We analysed the reported duration of incubation and symptomatic periods of norovirus for a dataset of 1022 outbreaks, 64 of which reported data on the average incubation period and 87 on the average symptomatic period. We found the mean and median incubation periods for norovirus to be 32·8 [95% confidence interval (CI) 30·9–34·6] hours and 33·5 (95% CI 32·0–34·0) hours, respectively. For the symptomatic period we found the mean and median to be 44·2 (95% CI 38·9–50·7) hours and 43·0 (95% CI 36·0–48·0) hours, respectively. We further investigated how these average periods were associated with several reported host, agent and environmental characteristics. We did not find any strong, biologically meaningful associations between the duration of incubation or symptomatic periods and the reported host, pathogen and environmental characteristics. Overall, we found that the distributions of incubation and symptomatic periods for norovirus infections are fairly constant and showed little differences with regard to the host, pathogen and environmental characteristics we analysed.

Data are rare on influenza outbreaks spreading through a workplace, but such transmission dynamics would be useful for comparison with the spread of the infection in other settings. We collected and compared infection data from two settings, a workplace and a university campus, during the 2009 pandemic influenza A(H1N1)pdm09 outbreak in a geographically contained community. Trajectories of infection were markedly alike in both settings. This suggests that transmission behaviour was similar in individuals in the two environments, despite the condition that individuals can leave the workplace setting in order to avoid transmission.

US public health laboratories began reporting Escherichia coli O157 isolates to CDC in 1996. We describe temporal and geographical patterns of isolates reported from 1996 to 2011 and demographics of persons whose specimens yielded isolates. We calculated annual E. coli O157 isolation rates/100 000 persons by patient's state of residence, county of residence, age, and sex using census data. The average annual isolation rate was 0·84. The average isolation rate in northern states (1·52) was higher than in southern states (0·43). Counties with ⩾76% rural population had a lower isolation rate (0·67) than counties with ⩽25%, 26–50%, and 51–75% rural populations (0·81, 0·92, and 0·81, respectively). The highest isolation rate (3·19) was in children aged 1–4 years. Infections were seasonal with 49% of isolates collected during July to September. Research into reasons for higher incidence in northern states and for seasonality could guide strategies to prevent illnesses.

Outbreak of Mycobacterium tuberculosis infections associated with acupuncture has not been reported. Thirteen patients with a painful swollen lump were referred to our hospital. The index patient received acupuncture and paraspinal muscular injection at a local acupuncture clinic in April 2011 and was diagnosed with M. tuberculosis 1 month later. From May 2011 to August 2011, 12 more patients with a swollen lump on the nuchal region or in the lower back or the buttocks region were referred to our hospital. Tuberculin skin test (TST), T-SPOT.TB, acid-fast stain, M. tuberculosis culture, chest radiograph, and lump magnetic resonance imaging (MRI) were performed and the patients were diagnosed with tuberculous abscess of the lump. All 13 patients received intramuscular injection at the paraspinal muscle by two acupuncturists at a local clinic and reported a swollen lump at the injection site. The needles and syringes were reused after autoclave sterilization. The TST was positive in all patients. Twelve patients had positive acid-fast stains. Mycobacterial cultures of abscess specimens were positive in all 13 patients. T-SPOT.TB tests were positive in all patients who underwent the test. The lesions and biopsies were subjected to polymerase chain reaction (PCR) and gene sequencing by the Disease Control Center of Zhejiang Province, China and the causative agent was identified as M. tuberculosis, Beijing type. In conclusion, physicians should consider the possibility of mycobacterial infections, apart from other bacterial agents, in patients with a swollen paraspinal lump following intramuscular injection.

Since early detection of pathogens and their virulence factors contribute to intervention and control strategies, we assessed the enteropathogens in diarrhoea disease and investigated the link between toxigenic strains of Escherichia coli from stool and drinking-water sources; and determined the expression of toxin genes by antibiotic-resistant E. coli in Lagos, Nigeria. This was compared with isolates from diarrhoeal stool and water from Wisconsin, USA. The new Luminex xTAG GPP (Gastroplex) technique and conventional real-time PCR were used to profile enteric pathogens and E. coli toxin gene isolates, respectively. Results showed the pathogen profile of stool and indicated a relationship between E. coli toxin genes in water and stool from Lagos which was absent in Wisconsin isolates. The Gastroplex technique was efficient for multiple enteric pathogens and toxin gene detection. The co-existence of antibiotic resistance with enteroinvasive E. coli toxin genes suggests an additional prognostic burden on patients.

