Several studies have reported evidence of interference between respiratory viruses: respiratory viruses rarely reach their epidemic peak concurrently and there appears to be a negative association between infection with one respiratory virus and co-infection with another. We used results spanning 16 years (2002–2017) of a routine diagnostic multiplex panel that tests for nine respiratory viruses to further investigate these interactions in Victoria, Australia. Time series analyses were used to plot the proportion positive for each virus. The seasonality of all viruses included was compared with respiratory syncytial virus (RSV) and influenza A virus using cross-correlations. Logistic regression was used to explore the likelihood of co-infection with one virus given infection with another. Seasonal peaks were observed each year for influenza A and RSV and less frequently for influenza B, coronavirus and parainfluenza virus. RSV circulated an average of 6 weeks before influenza A. Co-infection with another respiratory virus was less common with picornavirus, RSV or influenza A infection. Our findings provide further evidence of a temporal relationship in the circulation of respiratory viruses. A greater understanding of the interaction between respiratory viruses may enable better prediction of the timing and magnitude of respiratory virus epidemics.

In November 2016, a woman in her 30s who stayed at an insecure, temporary housing facility, a manga café in Tokyo, Japan, for a year was diagnosed with sputum smear-positive tuberculosis (TB). Since the café had 31 staff members and provided with accommodation to many people, the local health office initiated a contact investigation. This study aims to characterise the cases found in the outbreak. A TB case was defined as a person tested bacteriologically positive for TB, or was determined to have TB by a physician. A latent TB infection case was defined as a person tested positive by interferon-γ release assay. From January 2016 through November 2017, there were 31 staff members at the manga café, of which, six developed TB disease (one smear-negative, culture-positive and five smear- and culture-negative) in addition to seven LTBI. Another long-term customer was found having sputum smear-positive TB. Variable numbers tandem repeat (VNTR) test revealed that the index patient and the long-term customer had the identical type of VNTR; however, one staff member had a different VNTR. Local health authorities should intensify screening long-term customers of such facilities for TB regularly as well as once a TB outbreak occurs.

The association between methicillin-resistant Staphylococcus aureus (MRSA) colonisation and/or infection with increased morbidity and mortality among hospital patients has long been recognised. We sought to build on previous studies to identify modifiable risk factors associated with the acquisition of MRSA colonisation and infection by conducting a retrospective cohort study on patients admitted through the Emergency Department of an acute tertiary-care general hospital in Singapore which implemented universal on-admission MRSA screening. Patients were assigned to the acquisition or non-acquisition group depending on whether they acquired MRSA during their admission. We used logistic regression models with a patient being in the acquisition group as the binary outcome to identify factors associated with MRSA acquisition. A total of 1302 acquisition and 37 949 non-acquisition group patients were analysed. Fifteen variables were included in the multivariate model. A dose–response relationship between length of stay and odds of MRSA acquisition was observed, with a length of stay 3 weeks or more (Adj OR 11.78–57.36, all P < 0.001) being the single biggest predictor of MRSA acquisition. Other variables significantly associated with MRSA acquisition were: male gender, age 65 or greater, previous MRSA colonisation or infection, exposure to certain antibiotics and surgery, and history of diabetes.

Some European countries recently reported an increase in hepatitis E virus genotype 3 (HEV-3) of the subtype 3c. No link between HEV-3 subtypes and severity is established to date. Here, we report that patients infected with HEV-3c were at lower risk of hospitalisation, compared to those infected with HEV-3f, the other main subtype circulating in Belgium.

On 16 March 2018, a nursing home notified a possible acute gastroenteritis outbreak that affected 11 people. Descriptive and case–control studies and analysis of clinical and environmental samples were carried out to determine the characteristics of the outbreak, its aetiology, the transmission mechanism and the causal food. The extent of the outbreak in and outside the nursing home was determined and the staff factors influencing propagation were studied by multivariate analysis. A turkey dinner on March 14 was associated with the outbreak (OR 4.22, 95% CI 1.11–16.01). Norovirus genogroups I and II were identified in stool samples. The attack rates in residents, staff and household contacts of staff were 23.49%, 46.22% and 22.87%, respectively. Care assistants and cleaning staff were the staff most frequently affected. Cohabitation with an affected care assistant was the most important factor in the occurrence of cases in the home (adjusted OR 6.37, 95% CI 1.13–36.02). Our results show that staff in close contact with residents and their household contacts had a higher risk of infection during the norovirus outbreak.

