Tick-borne encephalitis (TBE) is peculiar due to its unstable dynamics with profound inter-annual fluctuations in case numbers – a phenomenon not well understood to date. Possible reasons – apart from variable human contact with TBE foci – include external factors, e.g. climatic forcing, autonomous oscillations of the disease system itself, or a combined action of both. Spectral analysis of TBE data from six regions of central Europe (CE) revealed that the ostensibly chaotic dynamics can be explained in terms of four superposed (quasi-)periodical oscillations: a quasi-biennial, triennial, pentennial, and a decadal cycle. These oscillations exhibit a high degree of regularity and synchrony across CE. Nevertheless, some amplitude and phase variations are responsible for regional differences in incidence patterns. In addition, periodic changes occur in the degree of synchrony in the regions: marked in-phase periods alternate with rather off-phase periods. Such a feature in the disease dynamics implies that it arises as basically diverging self-oscillations of local disease systems which, at intervals, receive synchronizing impulses, such as periodic variations in food availability for key hosts driven by external factors. This makes the disease dynamics synchronized over a large area during peaks in the synchronization signal, shifting to asynchrony in the time in between.

Human tuberculosis (TB) caused by Mycobacterium bovis surveillance is affected by a lack of data. The aims of the present study were: (i) to estimate the proportion of human TB caused by M. bovis over a period of 5 years in Bologna, Northern Italy, which, like most Western European countries, has been declared bovine TB-free; (ii) to compare the genetic profiles of M. bovis strains identified in humans with those circulating in cattle in the last 15 years in Italy. Among 511 TB patients, the proportion of human TB caused by M. bovis was 1·76%, significantly associated to extra-pulmonary localization (P = 0·004) and to being elderly (P < 0·001) and Italy-born (P = 0·036). The molecular epidemiology analysis by spoligotyping and Multilocus Variable Tandem Repeat Analysis confirmed that most M. bovis strains from Italy-born patients matched those circulating in cattle herds in Italy between 2001 and 2016. Two cases of Mycobacterium bovis BCG infection were also characterized. In conclusion, the rate of human TB caused by M. bovis was not negligible, highlighting the relevance of molecular typing in evaluating the effectiveness of programmes designed to eradicate TB in cattle in Italy.

Over the period 1995–2012, the incidence of invasive meningococcal disease (IMD) caused by Neisseria meningitidis serogroup Y (NmY) increased significantly in Sweden. This is mainly due to the emergence of a predominant cluster named strain type YI subtype 1, belonging to the ST-23 clonal complex (cc). The aim of this study was to examine the clinical picture of patients with invasive disease caused by NmY and to analyse whether the predominant cluster exhibits certain clinical characteristics that might explain the increased incidence. In this retrospective observational study, the medical records available from patients with IMD caused by Nm serogroup Y in Sweden between 1995 and 2012 were systematically reviewed. Patient characteristics, in-hospital findings and outcome were studied and differences between the dominating cluster and other isolates were analysed. Medical records from 175 of 191 patients were retrieved. The median age was 62 years. The all-cause mortality within 30 days of admission was 9% (15/175) in the whole material; 4% (2/54) in the cohort with strain type YI subtype 1 and 11% (12/121) among patients with other isolates. Thirty-three per cent of the patients were diagnosed with meningitis, 19% with pneumonia, 10% with arthritis and 35% were found to have bacteraemia but no apparent organ manifestation. This survey included cases with an aggressive clinical course as well as cases with a relatively mild clinical presentation. There was a trend towards lower mortality and less-severe disease in the cohort with strain type YI subtype 1 compared with the group with other isolates.

In Singapore, influenza vaccination is recommended for persons at higher risk of complications of seasonal influenza, including those with chronic medical conditions and the elderly (individuals aged ⩾65 years). We investigated the factors associated with influenza vaccine uptake based on a nationally representative sample of community-dwelling adults aged >50 years. The data for this study were obtained from the National Health Surveillance Survey (NHSS) 2013. The association between influenza vaccine uptake and socio-demographic and health-related variables was analysed using univariable and multivariable logistic regression models. Of 3700 respondents aged ⩾50 years in the NHSS, 15·2% had received seasonal influenza vaccination in the past year. Older age, single marital status and economic inactivity were the socio-demographic variables independently associated with vaccine uptake. Health-related factors which were predictive of influenza vaccine uptake were sufficient total physical activity, better self-rated health, having at least one medical condition at risk of influenza complications and a regular family doctor/general practitioner. Influenza vaccine uptake in community-dwelling older adults was low. Our findings are of relevance in the formulation of public health policies and targeted health promotion strategies to increase vaccine uptake in this population group.

