Showing papers in "Epidemiology and Infection in 2019"

Prevalence of comorbidities in cases of Middle East respiratory syndrome coronavirus: a retrospective study

Abstract: The Middle East respiratory syndrome coronavirus (MERS-CoV) is a life-threatening respiratory disease with a high case fatality rate; however, its risk factors remain unclear. We aimed to explore the influence of demographic factors, clinical manifestations and underlying comorbidities on mortality in MERS-CoV patients. Retrospective chart reviews were performed to identify all laboratory-confirmed cases of MERS-COV infection in Saudi Arabia that were reported to the Ministry of Health of Saudi Arabia between 23 April 2014 and 7 June 2016. Statistical analyses were conducted to assess the effect of sex, age, clinical presentation and comorbidities on mortality from MERS-CoV. A total of 281 confirmed MERS-CoV cases were identified: 167 (59.4%) patients were male and 55 (20%) died. Mortality predominantly occurred among Saudi nationals and older patients and was significantly associated with respiratory failure and shortness of breath. Of the 281 confirmed cases, 160 (56.9%) involved comorbidities, wherein diabetes mellitus, hypertension, ischemic heart disease, congestive heart failure, end-stage renal disease and chronic kidney disease were significantly associated with mortality from MERS-CoV and two or three comorbidities significantly affected the fatality rates from MERS-CoV. The findings of this study show that old age and the existence of underlying comorbidities significantly increase mortality from MERS-CoV.

Usutu virus: A new threat?

Abstract: 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.

The resurgence of syphilis in high-income countries in the 2000s : a focus on Europe

Abstract: Syphilis can cause severe complications and sequelae. Following a decrease in reported cases in European Union/European Economic Area (EU/EEA) and other high-income countries in the 1980s and 1990s as a result of the HIV epidemic and ensuing changes in sexual behaviour, trends started to increase in the 2000s in a number of EU/EEA Member States with higher rates among men and a large proportion of cases reported among men who have sex with men (MSM), particularly HIV-positive MSM. Trends in EU/EEA Member States vary however with some countries continuing to report decreases in the number of reported cases (mostly in the Eastern part of EU/EEA) whereas many Western European countries report increasing numbers of cases. Increasing rates among women, although still relatively low, have been observed in a number of countries leading to concerns around mother-to-child transmission of syphilis and congenital syphilis. Similar overall trends are observed in other high-income countries with the exception of Japan where rates among heterosexual men and women have been rising at alarming levels. Control of syphilis requires use of comprehensive, evidence-based strategies which take into account lessons learned from previous control efforts as well as consideration of biomedical interventions.

Diagnosis of spotted fever group Rickettsia infections: the Asian perspective.

Abstract: Spotted fever group rickettsiae (SFG) are a neglected group of bacteria, belonging to the genus Rickettsia, that represent a large number of new and emerging infectious diseases with a worldwide distribution. The diseases are zoonotic and are transmitted by arthropod vectors, mainly ticks, fleas and mites, to hosts such as wild animals. Domesticated animals and humans are accidental hosts. In Asia, local people in endemic areas as well as travellers to these regions are at high risk of infection. In this review we compare SFG molecular and serological diagnostic methods and discuss their limitations. While there is a large range of molecular diagnostics and serological assays, both approaches have limitations and a positive result is dependent on the timing of sample collection. There is an increasing need for less expensive and easy-to-use diagnostic tests. However, despite many tests being available, their lack of suitability for use in resource-limited regions is of concern, as many require technical expertise, expensive equipment and reagents. In addition, many existing diagnostic tests still require rigorous validation in the regions and populations where these tests may be used, in particular to establish coherent and worthwhile cut-offs. It is likely that the best strategy is to use a real-time quantitative polymerase chain reaction (qPCR) and immunofluorescence assay in tandem. If the specimen is collected early enough in the infection there will be no antibodies but there will be a greater chance of a PCR positive result. Conversely, when there are detectable antibodies it is less likely that there will be a positive PCR result. It is therefore extremely important that a complete medical history is provided especially the number of days of fever prior to sample collection. More effort is required to develop and validate SFG diagnostics and those of other rickettsial infections.

The fall and rise of group a Streptococcus diseases.