To control hepatitis A spread by vaccination, accurate estimation of transmissibility is vital. Regan et al. (2016) proposed a model of hepatitis A virus (HAV) transmission and used least squares to calibrate model to the 1991/1992 HAV outbreak in men who have sex with men (MSM) in Sydney, Australia. Based on the estimate of R0, they obtained the critical immunity of 70% and showed that when the proportion immune <70%, there is a definite chance for outbreaks to take place. The immunity level from previous surveys ranges from 32% to 64% after 1996 while no outbreaks in Australian MSMs have been reported since 1996. Further noticing the ill-distributed parameters, we argue that their estimate of R0 is not accurate. In this study, we revisited their model by Bayesian inference, which has privilege over least squares. We obtained the appropriate posterior distributions of parameters and the estimate of R0 ranges from 1.38 to 2.89, indicating a critical immunity of 65%. The reduction in critical immunity and outbreak probabilities predicts the absence of outbreaks in Australian MSMs since 1996. Our study shows the importance of using appropriate methods to provide reliable and accurate estimates of the model parameters especially the transmissibility.

Noroviruses, along with rotaviruses, are among the leading causes of gastroenteritis worldwide and novel strains are periodically emerging. In August 2015, an unusual increase of gastroenteritis cases occurred in a touristic district in Kassandra peninsula, Chalkidiki, Northern Greece. Seven stool specimens from cases were tested positive for norovirus. Molecular investigation and phylogenetic analysis identified that there was co-circulation of norovirus GI.P2_GI.2 and the recombinant strain GII.P16_GII.13. A 1:1 case–control study conducted and showed that tap water consumption significantly associated with developing symptoms of gastroenteritis (odds ratio = 36.9, P = 0.018). The results of the epidemiological investigation, the co-circulation of two different norovirus strains, the information of a pipeline breakage at the water supply system before the onset of cases, and reports on flooded wells and sewage overflow, indicated the possibility of water contamination by sewage during the pipeline breakage leading to a large outbreak with a peak at 10 August and a possible secondary person-to-person transmission after the 16th of August. Norovirus GI.P2_GI.2 strains are rarely reported in Europe, while it is the first time that infection from the recombinant strain GII.P16_GII.13 is recorded in Greece.

Meningococcal carriage dynamics drive patterns of invasive disease. The distribution of carriage by age has been well described in Europe, but not in the African meningitis belt, a region characterised by frequent epidemics of meningitis. We aimed to estimate the age-specific prevalence of meningococcal carriage by season in the African meningitis belt. We searched PubMed, Web of Science, the Cochrane Library and grey literature for papers reporting carriage of Neisseria meningitidis in defined age groups in the African meningitis belt. We used a mixed-effects logistic regression to model meningococcal carriage prevalence as a function of age, adjusting for season, location and year. Carriage prevalence increased from low prevalence in infants (0.595% in the rainy season, 95% CI 0.482–0.852%) to a broad peak at age 10 (1.94%, 95% CI 1.87–2.47%), then decreased in adolescence. The odds of carriage were significantly increased during the dry season (OR 1.5 95% CI 1.4–1.7) and during outbreaks (OR 6.7 95% CI 1.6–29). Meningococcal carriage in the African meningitis belt peaks at a younger age compared to Europe. This is consistent with contact studies in Africa, which show that children 10–14 years have the highest frequency of contacts. Targeting older children in Africa for conjugate vaccination may be effective in reducing meningococcal transmission.

Less than half of stool samples from people symptomatic with infectious intestinal disease (IID) will identify a causative organism. A secondary data analysis was undertaken to explore whether symptomology alone could be used to make inferences about causative organisms. Data were utilised from the Second Study of Infectious Intestinal Disease in the Community. A total of 844 cases were analysed. Few symptoms differentiated individual pathogens, but grouping pathogens together showed that viral IID was more likely when symptom onset was in winter (odds ratio (OR) 2.08, 95% confidence interval (CI) 1.16–3.75) or spring (OR 1.92, 95% CI 1.11–3.33), the patient was aged under 5 years (OR 3.63, 95% CI 2.24–6.03) and there was loss of appetite (OR 2.19, 95% CI 1.29–3.72). The odds of bacterial IID were higher with diarrhoea in the absence of vomiting (OR 3.54, 95% CI 2.37–5.32), diarrhoea which persisted for >3 days (OR 2.69, 95% CI 1.82–3.99), bloody diarrhoea (OR 4.17, 95% CI 1.63–11.83) and fever (OR 1.67, 95% CI 1.11–2.53). Symptom profiles could be of value to help guide clinicians and public health professionals in the management of IID, in the absence of microbiological confirmation.

