This study evaluated the spatio-temporal variation of Legionella spp. in New Zealand using notification and laboratory surveillance data from 1979 to 2009 and analysed the epidemiological trends. To achieve this we focused on changing incidence rates and occurrence of different species over this time. We also examined whether demographic characteristics such as ethnicity may be related to incidence. The annual incidence rate for laboratory-proven cases was 2·5/100 000 and 1·4/100 000 for notified cases. Incidence was highest in the European population and showed large geographical variations between 21 District Health Boards. An important finding of this study is that the predominant Legionella species causing disease in New Zealand differs from that found in other developed countries, with about 30–50% of cases due to L. longbeachae and a similar percentage due to L. pneumophila for any given year. The environmental risk exposure was identified in 420 (52%) cases, of which 58% were attributed to contact with compost; travel was much less significant as a risk factor (6·5%). This suggests that legionellosis has a distinctive epidemiological pattern in New Zealand.

Research in epidemiology may be concerned with assessing risk factors for complex health issues described by several variables. Moreover, epidemiological data are usually organized in several blocks of variables, consisting of a block of variables to be explained and a large number of explanatory variables organized in meaningful blocks. Usual statistical procedures such as generalized linear models do not allow the explanation of a multivariate outcome, such as a complex disease described by several variables, with a single model. Moreover, it is not easy to take account of the organization of explanatory variables into blocks. Here we propose an innovative method in the multiblock modelling framework, called multiblock redundancy analysis, which is designed to handle most specificities of complex epidemiological data. Overall indices and graphical displays associated with different interpretation levels are proposed. The interest and relevance of multiblock redundancy analysis is illustrated using a dataset pertaining to veterinary epidemiology.

Carbapenem-resistant Acinetobacter baumannii (CRAB) are an increasing infectious threat in hospitals. We investigated the clinical epidemiology of CRAB infections vs. colonization in patients, and examined the mechanisms of resistance associated with elevated minimum inhibitory concentrations (MICs) for carbapenems. From January to June 2009, 75 CRAB strains were collected. CRAB infection was significantly associated with malignancy and a high APACHE II score. The most dominant resistance mechanism was ISAba1 preceding OXA-51, producing strains with overexpression of efflux pump. Strains carrying blaOXA-23-like enzymes had higher carbapenem MICs than those carrying blaOXA-51-like enzymes; however, the presence of multiple mechanisms did not result in increased resistance to carbapenems. There was no difference in the resistance mechanisms in strains from infected and colonized patients. The majority of strains were genetically diverse by DNA macrorestriction although there was evidence of clonal spread of four clusters of strains in patients.

Multiple salmonellosis outbreaks have been linked to contaminated tomatoes. We investigated a multistate outbreak of Salmonella Typhimurium infections among 190 cases. For hypothesis generation, review of patients' food histories from four restaurant-associated clusters in four states revealed that large tomatoes were the only common food consumed by patients. Two case-control studies were conducted to identify food exposures associated with infections. In a study conducted in nine states illness was significantly associated with eating raw, large, round tomatoes in a restaurant [matched odds ratio (mOR) 3·1, 95% confidence interval (CI) 1·3–7·3]. In a Minnesota study, illness was associated with tomatoes eaten at a restaurant (OR 6·3, mid-P 95% CI 1·05–50·4, P=0·046). State, local and federal regulatory officials traced the source of tomatoes to Ohio tomato fields, a growing area not previously identified in past tomato-associated outbreaks. Because tomatoes are commonly eaten raw, prevention of tomato contamination should include interventions on the farm, during packing, and at restaurants.

This article describes the epidemiology of pandemic A(H1N1) 2009 influenza in all Canadian pregnant women admitted to hospital, and compares it with historical inter-pandemic influenza activity. We used weekly hospitalization and death counts of laboratory-confirmed pandemic A(H1N1) influenza cases reported to the Public Health Agency of Canada's (PHAC) 2009–2010 national pandemic influenza surveillance programme. Pregnant women infected and admitted with the pandemic strain were described and compared with: (1) confirmed admissions of all women of reproductive age; (2) all admitted cases reported to PHAC; and (3) to a historical average of inter-pandemic seasonal influenza admissions, and pneumonia and influenza (P&I) admissions for pregnant women. During the pandemic, 263 pregnant women with confirmed infections were admitted; four died in their third trimester. The median age for admitted pregnant cases was 27·5 years, which is consistent with the median age of the 3-year historical inter-pandemic pregnant comparison group. Aboriginal women appeared to be overrepresented but ethnicity was unavailable for 15·2% of all pregnant cases. Overall admission volumes were higher than those for seasonal influenza in the historical comparison group but were lower than those for P&I admissions. Despite increased admission volumes, severe outcomes in pregnant women were proportionally fewer than in all cases admitted for influenza A(H1N1) infection during the pandemic.

