Characterization of the incubation time from infection to onset is important for understanding the natural history of infectious diseases. Attempts to estimate the incubation time distribution for novel A(H1N1v) have been, up to now, based on limited data or peculiar samples. We characterized this distribution for a generic group of symptomatic cases using laboratory-confirmed swine influenza case-information. Estimates of the incubation distribution for the pandemic influenza were derived through parametric time-to-event analyses of data on onset of symptoms and exposure dates, accounting for interval censoring. We estimated a mean of about 1·6–1·7 days with a standard deviation of 2 days for the incubation time distribution in those who became symptomatic after infection with the A(H1N1v) virus strain. Separate analyses for the <15 years and ⩾15 years age groups showed a significant (P<0·02) difference with a longer mean incubation time in the older age group.

The lack of high-quality health information for accurately estimating burdens of disease in some Aboriginal populations is a challenge for developing effective and relevant public health programmes and for health research. We evaluated data from a health registry system that captured patient consultations, provided by Labrador Grenfell Health (Labrador, Canada). The goal was to evaluate the registry's utility and attributes using modified CDC guidelines for evaluating surveillance systems. Infectious gastrointestinal illness data were used as a reference syndrome to determine various aspects of data collection and quality. Key-informant interviews were conducted to provide information about system utility. The study uncovered limitations in data quality and accessibility, resulting in region-specific recommendations including conversion to an electronic system. More generally, this study emphasized how a systematic and standardized evaluation of health registry systems can help address challenges to obtaining quality health data in often remote areas where many Aboriginal communities are found.

Recently, multiple-locus variable-number tandem-repeat analysis (MLVA) has been proposed as an alternative to pulsed-field gel electrophoresis (PFGE) for characterization of Escherichia coli O157:H7. In this study we characterized 118 E. coli O157:H7 isolates from cases of gastrointestinal disease in New Zealand using XbaI PFGE profiles and a MLVA scheme that assessed variability in eight polymorphic loci. The 118 isolates characterized included all 80 E. coli O157:H7 referred to New Zealand's Enteric Reference Laboratory in 2006 and 29 phage-type 2 isolates from 2005. When applied to these isolates the discriminatory power of PFGE and MLVA was not significantly different. However, MLVA data may be more epidemiologically relevant as isolates from family clusters of disease had identical MLVA profiles, even when the XbaI PFGE profiles differed slightly. Furthermore, most isolates with indistinguishable XbaI PFGE profiles that did not appear to be epidemiologically related had distinct MLVA profiles.

We report the results of the New Zealand Acute Gastrointestinal Illness (AGI) Community Study, a representative cross-sectional community telephone survey of 3655 participants conducted over a 12-month period. Respondents were asked questions about vomiting and diarrhoea in the previous 4 weeks. At least one episode of diarrhoea and/or vomiting was reported by 8·6% of respondents, an incidence of 1·11 episodes/person per year. Prevalence was highest in children aged <5 years and lowest in those aged >64 years. The mean duration of illness was 2·5 days and most common symptoms were diarrhoea (82·5%), stomach cramps (75·7%), nausea (56·9%) and vomiting (49·0%). Extrapolation of the adjusted estimates indicates there are about 4·66 million episodes of AGI per year in New Zealand, nearly 1 million visits to the general medical practitioner, in excess of 300 000 courses of antibiotics being dispensed and more than 4·5 million days of paid work lost due to AGI. This represents a significant burden of disease.

Mycobacterium avium subsp. hominissuis (MAH) infection in swine may cause granulomatous lesions in lymph nodes that must undergo differential diagnosis with those caused by M. tuberculosis complex members. Moreover, MAH outbreaks can lead to severe economic losses due to condemnation of carcasses. A number of potential sources of infection for animals can usually be identified in contaminated farms. This report describes the application of several molecular characterization techniques in order to identify the possible environmental sources of MAH infection in an outbreak involving four breeding farms and six fattening farms. Molecular profiles obtained from MAH strains suggested a likely epidemiological link between clinical and environmental isolates cultured from sawdust and cooling systems from one breeding farm. These results highlight the potential risk posed by these environmental elements in the spread of infection and the need for implementation of adequate management practices in order to minimize this risk.

We examined the spatiotemporal distribution of laboratory-confirmed multidrug-resistant tuberculosis (MDR TB) cases and that of other TB cases in Lima, Peru with the aim of identifying mechanisms responsible for the rise of MDR TB in an urban setting. All incident cases of TB in two districts of Lima, Peru during 2005–2007 were included. The spatiotemporal distributions of MDR cases and other TB cases were compared with Ripley's K statistic. Of 11 711 notified cases, 1187 received drug susceptibility testing and 376 were found to be MDR. Spatial aggregation of patients with confirmed MDR disease appeared similar to that of other patients in 2005 and 2006; however, in 2007, cases with confirmed MDR disease were found to be more tightly grouped. Subgroup analysis suggests the appearance of resistance may be driven by increased transmission. Interventions should aim to reduce the infectious duration for those with drug-resistant disease and improve infection control.

