A cross-sectional survey was carried out in Bangladesh with the sampling of 514 Black Bengal goats on smallholdings to determine the presence of sorbitol non-fermenting (SNF) Shiga toxin-producing E. coli (STEC). Swab samples collected from the recto-anal junction were plated onto cefixime and potassium tellurite added sorbitol MacConkey (CT-SMAC) agar, a selective medium for STEC O157 serogroup, where this serogroup and other SNF STEC produce colourless colonies. The SNF E. coli (SNF EC) isolates obtained from the survey were investigated by PCR for the presence of Shiga toxin-producing genes, stx1 and stx2, and two other virulence genes, eae and hlyA that code for adherence factor (intimin protein) and pore-forming cytolysin, respectively. The SNF EC isolates were also assessed for the presence of the rfbO157 gene to verify their identity to O157 serogroup. The results revealed that the proportions of goats carrying SNF EC isolates and stx1 and stx2 genes were 6·2% (32/514) [95% confidence interval (CI) 4·4–8·7)], 1·2% (95% CI 0·5–2·6) and 1·2% (95% CI 0·5–2·6), respectively. All the SNF STEC tested negative for rfbO157, hlyA and eae genes. The risk for transmission of STEC from Black Bengal goats to humans is low.

We utilized a disease progression model to predict the number of viraemic infections, cirrhotic cases, and liver-related deaths in the state of Rhode Island (RI) under four treatment scenarios: (1) current HCV treatment paradigm (about 215 patients treated annually, Medicaid reimbursement criteria fibrosis stage ⩾F3); (2) immediate scale-up of treatment (to 430 annually) and less restrictive Medicaid reimbursement criteria (fibrosis stage ⩾F2); (3) immediate treatment scale-up and no fibrosis stage-specific Medicaid reimbursement criteria (⩾F0); (4) an ‘elimination’ scenario (i.e. a continued treatment scale-up needed to achieve >90% reduction in viraemic cases by 2030). Under current treatment models, the number of cirrhotic cases and liver-related deaths will plateau and peak by 2030, respectively. Treatment scale-up with ⩾F2 and ⩾F0 fibrosis stage treatment criteria could reduce the number of cirrhotic cases by 21·7% and 10·0%, and the number of liver-related deaths by 19·3% and 7·4%, respectively by 2030. To achieve a >90% reduction in viraemic cases by 2030, over 2000 persons will need to be treated annually by 2020. This strategy could reduce cirrhosis cases and liver-related deaths by 78·9% and 72·4%, respectively by 2030. Increased HCV treatment uptake is needed to substantially reduce the burden of HCV by 2030 in Rhode Island.

The incursion of influenza A(H1N1)pdm09 virus was detected by Norway's active serosurveillance of its pig population in 2009. Since then, surveillance data from 2010 to 2014 revealed that 54% of 5643 herd tests involving 1567 pig herds and 28% of 23 036 blood samples screened positive for antibodies against influenza A virus. Positive herds were confirmed to have influenza A(H1N1)pdm09 virus infection by haemagglutination inhibition test. In 50% of positive herd tests, ⩾60% of the sampled pigs in each herd had antibodies against influenza A(H1N1)pdm09 virus. This within-herd animal seroprevalence did not vary for type of production, herd size or year of test. The overall running mean of national herd seroprevalence, and annual herd incidence risks fluctuated narrowly around the means of 45% and 32%, respectively, with the highest levels recorded in the three densest pig-producing counties. The probability of a herd being seropositive varied in the five production classes, which were sow pools, multiplier herds, conventional sow herds, nucleus herds, and fattening herds in descending order of likelihood. Large herds were more likely to be seropositive. Seropositive herds were highly likely to be seropositive the following year. The study shows that influenza A(H1N1)pdm09 virus is established in the Norwegian pig population with recurrent and new herd infections every year with the national herd seroprevalence in 2014 hovering at around 43% (95% confidence interval 40–46%).