Between 1985 and 2008, a total of 102 387 wild boar sera originating from Eastern Germany covering an area of 108 589 km2 were tested for the presence of Aujeszky's disease virus (ADV)-specific antibodies. From 1985 until 1991 and from 1992 until 2008, wild boar sera were exclusively investigated using either conventional seroneutralization assays (n=39 621) or commercial gB and full antigen ELISAs (n=62 766), respectively. Spatial-temporal analysis revealed an increasing ADV seroprevalence from 0·4% to 15·9%, on average, during the 24-year observation period that went along with a continuous spread of the infection in a western direction. During 2006 and 2008, 18% of the 66 affected districts had ADV seroprevalences >30%. There was a significant correlation between ADV seroprevalence and the hunting index of population density (HIPD) of wild boar in the entire study area, although this did not hold true for some regions. Seroprevalences did not differ between sexes but were age-dependent. East Germany has been officially free of Aujeszky's disease (pseudorabies) in domestic pigs since 1985. Although a risk for domestic pigs cannot be completely ruled out, experience has shown that ADV in domestic pigs could be eliminated although the virus was present in the wild boar population. Despite increasing ADV seroprevalence in the East German wild boar population no spillover infections from wild boar to domestic pigs have been reported. To further trace ADV infections in the wild boar population in Germany, a nationwide serological monitoring programme should be implemented.

Contaminated water is one of the main sources of norovirus (NoV) gastroenteritis outbreaks globally. Waterborne NoV outbreaks are infrequently attributed to GII.4 NoV. In September 2009, a NoV outbreak affected a small school in Guangdong Province, China. Epidemiological investigations indicated that household use water, supplied by a well, was the probable source (relative risk 1·9). NoV nucleic acid material in concentrated well-water samples was detected using real-time RT–PCR. Nucleotide sequences of NoV extracted from diarrhoea and well-water specimens were identical and had the greatest sequence identity to corresponding sequences from the epidemic strain GII.4-2006b. Our report documents the first laboratory-confirmed waterborne outbreak caused by GII.4 NoV genotype in China. Our investigations indicate that well water, intended exclusively for household use but not for consumption, caused this outbreak. The results of this report serve as a reminder that private well water intended for household use should be tested for NoV.

We present a mathematical transmission model of tuberculosis in the USA. The model is calibrated to recent trends of declining incidence in the US-born and foreign-born populations and is used in assessing relative impacts of treatment of latently infected individuals on elimination time, where elimination is defined as annual incidence <1 case/million. Provided current control efforts are maintained, elimination in the US-born population can be achieved before the end of this century. However, elimination in the foreign-born population is unlikely in this timeframe even with higher rates of targeted testing and treatment of residents of and immigrants to the USA with latent tuberculosis infection. Cutting transmission of disease as an interim step would shorten the time to elimination in the US-born population but foreign-born rates would remain above the elimination target.

Salmonella is the second most commonly reported human foodborne pathogen in England and Wales, and antimicrobial-resistant strains of Salmonella are an increasing problem in both human and veterinary medicine. In this work we used a generalized linear spatial model to estimate the spatial and temporal patterns of antimicrobial resistance in Salmonella Typhimurium in England and Wales. Of the antimicrobials considered we found a common peak in the probability that an S. Typhimurium incident will show resistance to a given antimicrobial in late spring and in mid to late autumn; however, for one of the antimicrobials (streptomycin) there was a sharp drop, over the last 18 months of the period of investigation, in the probability of resistance. We also found a higher probability of resistance in North Wales which is consistent across the antimicrobials considered. This information contributes to our understanding of the epidemiology of antimicrobial resistance in Salmonella.

Microsporidia are spore-forming intracellular parasites that infrequently cause disease in immunocompetent persons. This study describes the first report of a foodborne microsporidiosis outbreak which affected persons visiting a hotel in Sweden. Enterocytozoon bieneusi was identified in stool samples from 7/11 case-patients, all six sequenced samples were genotype C. To confirm that this was not a chance finding, 19 stool samples submitted by healthy persons from a comparable group who did not visit the hotel on that day were tested; all were negative for microsporidia. A retrospective cohort study identified 135 case-patients (attack rate 30%). The median incubation period was 9 days. Consumption of cheese sandwiches [relative risk (RR) 4·1, 95% confidence interval (CI) 1·4–12·2] and salad (RR 2·1, 95% CI 1·1–4) were associated with illness. Both items contained pre-washed, ready-to-eat cucumber slices. Microsporidia may be an under-reported cause of gastrointestinal outbreaks; we recommend that microsporidia be explored as potential causative agents in food- and waterborne outbreaks, especially when no other organisms are identified.

