Influenza results in approximately 3–5 million annual cases of severe illness and 250 000–500 000 deaths. We urgently need an accurate multi-step-ahead time-series forecasting model to help hospitals to perform dynamical assignments of beds to influenza patients for the annually varied influenza season, and aid pharmaceutical companies to formulate a flexible plan of manufacturing vaccine for the yearly different influenza vaccine. In this study, we utilised four different multi-step prediction algorithms in the long short-term memory (LSTM). The result showed that implementing multiple single-output prediction in a six-layer LSTM structure achieved the best accuracy. The mean absolute percentage errors from two- to 13-step-ahead prediction for the US influenza-like illness rates were all <15%, averagely 12.930%. To the best of our knowledge, it is the first time that LSTM has been applied and refined to perform multi-step-ahead prediction for influenza outbreaks. Hopefully, this modelling methodology can be applied in other countries and therefore help prevent and control influenza worldwide.

Norovirus is one of the leading causes of viral gastroenteritis worldwide and responsible for substantial morbidity, mortality and healthcare costs. To further understanding of the epidemiology and control of norovirus, there has been much recent interest in describing the transmission dynamics of norovirus through mathematical models. In this study, we review the current modelling approaches for norovirus transmission. We examine the data and methods used to estimate these models that vary structurally and parametrically between different epidemiological contexts. Many of the existing studies at population level have focused on the same case notification dataset, whereas models from outbreak settings are highly specific and difficult to generalise. In this review, we explore the consistency in the description of norovirus transmission dynamics and the robustness of parameter estimates between studies. In particular, we find that there is considerable variability in estimates of key parameters such as the basic reproduction number, which may mean that the effort required to control norovirus at the population level may currently be underestimated.

Community-led total sanitation (CLTS) is an intervention that strives to end the practice of open defaecation. This study measured the effectiveness of CLTS in Nyando District by examining the association between community open defaecation-free (ODF) status and childhood diarrhoeal illness. A cross-sectional study design was used among households with children ⩽5 years old to ascertain information on acute diarrhoea in the past year (outcome), sanitation and health behaviours. Water testing was conducted to determine Escherichia coli and turbidity levels for 55 water sources. Data were obtained from 210 parents or caregivers from an ODF community and 216 parents or caregivers in a non-ODF community. The non-ODF participants reported a non-significant 16% increased risk of diarrhoea compared with the participants from the ODF community. Children's HIV positivity (adjusted prevalence ratio (aPR) = 2.29; 95% CI 2.07–2.53), unsafe child stool disposal (aPR = 1.92; 95% CI 1.74–2.12) and low household income (aPR = 1.93; 95% CI 1.46–2.56) were associated with diarrhoea, in the non-ODF community. The ODF location had a higher percentage of E. coli in the drinking water compared with the non-ODF location (76.7% vs. 60%). Diarrhoeal disease rates in children ⩽5 years old did not differ by whether a latrine intervention was implemented. Water sampling findings suggest water safety may have decreased the effectiveness of the CLTS’ improvement of childhood diarrhoea. Improved water treatment practices, safe stool disposal and education may improve the CLTS intervention in ODF communities and therefore reduced the risk of childhood diarrhoea.

Human parechoviruses (HPeVs) are known to cause various clinical manifestations including acute gastroenteritis. Although HPeV infections and their genotypes have been detected in human patients worldwide, no such reports are available from India to ascertain the association of HPeVs in acute gastroenteritis. The present study was conducted to determine the clinical features and genetic diversity of HPeVs detected in children hospitalised for acute gastroenteritis. Stool specimens (n = 979) collected from children aged ⩽5 years hospitalised for acute gastroenteritis in Pune, western India during January 2006–December 2010 were included. HPeV RNA was detected by reverse transcription-polymerase chain reaction (RT-PCR) (5′UTR) followed by genotyping using VP1 gene-based PCR and phylogenetic analysis. HPeV was detected in 13·9% (136/979) of the cases, co-infections with other enteric viruses were found in 43·4%. HPeV was more frequent in children ⩽1 year age with infections reported throughout the year. A total of 102/136 (75%) HPeV strains were genotyped, which comprised 13 different HPeV genotypes. Of these, HPeV1 was the most predominant genotype detected and phylogenetically clustered with the Harris strain which is rarely reported. The study documents circulation of heterogeneous HPeV genotypes. Two variant strains of HPeV4 and ‘RGD absent’ HPeV5 and 6 strains were also detected. This is the first report of HPeV with diversified genotypes identified in acute gastroenteritis patients from India.