Two global (re-)emerging zoonoses, leptospirosis and hantavirus infections, are clinically indistinguishable. Thirty-one patients, hospitalized in Sri Lanka for acute severe leptospirosis, were after exclusion of other potentially involved pathogens, prospectively screened with IgM ELISA for both pathogens. Of these, nine (29·0%) were positive for leptospirosis only, one (3·2%) for hantavirus only, seven (22·5%) for both pathogens concomitantly, whereas 13 (41·9%) remained negative for both. Moreover, in a retrospective study of 23 former patients, serologically confirmed for past leptospirosis, six (26·0%) were also positive in two different IgG ELISA hantavirus formats. Surprisingly, European Puumala hantavirus (PUUV) results were constantly higher, although statistically not significantly different, than Asian Hantaan virus (HTNV), suggesting an unexplained cross-reaction, since PUUV is considered absent throughout Asia. Moreover, RT–PCR on all hantavirus IgM ELISA positives was negative. Concomitant leptospirosis-hantavirus infections are probably heavily underestimated worldwide, compromising epidemiological data, therapeutical decisions, and clinical outcome.

In this study the putative protective seroprevalence (PPS) of IgG antibodies to the 27-kDa and 15/17-kDa Cryptosporidium antigens in sera of healthy participants who were and were not exposed to Cryptosporidium oocysts via surface water-derived drinking water was compared. The participants completed a questionnaire regarding risk factors that have been shown to be associated with infection. The PPS was significantly greater (49−61%) in settlements where the drinking water originated from surface water, than in the control city where riverbank filtration was used (21% and 23%). Logistic regression analysis on the risk factors showed an association between bathing/swimming in outdoor pools and antibody responses to the 15/17-kDa antigen complex. Hence the elevated responses were most likely due to the use of contaminated water. Results indicate that waterborne Cryptosporidium infections occur more frequently than reported but may derive from multiple sources.

In Taiwan, avian influenza virus (AIV) subtypes H5N2, H6N1 and H7N3 have been identified in domestic poultry, and several strains of these subtypes have become endemic in poultry. To evaluate the potential of avian-to-human transmission due to occupational exposure, an exploratory analysis of AIV antibody status in poultry workers was conducted. We enrolled 670 poultry workers, including 335 live poultry vendors (LPVs), 335 poultry farmers (PFs), and 577 non-poultry workers (NPWs). Serum antibody titres against various subtypes of viruses were analysed and compared. The overall seropositivity rates in LPVs and PFs were 2·99% (10/335) and 1·79% (6/335), respectively, against H5N2; and 0·6% (2/335) and 1·19% (4/335), respectively, for H7N3 virus. Of NPWs, 0·35% (2/577) and 0·17% (1/577) were seropositive for H5N2 and H7N3, respectively. Geographical analysis revealed that poultry workers whose workplaces were near locations where H5N2 outbreaks in poultry have been reported face greater risks of being exposed to viruses that result in elevated H5N2 antibody titres. H6N1 antibodies were detected in only one PF, and no H7N9 antibodies were found in the study subjects. Subclinical infections caused by H5N2, H6N1 and H7N3 viruses were thus identified in poultry workers in Taiwan. Occupational exposure is associated with a high risk of AIV infection, and the seroprevalence of particular avian influenza strains in humans reflects the endemic strains in poultry in this region.

Syndromic surveillance is an innovative surveillance tool used to support national surveillance programmes. Recent advances in the use of internet-based health data have demonstrated the potential usefulness of these health data; however, there have been limited studies comparing these innovative health data to existing established syndromic surveillance systems. We conducted a retrospective observational study to assess the usefulness of a national internet-based ‘symptom checker’ service for use as a syndromic surveillance system. NHS Direct online data were extracted for 1 August 2012 to 1 July 2013; a time-series analysis on the symptom categories self-reported by online users was undertaken and compared to existing telehealth syndromic data. There were 3·37 million online users of the internet-based self-checker compared to 1·43 million callers to the telephone triage health service. There was a good correlation between the online and telephone triage data for a number of syndromic indicators including cold/flu, difficulty breathing and eye problems; however, online data appeared to provide additional early warning over telephone triage health data. This assessment has illustrated some potential benefit of using internet-based symptom-checker data and provides the basis for further investigating how these data can be incorporated into national syndromic surveillance programmes.