The epidemiology of laboratory-confirmed respiratory syncytial virus (RSV) infections in young children has not recently been described in England, and is an essential step in identifying optimal target groups for future licensed RSV vaccines. We used two laboratory surveillance systems to examine the total number and number of positive RSV tests in children aged <5 years in England from 2010 to 2014. We derived odds ratios (ORs) with 95% confidence intervals (CIs) comparing children by birth month, using multivariable logistic regression models adjusted for age, season and sex. Forty-seven percent of RSV tests (29 851/63 827) and 57% (7405/13 034) of positive results in children aged <5 years were in infants aged <6 months. Moreover, 38% (4982/13 034) of positive results were in infants aged <3 months. Infants born in September, October and November had the highest odds of a positive RSV test during their first year of life compared to infants born in January (OR 2·1, 95% CI 1·7–2·7; OR 2·4, 95% CI 2·1–2·8; and OR 2·4, 95% CI 2·1–2·7, respectively). Our results highlight the importance of young age and birth month near the beginning of the RSV season to the risk of laboratory-confirmed RSV infection. Future control measures should consider protection for these groups.

Cholera is one of a number of infectious diseases that appears to be influenced by climate, geography and other natural environments. This study analysed the environmental factors of the spatial distribution of cholera in China. It shows that temperature, precipitation, elevation, and distance to the coastline have significant impact on the distribution of cholera. It also reveals the oceanic environmental factors associated with cholera in Zhejiang, which is a coastal province of China, using both remote sensing (RS) and geographical information systems (GIS). The analysis has validated the correlation between indirect satellite measurements of sea surface temperature (SST), sea surface height (SSH) and ocean chlorophyll concentration (OCC) and the local number of cholera cases based on 8-year monthly data from 2001 to 2008. The results show the number of cholera cases has been strongly affected by the variables of SST, SSH and OCC. Utilizing this information, a cholera prediction model has been established based on the oceanic and climatic environmental factors. The model indicates that RS and GIS have great potential for designing an early warning system for cholera.

Nursing homes (NHs) have been implicated as significant reservoirs of antibiotic-resistant organisms causing severe infectious disease. We investigated the prevalence and molecular epidemiology of, and risk factors for, faecal carriage of extended-spectrum β-lactamase-producing Enterobacteriaceae (ESBL-E). A multicentre cross-sectional study was conducted in seven NHs in Shanghai between March 2014 and May 2014. Antimicrobial susceptibility testing and polymerase chain reaction were used to detect genes coding for ESBLs and carbapenemases. NH records at individual-resident level and facility level were examined for potential risk factors. Four hundred and fifty-seven Enterobacteriaceae isolates were collected of which 183 (46·92%) were colonized by ESBL-E. CTX-M enzymes (198/200, 99%) predominated, with CTX-M-14 (84/200, 42%) the most common types. Two carbapenemase producers harboured blaKPC-2. Resistance rates to carbapenems, TZP, AK, FOS, CL and TGC were low. History of invasive procedures [odds ratio (OR) 2·384, 95% confidence interval (CI) 1·318–4·310, P = 0·004], narrow-spectrum cephalosporins (OR 1·635, 95% CI 1·045–2·558, P = 0·031) and broad-spectrum cephalosporins (OR 3·276, 95% CI 1·278–8·398, P = 0·014) were independently associated with ESBL-E carriage. In conclusion, NH residents have a very high prevalence of faecal carriage of ESBL-E. Continuous and active surveillance is important, as are prudent infection control measures and antibiotic use to prevent and control the spread of these antibiotic-resistant strains.

There is some suggestion that infection with pandemic influenza may increase long-term mortality risks. Therefore we aimed to determine if exposure to a severe outbreak of pandemic influenza on a troopship in 1918 impacted on lifespan in the survivors. The troopship with the outbreak cohort had 1107 personnel and the comparison cohort was from two contemporaneous troopships (1108 randomly selected personnel). Data were collected from online individual military files. The main finding was that there was no statistically significant difference in the lifespan of the outbreak cohort and the comparison cohort (means of 71·5 and 71·0 years, respectively). Indeed, the outbreak cohort was actually more likely to survive into the period from 1950 onwards (P = 0·036) and to participate in the Second World War (P = 0·043). There were no significant differences between the cohorts in terms of occupational class, but the comparison cohort had a higher proportion of rural occupations (33·3% vs. 27·0%, P < 0·001) and was very slightly older in mid-1918 (27·8 vs. 27·2 years, P = 0·028). In conclusion, this study found no support for the hypothesis that exposure to the 1918 influenza pandemic adversely impacted on the lifespan in the survivors, at least in this male and military-age population.