This study analysed the epidemiological characteristics of imported cases of acute infectious diseases and compared these features by nationality in 25 border counties of Yunnan Province from 2008 to 2017 to inform prevention strategies. Surveillance data for the imported cases collected in the border counties were analysed to determine disease variety, seasonal patterns, infection site and personal demographics and these features were compared by patient nationality. A total of 12 820 imported cases were reported in the 25 border counties, with 5610 foreign cases and 7210 native cases. The disease spectrum was more diverse among foreign cases than among native cases. Both foreign and native cases were mostly imported from Myanmar. The shift in the number of foreign cases was greater than that of native cases after 2016. Ruili, a city, that shares a border with Myanmar, exhibited the greatest number of imported infections. Farmers, businessmen, women and preschool children were frequently diagnosed with infections. Multiple prevention strategies including disease screening at the border, health education before departure and health service provision to foreigners should be carried out to reduce the risk of autochthonous spreading and to avoid potential outbreaks. Furthermore, international collaboration in terms of sharing infectious disease data should be improved between China and neighbouring countries.

A high degree of vigilance and appropriate diagnostic methods are required to detect Clostridioides difficile infection (CDI). We studied the effectiveness of a multimodal training program for improving CDI surveillance and prevention. Between 2011 and 2016, this program was made available to healthcare staff of acute care hospitals in Catalonia. The program included an online course, two face-to-face workshops and dissemination of recommendations on prevention and diagnosis. Adherence to the recommendations was evaluated through surveys administered to the infection control teams at the 38 participating hospitals. The incidence of CDI increased from 2.20 cases/10 000 patient-days in 2011 to 3.41 in 2016 (P < 0.001). The number of hospitals that applied an optimal diagnostic algorithm rose from 32.0% to 71.1% (P = 0.002). Hospitals that applied an optimal diagnostic algorithm reported a higher overall incidence of CDI (3.62 vs. 1.92, P < 0.001), and hospitals that were more active in searching for cases reported higher rates of hospital-acquired CDI (1.76 vs. 0.84, P < 0.001). The results suggest that the application of a multimodal training strategy was associated with a significant rise in the reporting of CDI, as well as with an increase in the application of the optimal diagnostic algorithm.

Usutu virus (USUV) is an emerging arbovirus that was first isolated in South Africa in 1959. This Flavivirus is maintained in the environment through a typical enzootic cycle involving mosquitoes and birds. USUV has spread to a large part of the European continent over the two decades mainly leading to substantial avian mortalities with a significant recrudescence of bird infections recorded throughout Europe within the few last years. USUV infection in humans is considered to be most often asymptomatic or to cause mild clinical signs. Nonetheless, a few cases of neurological complications such as encephalitis or meningoencephalitis have been reported. USUV and West Nile virus (WNV) share many features, like a close phylogenetic relatedness and a similar ecology, with co-circulation frequently observed in nature. However, USUV has been much less studied and in-depth comparisons of the biology of these viruses are yet rare. In this review, we discuss the main body of knowledge regarding USUV and compare it with the literature on WNV, addressing in particular virological and clinical aspects, and pointing data gaps.

We conducted probabilistic data linkage of three population datasets for the Northern Territory (NT), Australia, to describe the incidence of preterm births, stillbirths, low birthweight and small for gestational age (SGA) per 1000 NT births; and influenza and pertussis hospitalisations per 1 00 000 NT births in infants <7 months of age, in a pre-maternal vaccination era. The Perinatal Trends dataset (1994–2014) formed the cohort of 78 382 births. Aboriginal mother–infant pairs (37%) had disproportionately higher average annual rates (AR) for all adverse birth outcomes compared to their non-Aboriginal counterparts; rate ratios: preterm births 2.2 (AR 142.4 vs. 64.7); stillbirths 2.3 (AR 10.8 vs. 4.6); low birthweight 2.9 (AR 54 vs. 19); and SGA 1.7 (AR 187 vs. 111). Hospitalisation (2000–2015) and Immunisation Register datasets (1994–2015), showed that influenza hospitalisations (n = 53) and rates were 42.3 times higher in Aboriginal infants (AR 254 vs. 6); and that pertussis hospitalisations (n = 37) were 7.1 times higher in Aboriginal infants (AR 142.5 vs. 20.2) compared to non-Aboriginal infants. These baseline data are essential to assess the safety and effectiveness of influenza and pertussis vaccinations in pregnant women from the NT. Remote living Aboriginal women and infants stand to benefit the most from these vaccines.

