active contact tracing, the local public health authorities recruited the cohort of patients that had contact with either GP in their putative infectious period. In this cohort of patient contacts, we assess the frequency and determinants of SARS-CoV-2-transmission from GPs to patients. We calculated incidence rate ratios (IRR) to explore the type of contact as an explanatory variable for COVID-19 cases. Among the cohort of 83 patient contacts, we identified 22 (27%) COVID-19 cases including 17 (21%) possible, three (4%) probable and two (2%) confirmed cases. All 22 cases had contact with a GP when the GP did not wear a mask, and/or when contact was ≥10 min. Importantly, patients who had contact

An outbreak of SARS-CoV2 infection in a Barcelona prison was studied. One hundred and forty-eight inmates and 36 prison staff were evaluated by rt-PCR, and 24.1% (40 prisoners, two health workers and four non-health workers) tested positive. In all, 94.8% of cases were asymptomatic. The inmates were isolated in prison module 4, which was converted into an emergency COVID unit. There were no deaths. Generalised screening and the isolation and evaluation of the people infected were key measures. Symptom-based surveillance must be supplemented by rapid contact-based monitoring in order to avoid asymptomatic spread among prisoners and the community at large.

The effectiveness of screening travellers during times of international disease outbreak is contentious, especially as the reduction in the risk of disease importation can be very small. Border screening typically consists of travellers being thermally scanned for signs of fever and/or completing a survey declaring any possible symptoms prior to admission to their destination country; while more thorough testing typically exists, these would generally prove more disruptive to deploy. In this paper, we describe a simple Monte Carlo based model that incorporates the epidemiology of coronavirus disease-2019 (COVID-19) to investigate the potential decrease in risk of disease importation that might be achieved by requiring travellers to undergo screening upon arrival during the current pandemic. This is a purely theoretical study to investigate the maximum impact that might be attained by deploying a test or testing programme simply at the point of entry, through which we may assess such action in the real world as a method of decreasing the risk of importation. We, therefore, assume ideal conditions such as 100% compliance among travellers and the use of a ‘perfect’ test. In addition to COVID-19, we also apply the presented model to simulated outbreaks of influenza, severe acute respiratory syndrome (SARS) and Ebola for comparison. Our model only considers screening implemented at airports, being the predominant method of international travel. Primary results showed that in the best-case scenario, screening at the point of entry may detect a maximum of 8.8% of travellers infected with COVID-19, compared to 34.8.%, 9.7% and 3.0% for travellers infected with influenza, SARS and Ebola respectively. While results appear to indicate that screening is more effective at preventing disease ingress when the disease in question has a shorter average incubation period, our results suggest that screening at the point of entry alone does not represent a sufficient method to adequately protect a nation from the importation of COVID-19 cases.

Cholera is one of the major public health problems in the state of Odisha, India since centuries. The current paper is a comprehensive report on epidemiology of cholera in Odisha, which was documented from 1993. PubMed and Web of Knowledge were searched for publications reporting cholera in Odisha during the period 1993–2015. The search was performed using the keywords ‘Odisha’ and/or ‘Orissa’ and ‘Cholera’. In addition, manual search was undertaken to find out relevant papers. During the study period, a total of 37 cholera outbreaks were reported with an average of >1.5 cholera outbreaks per year and case fatality ratio was 0.3%. Vibrio cholerae O1 Ogawa serotype was the major causative agent in most of the cholera cases. The recent studies demonstrated the prevalence of V. cholerae O1, El Tor variants carrying ctxB1, ctxB7 and Haitian variant tcpA allele associated with polymyxin B sensitivity and these variants are replacing the proto type El Tor. The first report of variant ctxB7 in Odisha during super-cyclone 1999 predicted its emergence and subsequent spread causing cholera outbreaks. The prevalence of multidrug-resistant V. cholerae at different time periods created alarming situation. The efficacy trial of oral cholera vaccine (OCV, Shanchol) in a public health set-up in Odisha has shown encouraging results which should be deployed for community level vaccination among the vulnerable population. This paper has taken an effort to disseminate the valuable information of epidemiology of cholera that will influence the policy-makers and epidemiologists for constant surveillance in other parts of Odisha, India and around the globe.

