In this study, we estimate the burden of foodborne illness (FBI) caused by five major pathogens among nondeployed US Army service members. The US Army is a unique population that is globally distributed, has its own food procurement system and a food protection system dedicated to the prevention of both unintentional and intentional contamination of food. To our knowledge, the burden of FBI caused by specific pathogens among the US Army population has not been determined. We used data from a 2015 US Army population survey, a 2015 US Army laboratory survey and data from FoodNet to create inputs for two model structures. Model type 1 scaled up case counts of Campylobacter jejuni, Shigella spp., Salmonella enterica non-typhoidal and STEC non-O157 ascertained from the Disease Reporting System internet database from 2010 to 2015. Model type 2 scaled down cases of self-reported acute gastrointestinal illness (AGI) to estimate the annual burden of Norovirus illness. We estimate that these five pathogens caused 45 600 (5%–95% range, 30 300–64 000) annual illnesses among nondeployed active duty US Army Service members. Of these pathogens, Norovirus, Campylobacter jejuni and Salmonella enterica non-typhoidal were responsible for the most illness. There is a tremendous burden of AGI and FBI caused by five major pathogens among US Army Soldiers, which can have a tremendous impact on readiness of the force. The US Army has a robust food protection program in place, but without a specific active FBI surveillance system across the Department of Defence, we will never have the ability to measure the effectiveness of modern, targeted, interventions aimed at the reduction of specific foodborne pathogens.

Shiga-toxin producing Escherichia coli (STEC) is a pathogen that can cause bloody diarrhoea and severe complications. Cases occur sporadically but outbreaks are also common. Understanding the incubation period distribution and factors influencing it will help in the investigation of exposures and consequent disease control. We extracted individual patient data for STEC cases associated with outbreaks with a known source of exposure in England and Wales. The incubation period was derived and cases were described according to patient and outbreak characteristics. We tested for heterogeneity in reported incubation period between outbreaks and described the pattern of heterogeneity. We employed a multi-level regression model to examine the relationship between patient characteristics such as age, gender and reported symptoms; and outbreak characteristics such as mode of transmission with the incubation period. A total of 205 cases from 41 outbreaks were included in the study, of which 64 cases (31%) were from a single outbreak. The median incubation period was 4 days. Cases reporting bloody diarrhoea reported shorter incubation periods compared with cases without bloody diarrhoea, and likewise, cases aged between 40 and 59 years reported shorter incubation period compared with other age groups. It is recommended that public health officials consider the characteristics of cases involved in an outbreak in order to inform the outbreak investigation and the period of exposure to be investigated.

Influenza and respiratory syncytial virus (RSV) are common causes of respiratory tract infections and place a burden on health services each winter. Systems to describe the timing and intensity of such activity will improve the public health response and deployment of interventions to these pressures. Here we develop early warning and activity intensity thresholds for monitoring influenza and RSV using two novel data sources: general practitioner out-of-hours consultations (GP OOH) and telehealth calls (NHS 111). Moving Epidemic Method (MEM) thresholds were developed for winter 2017–2018. The NHS 111 cold/flu threshold was breached several weeks in advance of other systems. The NHS 111 RSV epidemic threshold was breached in week 41, in advance of RSV laboratory reporting. Combining the use of MEM thresholds with daily monitoring of NHS 111 and GP OOH syndromic surveillance systems provides the potential to alert to threshold breaches in real-time. An advantage of using thresholds across different health systems is the ability to capture a range of healthcare-seeking behaviour, which may reflect differences in disease severity. This study also provides a quantifiable measure of seasonal RSV activity, which contributes to our understanding of RSV activity in advance of the potential introduction of new RSV vaccines.