Leprosy still represents a serious health problem in a number of countries, including Brazil. Although leprosy has been associated with poverty for a long time, it is still difficult to accurately define this relationship. Here, we evaluated in an endemic municipality the progress from 1995 to 2015 of epidemiological indicators to establish if there were any strong associations between social indicators and the occurrence of leprosy. An ecological study was conducted using the SINAN database (Brazilian leprosy-national notifiable diseases information system) in combination with georeferencing of leprosy cases. The georeferencing used the ArcGis programme and occurrence of cases was evaluated in relation to the Health Vulnerability Index (HVI), an indicator that categorises socio-economic and sanitation factors. The data identified a marked decrease in the overall prevalence of leprosy, a reduction in the new case-detection rate and a reduction in the number of cases with grade 2 disabilities (albeit with transient peaks in 2007 and 2015). Logistic regression analysis showed association of detection rates with elevated HVI. Thus, while the epidemiological indicators point to the elimination of leprosy, there is evidence of hidden cases and an association between higher rates of leprosy detection and greater social vulnerability remain.

In this study, we describe the results of virological investigations carried out on cases of gastroenteritis reported in different communities within a 2-year pilot surveillance programme (January 2012 to December 2013) in the autonomous province of Bolzano (Northern Italy). Among the 162 norovirus (NoV)-positive cases out of 702 cases investigated, 76 were grouped in nine suspected outbreaks, 37 were hospital-acquired and 49 were community-acquired sporadic cases. NoV infections were found in all age groups in outbreak and community-acquired cases, while the highest peak of hospital-acquired infections occurred in the elderly. Sequence analyses helped to identify suspected outbreaks both in the community and in hospital wards. Although GII.4 is the predominant genotype, sequence data confirmed that at least seven genotypes circulate causing sporadic cases. Findings in this study confirmed the relevance of NoV infections as a cause of outbreaks, and impact of NoV infections in community-acquired sporadic cases in adults that are rarely described because of a lack of reporting.

Zika virus (ZIKV) infection is an emergent worldwide public health problem. Historically, 84 countries have reported vector-borne ZIKV transmission, 61 of which report on-going transmission. It is a Flavivirus transmitted through arthropods belonging to the Aedes genus. Since 2015, ZIKV infections have increased dramatically; with 1.3 million people infected during 2015 in Brazil alone. This paper's objective is to highlight the conjectural epidemiological points of the virus’ dissemination. The digital archives Pubmed, MEDLINE, EMBASE and Cochrane were searched for papers that assessed aspects of ZIKV transmission and epidemiology. The first isolation occurred in Uganda in 1947. Since then, important outbreaks were documented globally. Consequently, an emergent public health problem arose from a rapidly increasing incidence and its association with the development of neurological diseases such as microcephaly and Guillain–Barré syndrome. Key factors in the successful containment of outbreaks include surveillance of mosquitos in the neighbourhood, an early mosquito control treatment, an assertive information campaign, and the involvement of the local population and healthcare workers. As such, while ZIKV seems to be spreading globally in a similar manner to other arboviruses, such as Dengue and Chikungunya viruses, it can also be rapidly contained due to the pre-existing availability of necessary resources and regulatory tools as control measures. This review aims to provide a description of those characteristics of ZIKV infection that may be useful in the construction of effective outbreak control strategies.

Although Giardia, the aetiological agent of giardiasis, is one of the most prevalent intestinal parasitic infections world-wide, for industrialised countries, it is mainly appreciated as an imported disease with the minimal local transmission. However, the current evidence challenges this perception; Giardia has relevance beyond the high prevalence areas. This infection may be asymptomatic or cause gastrointestinal complains and long-term sequelae, including irritable bowel syndrome, chronic fatigue and impaired child growth and cognitive development. Its detection and diagnosis present a challenge to physicians who may not be familiar with this infection. To improve interventions to control this parasitosis, it is necessary to maintain a high index of suspicion and remain vigilant in finding cases at risk for infection. A better understanding of the characteristics of populations importing infections alongside improved methods to reliably classify infections as imported or acquired locally will help to ensure early and accurate diagnosis. The evidence shows that public health problems like giardiasis are global issues that need to be addressed collectively by both high and low prevalence countries.