As most children infected with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) present with mild symptoms or they are asymptomatic, the optimal strategy for molecular testing it is not well defined. The aim of the study was to determine the extent and aetiology of molecular testing for SARS-CoV-2 in Greek paediatric departments during the first phase of the pandemic and identify possible differences in incidence, depending on the age group and geographical area. We conducted a nationwide study of molecular testing for SARS-CoV-2 of children in paediatric departments between March and June 2020. A total of 65 paediatric departments participated in the study, representing 4901 children who were tested for SARS-CoV-2 and 90 (1.8%) were positive. Most paediatric cases were associated with topical outbreaks. Adolescents 11–16 years had the highest positivity rate (3.6%) followed by children 6–10 years (1.9%). However, since the testing rate significantly differed between age groups, the modified incidence of SARS-CoV-2 infection per age group was highest in infants 5 population). Most children tested presented with fever (70.9%), respiratory (50.1%) or gastrointestinal symptoms (28.1%). Significant differences were detected between public and private hospitals regarding the positivity rate (2.34% vs. 0.39%, P-value

Cyclosporiasis is an illness characterised by watery diarrhoea caused by the food-borne parasite Cyclospora cayetanensis. The increase in annual US cyclosporiasis cases led public health agencies to develop genotyping tools that aid outbreak investigations. A team at the Centers for Disease Control and Prevention (CDC) developed a system based on deep amplicon sequencing and machine learning, for detecting genetically-related clusters of cyclosporiasis to aid epidemiologic investigations. An evaluation of this system during 2018 supported its robustness, indicating that it possessed sufficient utility to warrant further evaluation. However, the earliest version of CDC's system had some limitations from a bioinformatics standpoint. Namely, reliance on proprietary software, the inability to detect novel haplotypes and absence of a strategy to select an appropriate number of discrete genetic clusters would limit the system's future deployment potential. We recently introduced several improvements that address these limitations and the aim of this study was to reassess the system's performance to ensure that the changes introduced had no observable negative impacts. Comparison of epidemiologically-defined cyclosporiasis clusters from 2019 to analogous genetic clusters detected using CDC's improved system reaffirmed its excellent sensitivity (90%) and specificity (99%), and confirmed its high discriminatory power. This C. cayetanensis genotyping system is robust and with ongoing improvement will form the basis of a US-wide C. cayetanensis genotyping network for clinical specimens.

Severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2) pandemic is still ongoing along with the global vaccination efforts against it. Here, we aimed to understand the longevity and strength of anti-SARS-CoV-2 IgG responses in a small community (n = 283) six months following local SARS-COV-2 outbreak in March 2020. Three serological assays were compared and neutralisation capability was also determined. Overall 16.6% (47/283) of the participants were seropositive and 89.4% (42/47) of the IgG positives had neutralising antibodies. Most of the symptomatic individuals confirmed as polymerase chain reaction (PCR) positive during the outbreak were seropositive (30/32, 93.8%) and 33.3% of the individuals who quarantined with a PCR confirmed patient had antibodies. Serological assays comparison revealed that Architect (Abbott) targeting the N protein LIASON® (DiaSorin) targeting the S protein and enzyme-linked immunosorbent assay (ELISA) targeting receptor binding domain detected 9.5% (27/283), 17.3% (49/283) and 17% (48/283), respectively, as IgG positives. The latter two assays highly agreed (kappa = 0.89) between each other. In addition, 95%, (19/20, by ELISA) and 90.9% (20/22, with LIASON) and only 71.4% (15/21, by Architect) of individuals that were seropositive in May 2020 were found positive also in September. The unexpected low rate of overall immunity indicates the absence of un-noticed, asymptomatic infections. Lack of overall high correlation between the assays is attributed mainly to target-mediated antibody responses and suggests that using a single serological assay may be misleading.