Linked administrative population data were used to estimate the burden of childhood respiratory syncytial virus (RSV) hospitalization in an Australian cohort aged <5 years. RSV-coded hospitalizations data were extracted for all children aged <5 years born in New South Wales (NSW), Australia between 2001 and 2010. Incidence was calculated as the total number of new episodes of RSV hospitalization divided by the child-years at risk. Mean cost per episode of RSV hospitalization was estimated using public hospital cost weights. The cohort comprised of 870 314 children. The population-based incidence/1000 child-years of RSV hospitalization for children aged <5 years was 4·9 with a rate of 25·6 in children aged <3 months. The incidence of RSV hospitalization (per 1000 child-years) was 11·0 for Indigenous children, 81·5 for children with bronchopulmonary dysplasia (BPD), 10·2 for preterm children with gestational age (GA) 32–36 weeks, 27·0 for children with GA 28–31 weeks, 39·0 for children with GA <28 weeks and 6·7 for term children with low birthweight. RSV hospitalization was associated with an average annual cost of more than AUD 9 million in NSW. RSV was associated with a substantial burden of childhood hospitalization specifically in children aged <3 months and in Indigenous children and children born preterm or with BPD.

Two cases of hospital-acquired listeriosis were linked to a commercially produced, pasteurized ice cream mix. Manufacturers should implement safety measures from the Food Safety Modernization Act to minimize the risk of Listeria contamination. Dietary guidelines for persons at high risk of listeriosis may need revision to recognize the potential risk from pasteurized products.

Escherichia albertii is a newly emerging enteric pathogen that has been associated with gastroenteritis in humans. Recently, E. albertii has also been detected in healthy and sick birds, animals, chicken meat and water. In the present study, the prevalence and characteristics of the eae-positive, lactose non-fermenting E. albertii strains in retail raw meat in China were evaluated. Thirty isolates of such strains of E. albertii were identified from 446 (6·73%) samples, including duck intestines (21·43%, 6/28), duck meat (9·52%, 2/21), chicken intestines (8·99%, 17/189), chicken meat (5·66%, 3/53), mutton meat (4·55%, 1/22) and pork meat (2·44%, 1/41). None was isolated from 92 samples of raw beef meat. Strains were identified as E. albertii by phenotypic properties, diagnostic PCR, sequence analysis of the 16S rRNA gene, and housekeeping genes. Five intimin subtypes were harboured by these strains. All strains possessed the II/III/V subtype group of the cdtB gene, with two strains carrying another copy of the I/IV subtype group. Pulsed-field gel electrophoresis showed high genetic diversity of E. albertii in raw meats. Our findings indicate that E. albertii can contaminate various raw meats, posing a potential threat to public health.

An outbreak of acute hepatitis recently occurred in a nursing home in Zhejiang Province, China. The objectives of this study were to confirm the outbreak and identify the aetiology, source and transmission patterns. All residents and staff in or near the nursing home during the period from 1 October 2014 to 21 May 2015 were investigated regarding hygiene and for epidemiological information including water and food (eating meat especially pork products). Serum and stool specimens were collected for detection of hepatitis E virus (HEV) antibodies using ELISA and RNA using RT–PCR. Samples that were RNA positive were genotyped. Of 185 senior residents and 24 staff in the nursing home, there were 37 laboratory-confirmed cases during the outbreak. Of these cases, 12 patients (three deaths) were symptomatic with jaundice, a common clinical symptom for hepatitis E infection. HEV strains were isolated from three cases and they formed a single cluster within genotype 4d. A case-control study was conducted to investigate potential risk factors for the outbreak and the results revealed that cases more often washed their dishes and rinsed their mouths using tap water than the controls (P < 0·05). Based on hygiene investigation and meteorological information, it is likely that HEV-infected sewage and faeces contaminated the water network on rainy days. Collectively, these results suggest that the outbreak of HEV genotype 4 infection was most likely caused by contaminated tap water rather than food.