An outbreak of rabies affected domestic raccoon dogs on an animal farm in Inner Mongolia, China in 2007. A study was conducted to characterize the aetiological agent and clarify the origin of the rabies virus. Brain tissues were obtained from five rabid raccoon dogs. Viral nucleoprotein antigen was detected in the brain tissues and five rabies viruses were isolated from these rabid animals. Phylogenetic analysis of the N and G gene sequences showed that these isolates were closely related to Arctic-like rabies viruses isolated from the far-eastern region of Russia and South Korea, but distinct from the rabies viruses that are widely distributed in endemic areas in China. Epidemiological data suggested that the likely source of infection was from one wild raccoon dog that was captured and placed in the same type of pen used for domestic raccoon dogs.

In members of the Bocavirus genus, that contain three open reading frames (ORFs) of the Parvovirinae subfamily, porcine bocaviruses (PoBoVs) exhibit the most genetic diversity. Based on the ORF2-encoded viral protein (VP1) classification, the six reported porcine bocaviruses were grouped into four species: PoBoV1 (porcine boca-like virus or PBoLV), PoBoV2 (porcine parvovirus 4 or PPV4), PoBoV3 (PBoV1/PBoV2) and PoBoV4 (6V/7V), with PoBoV3 and PoBoV4 each having two genotype viruses. All four PoBoV species were detected in the 166 samples collected in 2010 from swine herds located in ten provinces of China. The detection rates for PoBoV1-4 were 28·9%, 6·6%, 19·3% and 39·7%, respectively. The co-infection combinations involving these six porcine bocaviruses in the collected samples were very complex. Furthermore, mixed infections with viruses from other families (porcine reproductive and respiratory syndrome virus, classic swine fever virus and porcine circovirus type 2) were also detected.

Population-based studies of Gram-negative bloodstream infection (BSI) in children are lacking. Therefore, we performed this population-based investigation in Olmsted County, Minnesota, to determine the incidence rate, site of acquisition, and outcome of Gram-negative BSI in children aged ⩽18 years. We used Kaplan–Meier method and Cox proportional hazard regression for mortality analysis. We identified 56 unique children with Gram-negative BSI during the past decade. The gender-adjusted incidence rate of Gram-negative BSI per 100 000 person-years was 129·7 [95% confidence interval (CI) 77·8–181·6]) in infants, with a sharp decline to 14·6 (95% CI 6·0–23·2) and 7·6 (95% CI 4·3–10·9) in children aged 1–4 and 5–18 years, respectively. The urinary tract was the most commonly identified source of infection (34%) and Escherichia coli was the most common pathogen isolated (38%). Over two-thirds (68%) of children had underlying medical conditions that predisposed to Gram-negative BSI. The overall 28-day and 1-year all-cause mortality rates were 11% (95% CI 3–18) and 18% (95% CI 8–28), respectively. Younger age and number of underlying medical conditions were associated with 28-day and 1-year mortality, respectively. Nosocomial or healthcare-associated acquisition was associated with both 28-day and 1-year mortality.

Rubella, a mild, vaccine-preventable disease, can manifest as congenital rubella syndrome (CRS), a devastating disease of the fetus. To emphasize the inadequacy of the existing rubella vaccination programme in India, we evaluated epidemiological evidence of rubella virus activity with data available from a tertiary-care centre. The proportion of suspected CRS cases that were laboratory confirmed increased from 4% in 2000 to 11% in 2008. During the same period, 329 clinically suspected postnatal rubella cases were tested of which 65 (20%) were laboratory confirmed. Of women (n=770) of childbearing age, 12·5% were susceptible to rubella.

Mortality from influenza and pneumonia during the 1918–1919 pandemic was compared between subgroups of civilian and military populations from states in Australia and the USA. Exposures to crowded environments before and during the pandemic were used as proxies for exposure to respiratory infections. In three separate datasets, civilian mortality from influenza and pneumonia was higher in urban than rural populations. In contrast soldiers from these same urban backgrounds had significantly lower mortality than their rural counterparts. This suggests the lower mortality in rural civilians was due to the rural environment, probably due to the relative social isolation in rural areas. This is encouraging for pandemic planning, as it suggests social distancing interventions have the potential to reduce mortality in future pandemics. Soldiers recruited before 1918 had significantly lower mortality than those recruited in 1918, and this effect was separate from the protection given by urban origin to soldiers. Both these effects substantially reduced mortality in soldiers. Further research to identify the mechanisms of these separate protective effects may yield important evidence to inform pandemic planning strategies.