Abstract: Streptococcus pyogenes (or Group A Streptococcus, GAS) is a Gram-positive human pathogen responsible for a diverse array of superficial, invasive and immune-related diseases. GAS infections have historically been diseases of poverty and overcrowding, and remain a significant problem in the developing world and in disadvantaged populations within developed countries. With improved living conditions and access to antibiotics, the rates of GAS diseases in developed societies have gradually declined during the 20th century. However, genetic changes in circulating GAS strains and/or changes in host susceptibility to infection can lead to dramatic increases in the rates of specific diseases. No situations exemplify this more than the global upsurge of invasive GAS disease that originated in the 1980s and the regional increases in scarlet fever in north-east Asia and the UK. In each case, increased disease rates have been associated with the emergence of new GAS strains with increased disease-causing capability. Global surveillance for new GAS strains with increased virulence is important and determining why certain populations suddenly become susceptible to circulating strains remains a research priority. Here, we overview the changing epidemiology of GAS infections and the genetic alterations that accompany the emergence of GAS strains with increased capacity to cause disease.

Bayesian spatial and spatio-temporal approaches to modelling dengue fever: a systematic review

Abstract: Dengue fever (DF) is one of the world's most disabling mosquito-borne diseases, with a variety of approaches available to model its spatial and temporal dynamics. This paper aims to identify and compare the different spatial and spatio-temporal Bayesian modelling methods that have been applied to DF and examine influential covariates that have been reportedly associated with the risk of DF. A systematic search was performed in December 2017, using Web of Science, Scopus, ScienceDirect, PubMed, ProQuest and Medline (via Ebscohost) electronic databases. The search was restricted to refereed journal articles published in English from January 2000 to November 2017. Thirty-one articles met the inclusion criteria. Using a modified quality assessment tool, the median quality score across studies was 14/16. The most popular Bayesian statistical approach to dengue modelling was a generalised linear mixed model with spatial random effects described by a conditional autoregressive prior. A limited number of studies included spatio-temporal random effects. Temperature and precipitation were shown to often influence the risk of dengue. Developing spatio-temporal random-effect models, considering other priors, using a dataset that covers an extended time period, and investigating other covariates would help to better understand and control DF transmission.

Dengue, chikungunya and zika virus coinfection: results of the national surveillance during the zika epidemic in Colombia.

Abstract: Our objective was to determine the frequency of zika (ZIKV), chikungunya (CHIKV) and dengue (DENV) virus coinfection and describe the mortality cases that occurred during the epidemiologic surveillance of the ZIKV epidemic in Colombia. We analysed all cases of suspected ZIKV infection that were reported to the National Institute of Health (October 2015-December 2016). DENV, CHIKV and ZIKV RNA were detected in serum or tissue samples using polymerase chain reaction assay. Medical records of the fatal cases were reviewed. We identified that 23 871 samples were processed. The frequency of viral agents was 439 (1.84%) for DENV, 257 (1.07%) for CHIKV and 10118 (42.38%) for ZIKV. Thirty-four (0.14%) cases of coinfection were identified. The CHIKV-ZIKV coinfection was present in 28 cases (82.3%), DENV-CHIKV in three (8.8%) and DENV-ZIKV in three (8.8%). Seven (20.6%) coinfection cases were fatal (two DENV-CHIKV cases and five CHIKV-ZIKV cases). Two cases were foetal deaths and the others were related to neurological syndrome and sepsis. In conclusion, the frequency of arbovirus coinfection during epidemic of ZIKV was low, and CHIKV-ZIKV coinfection was the most common. Mortality was high among coinfection patients. The role of each virus in the mortality cases of coinfection warrants further studies.

Nipah virus infection: A review.

Abstract: Nipah virus (NiV) is an emerging bat-borne pathogen. It was first identified 20 years ago in Malaysia and has since caused outbreaks in other parts of South and Southeast Asia. It causes severe neurological and respiratory disease which is highly lethal. It is highly infectious and spreads in the community through infected animals or other infected people. Different strains of the virus show differing clinical and epidemiological features. Rapid diagnosis and implementation of infection control measures are essential to contain outbreaks. A number of serological and molecular diagnostic techniques have been developed for diagnosis and surveillance. Difficulties in diagnosis and management arise when a new area is affected. The high mortality associated with infection and the possibility of spread to new areas has underscored the need for effective management and control. However, no effective treatment or prophylaxis is readily available, though several approaches show promise. Given the common chains of transmission from bats to humans, a One Health approach is necessary for the prevention and control of NiV infection.

Global and regional source attribution of Shiga toxin-producing Escherichia coli infections using analysis of outbreak surveillance data

Abstract: 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.