Escherichia coli O157 is a human pathogen carried asymptomatically by cattle and shed in their faeces. Infection can occur from the consumption of contaminated beef or by direct contact. Large variations of E. coli O157 shedding in cattle exist and vary in the number of cattle positive for E. coli O157 and the amount of bacteria (c.f.u./g faeces) shed by positive animals. To investigate E. coli O157 shedding and super-shedding (>104 c.f.u./g) we used daily sampling over two 8-day periods; in January 2013 (n = 12) and February 2013 (n = 21). Samples were tested by direct faecal culture for enumeration and by immunomagnetic separation to detect lower levels of shedding. We identified three patterns of shedding, similar to previously observed descriptions: intermittent, transient and consistent. The most commonly observed pattern was intermittent shedding and variation in the level of shedding could be large. This extreme variation is demonstrated by a heifer from which E. coli O157 could be not detected one day, was super-shedding E. coli O157 the next and was detected as shedding >100 c.f.u./g the following day. Recto-anal mucosal swab testing did not predict super-shedding in this cohort of heifers. The variable individual patterns of shedding suggest that a common mechanism of infection may not operate within such a herd when considering previously described patterns and the inferred mechanisms. The sporadic and intermittent nature of shedding is a challenge to identifying risk factors and potential intervention strategies.

Helicobacter pylori imparts a considerable burden to public health. Infections are mainly acquired in childhood and can lead to chronic diseases, including gastric ulcers and cancer. The bacterium subsists in water, but the environment's role in transmission remains poorly understood. The nationally representative National Health and Nutrition Examination Survey (NHANES) was examined for environmental risk factors associated with H. pylori seroprevalence. Data from 1999–2000 were examined and weighted to represent the US population. Multivariable logistic regression estimated adjusted odds ratios (aOR) and 95% confidence intervals (CI) for associations with seropositivity. Self-reported general health condition was inversely associated with seropositivity. Of participants aged <20 years, seropositivity was significantly associated with having a well as the source of home tap water (aOR 1·7, 95% CI 1·1–2·6) and living in a more crowded home (aOR 2·3, 95% CI 1·5–3·7). Of adults aged ⩾20 years, seropositivity was not associated with well water or crowded living conditions, but adults in soil-related occupations had significantly higher odds of seropositivity compared to those in non-soil-related occupations (aOR 1·9, 95% CI 1·2–2·9). Exposures to both well water and occupationally related soil increased the effect size of adults' odds of seropositivity compared to non-exposed adults (aOR 2·7, 95% CI 1·3-5·6). Environmental exposures (well-water usage and occupational contact with soil) play a role in H. pylori transmission. A disproportionate burden of infection is associated with poor health and crowded living conditions, but risks vary by age and race/ethnicity. These findings could help inform interventions to reduce the burden of infections in the United States.

Microbial subtyping approaches are commonly used for source attribution of human salmonellosis. Such methods require data on Salmonella in animals and humans, outbreaks, infection abroad and amounts of food available for consumption. A source attribution model was applied to 24 European countries, requiring special data management to produce a standardized dataset. Salmonellosis data on animals and humans were obtained from datasets provided by the European Food Safety Authority. The amount of food available for consumption was calculated based on production and trade data. Limitations included different types of underreporting, non-participation in prevalence studies, and non-availability of trade data. Cases without travel information were assumed to be domestic; non-subtyped human or animal records were re-identified according to proportions observed in reference datasets; missing trade information was estimated based on previous years. The resulting dataset included data on 24 serovars in humans, broilers, laying hens, pigs and turkeys in 24 countries.