A multistate outbreak of Escherichia coli O157:H7 infections occurred in the USA in November–December 2006 in patrons of restaurant chain A. We identified 77 cases with chain A exposure in four states – Delaware, New Jersey, New York, and Pennsylvania. Fifty-one (66%) patients were hospitalized, and seven (9%) developed haemolytic uraemic syndrome; none died. In a matched analysis controlling for age in 31 cases and 55 controls, illness was associated with consumption of shredded iceberg lettuce [matched odds ratio (mOR) 8·0, 95% confidence interval (CI) 1·1–348·1] and shredded cheddar cheese (mOR 6·2, CI 1·7–33·7). Lettuce, an uncooked ingredient, was more commonly consumed (97% of patients) than cheddar cheese (84%) and a single source supplied all affected restaurants. A single source of cheese could not explain the regional distribution of outbreak cases. The outbreak highlights challenges in conducting rapid multistate investigations and the importance of incorporating epidemiological study results with other investigative findings.

Annual overviews of waterborne disease outbreaks associated with untreated recreational water use provided by authorities responsible for bathing-water quality and public health in The Netherlands revealed 742 outbreaks during 1991–2007 mainly comprising of skin conditions (48%) and gastroenteritis (31%) and involving at least 5623 patients. The number of outbreaks per bathing season correlated with the number of days with temperatures over 25°C (r=0·8–0·9), but was not reduced through compliance with European bathing-water legislation (r=0·1), suggesting that monitoring of faecal indicator parameters and striving for compliance with water-quality standards may not sufficiently protect bathers. Bathing sites were prone to incidental faecal contamination events or environmental conditions that favoured the growth of naturally occurring pathogens. Identification of all possible contamination sources, awareness of changes that might negatively affect water quality, and provision of adequate information to the public are important preventive measures to protect public health.

In 1996 an outbreak of severe soft tissue infections caused by Vibrio vulnificus unexpectedly erupted in fish consumers in Israel with relatively little morbidity in fish farmers. To test the hypothesis that recurrent exposure of fishermen to the virulent strain may have provided protection against severe or symptomatic disease, we investigated the association between the immune response to V. vulnificus biotype 3 lipopolysaccharide (BT3 LPS) and disease susceptibility in fish farmers and fish consumers. Serum samples were tested for IgA and IgG of anti-BT3 LPS in fishermen and fish consumers who suffered from V. vulnificus BT3 infections and their matched controls. Pre-existing levels of IgG (IgG0) of anti-BT3 LPS were significantly lower in diseased fishermen who developed disease associated with the homologous biotype, compared to controls. In multivariate analysis, levels of IgG0 anti-BT3 LPS remained the only variable significantly associated with disease occurrence in fishermen. Higher levels of pre-existing IgG anti-BT 3 LPS antibodies may be associated with protection against severe or symptomatic disease with the homologous biotype in fishermen but not in subjects from the general public.

We report the first large-scale serosurvey for West Nile virus (WNV) conducted in the equine population in Iran. Blood samples were obtained in 2008–2009 from 1054 equines collected from 260 districts located in 27 provinces. The overall seroprevalence rate for WNV neutralizing antibodies was 23·7%. Marked geographical variations were observed as province-specific seroprevalence rates ranged from 1% to 88%, the highest values being observed in the southern and western parts of the country. The presence of IgM-positive animals (n=9) indicated a recent circulation of WNV in several provinces. Logistic modelling confirmed this result with a significant effect of age on seropositivity. This study revealed extensive circulation of WNV in Iran particularly in southwestern provinces where the virus probably circulates every year.

This study estimated the frequency of exposure of meat workers to carcasses infected with Leptospira serovars Hardjobovis or Pomona in a sheep-only abattoir in New Zealand. A stochastic spreadsheet model was developed to assess the daily risk of exposure of eviscerators, meat inspectors and offal handlers to live leptospires in sheep carcasses from May to November 2004 (high-risk period), and from December 2004 to June 2005 (low-risk period). The average sheep processed per day were 225 for an eviscerator, 374 for a meat inspector, and 1123 for an offal handler. The median daily exposures during high- and low-risk periods were 11 [95% distribution interval (DI) 5–19] and three (95% DI 1–8) infected carcasses/day for eviscerators, 18 (95% DI 9–29) and six (95% DI 2–12) for meat inspectors, and 54 (95% DI 32–83) and 18 (95% DI 8–31) for offal handlers, respectively. Stochastic risk modelling provided evidence that processing of sheep carcasses exposed meat workers regularly to live leptospires with substantial seasonal variation.

We present the results from a novel surveillance system for detecting excess all-cause mortality by age group in England and Wales developed during the pandemic influenza A(H1N1) 2009 period from April 2009 to March 2010. A Poisson regression model was fitted to age-specific mortality data from 1999 to 2008 and used to predict the expected number of weekly deaths in the absence of extreme health events. The system included adjustment for reporting delays. During the pandemic, excess all-cause mortality was seen in the 5–14 years age group, where mortality was flagged as being in excess for 1 week after the second peak in pandemic influenza activity; and in age groups >45 years during a period of very cold weather. This new system has utility for rapidly estimating excess mortality for other acute public health events such as extreme heat or cold weather.