Diarrhoeagenic Escherichia coli and Escherichia albertii in Brazil: pathotypes and serotypes over a 6-year period of surveillance.

Abstract: Diarrhoeagenic Escherichia coli (DEC) is a leading cause of infectious diarrhoea worldwide. In recent years, Escherichia albertii has also been implicated as a cause of human enteric diseases. This study describes the occurrence of E. coli pathotypes and serotypes associated with enteric illness and haemolytic uremic syndrome (HUS) isolated in Brazil from 2011 to 2016. Pathotypes isolated included enteropathogenic E. coli (EPEC), enteroaggregative E. coli (EAEC), enterotoxigenic E. coli (ETEC), enteroinvasive E. coli (EIEC) and Shiga toxin-producing E. coli (STEC). PCR of stool enrichments for DEC pathotypes was employed, and E. albertii was also sought. O:H serotyping was performed on all DEC isolates. A total of 683 DEC and 10 E. albertii strains were isolated from 5047 clinical samples. The frequencies of DEC pathotypes were 52.6% (359/683) for EPEC, 32.5% for EAEC, 6.3% for ETEC, 4.4% for EIEC and 4.2% for STEC. DEC strains occurred in patients from 3 months to 96 years old, but EPEC, EAEC and STEC were most prevalent among children. Both typical and atypical isolates of EPEC and EAEC were recovered and presented great serotype heterogeneity. HUS cases were only associated with STEC serotype O157:H7. Two E. albertii isolates belonged to serogroup O113 and one had the stx2f gene. The higher prevalence of atypical EPEC in relation to EAEC in community-acquired diarrhoea in Brazil suggests a shift in the trend of DEC pathotypes circulation as previously EAEC predominated. This is the first report of E. albertii isolation from active surveillance. These results highlight the need of continuing DEC and E. albertii surveillance, as a mean to detect changes in the pattern of pathotypes and serotypes circulation and provide useful information for intervention and control strategies.

Rates of asymptomatic respiratory virus infection across age groups.

Abstract: Respiratory viral infections are a leading cause of disease worldwide. A variety of respiratory viruses produce infections in humans with effects ranging from asymptomatic to life-treathening. Standard surveillance systems typically only target severe infections (ED outpatients, hospitalisations, deaths) and fail to track asymptomatic or mild infections. Here we performed a large-scale community study across multiple age groups to assess the pathogenicity of 18 respiratory viruses. We enrolled 214 individuals at multiple New York City locations and tested weekly for respiratory viral pathogens, irrespective of symptom status, from fall 2016 to spring 2018. We combined these test results with participant-provided daily records of cold and flu symptoms and used this information to characterise symptom severity by virus and age category. Asymptomatic infection rates exceeded 70% for most viruses, excepting influenza and human metapneumovirus, which produced significantly more severe outcomes. Symptoms were negatively associated with infection frequency, with children displaying the lowest score among age groups. Upper respiratory manifestations were most common for all viruses, whereas systemic effects were less typical. These findings indicate a high burden of asymptomatic respiratory virus infection exists in the general population.

The epidemiology of paediatric Mycoplasma pneumoniae pneumonia in North China: 2006 to 2016

Abstract: Paediatric Mycoplasma pneumoniae pneumonia (MPP) is a major cause of community-acquired pneumonia in China. Data on epidemiology of paediatric MPP from China are little known. This study retrospectively collected data from June 2006 to June 2016 in Beijing Children's Hospital, Capital Medical University of North China and aims to explore the epidemiological features of paediatric MPP and severe MPP (SMPP) in North China during the past 10 years. A total of 27 498 paediatric patients with pneumonia were enrolled. Among them, 37.5% of paediatric patients had MPP. In this area, an epidemic took place every 2–3 years at the peak, and the positive rate of MPP increased during these peak years over time. The peak age of MPP was between the ages of 6 and 10 years, accounting for 75.2%, significantly more compared with other age groups (χ2 = 1384.1, P < 0.0001). The epidemics peaked in September, October and November (χ2 = 904.9, P < 0.0001). Additionally, 13.0% of MPP paediatric patients were SMPP, but over time, the rate of SMPP increased, reaching 42.6% in 2016. The mean age of paediatric patients with SMPP (6.7 ± 3.0 years old) was younger than that of patients with non-SMPP (7.4 ± 3.2 years old) (t = 3.60, P = 0.0001). The prevalence of MPP and SMPP is common in China, especially in children from 6 to 10 years old. Paediatric patients with SMPP tend to be younger than those with non-SMPP. MPP outbreaks occur every 2–3 years in North China. September, October and November are the peak months, unlike in South China. Understanding the epidemiological characteristics of paediatric MPP can contribute to timely treatment and diagnosis, and may improve the prognosis of children with SMPP.