In 2014–2016, we conducted a cross-sectional survey in 115 sheep, 104 beef and 82 dairy cattle herds to estimate Shiga toxin-producing Escherichia coli (STEC) prevalence, and collected data on human clinical cases of infection. Isolates were characterised (stx1, stx2, eae, ehxA) and serogroups O157 and O111 identified by PCR, and their antimicrobial resistance (AMR) profiles were determined by broth microdilution. STEC were more frequently isolated from beef cattle herds (63.5%) and sheep flocks (56.5%) than from dairy cattle herds (30.5%) (P < 0.001). A similar but non-significant trend was observed for O157:H7 STEC. In humans, mean annual incidence rate was 1.7 cases/100 000 inhabitants for O157 STEC and 4.7 for non-O157 STEC, but cases concentrated among younger patients. Distribution of virulence genes in STEC strains from ruminants differed from those from human clinical cases. Thus, stx2 was significantly associated with animal STEC isolates (O157 and non-O157), ehxA to ruminant O157 STEC (P = 0.004) and eae to human non-O157 STEC isolates (P < 0.001). Resistance was detected in 21.9% of human and 5.2% of animal O157 STEC isolates, whereas all non-O157 isolates were fully susceptible. In conclusion, STEC were widespread in ruminants, but only some carried virulence genes associated with severe disease in humans; AMR in ruminants was low but profiles were similar to those found in human isolates.

Information on the kinetics of the serum antibody response to infection with Yersinia enterocolitica is essential to allow the estimation and comparison of seroconversion rates in a diversity of pools of cross-sectional serum antibody measurements. Data from 94 patients with acute enteritis caused by Yersinia infection were used. The follow-up period for the longitudinal study was 36 months, addressed by questionnaire. An indirect enzyme-linked immunosorbent assay method was adapted to determine the concentration of antibodies against Y. enterocolitica in human sera. A mathematical within-host model was used to describe the interaction between pathogen and immune system and the waning of immunity after clearing of the pathogen. All observed antibodies (IgG, IgM, IgA) reached peak levels shortly after infection and then decayed slowly indicating that the median levels decreased only little during the observation period. Estimated maximum peak antibody levels were highest in IgG. Seroresponse curves of all antibodies showed large individual variation between patients. There was no apparent pattern of variation with age, nor any notable difference between genders. Estimated half-times were very long for all antibodies, and their posterior distributions were highly skewed. IgA appeared to have the most persistent antibody response, compared with IgG and IgM. Median peak levels of all three antibodies were similar. There was no significance found between peak antibody levels and severity of symptoms of gastrointestinal infection and severity of joint pain. Our findings allow the use of cross-sectional serum antibody measurements as biomarkers, to estimate seroconversion rates. Such seroincidence estimates include asymptomatic seroconversions, thereby avoiding under-reporting, and allows the comparison of infection pressures among countries, independent of their healthcare and surveillance systems.

Toxigenic Clostridium difficile (C. difficile) carriers represent an important source in the transmission of C. difficile infection (CDI) during hospitalisation, but its prevalence and mode in patients with hepatic cirrhosis are not well established. We investigated longitudinal changes in carriage rates and strain types of toxigenic C. difficile from admission to discharge among hepatic cirrhosis patients. Toxigenic C. difficile was detected in 104 (19.8%) of 526 hepatic cirrhosis patients on admission, and the carriage status changed in a portion of patients during hospitalisation. Approximately 56% (58/104) of patients lost the colonisation during their hospital stay. Among the remaining 48 patients who remained positive for toxigenic C. difficile, the numbers of patients who were positive at one, two, three and four isolations were 10 (55.6%), three (16.7%), two (11.1%) and three (16.7%), respectively. Twenty-eight patients retained a particular monophyletic strain at multiple isolations. The genotype most frequently identified was the same as that frequently identified in symptomatic CDI patients. A total of 25% (26/104) of patients were diagnosed with CDI during their hospital stay. Conclusions: Colonisation with toxigenic C. difficile strains occurs frequently in cirrhosis patients and is a risk factor for CDI.