Over the recent years, potential associations between Toxoplasma gondii (T. gondii) infection and cancer risk have attracted a lot of attention. Nevertheless, the association between T. gondii infection and oral cancer remains relatively unexplored. We performed a case–control study of 861 oral cancer patients and 861 control subjects from eastern China with the aim to detect antibodies to T. gondii by enzyme-linked immunosorbent assay (ELISA) in these patients. The results showed that oral cancer patients (21.72%, 187/861) had a significantly higher seroprevalence than control subjects (8.25%, 71/861) (P < 0.001). Among them, 144 (16.72%) oral cancer patients and 71 (8.25%) control subjects were positive for IgG antibodies to T. gondii, while 54 (6.27%) oral cancer patients and 9 (1.05%) controls were positive for IgM antibodies to T. gondii. In addition, multiple logistic analysis showed that T. gondii infection in oral cancer patients was associated with blood transfusion history, keeping cats at home, and oyster consumption. To our knowledge, this is the first study that provided a serological evidence of an association between T. gondii infection and oral cancer patients. However, further studies are necessary to elucidate the role of T. gondii in oral cancer patients.

The ability to predict upper respiratory infections (URI), lower respiratory infections (LRI), and gastrointestinal tract infections (GI) in independently living older persons would greatly benefit population and individual health. Social network parameters have so far not been included in prediction models. Data were obtained from The Maastricht Study, a population-based cohort study (N = 3074, mean age (±s.d.) 59.8 ± 8.3, 48.8% women). We used multivariable logistic regression analysis to develop prediction models for self-reported symptomatic URI, LRI, and GI (past 2 months). We determined performance of the models by quantifying measures of discriminative ability and calibration. Overall, 953 individuals (31.0%) reported URI, 349 (11.4%) LRI, and 380 (12.4%) GI. The area under the curve was 64.7% (95% confidence interval (CI) 62.6–66.8%) for URI, 71.1% (95% CI 68.4–73.8) for LRI, and 64.2% (95% CI 61.3–67.1%) for GI. All models had good calibration (based on visual inspection of calibration plot, and Hosmer–Lemeshow goodness-of-fit test). Social network parameters were strong predictors for URI, LRI, and GI. Using social network parameters in prediction models for URI, LRI, and GI seems highly promising. Such parameters may be used as potential determinants that can be addressed in a practical intervention in older persons, or in a predictive tool to compute an individual's probability of infections.

Our objective was to identify predictors of severe acute respiratory infection in hospitalised patients and understand the impact of vaccination and neuraminidase inhibitor administration on severe influenza. We analysed data from a study evaluating influenza vaccine effectiveness in two Michigan hospitals during the 2014–2015 and 2015–2016 influenza seasons. Adults admitted to the hospital with an acute respiratory infection were eligible. Through patient interview and medical record review, we evaluated potential risk factors for severe disease, defined as ICU admission, 30-day readmission, and hospital length of stay (LOS). Two hundred sixteen of 1119 participants had PCR-confirmed influenza. Frailty score, Charlson score and tertile of prior-year healthcare visits were associated with LOS. Charlson score >2 (OR 1.5 (1.0–2.3)) was associated with ICU admission. Highest tertile of prior-year visits (OR 0.3 (0.2–0.7)) was associated with decreased ICU admission. Increasing tertile of visits (OR 1.5 (1.2–1.8)) was associated with 30-day readmission. Frailty and prior-year healthcare visits were associated with 30-day readmission among influenza-positive participants. Neuraminidase inhibitors were associated with decreased LOS among vaccinated participants with influenza A (HR 1.6 (1.0–2.4)). Overall, frailty and lack of prior-year healthcare visits were predictors of disease severity. Neuraminidase inhibitors were associated with reduced severity among vaccine recipients.

This research investigates the long-forgotten relationship between diphtheria and tuberculosis. Historical medical reports from the late 19th century are reviewed followed by a statistical regression analysis of the relationship between the two diseases in the early 20th century. Historical medical reports show a consistent association between diphtheria and tuberculosis that can increase the likelihood and severity of either disease in a co-infection. The statistical analysis uses historical weekly public health data on reported cases in five American cities over a period of several years, finding a modest but statistically significant relationship between the two diseases. No current medical theory explains the association between diphtheria and tuberculosis. Alternative explanations are explored with a focus on how the diseases assimilate iron. In a co-infection, the effectiveness of tuberculosis at assimilating extracellular iron may lead to increased production of diphtheria toxin, worsening that disease, which may, in turn, exacerbate tuberculosis. Iron-dependent repressor genes connect both diseases.

