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.

We retrospectively analysed the epidemiological data of all hand, foot, and mouth disease (HFMD) cases from the largest paediatric infectious diseases centre in Shanghai between 2007 and 2010. A total of 28 058 outpatients were diagnosed with HFMD, of which 3948 (14·07%) were hospitalized, 730 (2·60%) had complications with neurological disorders and pulmonary oedema/haemorrhage, and 11 (0·04%) died. The peak season was the summer months. Boys were more affected than girls. Since 2008, the major population group affected has shifted from native Shanghainese children attending preschool to migrant children and younger children cared for at home. Children aged 1–4 years constituted 82·27% of cases. EV-A71 was tested in clinical samples taken from severe cases in 2009 and 2010, and from most inpatients in 2010. EV-A71 was positive in 99·17% and 86·31% of severe cases, respectively in 2009 and 2010. All 12 cases with pulmonary oedema or haemorrhage were infected with EV-A71. Ten (90·90%) of 11 fatal cases were attributable to EV-A71 infection. In 2010, EV-A71-positive cases accounted for 54·12% of inpatients. The dominant circulation of EV-A71 led to the outbreak of HFMD and occurrence of severe and fatal cases.

Childhood rubella infection in early pregnancy can lead to fetal death or congenital rubella syndrome (CRS) with multiple disabilities. Reduction of transmission via universal vaccination can prevent CRS, but inadequate coverage may increase CRS numbers by increasing the average age at infection. Consequently, many countries do not vaccinate against rubella. The World Health Organization recommends that for safe rubella vaccination, at least 80% coverage of each birth cohort should be sustained. The nonlinear relationship between CRS burden and infection dynamics has been much studied; however, how the complex interaction between epidemic and demographic dynamics affects minimum safe levels of coverage has not been quantitatively evaluated across scales necessary for a global assessment. We modelled 30-year CRS burdens across epidemiological and demographic settings, including the effect of local interruption of transmission via stochastic fadeout. Necessary minimum vaccination coverage increases markedly with birth and transmission rates, independent of amplitude of seasonal fluctuations in transmission. Susceptible build-up in older age groups following local stochastic extinction of rubella increased CRS burden, indicating that spatial context is important. In low birth-rate settings, 80% routine coverage is a conservative guideline, particularly if supplemented with campaigns and vaccination of women of childbearing age. Where birth and transmission rates are high, immunization coverage must be well above 80% and campaigns may be needed. Policy-makers should be aware of the potential negative effect of local extinction of rubella, since heterogeneity in vaccination coverage will shape extinction patterns, potentially increasing CRS burdens.

Certain influenza outbreaks, including the 2009 influenza A(H1N1) pandemic, can predominantly affect school-age children. Therefore the use of school absenteeism data has been considered as a potential tool for providing early warning of increasing influenza activity in the community. This study retrospectively evaluates the usefulness of these data by comparing them with existing syndromic surveillance systems and laboratory data. Weekly mean percentages of absenteeism in 373 state schools (children aged 4–18 years) in Birmingham, UK, from September 2006 to September 2009, were compared with established syndromic surveillance systems including a telephone health helpline, a general practitioner sentinel network and laboratory data for influenza. Correlation coefficients were used to examine the relationship between each syndromic system. In June 2009, school absenteeism generally peaked concomitantly with the existing influenza surveillance systems in England. Weekly school absenteeism surveillance would not have detected pandemic influenza A(H1N1) earlier but daily absenteeism data and the development of baselines could improve the timeliness of the system.

The objective of this study was to compare the occurrence of Salmonella spp. found in the animal environment in pig herds with different Salmonella risks (61 herds with low seroprevalence, 81 herds with high seroprevalence) on a broad scale. The environmental samples were divided into two types: direct (n=1105) and indirect (n=1220) environmental samples. All samples were tested for Salmonella spp. via real-time polymerase chain reaction. Most of the indirect environments were more often Salmonella-positive in the high-seroprevalence herds than in the low-seroprevalence herds; significantly higher were compartment aisles [odds ratio (OR) 3·45, 95% confidence interval (CI) 1·61–7·41], driving boards (OR 3·06, 95% CI 1·38–6·92) and the central aisle of the barn (OR 3·03, 95% CI 1·35–6·83). The overall results show that especially areas in the indirect environment are the major, but mostly underestimated causes of residual Salmonella.

This study used linked national tuberculosis (TB) and HIV surveillance data to investigate recent trends and factors associated with HIV co-infection (TB-HIV) in healthcare workers (HCWs) with TB in England and Wales. Methods applied were the χ2 trend test and logistic regression. Overall 14% (231/1627) of HCWs with TB were co-infected with HIV, increasing from 8% in 1999 to 14% in 2005 (P<0·001). Most (78%) HCWs were non-UK born and 74% of these developed TB ⩾2 years post-entry. Being born in Sub-Saharan Africa was an independent predictor for TB-HIV, especially for female HCWs (odds ratio 66·5, 95% confidence interval 16·3–271·1), who also had a lower median CD4 count than other co-infected women (106/mm3, interquartile range 40–200, P<0·01). Voluntary HIV testing of new HCWs should be encouraged as an opportunity for early diagnosis. Post-entry, a high index of clinical suspicion for TB in those most at risk remains important.