A history of FMD research and control programmes in Southeast Asia: Lessons from the past informing the future

Abstract: Foot and Mouth Disease (FMD) is a major animal health problem within Southeast Asia (SEA). Although Indonesia and more recently the Philippines have achieved freedom from FMD, the disease remains endemic on continental SEA. Control of FMD within SEA would increase access to markets in more developed economies and reduce lost productivity in smallholder and emerging commercial farmer settings. However, despite many years of vaccination by individual countries, numerous factors have prevented the successful control of FMD within the region, including: unregulated 'informal' transboundary movement of livestock and their products, difficulties implementing vaccination programmes, emergence of new virus topotypes and lineages, low-level technical capacity and biosecurity at national levels, limited farmer knowledge on FMD disease recognition, failure of timely outbreak reporting and response, and limitations in national and international FMD control programmes. This paper examines the published research of FMD in the SEA region, reviewing the history, virology, epidemiology and control programmes and identifies future opportunities for FMD research aimed at the eventual eradication of FMD from the region.

Global status of Middle East respiratory syndrome coronavirus in dromedary camels: a systematic review

Abstract: Dromedary camels have been shown to be the main reservoir for human Middle East respiratory syndrome (MERS) infections. This systematic review aims to compile and analyse all published data on MERS-coronavirus (CoV) in the global camel population to provide an overview of current knowledge on the distribution, spread and risk factors of infections in dromedary camels. We included original research articles containing laboratory evidence of MERS-CoV infections in dromedary camels in the field from 2013 to April 2018. In general, camels only show minor clinical signs of disease after being infected with MERS-CoV. Serological evidence of MERS-CoV in camels has been found in 20 countries, with molecular evidence for virus circulation in 13 countries. The seroprevalence of MERS-CoV antibodies increases with age in camels, while the prevalence of viral shedding as determined by MERS-CoV RNA detection in nasal swabs decreases. In several studies, camels that were sampled at animal markets or quarantine facilities were seropositive more often than camels at farms as well as imported camels vs. locally bred camels. Some studies show a relatively higher seroprevalence and viral detection during the cooler winter months. Knowledge of the animal reservoir of MERS-CoV is essential to develop intervention and control measures to prevent human infections.

Infectious disease outbreaks in the African region: overview of events reported to the World Health Organization in 2018

Abstract: The WHO African region is characterised by the largest infectious disease burden in the world. We conducted a retrospective descriptive analysis using records of all infectious disease outbreaks formally reported to the WHO in 2018 by Member States of the African region. We analysed the spatio-temporal distribution, the notification delay as well as the morbidity and mortality associated with these outbreaks. In 2018, 96 new disease outbreaks were reported across 36 of the 47 Member States. The most commonly reported disease outbreak was cholera which accounted for 20.8% (n = 20) of all events, followed by measles (n = 11, 11.5%) and Yellow fever (n = 7, 7.3%). About a quarter of the outbreaks (n = 23) were reported following signals detected through media monitoring conducted at the WHO regional office for Africa. The median delay between the disease onset and WHO notification was 16 days (range: 0-184). A total of 107 167 people were directly affected including 1221 deaths (mean case fatality ratio (CFR): 1.14% (95% confidence interval (CI) 1.07%-1.20%)). The highest CFR was observed for diseases targeted for eradication or elimination: 3.45% (95% CI 0.89%-10.45%). The African region remains prone to outbreaks of infectious diseases. It is therefore critical that Member States improve their capacities to rapidly detect, report and respond to public health events.

Lag effect of climatic variables on dengue burden in India.