Hebei Province was affected by two coronavirus disease 2019 (COVID-19) outbreak waves during the period 22 January 2020 through 27 February 2020 (wave 1) and 2 January 2021 through 14 February 2021 (wave 2). To evaluate and compare the epidemiological characteristics, containment delay, cluster events and social activity, as well as non-pharmaceutical interventions of the two COVID-19 outbreak waves, we examined real-time update information on all COVID-19-confirmed cases from a publicly available database. Wave 1 was closely linked with the COVID-19 pandemic in Wuhan, whereas wave 2 was triggered, to a certain extent, by the increasing social activities such as weddings, multi-household gatherings and church events during the slack agricultural period. In wave 2, the epidemic spread undetected in the rural areas, and people living in the rural areas had a higher incidence rate than those living in the urban areas (5.3 vs. 22.0 per 1 000 000). Furthermore, Rt was greater than 1 in the early stage of the two outbreak waves, and decreased substantially after massive non-pharmaceutical interventions were implemented. In China's ‘new-normal’ situation, development of targeted and effective intervention remains key for COVID-19 control in consideration of the potential threat of new coronavirus strains.

In August 2017, a cluster of four persons infected with genetically related strains of Shiga toxin-producing Escherichia coli (STEC) O157:H7 was identified. These strains possessed the Shiga toxin (stx) subtype stx2a, a toxin type known to be associated with severe clinical outcome. One person died after developing haemolytic uraemic syndrome. Interviews with cases revealed that three of the cases had been exposed to dogs fed on a raw meat-based diet (RMBD), specifically tripe. In two cases, the tripe had been purchased from the same supplier. Sampling and microbiological screening of raw pet food was undertaken and indicated the presence of STEC in the products. STEC was isolated from one sample of raw tripe but was different from the strain causing illness in humans. Nevertheless, the detection of STEC in the tripe provided evidence that raw pet food was a potential source of human STEC infection during this outbreak. This adds to the evidence of raw pet food as a risk factor for zoonotic transmission of gastrointestinal pathogens, which is widely accepted for Salmonella, Listeria and Campylobacter spp. Feeding RMBD to companion animals has recently increased in popularity due to the belief that they provide health benefits to animals. Although still rare, an increase in STEC cases reporting exposure to RMBDs was detected in 2017. There has also been an increased frequency of raw pet food incidents in 2017, suggesting an increasing trend in potential risk to humans from raw pet food. Recommendations to reduce the risk of infection included improved awareness of risk and promotion of good hygiene practices among the public when handling raw pet food.

We report the events of an Italian top league soccer club that took place in 1 year (from March 2020 to February 2021) at the time of coronavirus disease 2019 (COVID-19) pandemic. In early March 2020, just before sport competitions were called off due to the national lockdown in Italy, the team, which included 27 players and 26 staff at the time, faced a COVID-19 outbreak, with 16 confirmed and seven probable cases, including three staff members who had to be hospitalised. In May 2020, at the resumption of the training sessions, a high prevalence of anti-severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) immunoglobulin G positivity (35/53, 66%) was detected among the members of the group. In the following months, sport activities were organised behind closed doors with stringent risk mitigation procedures in place. As of February 2021, only two new cases of SARS-CoV-2 infection were detected within the group, against more than 3500 nasopharyngeal swabs and 1000 serological tests.