We describe the investigation of two temporally coincident illness clusters involving salmonella and Staphylococcus aureus in two states. Cases were defined as gastrointestinal illness following two meal events. Investigators interviewed ill persons. Stool, food and environmental samples underwent pathogen testing. Alabama: Eighty cases were identified. Median time from meal to illness was 5·8 h. Salmonella Heidelberg was identified from 27 of 28 stool specimens tested, and coagulase-positive S. aureus was isolated from three of 16 ill persons. Environmental investigation indicated that food handling deficiencies occurred. Colorado: Seven cases were identified. Median time from meal to illness was 4·5 h. Five persons were hospitalised, four of whom were admitted to the intensive care unit. Salmonella Heidelberg was identified in six of seven stool specimens and coagulase-positive S. aureus in three of six tested. No single food item was implicated in either outbreak. These two outbreaks were linked to infection with Salmonella Heidelberg, but additional factors, such as dual aetiology that included S. aureus or the dose of salmonella ingested may have contributed to the short incubation periods and high illness severity. The outbreaks underscore the importance of measures to prevent foodborne illness through appropriate washing, handling, preparation and storage of food.

Aedes aegypti, historically known as yellow fever (YF) mosquito, transmits a great number of other viruses such as Dengue, West Nile, Chikungunya, Zika, Mayaro and perhaps Oropouche, among others. Well established in Africa and Asia, Aedes mosquitoes are now increasingly invading large parts of the American continent, and hence the risk of urban YF resurgence in the American cities should because of great concern to public health authorities. Although no new urban cycle of YF was reported in the Americas since the end of an Aedes eradication programme in the late 1950s, the high number of non-vaccinated individuals that visit endemic areas, that is, South American jungles where the sylvatic cycle of YF is transmitted by canopy mosquitoes, and return to Aedes-infested urban areas, increases the risk of resurgence of the urban cycle of YF. We present a method to estimate the risk of urban YF resurgence in dengue-endemic cities. This method consists in (1) to estimate the number of Aedes mosquitoes that explains a given dengue outbreak in a given region; (2) calculate the force of infection caused by the introduction of one infective individual per unit area in the endemic area under study; (3) using the above estimates, calculate the probability of at least one autochthonous YF case per unit area produced by one single viraemic traveller per unit area arriving from a YF endemic or epidemic sylvatic region at the city studied. We demonstrate that, provided the relative vector competence, here defined as the capacity to being infected and disseminate the virus, of Ae. aegypti is greater than 0.7 (with respect to dengue), one infected traveller can introduce urban YF in a dengue endemic area.

The main feature of the epidemiological transition is a shift in the recorded causes of death from infectious diseases to other morbid conditions. This paper outlines modifications made to Omran's original model and stages of transition, and suggests that without a focus on aetiology and morbidity, these have been basically descriptive rather than explanatory, and potentially misleading because infections have been confirmed as causes of various chronic diseases. Common infections and related immune responses or inflammatory processes contribute to the multifactorial aetiology of morbid conditions that together make a substantial contribution to overall mortality, and infectious causation is suspected for many others because of strong evidence of association. Investigation into possible infectious causes of conditions frequently recorded as the underlying cause of death can be integrated into a framework for comparative research on patterns of disease and mortality in support of public health and prevention. A theory of epidemiological transition aimed at understanding changes in disease patterns can encompass the role in different conditions and chronic diseases of infections contracted over the life course, and their contribution to disability, morbidity and mortality relative to other causes and determinants.

A salmonellosis outbreak occurred at a California prison in April and May 2016. In a cohort study of 371 inmates, persons who consumed dishes from the prison kitchen made from ground meat had a higher attack rate (15%) than those who did not (4%) (risk ratio 3.4, 95% CI 1.1–10.6). The ground meat product was composed exclusively of beef, mechanically separated chicken (MSC) and textured vegetable protein; eight of eight lots of the product collected from the prison and processing facility were contaminated with Salmonella enterica of eight serotypes and 17 distinct PFGE patterns, including multidrug-resistant S. Infantis. Either the MSC or the beef could have been the source of the particular strains of S. enterica isolated from patients or the product. The microbiological evidence is most consistent with MSC as the source of the high levels of S. enterica in the epidemiologically linked meat product. Our findings contribute to the growing body of evidence about the hazard posed by the use of products containing raw mechanically separated poultry in kitchens in institutions.