Although viral acute lower respiratory infections (ALRIs) are a major public health problem in tropical low- and middle-income countries (LMICs), and there is growing evidence showing their relationship with meteorological parameters, studies performed in these countries are scarce. In an analytical cross-sectional study, we determined which of the main meteorological parameters (temperature, absolute humidity, rainfall, wind speed, and solar radiation) predicted respiratory syncytial virus (RSV) activity in a population of hospitalized children with ALRI during a 5-year period, from January 2009 to December 2013. Out of a total of 4559 children included in the study (mean age 9·2 ± 8·5 months), 2953 (64·8%) presented RSV infection during the 3-month period from March to May. In the multivariate analysis, after controlling for absolute humidity, wind speed, and solar radiation, temperature [incidence rate ratio (IRR) 2·25, 95% confidence interval (CI) 1·11–4·53, P = 0·024], and rainfall (IRR 1·01, 95% CI 1·00–1·02, P = 0·044) were independently associated with the monthly number of RSV infections. In conclusion, in Bogota, the capital of a tropical LMIC lying slightly above the equator, RSV activity peaks in the 3-month period from March to May, the main rainy period of the year in the city. In addition, rainfall and temperature are the two most important meteorological parameters that are independently associated with RSV activity in hospitalized children with ALRI in the city.

The aim of this study was to examine the population structure, transmission and spatial relationship between genotypes of Shiga toxin-producing Escherichia coli (STEC) and Campylobacter jejuni, on 20 dairy farms in a defined catchment. Pooled faecal samples (n = 72) obtained from 288 calves were analysed by real-time polymerase chain reaction (rtPCR) for E. coli serotypes O26, O103, O111, O145 and O157. The number of samples positive for E. coli O26 (30/72) was high compared to E. coli O103 (7/72), O145 (3/72), O157 (2/72) and O111 (0/72). Eighteen E. coli O26 and 53 C. jejuni isolates were recovered from samples by bacterial culture. E. coli O26 and C. jejuni isolates were genotyped using pulsed-field gel electrophoresis and multilocus sequence typing, respectively. All E. coli O26 isolates could be divided into four clusters and the results indicated that E. coli O26 isolates recovered from calves on the same farm were more similar than isolates recovered from different farms in the catchment. There were 11 different sequence types of C. jejuni isolated from the cattle and 22 from water. An analysis of the population structure of C. jejuni isolated from cattle provided evidence of clustering of genotypes within farms, and among groups of farms separated by road boundaries.

The incidence of reported infections of non-typhoid Salmonella is affected by biases inherent to passive laboratory surveillance, whereas analysis of blood sera may provide a less biased alternative to estimate the force of Salmonella transmission in humans. We developed a mathematical model that enabled a back-calculation of the annual seroincidence of Salmonella based on measurements of specific antibodies. The aim of the present study was to determine the seroincidence in two convenience samples from 2012 (Danish blood donors, n = 500, and pregnant women, n = 637) and a community-based sample of healthy individuals from 2006 to 2007 (n = 1780). The lowest antibody levels were measured in the samples from the community cohort and the highest in pregnant women. The annual Salmonella seroincidences were 319 infections/1000 pregnant women [90% credibility interval (CrI) 210–441], 182/1000 in blood donors (90% CrI 85–298) and 77/1000 in the community cohort (90% CrI 45–114). Although the differences between study populations decreased when accounting for different age distributions the estimates depend on the study population. It is important to be aware of this issue and define a certain population under surveillance in order to obtain consistent results in an application of serological measures for public health purposes.

Heptavalent pneumococcal conjugate vaccine (PCV7) was introduced to Japan in 2010. We investigated the impact of PCV7 on childhood community-acquired pneumonia (CAP) and pneumococcal pneumonia (PP). Children aged <5 years living in Chiba city, Japan, who were admitted to hospitals were enrolled to estimate the incidence of CAP based on the mid-year population. PP was determined by the presence of Streptococcus pneumoniae in cultured blood and/or sputum samples of CAP patients. The incidence of CAP and S. pneumoniae isolated from PP patients was compared before (April 2008–March 2009) and after (April 2012–March 2013) the introduction of PCV7 immunization. The annual incidence of CAP was reduced [incidence rate ratio 0·81, 95% confidence interval (CI) 0·73–0·90]. When comparing post-vaccine with pre-vaccine periods, the odds ratio for PP incidence was 0·60 (95% CI 0·39–0·93, P = 0·024). PCV7-covered serotypes markedly decreased (66·6% in pre-vaccine vs. 15·6% in post-vaccine, P < 0·01), and serotypes 6C, 15A, 15C and 19A increased. Multidrug-resistant international clones in the pre-vaccine period (Spain6B-2/ST90, Taiwan19F-14/ST236) decreased, while Sweden15A-25/ST63 was the dominant clone in the post-vaccine period. A significant reduction in the incidence of both CAP hospitalizations and culture-confirmed PP of vaccine serotypes was observed at 2 years after PCV7 vaccination.