Treatment options for Hepatitis C infection have greatly improved with direct-acting antiviral (DAA) combinations achieving high cure rates. Nevertheless, the cost of this treatment is still high and access to treatment in many countries has been preferentially reserved for patients with more severe fibrosis (F3 and F4). In this French nationwide study, we investigated the epidemiological characteristics and genotype distribution of hepatitis C virus (HCV) in treatment-naive patients with METAVIR fibrosis stages between F0 and F2 in order to identify patient profiles that became eligible for unrestricted treatment in a second period. Between 2015 and 2016 we collected data from nine French university hospitals on a total of 584 HCV positive patients with absent, mild or moderate liver fibrosis. The most represented genotypes were genotype 1b (159/584; 27.2%), followed by genotype 1a (150/584; 25.7%); genotype 3 (87/584: 14.9%); genotype 4 (80/584; 13.7%). Among genotype 4: 4a was predominantly encountered with 22 patients (27.5% of genotype 4). Genotypes 1b and 1a are currently the most frequent virus types present in treatment-naive patients with mild fibrosis in France. They can be readily cured using the available DAA. Nevertheless, non-a/non-d genotype 4 is also frequent in this population and clinical data on the efficacy of DAA on these subtypes is missing. The GEMHEP is the French group for study and evaluation of viral hepatitis on a national scale. Data collection on epidemiological and molecular aspects of viral hepatitis is performed on a regular basis in all main French teaching hospitals and serves as a basis for surveillance of these infections. Analysis and trends are regularly published on behalf of the GEMHEP group. Data collection was performed retrospectively over the 2015–2016 period, covering nine main university hospitals in France. A total of 584 hepatitis C positive patients were included in this study. Genotyping of the circulating viruses showed a high prevalence of genotypes 1b and 1a in our population. The epidemiology of hepatitis C is slowly changing in France, particularly as a consequence of the rise of ‘non-a non-d’ genotype 4 viruses mainly originating from African populations. More data concerning treatment efficacy of these genotypes is needed in order to guide clinical care.

Shiga toxin-producing Escherichia coli (STEC) infections are a significant public health issue, with foodborne transmission causing >1 million illnesses worldwide each year. We conducted a systematic review and meta-analysis (PROSPERO registry # CRD42017074239), to determine the relative association of different food types with sporadic illnesses caused by STEC. Searches were conducted from 01 August to 30 September 2017, using bibliographic and grey literature databases, websites and expert consultation. We identified 22 case-control studies of sporadic STEC infection in humans, from 10 countries within four World Health Organization subregions, from 1985 to 2012. We extracted data from 21 studies, for 237 individual measures in 11 food categories and across three status types (raw or undercooked, not raw and unknown). Beef was the most significant food item associated with STEC illness in the Americas and Europe, but in the Western Pacific region, chicken was most significant. These findings were not significantly moderated by the raw or cooked status of the food item, nor the publication year of the study. Data from the African, South-East Asian and Eastern Mediterranean subregions were lacking and it is unclear whether our results are relevant to these regions.

Shiga toxin-producing Escherichia coli (STEC) infections pose a substantial health and economic burden worldwide. To target interventions to prevent foodborne infections, it is important to determine the types of foods leading to illness. Our objective was to determine the food sources of STEC globally and for the six World Health Organization regions. We used data from STEC outbreaks that have occurred globally to estimate source attribution fractions. We categorised foods according to their ingredients and applied a probabilistic model that used information on implicated foods for source attribution. Data were received from 27 countries covering the period between 1998 and 2017 and three regions: the Americas (AMR), Europe (EUR) and Western-Pacific (WPR). Results showed that the top foods varied across regions. The most important sources in AMR were beef (40%; 95% Uncertainty Interval 39–41%) and produce (35%; 95% UI 34–36%). In EUR, the ranking was similar though with less marked differences between sources (beef 31%; 95% UI 28–34% and produce 30%; 95% UI 27–33%). In contrast, the most common source of STEC in WPR was produce (43%; 95% UI 36–46%), followed by dairy (27%; 95% UI 27–27%). Possible explanations for regional variability include differences in food consumption and preparation, frequency of STEC contamination, the potential of regionally predominant STEC strains to cause severe illness and differences in outbreak investigation and reporting. Despite data gaps, these results provide important information to inform the development of strategies for lowering the global burden of STEC infections.