Abstract: Dengue is a widespread vector-borne disease believed to affect between 100 and 390 million people every year. The interaction between vector, host and pathogen is influenced by various climatic factors and the relationship between dengue and climatic conditions has been poorly explored in India. This study explores the relationship between El Nino Southern Oscillation (ENSO), the Indian Ocean Dipole (IOD) and dengue cases in India. Additionally, distributed lag non-linear model was used to assess the delayed effects of climatic factors on dengue cases. The weekly dengue cases reported by the Integrated Disease Surveillance Program (IDSP) over India during the period 2010-2017 were analysed. The study shows that dengue cases usually follow a seasonal pattern, with most cases reported in August and September. Both temperature and rainfall were positively associated with the number of dengue cases. The precipitation shows the higher transmission risk of dengue was observed between 8 and 15 weeks of lag. The highest relative risk (RR) of dengue was observed at 60 mm rainfall with a 12-week lag period when compared with 40 and 80 mm rainfall. The RR of dengue tends to increase with increasing mean temperature above 24 °C. The largest transmission risk of dengue was observed at 30 °C with a 0-3 weeks of lag. Similarly, the transmission risk increases more than twofold when the minimum temperature reaches 26 °C with a 2-week lag period. The dengue cases and El Nino were positively correlated with a 3-6 months lag period. The significant correlation observed between the IOD and dengue cases was shown for a 0-2 months lag period.

Foodborne viral outbreaks associated with frozen produce.

Abstract: Over the past decade, frozen fruits have been a major vehicle of foodborne illnesses mainly attributed to norovirus (NoV) and hepatitis A virus (HAV) infections. Fresh produce may acquire viral contamination by direct contact with contaminated surface, water or hands, and is then frozen without undergoing proper decontamination. Due to their structural integrity, foodborne viruses are able to withstand hostile conditions such as desiccation and freezing, and endure for a long period of time without losing their infectivity. Additionally, these foods are often consumed raw or undercooked, which increases the risk of infection. Herein, we searched published literature and databases of reported outbreaks as well as the databases of news articles for the viral outbreaks associated with the consumption of frozen produce between January 2008 and December 2018; recorded the worldwide distribution of these outbreaks; and analysed the implication of consumption of different types of contaminated frozen food. In addition, we have briefly discussed the factors that contribute to an increased risk of foodborne viral infection following the consumption of frozen produce. Our results revealed that frozen fruits, especially berries and pomegranate arils, contributed to the majority of the outbreaks, and that most outbreaks were reported in industrialised countries.

Using routine testing data to understand circulation patterns of influenza A, respiratory syncytial virus and other respiratory viruses in Victoria, Australia.

Abstract: 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.

Human toxoplasmosis: a systematic review for genetic diversity of Toxoplasma gondii in clinical samples.

Abstract: Toxoplasma gondii (T. gondii) as an obligate intracellular protozoan with a worldwide distribution can infect virtually all warm-blooded animals and humans. This study aims to provide a summary of the available data on genotypes of T. gondii in human. Five databases including MEDLINE in PubMed, Scopus, Science Direct, Web of Science and Google Scholar were searched for the T. gondii genotyping in human during 1995-August 2017. Next, we screened all the articles based on the inclusion and exclusion criteria. Overall, 26 studies were eligible regarding genotyping T. gondii in human samples. In clonal genotyping, 167 out of 286 cases (58%) were infected with type II. Genetic characterisation of T. gondii isolates displayed that type II was the most predominant genotype in human with the prevalence of 64.3%, 62.1% and 41.7% in patients with AIDS, congenital and ocular toxoplasmosis, respectively. In ToxoDB genotyping, most individuals were infected with genotypes #9 and #65 (21.2%). Based on these results, genotype profile of T. gondii isolates is different throughout the world. The strains in Asian and African countries are characterised by low genetic diversity, while in North and South America a wide diversity of this parasite is found. In countries without any data (e.g. Australia, Western and Southern Africa and Western Asia), identification of T. gondii genotypes might discover higher genetic diversity.

The changing epidemiology worldwide of Mycobacterium ulcerans.

Abstract: Mycobacterium ulcerans is recognised as the third most common mycobacterial infection worldwide. It causes necrotising infections of skin and soft tissue and is classified as a neglected tropical disease by the World Health Organization (WHO). However, despite extensive research, the environmental reservoir of the organism and mode of transmission of the infection to humans remain unknown. This limits the ability to design and implement public health interventions to effectively and consistently prevent the spread and reduce the incidence of this disease. In recent years, the epidemiology of the disease has changed. In most endemic regions of the world, the number of cases reported to the WHO are reducing, with a 64% reduction in cases reported worldwide in the last 9 years. Conversely, in a smaller number of countries including Australia and Nigeria, reported cases are increasing at a rapid rate, new endemic areas continue to appear, and in Australia cases are becoming more severe. The reasons for this changing epidemiology are unknown. We review the epidemiology of M. ulcerans disease worldwide, and document recent changes. We also outline and discuss the current state of knowledge on the ecology of M. ulcerans, possible transmission mechanisms to humans and what may be enabling the spread of M. ulcerans into new endemic areas.