The Infectious Diseases and Beliaghata General Hospital, Kolkata, India witnessed a sudden increase in admissions of diarrhoea cases during the first 2 weeks of August 2015 following heavy rainfall. This prompted us to investigate the event. Cases were recruited through hospital-based surveillance along with the collection of socio-demographic characteristics and clinical profile using a structured questionnaire. Stool specimens were tested at bacteriological laboratory of the National Institute of Cholera and Enteric Diseases (NICED), Kolkata. Admission of 3003 diarrhoea cases, clearly indicated occurrence of outbreak in Kolkata municipal area as it was more than two standard deviation of the mean number (911; s.d. = 111) of diarrhoea admissions during the same period in previous 7 years. Out of 164 recruited cases, 25% were under-5 children. Organisms were isolated from 80 (49%) stool specimens. Vibrio cholerae O1 was isolated from 50 patients. Twenty-eight patients had this organism as the sole pathogen. Among 14 infants, five had cholera. All V. cholerae O1 isolates were resistant to nalidixic acid, followed by co-trimoxazole (96%), streptomycin (92%), but sensitive to fluroquinolones. We confirmed the occurrence of a cholera outbreak in Kolkata during August 2015 due to V. cholerae O1 infection, where infants were affected.

This invited editorial introduces a special issue of Epidemiology & Infection while also discussing advances in emerging infectious diseases.

Disease surveillance in wildlife populations presents a logistical challenge, yet is critical in gaining a deeper understanding of the presence and impact of wildlife pathogens. Erinaceus coronavirus (EriCoV), a clade C Betacoronavirus, was first described in Western European hedgehogs (Erinaceus europaeus) in Germany. Here, our objective was to determine whether EriCoV is present, and if it is associated with disease, in Great Britain (GB). An EriCoV-specific BRYT-Green® real-time reverse transcription PCR assay was used to test 351 samples of faeces or distal large intestinal tract contents collected from casualty or dead hedgehogs from a wide area across GB. Viral RNA was detected in 10.8% (38) samples; however, the virus was not detected in any of the 61 samples tested from Scotland. The full genome sequence of the British EriCoV strain was determined using next generation sequencing; it shared 94% identity with a German EriCoV sequence. Multivariate statistical models using hedgehog case history data, faecal specimen descriptions and post-mortem examination findings found no significant associations indicative of disease associated with EriCoV in hedgehogs. These findings indicate that the Western European hedgehog is a reservoir host of EriCoV in the absence of apparent disease.

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 Niño 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 Niño 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.

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.

The majority of paediatric Clostridioides difficile infections (CDI) are community-associated (CA), but few data exist regarding associated risk factors. We conducted a case–control study to evaluate CA-CDI risk factors in young children. Participants were enrolled from eight US sites during October 2014–February 2016. Case-patients were defined as children aged 1–5 years with a positive C. difficile specimen collected as an outpatient or ⩽3 days of hospital admission, who had no healthcare facility admission in the prior 12 weeks and no history of CDI. Each case-patient was matched to one control. Caregivers were interviewed regarding relevant exposures. Multivariable conditional logistic regression was performed. Of 68 pairs, 44.1% were female. More case-patients than controls had a comorbidity (33.3% vs. 12.1%; P = 0.01); recent higher-risk outpatient exposures (34.9% vs. 17.7%; P = 0.03); recent antibiotic use (54.4% vs. 19.4%; P < 0.0001); or recent exposure to a household member with diarrhoea (41.3% vs. 21.5%; P = 0.04). In multivariable analysis, antibiotic exposure in the preceding 12 weeks was significantly associated with CA-CDI (adjusted matched odds ratio, 6.25; 95% CI 2.18–17.96). Improved antibiotic prescribing might reduce CA-CDI in this population. Further evaluation of the potential role of outpatient healthcare and household exposures in C. difficile transmission is needed.