Different countries, especially Brazil, that have faced recurrent dengue epidemics for decades and chikungunya epidemics since 2014, have had to restructure their health services to combat a triple epidemic of arboviruses – Zika, dengue and Chikungunya – transmitted by the same vector, mainly Aedes aegypti, in 2015–2016. Several efforts have been made to better understand these three arboviruses. Spatial analysis plays an important role in the knowledge of disease dynamics. The knowledge of the patterns of spatial diffusion of these three arboviruses during an epidemic can contribute to the planning of surveillance actions and control of these diseases. This study aimed to identify the spatial diffusion processes of these viruses in the context of the triple epidemic in 2015–2016 in Rio de Janeiro, Brazil. Two study designs were used: cross-sectional and ecological. Sequential Kernel maps, nearest-neighbour ratios calculated cumulatively over time, Moran global autocorrelation correlograms, and local autocorrelation changes over time were used to identify spatial diffusion patterns. The results suggested an expansion diffusion pattern for the three arboviruses during 2015–2016 in Rio de Janeiro. These findings can be considered for more effective control measures and for new studies on the dynamics of these three arboviruses.

In recent decades, the invasive Aedes albopictus vector has spread across Europe and is responsible for numerous outbreaks of autochthonous arboviral disease. The aim of this study was to identify epidemiological and sociological risk factors related to individual levels of exposure to Aedes albopictus bites. A multidisciplinary survey was conducted with volunteer blood donors living in areas either colonised or not by Aedes albopictus in mainland France. Individual levels of exposure were evaluated by measuring the IgG level specific to Aedes albopictus saliva. The most striking risk factors concerned the localisation and characteristics of the dwelling. Individuals living in areas colonised prior to 2009 or recently colonised (between 2010 and 2012) had higher anti-salivary gland extract IgG levels compared with those who were living in areas not yet colonised by Ae. albopictus. The type of dwelling did not seem to impact the level of exposure to Aedes bites. People living in apartments had a higher anti-salivary gland extract IgG level than those living in individual houses but the difference was not statistically significant. Interestingly, the presence of air conditioning or window nets was associated with a noticeable reduction in bite intensity.

Scabies is a contagious skin infection commonly occurring in institutions such as care homes. However, a large proportion of vulnerable people in England receive domiciliary care in the community and their experience of scabies has not been described. We undertook a pragmatic cross-sectional survey of Health Protection Teams (HPTs) in England to determine the burden of scabies related to domiciliary care. Fifteen cases or outbreaks were notified to HPTs between January 2013 and December 2017. Although a relatively uncommon event for individual HPTs, they were complex to manage and required the co-ordination of multiple stakeholders. Diagnosis was often delayed and required several clinical consultations. A lack of guidance led to difficulties establishing stakeholder roles and responsibilities and sources of funding for treatment. The stigmatisation of scabies sometimes affected the quality of care provided to patients, such as use of excessive personal protective equipment. Our study demonstrates that scabies is an issue of public health importance for domiciliary care service providers and users, and research is required to better understand the impacts of the disease and to develop evidence-based guidance. More generally, there is a need for simpler treatment regimens and methods of diagnosing scabies.

Hendra virus (HeV) continues to cause fatal infection in horses and threaten infection in close-contact humans in eastern Australia. Species of Pteropus bats (flying-foxes) are the natural reservoir of the virus. We caught and sampled flying-foxes from a multispecies roost in southeast Queensland, Australia on eight occasions between June 2013 and June 2014. The effects of sample date, species, sex, age class, body condition score (BCS), pregnancy and lactation on HeV antibody prevalence, log-transformed median fluorescent intensity (lnMFI) values and HeV RNA status were assessed using unbalanced generalised linear models. A total of 1968 flying-foxes were sampled, comprising 1012 Pteropus alecto, 742 P. poliocephalus and 214 P. scapulatus. Sample date, species and age class were each statistically associated with HeV RNA status, antibody status and lnMFI values; BCS was statistically associated with HeV RNA status and antibody status. The findings support immunologically naïve sub-adult P. alecto playing an important role in maintaining HeV infection at a population level. The biological significance of the association between BCS and HeV RNA status, and BCS and HeV antibody status, is less clear and warrants further investigation. Contrary to previous studies, we found no direct association between HeV infection and pregnancy or lactation. The findings in P. poliocephalus suggest that HeV exposure in this species may not result in systemic infection and virus excretion, or alternatively, may reflect assay cross-reactivity with another (unidentified) henipavirus.