Salmonella enterica serovar Typhimurium definitive phage type (DT) 8 is uncommon in humans in the UK. In July 2010, the Health Protection Agency reported an excess isolation rate of pan-susceptible S. Typhimurium DT8 in England and Northern Ireland. By the end of October, this amounted to 81 laboratory-confirmed human cases for all regions of England and Northern Ireland in 2010, an increase of 26% and 41% on 2009 and 2008, respectively. Descriptive epidemiological investigation found a strong association with infection and consumption of duck eggs. Duck eggs contaminated with S. Typhimurium DT8 were collected from a patient's home and also at farms in the duck-egg supply chain. Although duck eggs form a small part of total UK eggs sales, there has been significant growth in sales in recent years. This is the first known outbreak of salmonellosis linked to duck eggs in the UK since 1949 and highlighted the impact of a changing food source and market on the re-emergence of salmonellosis linked to duck eggs. Control measures by the duck-egg industry should be improved along with a continued need to remind the public and commercial caterers of the potential high risks of contracting salmonellosis from duck eggs.

We studied a cross-sectional sample of the population of Kech, a small rural town in Pakistan to determine the prevalence and risk factors for hepatitis C infection. The prevalence of hepatitis C was 110 out of 2000 persons (5·5%, 95% confidence interval 4·5–6·5). Higher rates were identified in males. Independent risk factors identified were age ⩾75 years, being a healthcare worker, and injecting drug use. There was a high prevalence of many potential routes of transmission of bloodborne viruses and most people reported at least one potential risk factor.

This study describes the epidemiology of human salmonellosis in New Zealand using notified, hospitalized and fatal cases over a 12-year period (1997–2008). The average annual incidence for notifications was 42·8/100 000 population and 3·6/100 000 population for hospitalizations. Incidence was about twice as high in summer as in winter. Rural areas had higher rates than urban areas (rate ratio 1·23, 95% confidence interval 1·22–1·24 for notifications) and a distinct spring peak. Incidence was highest in the 0–4 years age group (154·2 notifications/100 000 and 11·3 hospitalizations/100 000). Hospitalizations showed higher rates for Māori and Pacific Island populations compared to Europeans, and those living in more deprived areas, whereas notifications showed the reverse, implying that notifications are influenced by health-seeking behaviours. Salmonella Typhimurium was the dominant serotype followed by S. Enteritidis. For a developed country, salmonellosis rates in New Zealand have remained consistently high suggesting more work is needed to investigate, control and prevent this disease.

Meningococcal meningitis is a major public health problem in a large area of sub-Saharan Africa known as the meningitis belt. Disease incidence increases every dry season, before dying out with the first rains of the year. Large epidemics, which can kill tens of thousands of people, occur frequently but unpredictably every 6–14 years. It has been suggested that these patterns may be attributable to complex interactions between the bacteria, human hosts and the environment. We used deterministic compartmental models to investigate how well simple model structures with seasonal forcing were able to qualitatively capture these patterns of disease. We showed that the complex and irregular timing of epidemics could be caused by the interaction of temporary immunity conferred by carriage of the bacteria together with seasonal changes in the transmissibility of infection. This suggests that population immunity is an important factor to include in models attempting to predict meningitis epidemics.

We examined pertussis hospitalizations among infants aged <1 year between 2006 and 2008 using the nationwide inpatient database in Japan. A total of 660 infants hospitalized for pertussis were identified. Peak incidence occurred at age 1 month and infants aged 0–2 months (too young for pertussis vaccination) and ⩾3 months (eligible for at least one dose of vaccination) accounted for 44·5% and 55·5% of hospitalizations, respectively. Complications related to pertussis were found in 165 (25·0%) cases, including one death; the age at admission did not differ significantly between patients with and those without complications (mean age 4·1 vs. 4·5 months, P=0·12). Seventeen patients required mechanical ventilation. Of the 17 cases, 14 infants were aged <3 months and three infants were aged ⩾3 months. Our findings highlight that the vaccination schedule against pertussis may often be delayed in Japan.