Social network characteristics of people who inject drugs (PWID) have previously been flagged as potential risk factors for HCV transmission such as increased injection frequency. To understand the role of the injecting network on injection frequency, we investigated how changes in an injecting network over time can modulate injecting risk behaviour. PWID were sourced from the Networks 2 Study, a longitudinal cohort study of PWID recruited from illicit drug street markets across Melbourne, Australia. Network-related correlates of injection frequency and the change in frequency over time were analysed using adjusted Cox Proportional Hazards and Generalised Estimating Equations modelling. Two-hundred and eighteen PWID followed up for a mean (s.d.) of 2.8 (1.7) years were included in the analysis. A greater number of injecting partners, network closeness centrality and eigenvector centrality over time were associated with an increased rate of infection frequency. Every additional injection drug partner was associated with an increase in monthly injection frequency. Similarly, increased network connectivity and centrality over time was also associated with an increase in injection frequency. This study observed that baseline network measures of connectivity and centrality may be associated with changes in injection frequency and, by extension, may predict subsequent HCV transmission risk. Longitudinal changes in network position were observed to correlate with changes in injection frequency, with PWID who migrate from the densely-connected network centre out to the less-connected periphery were associated with a decreased rate of injection frequency.

A cross-sectional study was conducted from 2014 to 2017 in 13 organised pig farms located in eight states of India (Northern, North-Eastern and Southern regions) to identify the risk factors, pathotype and antimicrobial resistance of Escherichia coli associated with pre- and post-weaning piglet diarrhoea. The data collected through questionnaire survey were used to identify the risk factors by univariable analysis, in which weaning status, season, altitude, ventilation in the shed, use of heater/cooler for temperature control in the sheds, feed type, water source, and use of disinfectant, were the potential risk factors. In logistic regression model, weaning and source of water were the significant risk factors. The piglet diarrhoea prevalence was almost similar across the regions. Of the 909 faecal samples collected (North – 310, North-East – 194 and South – 405) for isolation of E. coli, pathotyping and antibiotic screening, 531 E. coli were isolated in MacConkey agar added with cefotaxime, where 345 isolates were extended spectrum β-lactamase (ESBL) producers and were positive for blaCTX-M-1 (n = 147), bla TEM (n = 151), qnrA (n = 98), qnrB (n = 116), qnrS (n = 53), tetA (n = 46), tetB (n = 48) and sul1 (n = 54) genes. Multiple antibiotic resistance (MAR) index revealed that 14 (2.64%) isolates had MAR index of 1. On the virulence screening of E. coli, 174 isolates harboured alone or combination of Stx1, Stx2, eaeA, hlyA genes. The isolates from diarrhoeic and post-weaning samples harboured higher number of virulence genes than non-diarrhoeic and pre-weaning. Alleviating the risk factors might reduce the piglet diarrhoea cases. The presence of multidrug-resistant and ESBL-producing pathogenic E. coli in piglets appears a public health concern.

Declining mortality following invasive pneumococcal disease (IPD) has been observed concurrent with a reduced incidence due to effective pneumococcal conjugate vaccines. However, with IPD now increasing due to serotype replacement, we undertook a statistical analysis to estimate the trend in all-cause 30-day case fatality rate (CFR) in the North East of England (NEE) following IPD. Clinical, microbiological and demographic data were obtained for all laboratory-confirmed IPD cases (April 2006–March 2016) and the adjusted association between CFR and epidemiological year estimated using logistic regression. Of the 2510 episodes of IPD included in the analysis, 486 died within 30 days of IPD (CFR 19%). Increasing age, male sex, a diagnosis of septicaemia, being in ⩾1 clinical risk groups, alcohol abuse and individual serotypes were independently associated with increased CFR. A significant decline in CFR over time was observed following adjustment for these significant predictors (adjusted odds ratio 0.93, 95% confidence interval 0.89–0.98; P = 0.003). A small but significant decline in 30-day all-cause CFR following IPD has been observed in the NEE. Nonetheless, certain population groups remain at increased risk of dying following IPD. Despite the introduction of effective vaccines, further strategies to reduce the ongoing burden of mortality from IPD are needed.

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.