We present a mathematical model for the simulation of the development of an outbreak of coronavirus disease 2019 (COVID-19) in a slum area under different interventions. Instead of representing interventions as modulations of the parameters of a free-running epidemic, we introduce a model structure that accounts for the actions but does not assume the results. The disease is modelled in terms of the progression of viraemia reported in scientific studies. The emergence of symptoms in the model reflects the statistics of a nation-wide highly detailed database consisting of more than 62 000 cases (about a half of them confirmed by reverse transcription-polymerase chain reaction tests) with recorded symptoms in Argentina. The stochastic model displays several of the characteristics of COVID-19 such as a high variability in the evolution of the outbreaks, including long periods in which they run undetected, spontaneous extinction followed by a late outbreak and unimodal as well as bimodal progressions of daily counts of cases (second waves without ad-hoc hypothesis). We show how the relation between undetected cases (including the ‘asymptomatic’ cases) and detected cases changes as a function of the public policies, the efficiency of the implementation and the timing with respect to the development of the outbreak. We show also that the relation between detected cases and total cases strongly depends on the implemented policies and that detected cases cannot be regarded as a measure of the outbreak, being the dependency between total cases and detected cases in general not monotonic as a function of the efficiency in the intervention method. According to the model, it is possible to control an outbreak with interventions based on the detection of symptoms only in the case when the presence of just one symptom prompts isolation and the detection efficiency reaches about 80% of the cases. Requesting two symptoms to trigger intervention can be enough to fail in the goals.

Cyclospora cayetanensisis a parasite causing cyclosporiasis (an illness in humans). Produce (fruits, vegetables, herbs), water and soil contaminated withC. cayetanensishave been implicated in human infection. The objective was to conduct a scoping review of primary research in English on the detection, epidemiology and control ofC. cayetanensiswith an emphasis on produce, water and soil. MEDLINE® (Web of ScienceTM), Agricola (ProQuest), CABI Global Health, and Food Science and Technology Abstracts (EBSCOhost) were searched from 1979 to February 2020. Of the 349 relevant primary research studies identified, there were 75 detection-method studies, 40 molecular characterisation studies, 38 studies ofCyclosporain the environment (33 prevalence studies, 10 studies of factors associated with environmental contamination), 246 human infection studies (212 prevalence/incidence studies, 32 outbreak studies, 60 studies of environmental factors associated with non-outbreak human infection) and eight control studies. There appears to be sufficient literature for a systematic review of prevalence and factors associated with human infection withC. cayetanensis. There is a dearth of publicly available detection-method studies in soil (n= 0) and water (n= 2), prevalence studies on soil (n= 1) and studies of the control ofCyclospora(particularly on produce prior to retail (n= 0)).

The global outbreak of coronavirus disease 2019 (COVID-19) is greatly threatening the public health in the world. We reconstructed global transmissions and potential demographic expansions of severe acute respiratory syndrome coronavirus 2 based on genomic information. We found that intercontinental transmissions were rare in January and early February but drastically increased since late February. After world-wide implements of travel restrictions, the transmission frequencies decreased to a low level in April. We identified a total of 88 potential demographic expansions over the world based on the star-radiative networks and 75 of them were found in Europe and North America. The expansion numbers peaked in March and quickly dropped since April. These findings are highly concordant with epidemic reports and modelling results and highlight the significance of quarantine validity on the global spread of COVID-19. Our analyses indicate that the travel restrictions and social distancing measures are effective in containing the spread of COVID-19.

Almost all hospitals are equipped with air-conditioning systems to provide a comfortable environment for patients and staff. However, the accumulation of dust and moisture within these systems increases the risk of transmission of microbes and have on occasion been associated with outbreaks of infection. Nevertheless, the impact of air-conditioning on the transmission of microorganisms leading to infection remains largely uncertain. We conducted a scoping review to screen systematically the evidence for such an association in the face of the coronavirus disease 2019 epidemic. PubMed, Embase and Web of Science databases were explored for relevant studies addressing microbial contamination of the air, their transmission and association with infectious diseases. The review process yielded 21 publications, 17 of which were cross-sectional studies, three were cohort studies and one case−control study. Our analysis showed that, compared with naturally ventilated areas, microbial loads were significantly lower in air-conditioned areas, but the incidence of infections increased if not properly managed. The use of high-efficiency particulate air (HEPA) filtration not only decreased transmission of airborne bioaerosols and various microorganisms, but also reduced the risk of infections. By contrast, contaminated air-conditioning systems in hospital rooms were associated with a higher risk of patient infection. Cleaning and maintenance of such systems to recommended standards should be performed regularly and where appropriate, the installation of HEPA filters can effectively mitigate microbial contamination in the public areas of hospitals.