On 6 December 2010 a fire in Hemiksem, Belgium, was extinguished by the fire brigade with both river water and tap water. Local physicians were asked to report all cases of gastroenteritis. We conducted a retrospective cohort study among 1000 randomly selected households. We performed a statistical and geospatial analysis. Human stool samples, tap water and river water were tested for pathogens. Of the 1185 persons living in the 528 responding households, 222 (18·7%) reported symptoms of gastroenteritis during the time period 6–13 December. Drinking tap water was significantly associated with an increased risk for gastroenteritis (relative risk 3·67, 95% confidence interval 2·86–4·70) as was place of residence. Campylobacter sp. (2/56), norovirus GI and GII (11/56), rotavirus (1/56) and Giardia lamblia (3/56) were detected in stool samples. Tap water samples tested positive for faecal indicator bacteria and protozoa. The results support the hypothesis that a point-source contamination of the tap water with river water was the cause of the multi-pathogen waterborne outbreak.

Parrots are one of the most popular pet birds in China, and can harbour Chlamydia which has significance for human and animal health. We investigated, by indirect haemagglutination assay, the seroprevalence of Chlamydia infection in four species of parrots, namely budgerigars (Melopsittacus undulatus), lovebirds (Agapornis sp.), cockatiels (Nymphicus hollandicus) and Alexandrine parakeets (Psittacula eupatria) that were collected from Weifang and Beijing cities, North China and explored the association between potential risk factors and chlamydial seropositivity. We further determined the genotype of Chlamydia in 21 fresh faecal samples based on the ompA sequence by reconstruction of phylogenetic relationships. Of the 311 parrots examined, 35·37% (95% confidence interval 30·06–40·68) were seropositive, and species, gender, age, season and geographical location were identified as risk factors. Two PCR-positive samples represented Chlamydia psittaci genotype A. The occurrence of C. psittaci genotype A in the droppings of two pet parrots in China suggests potential environmental contamination with Chlamydiaceae and may raise a public health concern.

We compared the epidemiological and clinical features of avian influenza A(H7N9) virus infections in the population in Zhejiang province, China, between March and April 2013 (first wave) and October 2013 and February 2014 (second wave). No statistical difference was found for age, sex, occupation, presence of underlying conditions, exposure history, white blood cell count, lymphocyte percentage and illness timeline and duration (all P > 0·05). The virus spread to 30 new counties compared to the first wave. The case-fatality rate was 22% in the first wave and 42% in the second (P = 0·023). Of those infected, 66% in the first wave and 62% in the second wave had underlying conditions. The proportion of those exposed to live poultry markets were 80% and 66%, respectively. We recommend permanent closure of live poultry markets and reformation of poultry supply and sales.

The incidence of tuberculosis (TB) in native ethnic minorities remains high in developed countries. Arabs, the major ethnic minority in Israel, comprise 21% of its population. This retrospective study compared TB incidence, demographic, clinical, laboratory, genotyping characteristics and treatment outcomes in all Israeli-born citizens diagnosed with TB between 1999 and 2011 by ethnicity, i.e. Israeli-born Arabs (IA) and Jews (IJ). A total of 831 Israeli-born TB patients were reported. Of those, there were 530 (64%) IJ and 301 (36%) IA, with an average annual TB rate of 1·1 and 1·6 cases/100 000 population, respectively, lower than the national average (7·0 cases/100 000 population). TB rates in IA and IJ declined and converged to 1 case/100 000 residents. IA TB patients were more likely to be older, have more pulmonary TB and have lower treatment success rates than IJ. Older age and HIV co-infection, but not ethnicity, were predictive of non-success in TB treatment. Ten mixed IA–IJ clades were detected by spoligotyping and three mixed IA–IJ clusters were identified by MIRU-VNTR typing. Only one IA–IJ couple recalled mutual contact. In conclusion, TB rate in IA was higher than in IJ, but declined and converged in both to 1 case/100 000. Treatment success was high in both groups, and was unrelated to ethnicity.