Reconstruction and prediction of viral disease epidemics.

Abstract: A growing number of infectious pathogens are spreading among geographic regions. Some pathogens that were previously not considered to pose a general threat to human health have emerged at regional and global scales, such as Zika and Ebola Virus Disease. Other pathogens, such as yellow fever virus, were previously thought to be under control but have recently re-emerged, causing new challenges to public health organisations. A wide array of new modelling techniques, aided by increased computing capabilities, novel diagnostic tools, and the increased speed and availability of genomic sequencing allow researchers to identify new pathogens more rapidly, assess the likelihood of geographic spread, and quantify the speed of human-to-human transmission. Despite some initial successes in predicting the spread of acute viral infections, the practicalities and sustainability of such approaches will need to be evaluated in the context of public health responses.

Antimicrobial resistance patterns of bacteria isolated from dogs with otitis.

Abstract: Antimicrobial-resistant bacteria in dogs can be transmitted to humans and close contact between dogs and people might foster dissemination of resistance determinants. The aim of our study was to describe the antimicrobial resistance (AMR) pattern of the major causative agents of canine otitis - one of the most common diseases in dogs - isolated in France. Data collected between 2012 and 2016 by the French national surveillance network for AMR, referred to as RESAPATH, were analysed. Resistance trends were investigated using non-linear analysis (generalised additive models). A total of 7021 antibiograms were analysed. The four major causative agents of canine otitis in France were coagulase-positive staphylococci, Pseudomonas aeruginosa, Proteus mirabilis and streptococci. Since 2013, resistance to fluoroquinolones has been on the decrease in both P. aeruginosa and Staphylococcus pseudintermedius isolates. For P. aeruginosa, 19.4% of isolates were resistant to both enrofloxacin and gentamicin. The levels of multidrug resistance (acquired resistance to at least one antibiotic in three or more antibiotic classes) ranged between 11.9% for P. mirabilis and 16.0% for S. pseudintermedius. These results are essential to guide prudent use of antibiotics in veterinary medicine. They will also help in designing efficient control strategies and in measuring their effectiveness.

Disgust as an emotional driver of vaccine attitudes and uptake? A mediation analysis.

Abstract: Research on the drivers of vaccine acceptance has expanded but most interventions fall short of coverage targets. We explored whether vaccine uptake is driven directly or indirectly by disgust with attitudes towards vaccines acting as a possible mediator. An online cross-sectional study of 1007 adults of the USA via Amazon's Mechanical Turk was conducted in January 2017. The questionnaire consisted of four sections: (1) items assessing attitudes towards vaccines and vaccine uptake, (2) revised Disgust Scale (DS-R) to measure Disgust Sensitivity, (3) Perceived Vulnerability to Disease scale (PVD) to measure Germ Aversion and Perceived Susceptibility, and (4) socio-demographic information. Using mediation analysis, we assess the direct, the indirect (through Vaccine Attitudes) and the total effect of Disgust Sensitivity, Germ Aversion and Perceived Susceptibility on 2016 self-reported flu vaccine uptake. Mediation analysis showed the effect of Disgust Sensitivity and Germ Aversion on vaccine uptake to be twofold: a direct positive effect on vaccine uptake and an indirect negative effect through Vaccine Attitudes. In contrast, Perceived Susceptibility was found to have only a direct positive effect on vaccine uptake. Nonetheless, these effects were attenuated and small compared to economic, logistic and psychological determinants of vaccine uptake.

Incubation periods of enteric illnesses in foodborne outbreaks, United States, 1998-2013.

Abstract: Early in a foodborne disease outbreak investigation, illness incubation periods can help focus case interviews, case definitions, clinical and environmental evaluations and predict an aetiology. Data describing incubation periods are limited. We examined foodborne disease outbreaks from laboratory-confirmed, single aetiology, enteric bacterial and viral pathogens reported to United States foodborne disease outbreak surveillance from 1998-2013. We grouped pathogens by clinical presentation and analysed the reported median incubation period among all illnesses from the implicated pathogen for each outbreak as the outbreak incubation period. Outbreaks from preformed bacterial toxins (Staphylococcus aureus, Bacillus cereus and Clostridium perfringens) had the shortest outbreak incubation periods (4-10 h medians), distinct from that of Vibrio parahaemolyticus (17 h median). Norovirus, salmonella and shigella had longer but similar outbreak incubation periods (32-45 h medians); campylobacter and Shiga toxin-producing Escherichia coli had the longest among bacteria (62-87 h medians); hepatitis A had the longest overall (672 h median). Our results can help guide diagnostic and investigative strategies early in an outbreak investigation to suggest or rule out specific etiologies or, when the pathogen is known, the likely timeframe for exposure. They also point to possible differences in pathogenesis among pathogens causing broadly similar syndromes.