We analyze the Covid-19 epidemic curve from March to end of April 2020 in Germany. We use statistical models to estimate the number of cases with disease onset on a given day and use back-projection techniques to obtain the number of new infections per day. The respective time series are analyzed by a Poisson trend regression model with change points. The change points are estimated directly from the data without further assumptions. We carry out the analysis for the whole of Germany and the federal state of Bavaria, where we have more detailed data. Both analyses show a major change between March 9th and 13th for the time series of infections: from a strong increase to a stagnation or a slight decrease. Another change was found between March 24th and March 31st, where the decline intensified. These two major changes can be related to different governmental measures. On March, 11th, Chancellor Merkel appealed for social distancing in a press conference with the Robert Koch Institute (RKI) and a ban on major events with more than 1000 visitors (March 10th) was issued. The other change point at the end of March could be related to the shutdown in Germany. Our results differ from those by other authors as we take into account the reporting delay, which turned out to be time dependent and therefore changes the structure of the epidemic curve compared to the curve of newly reported cases.

Since 1993, reports on tuberculosis (TB) outbreaks have been collected in Japan; however, there has never been an overall analysis of these TB outbreaks. We aim to provide one here. The TB outbreak data were obtained from the Ministry of Health, Labour and Welfare and are described in terms of time, place and transmission site. The average number of TB cases and latent tuberculosis infection (LTBI) were compared by the transmission site. Some 605 TB outbreaks with 3491 TB cases were reported in 1993–2015 with an increasing trend (r = 0.45), during which time 728 777 TB cases were reported nationwide. On an average, TB outbreaks occurred more often in April to May (5.5 outbreaks per 2 months) than in December to January (3.4). The most common transmission sites were workplaces (n = 255), followed by health facilities (n = 144), schools (n = 60) and welfare facilities (n = 48). Psychiatric hospitals and nursing homes had the highest average number of TB cases per outbreak (8.5 each), whereas schools and prisons had the highest numbers of LTBI cases (29.1 and 38.9, respectively). Countries, particularly those that have resources to investigate TB outbreaks, should collect and analyse findings of TB outbreaks, as it informs surveillance systems and eventually strengthens general health systems.

About 800 foodborne disease outbreaks are reported in the United States annually. Few are associated with food recalls. We compared 226 outbreaks associated with food recalls with those not associated with recalls during 2006–2016. Recall-associated outbreaks had, on average, more illnesses per outbreak and higher proportions of hospitalisations and deaths than non-recall-associated outbreaks. The top confirmed aetiology for recall-associated outbreaks was Salmonella. Pasteurised and unpasteurised dairy products, beef and molluscs were the most frequently implicated foods. The most common pathogen−food pairs for outbreaks with recalls were Escherichia coli-beef and norovirus-molluscs; the top pairs for non-recall-associated outbreaks were scombrotoxin-fish and ciguatoxin-fish. For outbreaks with recalls, 48% of the recalls occurred after the outbreak, 27% during the outbreak, 3% before the outbreak, and 22% were inconclusive or had unknown recall timing. Fifty per cent of recall-associated outbreaks were multistate, compared with 2% of non-recall-associated outbreaks. The differences between recall-associated outbreaks and non-recall-associated outbreaks help define the types of outbreaks and food vehicles that are likely to have a recall. Improved outbreak vehicle identification and traceability of rarely recalled foods could lead to more recalls of these products, resulting in fewer illnesses and deaths.