Human campylobacteriosis is the most commonly reported gastrointestinal bacterial infection in the EU; poultry meat has been identified as the main source of infection. We tested the hypothesis that enhanced biosecurity and other factors such as welfare status, breed, the practice of partial depopulation and number of empty days between flocks may prevent Campylobacter spp. caecal colonization of poultry batches at high levels (>123 000 c.f.u./g in pooled caecal samples). We analysed data from 2314 poultry batches sampled at slaughter in the UK in 2011–2013. We employed random-effects logistic regression to account for clustering of batches within farms and adjust for confounding. We estimated population attributable fractions using adjusted risk ratios. Enhanced biosecurity reduced the odds of colonization at partial depopulation [odds ratio (OR) 0·25, 95% confidence interval (CI) 0·14–0·47] and, to a lesser extent, at final depopulation (OR 0·47, 95% CI 0·25–0·89). An effect of the type of breed was also found. Under our assumptions, approximately 1/3 of highly colonized batches would be avoided if they were all raised under enhanced biosecurity or without partial depopulation. The results of the study indicate that on-farm measures can play an important role in reducing colonization of broiler chickens with Campylobacter spp. and as a result human exposure.

Many infectious diseases in humans may manifest with no or mild symptoms. While numerous studies have estimated the proportion of infectious individuals in whom symptoms are absent during the entire course of infection, the contribution of asymptomatic cases to the overall cumulative incidence is difficult to untangle. Here, with a mathematical model, we provide a simple analytical formula to quantify this contribution and highlight the potential for large errors that can arise when naively estimating it.

Prior studies suggest that the influenza vaccine is protective against some outcomes in hospitalized patients infected with influenza despite vaccination. We utilized surveillance data from Columbus, Ohio to investigate this association over multiple influenza seasons and age groups. Data on laboratory-confirmed influenza-associated hospitalizations were collected as a part of the Influenza Hospitalization Surveillance Project for the 2012–2013, 2013–2014, and 2014–2015 influenza seasons. The association between influenza vaccination status was examined in relation to the outcomes of severe influenza and diagnosis of pneumonia among patients receiving antiviral treatment. Data were analyzed using multivariable logistic regression. We observed no overall association between influenza vaccination status and severe influenza among hospitalized patients. During the 2013–2014 season, those who were vaccinated were 41% less likely to be diagnosed with pneumonia compared with those who were unvaccinated (OR = 0·59 95% CI 0·41–0·86). The influenza vaccine may provide a secondary preventive function against pneumonia among influenza cases requiring hospitalization. However, a protective effect was only observed in 2013–2014, an influenza H1N1 dominant year. Differences in circulating influenza virus strains and vaccine matching to the circulating strains during influenza seasons may impact this association.

Migrants are considered a key group at risk for HIV infection. This study describes differences between migrants and the Spanish-born population as they progress through the HIV care cascade in Catalonia, Spain. This study found that among people reached by prevention activities, migrants had a higher number of barriers to access HIV testing services than Spanish-born people, driven primarily by shared risk factors. Between 2001 and 2013, 9829 new HIV diagnoses were reported in Catalonia, the proportion of migrants increasing from 24% in 2001 to 41% in 2013. Compared with Spanish-born people, migrants had a higher proportion of women at diagnosis (24·6% vs. 16·7%), and were younger (median age of 33 vs. 37). The most frequent at-risk population was MSM (men who have sex with men) in both migrants and Spanish-born people, (40% and 43%, respectively), although there were significant differences by region of origin. People from sub-Saharan Africa had the highest proportion of late diagnosis (63·7%). Compared with the Spanish-born population, migrants on follow-up had a lower proportion of people on antiretroviral therapy (ART) (93·7% vs. 90·8%, P < 0·001) and with viral suppression (87·2% vs. 82·9%, P < 0·001). Migrants have higher number of barriers to access HIV testing services, lower retention rates and proportions on ART as compared with Spanish-born people, these differences not being uniform between migrants from different regions.