The possible association between Toxoplasma gondii infection and paediatric haematological malignancies in a group of patients and control subjects was evaluated in the present study. We performed an age-, gender- and residence frequency-matched case–control study of 101 blood cancer patients under 18 years of age, all of which were treated in Amirkola Pediatric Hospital. One hundred and thirty-eight control samples were gathered from the outpatient clinic in the hospital. All cases and controls were tested for the presence of anti-Toxoplasma IgG antibodies and then IgG-positive subjects were evaluated for IgM antibodies by enzyme-linked immunoassays. Anti-T. gondii IgG antibodies were found in 37 (36.6%) of the cases and 12 (8.7%) subjects in the control group (odds ratio 6.07, 95% confidence interval 2.963–12.437, P < 0.0001). The median and interquartile range (IQR) of IgG titre from case group (7.7 (IQR 0.25–13.5)) was higher than the control (0.2 (IQR 0.1–0.5)) (P < 0.0001). The frequency of anti-T. gondii antibodies (IgG) in lymphoblastic leukaemia (acute lymphoblastic leukaemia), Hodgkin's lymphoma and T–cell lymphoma were 33 (31.9%), 3 (50%) and 1(100%), respectively. Anti–T. gondii IgM was not detected in the IgG-positive patients in case group. In the case subjects, no significant difference was seen in the positive rates of T. gondii infection between genders (37.3% in male; 35.7% in female; P = 0.52) and ages groups (P = 0.31). This study demonstrated that T. gondii infection is prevalent in children with blood cancer. It also showed that toxoplasmosis may possibly be linked with an increased risk of childhood haematologic malignancies. Furthermore, these results may be helpful in research on blood neoplasia aetiology.

In July 2014, an outbreak of gastroenteritis occurred among visitors to lakes in Tampere, Finland. We conducted a retrospective cohort study using an internet-based survey, solicited by public announcement, to identify source of infection and to implement control measures. Of 1453 persons enrolled in the study, 244 met the case definition (attack rate, 17%). In the pooled univariate analysis, risk factors for gastroenteritis included getting water in the mouth while swimming (Risk ratio (RR) 3.32; 95% Confidence interval (CI), 2.36–4.68) and playing on the wet sand at the beach (RR 1.90; 95% CI 1.50–2.41). In a multivariable analysis (logistic regression), the source of the infection was likely at two lakes (lake A Odds ratio (OR) 1.66; 95% CI 1.15–2.39 and lake B, OR 2.35; 95% CI 1.49–3.72). Norovirus (NoV) was found in 19 stool samples. All water samples from implicated beaches had acceptable values of fecal indicator bacteria and were negative for NoV. The likely source of the outbreak was lake-water contaminated with NoV at two popular lakes. Closure of swimming beaches, advice on hygienic precautions and rapid outbreak alerts were efficient in controlling the outbreak. Results suggest a need for new indicators of water quality and development of evidence-based recommendations regarding timing of safe reopen of recreational water venues associated with outbreaks.

A large outbreak of Legionnaires’ disease occurred at a California state prison in August 2015. We conducted environmental and epidemiological investigations to identify the most likely source of exposure and characterise morbidity. Sixty-four inmates had probable Legionnaires’ disease; 14 had laboratory-confirmed legionellosis. Thirteen (17%) inmates were hospitalised; there were no deaths. Ill inmates were more likely to be ⩾65 years old (P < 0.01), have the chronic obstructive pulmonary disease (P < 0.01), diabetes mellitus (P = 0.02), hepatitis C infection (P < 0.01), or end-stage liver disease (P < 0.01). The case-patients were in ten housing units throughout the prison grounds. All either resided in or were near the central clinical building (for appointments or yard time) during their incubation periods. Legionella pneumophila serogroup 1 was cultured from three cooling towers on top of the central medical clinic (range, 880–1200 cfu/ml). An inadequate water management program, dense biofilm within the cooling towers, and high ambient temperatures preceding the outbreak created an ideal environment for Legionella sp. proliferation. All state prisons were directed to develop local operating procedures for maintaining their cooling towers and the state health department added a review of the maintenance plans to their environmental inspection protocol.

Norovirus is the leading cause of acute gastroenteritis in the USA. Although secondary household transmission of norovirus is frequently reported in outbreaks, little is known about specific risk factors for susceptibility and infectiousness in the household. Three norovirus outbreaks were investigated and data were collected on individuals exposed in the primary outbreak setting and their household members. Potential individual- and household-level risk factors for susceptibility and infectiousness were assessed using univariate and multivariate generalised linear mixed models. In the univariate models, the secondary attack rate (SAR) was significantly higher when living in a household with two or more primary cases (incidence rate ratio (IRR) = 2·1; 95% confidence interval (CI) 1·37–3·29), more than one primary case with vomiting (IRR = 1·9; CI 1·11–3·37), and at least one primary case with diarrhoea (IRR = 3·0; CI 1·46–6·01). After controlling for other risk factors in the multivariate models, the SAR was significantly higher among those living in a household with two or more primary cases (adjusted IRR = 2·0; CI 1·17–3·47) and at least one primary case with diarrhoea (adjusted IRR = 2·8; CI 1·35–5·93). These findings underscore the importance of maintaining proper hygiene and isolating ill household members to prevent norovirus transmission in the household.