An acute gastroenteritis (AGE) outbreak caused by a norovirus occurred at a hospital in Shanghai, China, was studied for molecular epidemiology, host susceptibility and serological roles. Rectal and environmental swabs, paired serum samples and saliva specimens were collected. Pathogens were detected by real-time polymerase chain reaction and DNA sequencing. Histo-blood group antigens (HBGA) phenotypes of saliva samples and their binding to norovirus protruding proteins were determined by enzyme-linked immunosorbent assay. The HBGA-binding interfaces and the surrounding region were analysed by the MegAlign program of DNAstar 7.1. Twenty-seven individuals in two care units were attacked with AGE at attack rates of 9.02 and 11.68%. Eighteen (78.2%) symptomatic and five (38.4%) asymptomatic individuals were GII.6/b norovirus positive. Saliva-based HBGA phenotyping showed that all symptomatic and asymptomatic cases belonged to A, B, AB or O secretors. Only four (16.7%) out of the 24 tested serum samples showed low blockade activity against HBGA-norovirus binding at the acute phase, whereas 11 (45.8%) samples at the convalescence stage showed seroconversion of such blockade. Specific blockade antibody in the population played an essential role in this norovirus epidemic. A wide HBGA-binding spectrum of GII.6 supports a need for continuous health attention and surveillance in different settings.

The outbreak of coronavirus disease-2019 (COVID-19) impacts public health dramatically around the world. The demographic characteristics, exposure history, dates of illness onset and dates of confirmed diagnosis were collected from the data of 24 family clusters from Beijing. The characteristics of the cases and the estimated key epidemiologic time-to-event distributions were described. The basic reproductive number (R0) was calculated. Among 89 confirmed COVID-19 patients from 24 family clusters, the median age was 38.0 years and 43.8% were male. The median of incubation period was 5.08 days (95% confidence interval (CI) 4.17–6.21). The median of serial interval was 6.00 days (95% CI 5.00–7.00). The basic reproductive number (R0) was 2.06 (95% CI 2.02–2.08). The median of onset-to-care-seeking days and the median of onset-to-hospital admission days were significantly reduced after 23 January 2020, which implied the enhanced public health awareness among families. With epidemic containment measures in place, the results can inform health authorities about possible extent of epidemic transmission within families. Furthermore, following initiation of interventions, public health measures are not only important for curbing the epidemic spread at the community level but also improve health seeking behaviour at the individual level.

A cluster of 18 scarlet fever cases and large illness absenteeism (32%, 58/184) in a school prompted concern and further investigation. We conducted telephone interviews with parents to ascertain cases and better comprehend parents' views. We identified 19 cases, of which 13 reported scarlet fever diagnosis by a physician and only seven fulfilled the probable case definition. We concluded that the outbreak was far smaller than suspected and found that communication and reporting could be improved. Accurate information and communication is essential in an outbreak; the school's concern could have been alleviated sooner and response measures better targeted.

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.

The outbreak of the novel coronavirus severe acute respiratory syndrome-coronavirus-2 has raised major health policy questions and dilemmas. Whilst respiratory droplets are believed to be the dominant transmission mechanisms, indirect transmission may also occur through shared contact of contaminated common objects that is not directly curtailed by a lockdown. The conditions under which contaminated common objects may lead to significant spread of coronavirus disease 2019 during lockdown and its easing is examined using the susceptible-exposed-infectious-removed model with a fomite term added. Modelling the weekly death rate in the UK, a maximum-likelihood analysis finds a statistically significant fomite contribution, with 0.009 ± 0.001 (95% CI) infection-inducing fomites introduced into the environment per day per infectious person. Post-lockdown, comparison with the prediction of a corresponding counterfactual model with no fomite transmission suggests fomites, through enhancing the overall transmission rate, may have contributed to as much as 25% of the deaths following lockdown. It is suggested that adding a fomite term to more complex simulations may assist in the understanding of the spread of the illness and in making policy decisions to control it.