Risk factors and epidemiologic predictors of blood stream infections with New Delhi Metallo-b-lactamase (NDM-1) producing Enterobacteriaceae.

Abstract: Carbapenem-resistant Enterobacteriaceae conferred by New Delhi metallo-b-lactamase (NDM-1) resistance mechanism are endemic in India and Southeast Asia. An understanding of risk factors for NDM-1 infections is necessary to guide prevention strategies. We performed a retrospective case-control study of patients admitted at Christian Medical College Hospital, Vellore, India between May 2010 and August 2014 with Klebsiella pneumoniae blood stream infection (BSI). We compared patients with BSI caused by NDM-1 producing strains to two control groups: BSI with other multidrug resistant (MDR) strains and BSI with pan-susceptible strains. The study groups were assessed for risk factors for the outcomes: (1) infection with any MDR strain compared to pan-susceptible; and, (2) infection with NDM-1 strain as compared with other MDR and (3) Mortality. A total of 101 patients with BSI with NDM-1 producing Klebsiella pneumoniae were matched to two groups of controls: 112 with non-NDM-1 MDR strains and 101 with pan-susceptible strains. Medical (OR 10.4) and neonatal (OR 0.7) ICU admission, central venous catheter placement (CVC, OR 7.4) predicted MDR BSI. Prior carbapenem use (OR 8.4) and CVC (OR 4.8) predicted acquisition of an NDM-1 strain. Significant predictors for mortality included ICU stay (OR 3.0), mechanical ventilation (OR 3.2), female gender (OR 2.2), diabetes (OR 0.4). CVC placement, prior carbapenem use and ICU admission were significantly associated with BSI with NDM-1 producing and other MDR strains.

Louse-borne relapsing fever (Borrelia recurrentis infection).

Abstract: Louse-borne relapsing fever (LBRF) is an epidemic disease with a fascinating history from Hippocrates' times, through the 6th century 'Yellow Plague', to epidemics in Ireland, Scotland and England in the 19th century and two large Afro-Middle Eastern pandemics in the 20th century. An endemic focus persists in Ethiopia and adjacent territories in the Horn of Africa. Since 2015, awareness of LBRF in Europe, as a re-emerging disease, has been increased dramatically by the discovery of this infection in dozens of refugees arriving from Africa.The causative spirochaete, Borrelia recurrentis, has a genome so similar to B. duttonii and B. crocidurae (causes of East and West African tick-borne relapsing fever), that they are now regarded as merely ecotypes of a single genomospecies. Transmission is confined to the human body louse Pediculus humanus corporis, and, perhaps, the head louse P. humanus capitis, although the latter has not been proved. Infection is by inoculation of louse coelomic fluid or faeces by scratching. Nosocomial infections are possible from contamination by infected blood. Between blood meals, body lice live in clothing until the host's body temperature rises or falls, when they seek a new abode.The most distinctive feature of LBRF, the relapse phenomenon, is attributable to antigenic variation of borrelial outer-membrane lipoprotein. High fever, rigors, headache, pain and prostration start abruptly, 2-18 days after infection. Petechial rash, epistaxis, jaundice, hepatosplenomegaly and liver dysfunction are common. Severe features include hyperpyrexia, shock, myocarditis causing acute pulmonary oedema, acute respiratory distress syndrome, cerebral or gastrointestinal bleeding, ruptured spleen, hepatic failure, Jarisch-Herxheimer reactions (J-HR) and opportunistic typhoid or other complicating bacterial infections. Pregnant women are at high risk of aborting and perinatal mortality is high.Rapid diagnosis is by microscopy of blood films, but polymerase chain reaction is used increasingly for species diagnosis. Severe falciparum malaria and leptospirosis are urgent differential diagnoses in residents and travellers from appropriate geographical regions.High untreated case-fatality, exceeding 40% in some historic epidemics, can be reduced to less than 5% by antibiotic treatment, but elimination of spirochaetaemia is often accompanied by a severe J-HR.Epidemics are controlled by sterilising clothing to eliminate lice, using pediculicides and by improving personal hygiene.