Human papillomavirus (HPV) is the agent of the most common sexually transmitted diseases causing a variety of clinical manifestations ranging from warts to cancer. Oncogenic HPV infection is the major cause of cervical cancer and less frequently of penile cancers. Its presence in semen is widely known, but the effects on fertility are still controversial. We developed a new approach to evaluate virus localisation in the different semen components. We analysed also the specific genotype localisation and viral DNA quantity by qPCR. Results show that HPV DNA can be identified in every fraction of semen: spermatozoa, somatic cells and seminal plasma. Different samples can contain the HPV DNA in different fractions and several HPV genotypes can be found in the same fraction. Additionally, different fractions may contain multiple HPV genotypes in different relative quantity. We analysed the wholeness of HPV DNA in sperm cells by qPCR. In one sample more than half of viral genomes were defective, suggesting a possible recombination event. The new method allows to easily distinguish different sperm infections and to observe the possible effects on semen. The data support the proposed role of HPV in decreased fertility and prompt new possible consequences of the infection in semen.

Understanding endemic infectious disease risk factors through traditional epidemiological tools is challenging. Population-based case–control studies are costly and time-consuming. A case–case analyses using surveillance data addresses these limitations by using resources more efficiently. We conducted a case–case analyses using routine surveillance data reported by 16 U.S. states (2005–2015), wherein reported cases of salmonellosis were used as a comparison group to identify exposure associations with reported cases of cryptosporidiosis and giardiasis. Odds ratios adjusted for age and reporting state (aOR) and 95% confidence intervals (95% CI) were calculated. A total of 10 704 cryptosporidiosis cases, 17 544 giardiasis cases, and 106 351 salmonellosis cases were included in this analyses. When compared with cases of salmonellosis, exposure to treated recreational water (aOR 4.7, 95% CI 4.3–5.0) and livestock (aOR: 3.2; 95% CI: 2.9–3.5) were significantly associated with cryptosporidiosis and exposure to untreated drinking (aOR 4.1, 95% CI 3.6–4.7) and recreational water (aOR 4.1, 95% CI 3.7–4.5) were associated with giardiasis. Our analyses shows that routine surveillance data with standardised exposure information can be used to identify associations of interest for cryptosporidiosis and giardiasis.

Better control of highly pathogenic avian influenza (HPAI) outbreaks requires deeper understanding of within-flock virus transmission dynamics. For such fatal diseases, daily mortality provides a proxy for disease incidence. We used the daily mortality data collected during the 2015 H5N2 HPAI outbreak in Minnesota turkey flocks to estimate the within-flock transmission rate parameter (β). The number of birds in Susceptible, Exposed, Infectious and Recovered compartments was inferred from the data and used in a generalised linear mixed model (GLMM) to estimate the parameters. Novel here was the correction of these data for normal mortality before use in the fitting process. We also used mortality threshold to determine HPAI-like mortality to improve the accuracy of estimates from the back-calculation approach. The estimated β was 3.2 (95% confidence interval (CI) 2.3–4.3) per day with a basic reproduction number of 12.8 (95% CI 9.2–17.2). Although flock-level estimates varied, the overall estimate was comparable to those from other studies. Sensitivity analyses demonstrated that the estimated β was highly sensitive to the bird-level latent period, emphasizing the need for its precise estimation. In all, for fatal poultry diseases, the back-calculation approach provides a computationally efficient means to obtain reasonable transmission parameter estimates from mortality data.

Pathogen spillover from wildlife to humans or domestic animals requires a series of conditions to align with space and time. Comparing these conditions between times and locations where spillover does and does not occur presents opportunities to understand the factors that shape spillover risk. Bovine rabies transmitted by vampire bats was first confirmed in 1911 and has since been detected across the distribution of vampire bats. However, Uruguay is an exception. Uruguay was free of bovine rabies until 2007, despite high-cattle densities, the presence of vampire bats and a strong surveillance system. To explore why Uruguay was free of bovine rabies until recently, we review the historic literature and reconstruct the conditions that would allow rabies invasion into Uruguay. We used available historical records on the abundance of livestock and wildlife, the vampire bat distribution and occurrence of rabies outbreaks, as well as environmental modifications, to propose four alternative hypotheses to explain rabies virus emergence and spillover: bat movement, viral invasion, surveillance failure and environmental changes. While future statistical modelling efforts will be required to disentangle these hypotheses, we here show how a detailed historical analysis can be used to generate testable predictions for the conditions leading to pathogen spillover.