The UK Severe Influenza Surveillance System (USISS) was established following the 2009 influenza pandemic to monitor severe seasonal influenza. This article describes the severity of influenza observed in five post-2009 pandemic seasons in England. Two key measures were used to assess severity: impact measured through the cumulative incidence of laboratory-confirmed hospitalised influenza and case severity through the proportion of confirmed hospitalised cases admitted into intensive care units (ICU)/high dependency units (HDU). The impact of influenza varied by subtype and age group across the five seasons with the highest crude cumulative hospitalisation incidence for influenza A/H1N1pdm09 cases in 2010/2011 and in 0–4 year olds each season for all-subtypes. Case severity also varied by subtype and season with a higher hospitalisation: ICU ratio for A/H1N1pdm09 and older age groups (older than 45 years). The USISS system provides a tool for measuring severity of influenza each year. Such seasonal surveillance can provide robust baseline estimates to allow for rapid assessment of the severity of seasonal and emerging influenza viruses.

We compared the impact of a commercial chlorination product (brand name Air RahMat) in stored drinking water to traditional boiling practices in Indonesia. We conducted a baseline survey of all households with children <5 years in four communities, made 11 subsequent weekly home visits to assess acceptability and use of water treatment methods, measured Escherichia coli concentration in stored water, and determined diarrhoea prevalence among children <5 years. Of 281 households surveyed, boiling (83%) and Air RahMat (7%) were the principal water treatment methods. Multivariable log-binomial regression analyses showed lower risk of E. coli in stored water treated with Air RahMat than boiling (risk ratio (RR) 0·75, 95% confidence interval (CI) 0·56–1·00). The risk of diarrhoea in children <5 years was lower among households using Air RahMat (RR 0·43, 95% CI 0·19–0·97) than boiling, and higher in households with E. coli concentrations of 1–1000 MPN/100 ml (RR 1·54, 95% CI 1·04–2·28) or >1000 MPN/100 ml (RR 1·86, 95% CI 1·09–3·19) in stored water than in households without detectable E. coli. Although results suggested that Air RahMat water treatment was associated with lower E. coli contamination and diarrhoeal rates among children <5 years than water treatment by boiling, Air RahMat use remained low.

Pertussis is a vaccine-preventable respiratory infection caused by Bordetella pertussis which can be fatal in infants. Although high vaccine coverage led to prolonged disease control in England, a national outbreak of pertussis in 2011 led to the largest increase in over two decades, including a marked increase in cases aged ⩾15 years. A case-control study in four regions of England was undertaken to investigate risk factors for pertussis in adolescents and adults, specifically employment type and professional and household contact with children. Pertussis cases were laboratory-confirmed and aged ⩾15 years. Controls were recruited through general practitioner nomination. Demographic and risk factor information were collected using an online survey. Multivariable logistic regression was used to estimate independent associations with outcome. Two hundred and thirty-one cases and 190 controls were recruited. None of the four employment variables (social care, education, health sector, patient contact) were significantly associated with pertussis. Professional contact with children aged < 1 year was associated with a significantly reduced odds of pertussis [odds ratio (OR) 0·25, 95% confidence interval (CI) 0·08–0·78, P = 0·017]. Household contact with ⩾1 child aged 10–14 years was associated with significantly increased odds of pertussis (OR 2·61, 95% CI 1·47–4·64, P = 0·001). Occupational contact with very young children was associated with reduced odds of pertussis, probably due to immune boosting by low-level exposures to B. pertussis. Sharing a household with a young adolescent was a significant risk factor for pertussis in adults and older teenagers. The primary focus of the childhood pertussis vaccination programmes is to prevent infant disease. Although evidence is emerging that adolescent vaccination does not provide indirect protection to infants, our results highlight the importance of children aged 10–14 years in pertussis transmission to older adolescents and adults.