Bartonella spp. are endemic in wild rodents in many parts of the world. A study conducted in two northern California counties (Sonoma and Yolo) sampling California ground squirrels (Otospermophilus beecheyi) and four other rodent species (Peromyscus maniculatus, P. boylii, P. truei and Neotoma fuscipes) led to the isolation of small Gram-negative bacilli which were identified as Bartonella spp. based on colony morphology, polymerase chain reaction–restriction fragment length polymorphism (PCR–RFLP) and partial gene sequencing. Overall, Bartonella spp. were isolated from the blood of 71% (32/45) of the ground squirrels and one third (22/66) of the other rodents. PCR–RFLP analysis of the gltA and 16S rRNA genes yielded seven unique profiles, four for the ground squirrels and three for the other rodents. Isolates from each PCR–RFLP profiles were submitted for partial sequencing. Ground squirrel isolates were most closely related to B. washoensis, whereas the other rodent isolates were closest to B. vinsonii subsp. vinsonii and B. vinsonii subsp. arupensis. Two of these three species or subspecies are known zoonotic agents.

This study aimed to describe the diurnal shedding dynamics of Escherichia coli O157 in cattle managed on pasture. The purpose was to identify the value of a single measurement for predicting the shedding status on subsequent days. Over a 14-day period, 24 beef cows with known E. coli O157 shedding status were sampled twice daily or daily (21 sampling points) and E. coli O157 was enumerated from faeces. No association between shedding status of individual animals within a 7-h period was identified (odds ratio 1·5, P = 0·08). Short-interval sampling demonstrated substantial diurnal volatility in shedding of E. coli O157 that is not evident in studies based on long-interval (>7 days) sampling. The findings contribute to and support previous findings on the question why it has been difficult to achieve progress in understanding the epidemiology of E. coli O157 infection in cattle.

Over 10% of acute rotavirus gastroenteritis (ARGE) requires hospitalization because of complications. The aggravating factors have been widely analysed, but in an isolated way. We aimed to explore the interrelationship between the clinical and epidemiological factors that characterize rotavirus hospitalizations in Spain using information from the Minimum Basic Data Set (MBDS). Using ICD-9-CM codes, we classified acute gastroenteritis (AGE) cases by principal diagnosis fields and then categorized their comorbidities, complications, and epidemiological features by secondary fields. A multivariable, logistic, step-wise regression model was then constructed. We identified 1657 ARGE cases from 17 415 cases of AGE. Rotavirus hospitalizations were associated with place of residence, age, and season (P < 0·0001), as well as with dehydration [odds ratio (OR) 12·44, 95% confidence interval (CI) 1·52–40·38], intravenous rehydration (OR 1·74, 95% CI 1·29–2·35), metabolic acidosis (OR 1·51, 95% CI 1·24–1·83), respiratory tract infections (RTIs) (OR 1·60, 95% CI 1·09–1·98), and concomitant AGE (OR 1·52, 95% CI 1·03–2·25). Dehydration was four times more likely in patients aged <5 years (OR 4·36, 95% CI 1·20–12·96) and was associated with acidosis when ARGE and RTI were present simultaneously (P < 0·0001). Specific co-infecting viruses may play a role in acute respiratory symptoms and aggravation of gastrointestinal manifestations of rotaviruses, thus leading to complications requiring hospitalization.

Dengue has become a global problem in past few decades, with half of the world's population at risk of infection. For some countries of Asia and Latin America, severe dengue is a major cause of serious illness and even death in children. Pakistan has been reported as a hyperendemic area for dengue infection. Our study aimed to find seroprevalence of past dengue infection in asymptomatic children of Lahore with no previous history of dengue infection. A total of 400 samples were collected from children aged 1–12 years in Lahore using random sampling. The inclusion criteria were children aged 1–12 years, who had no previous symptoms of dengue fever during their lives. Children with known immunodeficiency status or fever at the time of recruitment were excluded from the study. Commercially available ELISA kits were used to determine the IgG status in sera of children. The data obtained was entered and analysed using SPSS v. 20.0. The overall prevalence of asymptomatic dengue infection was found to be 25%. There was no statistically significant difference between prevalence of infection in male and female children. There was, however, a strong relationship between increasing age of the child and number of cases with infection, with low incidence in children aged ⩽5 years.