Chronic hepatitis B and C infections in the Netherlands: estimated prevalence in risk groups and the general population.

Abstract: Chronic hepatitis B virus (HBV) and hepatitis C virus (HCV) infections are usually asymptomatic for decades, thus targeted screening can prevent liver disease by timely diagnosis and linkage to care. More robust estimates of chronic HBV and HCV infections in the general population and risk groups are needed. Using a modified workbook method, the total number of ever chronically infected individuals in the Netherlands in 2016 was determined using population size and prevalence estimates from studies in the general and high-risk population. The estimated 2016 chronic HBV infection prevalence is 0.34% (low 0.22%, high 0.47%), corresponding to approximately 49 000 (low 31 000, high 66 000) HBV-infected individuals aged 15 years and older. The estimated ever-chronic HCV infection prevalence is 0.16% (low 0.06%, high 0.27%), corresponding to approximately 23 000 (low 8000, high 38 000) ever-chronic HCV-infected individuals. The prevalence of chronic HBV and HCV infections in the Netherlands is low. First-generation migrants account for most infections with 81% and 60% of chronic HBV and HCV infections, respectively. However, about one-fifth of HCV infections is found in the general population at low risk. This method can serve as an example for countries in need of more accurate prevalence estimates, to help the design and evaluation of prevention and control policies.

Depletion-of-susceptibles bias in influenza vaccine waning studies: how to ensure robust results.

Abstract: Vaccine effectiveness studies are subject to biases due to depletion-of-persons at risk of infection, or at especially high risk of infection, at different rates from different groups (depletion-of-susceptibles bias), a problem that can also lead to biased estimates of waning effectiveness, including spurious inference of waning when none exists. An alternative study design to identify waning is to study only vaccinated persons, and compare for each day the incidence in persons with earlier or later dates of vaccination to assess waning in vaccine protection as a function of vaccination time (namely whether earlier vaccination would result in lower subsequent protection compared to later vaccination). Prior studies suggested under what conditions this alternative would yield correct estimates of waning. Here we define the depletion-of-susceptibles process formally and show mathematically that for influenza vaccine waning studies, a randomised trial or corresponding observational study that compares incidence at a specific calendar time among individuals vaccinated at different times before the influenza season begins will not be vulnerable to depletion-of-susceptibles bias in its inference of waning as a function of vaccination time under the null hypothesis that none exists, and will - if waning does actually occur - underestimate the extent of waning. Such a design is thus robust in the sense that a finding of waning in that inference framework reflects actual waning of vaccine-induced immunity. We recommend such a design for future studies of waning, whether observational or randomised.

Syndromic surveillance: two decades experience of sustainable systems - its people not just data!

Abstract: Syndromic surveillance is a form of surveillance that generates information for public health action by collecting, analysing and interpreting routine health-related data on symptoms and clinical signs reported by patients and clinicians rather than being based on microbiologically or clinically confirmed cases. In England, a suite of national real-time syndromic surveillance systems (SSS) have been developed over the last 20 years, utilising data from a variety of health care settings (a telehealth triage system, general practice and emergency departments). The real-time systems in England have been used for early detection (e.g. seasonal influenza), for situational awareness (e.g. describing the size and demographics of the impact of a heatwave) and for reassurance of lack of impact on population health of mass gatherings (e.g. the London 2012 Olympic and Paralympic Games).We highlight the lessons learnt from running SSS, for nearly two decades, and propose questions and issues still to be addressed. We feel that syndromic surveillance is an example of the use of 'big data', but contend that the focus for sustainable and useful systems should be on the added value of such systems and the importance of people working together to maximise the value for the public health of syndromic surveillance services.

Outbreaks of Salmonella illness associated with frozen raw breaded chicken products in Canada, 2015-2019.

Abstract: Frozen raw breaded chicken products (FRBCP) have been identified as a risk factor for Salmonella infection in Canada. In 2017, Canada implemented whole genome sequencing (WGS) for clinical and non-clinical Salmonella isolates, which increased understanding of the relatedness of Salmonella isolates, resulting in an increased number of Salmonella outbreak investigations. A total of 18 outbreaks and 584 laboratory-confirmed cases have been associated with FRBCP or chicken since 2017. The introduction of WGS provided the evidence needed to support a new requirement to control the risk of Salmonella in FRBCP produced for retail sale.