Australian abattoir workers, farmers, veterinarians and people handling animal birthing products or slaughtering animals continue to be at high risk of Q fever despite an effective vaccine being available. National Notifiable Diseases Surveillance System data were analysed for the period 1991–2014, along with enhanced risk factor data from notified cases in the states of New South Wales and Queensland, to examine changes in the epidemiology of Q fever in Australia. The national Q fever notification rate reduced by 20% [incident rate ratio (IRR) 0·82] following the end of the National Q fever Management Program in 2006, and has increased since 2009 (IRR 1·01–1·34). Highest rates were in males aged 40–59 years (5·9/100 000) and 87% of Q fever cases occurred in New South Wales and Queensland. The age of Q fever cases and proportion of females increased over the study period. Based on the enhanced risk factor data, the most frequently listed occupation for Q fever cases involved contact with livestock, followed by ‘no known risk’ occupations. More complete and comparable enhanced risk factor data, at the State/Territory and national levels, would aid in further understanding of the epidemiology of Q fever.

South Africa's paediatric antiretroviral therapy (ART) programme is managed using a monitoring and evaluation tool known as TIER.Net. This electronic system has several advantages over paper-based systems, allowing profiling of the paediatric ART programme over time. We analysed anonymized TIER.Net data for HIV-infected children aged <15 years who had initiated ART in a rural district of South Africa between 2005 and 2014. We performed Kaplan–Meier survival analysis to assess outcomes over time. Records of 5461 children were available for analysis; 3593 (66%) children were retained in care. Losses from the programme were higher in children initiated on treatment in more recent years (P < 0·0001) and in children aged ≤1 year at treatment initiation (P < 0·0001). For children aged <3 years, abacavir was associated with a significantly higher rate of loss from the programme compared to stavudine (hazard ratio 1·9, P < 0·001). Viral load was suppressed in 48–52% of the cohort, with no significant change over the years (P = 0·398). Analysis of TIER.Net data over time provides enhanced insights into the performance of the paediatric ART programme and highlights interventions to improve programme performance.

The importance of pork in the transmission of Salmonella spp. to humans has led to the development of control programmes worldwide. For this, knowledge on the epidemiology of the infection in the production system is fundamental to the efficacy of the regulations. Our objective was to determine the prevalence and spatial distribution of Salmonella-infected farms in the central region of Argentina, and to identify the predominant serotypes and epidemiological factors associated with an increased risk of infection. Salmonella was isolated from 22 of 52 sampled farms, for a farm prevalence of 42·3% (95% confidence interval 28·4–56·1). The most frequent serotypes isolated were S. Typhimurium and S. Derby, which have often been considered of public health concern in the region. Limited evidences of global and local clustering in the region under study were found, and the type of feed and presence of diarrhoeic pigs were significantly associated with having Salmonella shedders in the farm. This highlights the need to evaluate microbiological controls at the farm level, and demonstrates the usefulness of the spatial tools to identify areas of greatest risk when processing pork at slaughterhouse, which could contribute to increasing the food safety of pork products.

People who use drugs (PWUD) are a key population for hepatitis B virus (HBV) vaccination and screening. We aimed to estimate the seroprevalence of HBs antigen (HBsAg) and self-reported HBV vaccination history in French PWUD attending harm reduction centres using data from the ANRS-Coquelicot multicentre survey conducted in 2011–2013 in 1718 PWUD. Self-fingerprick blood samples were collected on dried blood spots to detect the presence of HBsAg. HBsAg seroprevalence was estimated at 1·4% [95% confidence interval (CI) 0·8–2·5]. It varied between PWUD born in high (7·6%, 95% CI 2·7–19·1), moderate (2·2%, 95% CI 0·8–5·7) and low (0·7%, 95% CI 0·3–1·5) endemic zones. Factors independently associated with HBsAg carriage were being born in a moderate or high endemic zone or reporting precarious housing. Self-reported HBV vaccination history varied from 47·4% in high endemic zones, to 59·3% and 62·6% for moderate and low endemic zones, respectively. Our results suggest that drug use plays a small and substantial role, respectively, in HBsAg carriage in PWUD born in high/moderate and low endemic zones.