The interferon-inducible transmembrane protein 3 (IFITM3), as one of the key genes involved in the interferon pathway, is critical for defending the host against influenza virus, and the rs12252 T>C variant in IFITM3 might be associated with susceptibility to severe influenza. Owing to contradictory and inconclusive results, we performed a meta-analysis to assess the association between rs12252 T>C polymorphism and severe influenza risk. A comprehensive literature search up to 1 August 2014 was conducted in EMBASE, Pubmed, Web of Science, VIP, Wanfang and CNKI databases. Four eligible studies with a total of 445 influenza patients and 3396 controls were included in this meta-analysis. Overall, our results demonstrated a significant association between the IFITM3 rs12252 T>C polymorphism and influenza risk [C vs. T: odds ratio (OR) 1·68, 95% confidence interval (CI) 1·32–2·13; CC vs. CT+TT: OR 2·38, 95% CI 1·52–3·73; CC+CT vs. TT: OR 1·62, 95% CI 1·18–2·22]. Stratification by ethnicity indicated that the variant C allele was associated with an 88% increased risk of influenza in Asians (C vs. T: OR 1·88, 95% CI 1·34–2·62). Moreover, subjects carrying the variant C allele had an increased risk of developing severe illness upon influenza infection (C vs. T: OR 2·70, 95% CI 1·86–3·94). However, no significant association was observed in patients with mild infection (C vs. T: OR 1·26, 95% CI 0·93–1·71). Our meta-analysis suggests that IFITM3 rs12252 T>C polymorphism is significantly associated with increased risk of severe influenza but not with the chance of initial virus infection.

To investigate the frequencies of dendritic cells (DCs) and Toll-like receptor 3 (TLR3) in neonates of HBsAg-positive mothers with different HBV serological profiles, we conducted a study in Taiyuan, China. The study included 144 HBsAg-positive mothers and their neonates. The frequencies of DCs and TLR3 were determined using four-colour flow-cytometric analysis. DC and TLR3 frequencies were not related to HBV intrauterine transmission, maternal HBeAg positivity, maternal HBV DNA positivity and HBeAg/HBV DNA double-positivity. The plasmacytoid dendritic cell (pDC) frequencies in neonates whose maternal HBV DNA was >5 × 107 copies/ml decreased significantly compared to that in neonates whose maternal HBV DNA was ⩽5 × 107 copies/ml (Z = − 2·170, P = 0·03) or whose maternal HBV DNA was negative (Z = − 1·981 P = 0·048). This study suggests that neonatal pDC frequencies decrease when maternal HBV DNA loads are >5 × 107 copies/ml.

A better understanding of physician practices in requesting stool samples for patients with acute gastroenteritis (AG) is needed to more accurately interpret laboratory-based surveillance data. A survey was conducted in General Practitioners (GPs) between August 2013 and July 2014 to estimate the proportion of stool samples requested for patients with AG and to identify factors associated with GP requests for a stool sample. National health insurance (NHI) data together with surveillance data from a French Sentinel GP network were also used to estimate the proportion of stool samples requested. This proportion was estimated at 4·3% in the GP survey and 9·1% (95% confidence interval 8·7–9·6) using NHI data. Multivariate analysis indicated that the ratio of stool samples requested was almost five times higher in patients with bloody diarrhoea and 10–20 times higher in patients with a long duration of illness before consultation. Laboratory-based surveillance data underestimates the actual burden of disease as fewer than one in 10 AG cases consulting their GP will be requested to submit a stool sample for laboratory testing. This underestimation varies by pathogen as stool samples are more frequently requested for severe illness.

A pen infection-transmission experiment was conducted to elucidate the role of pathogen strain and environmental contamination in transmission of Escherichia coli O157:H7 (ECO157) in cattle. Five steers were inoculated with a three-strain mixture of ECO157 and joined with five susceptible steers in each of two experimental replicates. Faecal and environmental samples were monitored for ECO157 presence over 30 days. One ECO157 strain did not spread. Transmission rates for the other two strains were estimated using a generalized linear model developed based on a modified ‘Susceptible–Infectious–Susceptible’ mathematical model. Transmission rates estimated for the two strains (0·11 and 0·14) were similar. However, the rates significantly (P = 0·0006) increased 1·5 times for every 1-unit increase in the level of environmental contamination measured as log10 c.f.u. Depending on the level of environmental contamination, the estimated basic reproduction numbers varied from <1 to 8. The findings indicate the importance of on-farm measures to reduce environmental contamination for ECO157 control in cattle that should be validated under field conditions.