The 7-valent pneumococcal conjugate vaccine (PCV7) is reported to decrease the incidence of community-acquired pneumonia (CAP) in children. To determine the annual incidence of CAP before the introduction of PCV7, we counted the number of children hospitalized with CAP between 2008 and 2009 in Chiba City, Japan. We investigated serotype and multilocus sequence typing (MLST) for Streptococcus pneumoniae isolates in CAP cases. The annual incidence of hospitalized CAP in children aged <5 years was 17·6 episodes/1000 child-years. In 626 episodes, S. pneumoniae was dominant in 14·7% and 0·8% of sputum and blood samples, respectively. The most common serotypes were 6B, 23F and 19F. The coverage rates of PCV7 were 66·7% and 80% in sputum samples and blood samples, respectively. MLST analysis revealed 37 sequence types. Furthermore, 54·1% of the sputum isolates and 40% of the blood isolate were related to international multidrug-resistant clones.

A prospective surveillance system for extended-spectrum beta-lactamase-producing Escherichia coli (ESBL-E) and ESBL-producing Klebsiella spp. (ESBL-K) was implemented in 39 German hospitals with the aim of determining the incidence densities (IDs) of community-onset and hospital-onset cases and of identifying risk factors for high IDs of hospital-onset cases. During 2008, 2081 ESBL-E/K cases were documented. ESBL-E cases (n=1330, 63·9%) were more common than ESBL-K cases (n=751, 36·1%), but a higher proportion of ESBL-K cases (59%) than of ESBL-E cases (39·5%) were hospital-onset cases. The mean IDs were 0·54 (range 0–2·53) per 1000 patient-days for all ESBL-EK cases, 0·29 (range 0–1·81) per 1000 patient-days for community-onset ESBL-EK cases and 0·25 (range 0–1·82) per 1000 patient-days for hospital-onset ESBL-EK cases. Regression analysis showed a linear association between the IDs of community-onset and hospital-onset cases. The wide dissemination of ESBL-E and ESBL-K emphasizes the need for hospital-wide surveillance to guide control measures.

An outbreak of gastroenteritis affected at least 240 persons who had eaten at a gourmet restaurant over a period of 7 weeks in 2009 in England. Epidemiological, microbiological, and environmental studies were conducted. The case-control study demonstrated increased risk of illness in those who ate from a special ‘tasting menu’ and in particular an oyster, passion fruit jelly and lavender dish (odds ratio 7·0, 95% confidence interval 1·1–45·2). Ten diners and six staff members had laboratory-confirmed norovirus infection. Diners were infected with multiple norovirus strains belonging to genogroups I and II, a pattern characteristic of molluscan shellfish-associated outbreaks. The ongoing risk from dining at the restaurant may have been due to persistent contamination of the oyster supply alone or in combination with further spread via infected food handlers or the restaurant environment. Delayed notification of the outbreak to public health authorities may have contributed to outbreak size and duration.

The aim of this study was to investigate the optimal pertussis booster vaccination strategy for The Netherlands. A realistic age-structured deterministic model was designed. Assuming a steady-state situation and correcting for underreporting, the model was calibrated using notification data from the period 1996–2000. Several sensitivity analyses were performed to explore the impact of different assumptions for parameters surrounded by uncertainty (e.g. duration of protection after natural infection, underreporting factors, and transmission probabilities). The optimal age of an additional booster dose is in the range of 10–15 years, and implementation of this booster dose will reduce both symptomatic and asymptomatic infections, although the incidence of symptomatic infections in older age groups will increase. The impact of the different assumptions used in the model was in general limited. We conclude that over a wide range of assumptions, an additional booster dose can reduce the incidence of pertussis in the population.

An outbreak of meningococcal disease (MD) with severe morbidity and mortality was investigated in midwestern Brazil in order to identify control measures. A MD case was defined as isolation of Neisseria meningitidis, or detection of polysaccharide antigen in a sterile site, or presence of clinical purpura fulminans, or an epidemiological link with a laboratory-confirmed case-patient, between June and August 2008. In 8 out of 16 MD cases studied, serogroup C ST103 complex was identified. Five (31%) cases had neurological findings and five (31%) died. The attack rate was 12 cases/100 000 town residents and 60 cases/100 000 employees in a large local food-processing plant. We conducted a matched case-control study of eight primary laboratory-confirmed cases (1:4). Factors associated with illness in single variable analysis were work at the processing plant [matched odds ratio (mOR) 22, 95% confidence interval (CI) 2·3–207·7, P<0·01], and residing <1 year in Rio Verde (mOR 7, 95% CI 1·11–43·9, P<0·02). Mass vaccination (>10 000 plant employees) stopped propagation in the plant, but not in the larger community.