In England, dual tests detecting chlamydia and gonorrhoea are used in specialist and community-based sexual health services (SHSs). Test performance is poor when prevalence is low, therefore UK national guidelines recommend against opportunistic gonorrhoea screening unless there is a clear local public health need. While surveillance data on gonorrhoea prevalence is comprehensive in specialist SHSs, it is sparse in community SHSs. We aimed to estimate gonorrhoea prevalence in heterosexual men and women aged 15–24 attending community SHSs to inform testing care pathways. We used linear and quadratic regression to model the relationship between prevalence in community and specialist SHSs in local authorities (LAs) with available surveillance data. We applied best-fitting models to predict prevalence in community SHSs in remaining LAs. Data from community SHSs were available for 102/326 LAs. There was a weak positive association between gonorrhoea prevalence in community and specialist SHSs in corresponding LAs within (R2 = 0·13, P = 0·058) and outside (R2 = 0·07, P = 0·02) London. Applying best-fitting models, we estimated a median gonorrhoea prevalence of 0·5% (mean 0·6%; range 0·2%–2·7%) in heterosexuals attending community SHSs. Despite some unexplained variation, our analyses suggest gonorrhoea prevalence in young heterosexuals attending community SHSs is below 1% in most English LAs. Our findings re-inforce the current national guidelines that recommend care pathways for gonorrhoea testing in community SHSs include confirmatory testing to reduce the risk of misdiagnosis and inappropriate management.

Ignác Fülöp Semmelweis is famous for dramatically reducing puerperal mortality while he was an Assistant in Vienna's largest hospital, the Allgemeines Krankenhaus; he did this, mainly, by requiring medical personnel to disinfect their hands by washing in a chlorine solution. But Semmelweis was soon removed from his post as assistant. The conventional view, which is suggested by Semmelweis's own account, is that his contemporaries were skeptical of his results, that he was marginalized and that once he was no longer directly responsible for caring for maternity patients, puerperal mortality returned to its former high levels. In fact, the situation appears to have been quite different. In this paper, we calculate and discuss the number of deaths at the Allgemeines maternity clinic after Semmelweis was removed from his position. As we will see, his successors maintained a relatively low mortality rate roughly consistent with the rate Semmelweis himself achieved. This suggests that the chlorine washings were probably still used conscientiously after he left and that the opposition he encountered had other sources than doubts about the effectiveness of the chlorine washings.

The surveillance of Clostridium difficile (CD) in Denmark consists of laboratory based data from Departments of Clinical Microbiology (DCMs) sent to the National Registry of Enteric Pathogens (NREP). We validated a new surveillance system for CD based on the Danish Microbiology Database (MiBa). MiBa automatically collects microbiological test results from all Danish DCMs. We built an algorithm to identify positive test results for CD recorded in MiBa. A CD case was defined as a person with a positive culture for CD or PCR detection of toxin A and/or B and/or binary toxin. We compared CD cases identified through the MiBa-based surveillance with those reported to NREP and locally in five DCMs representing different Danish regions. During 2010–2014, NREP reported 13 896 CD cases, and the MiBa-based surveillance 21 252 CD cases. There was a 99·9% concordance between the local datasets and the MiBa-based surveillance. Surveillance based on MiBa was superior to the current surveillance system, and the findings show that the number of CD cases in Denmark hitherto has been under-reported. There were only minor differences between local data and the MiBa-based surveillance, showing the completeness and validity of CD data in MiBa. This nationwide electronic system can greatly strengthen surveillance and research in various applications.

The type identity of strains of Pseudomonas aeruginosa from primary and recurrent blood stream infection (BSI) has not been widely studied. Twenty-eight patients were identified retrospectively from 2008 to 2013 from five different laboratories; available epidemiological, clinical and microbiological data were obtained for each patient. Isolates were genotyped by iPLEX MassARRAY MALDI-TOF MS and rep-PCR. This showed that recurrent P. aeruginosa BSI was more commonly due to the same genotypically related strain as that from the primary episode. Relapse due to a genotypically related strain occurred earlier in time than a relapsing infection from an unrelated strain (median time: 26 vs. 91 days, respectively). Line related infections were the most common source of suspected BSI and almost half of all BSI episodes were associated with neutropenia, possibly indicating translocation of the organism from the patient's gut in this setting. Development of meropenem resistance occurred in two relapse isolates, which may suggest that prior antibiotic therapy for the primary BSI was a driver for the subsequent development of resistance in the recurrent isolate.