This study determined the prevalence and antimicrobial susceptibility of Salmonella isolated from broiler flocks in Japan. Caecal dropping samples were collected from 288 broiler flocks between November 2007 and February 2010. Salmonella was prevalent in 248 (86·1%) broiler flocks. The top three serovars were S. Infantis, S. Manhattan and S. Schwarzengrund. S. Infantis was found in all regions tested in this study. However, S. Manhattan and S. Schwarzengrund were frequently found only in the western part of Japan. High antimicrobial resistance rates were observed against oxytetracycline (90·2%), dihydrostreptomycin (86·7%) and ampicillin (36·5%), and 258 (90·5%) of 285 isolates were resistant to two or more antimicrobial agents. Interestingly, 26·3% of isolates were resistant to ceftiofur, especially 38·1% of S. Infantis isolates, although its use in broilers has not been approved in Japan. This study showed that Salmonella is highly prevalent (86·1%) in Japanese broiler flocks, that 90·5% of Salmonella isolates were multidrug-resistant, and that S. Infantis frequently exhibited resistance to cephalosporin antimicrobial agents.

In Australia, Ross River virus (RRV) is predominantly identified and managed through passive health surveillance. Here, the proactive use of environmental datasets to improve community-scale public health interventions in southeastern Tasmania is explored. Known environmental drivers (temperature, rainfall, tide) of the RRV vector Aedes camptorhynchus are analysed against cumulative case records for five adjacent local government areas (LGAs) from 1993 to 2009. Allowing for a 0- to 3-month lag period, temperature was the most significant driver of RRV cases at 1-month lag, contributing to a 23·2% increase in cases above the long-term case average. The potential for RRV to become an emerging public health issue in Tasmania due to projected climate changes is discussed. Moreover, practical outputs from this research are proposed including the development of an early warning system for local councils to implement preventative measures, such as public outreach and mosquito spray programmes.

This study used statistical methods to investigate linkages in phenotypic resistance profiles in a population sample of 321 Salmonella Typhimurium isolates from sporadic salmonellosis cases in Lower Saxony, Germany, collected during 2008–2010. A resistance index was applied to calculate the conditional probability of resistance to one antimicrobial agent given the resistance to one or more other antimicrobial agent(s). A susceptibility index was defined analogously. A contingency plot, which visualizes the association between resistances to two antimicrobial agents, facilitated the interpretation. Linkages between minimum inhibitory concentrations (MIC) were analysed using Spearman's rank correlation coefficient and jittered scatter plots. Applying these methods provided a compact description of multi-resistance and linkages between resistance properties in large datasets. Moreover, this approach will improve monitoring of antimicrobial resistance dynamics of bacteria in human or animal populations by identifying linked resistance to antimicrobial agents (cross- or co-resistance) with a non-molecular method.

This study reports on gastroenteritis outbreaks suspected of being norovirus infections in eight long-term care facilities. A descriptive epidemiological investigation was used to depict sources of infections and control measures. Outbreaks affected 299 (31%) of 954 residents and 95 (11%) of 843 staff. Attack rates were higher in residents (range 17–55%) than staff (range 3–35%). Person-to-person spread was suspected. The case-hospitalization rate was 2·5%, and no death occurred. Eight staff members were employed at multiple affected facilities and may have introduced disease into three facilities. Thirty-two stool specimens were positive for norovirus by real-time reverse transcriptase–polymerase chain reaction or enzyme immunoassay. Sequenced specimens were closely related to GII.4 New Orleans. A concurrent Clostridium difficile outbreak was also detected at one facility. Staff members who work at multiple facilities may transmit norovirus between them. Regulatory agencies should consider precluding ill staff from working in multiple facilities during outbreaks. Guidelines to control norovirus must be applied promptly and meticulously by facilities.

Historically, Shigella sonnei has dominated other Shigella species infection in men who have sex with men (MSM) in Montréal. In early 2010, Toronto reported increased proportions of the more pathogenic S. flexneri, HIV co-infection and MSM in shigellosis cases since 2009. Analytical methods were used to assess whether S. flexneri had dominated Montréal's MSM cases since 2009 and whether changes had occurred in notifications in MSM and HIV-co-infected MSM. S. flexneri increased by 6·7% per month since 2007 and predominated in MSM since 2009 without changes in HIV co-infection or similar shifts in the general population. The results suggest that the surveillance of Shigella species in order to detect species shifts is beneficial for surveillance, given the potential for increased transmission and severity of S. flexneri in HIV-positive MSM.

This study reports on the clinical profiles of herpes simplex encephalitis (HSE) case-patients and the management of acyclovir prescriptions. We designed a study on the causes of encephalitis in France in 2007. Case-patients fulfilling the inclusion criteria were enrolled in all the hospitals that volunteered to participate. Fifty-five of 253 enrolled case-patients were diagnosed with HSE. Three (5%) HSE patients died and 48 (89%) were discharged with persistent neurological symptoms. All HSE patients were prescribed acyclovir, 10 of whom had a 2-week course; 42 a 3-week course; two received incomplete courses; and one received two courses of 21 days each due to relapse. The acyclovir dosage was reported for 45 adult HSE patients, 25 (53%) of whom received 10 mg/kg t.i.d. and 22 (47%) received 15 mg/kg t.i.d. The mortality rate was low despite 49% of patients being admitted to intensive-care units. A high dose of acyclovir was not associated with a better outcome in HSE patients. Most patients had persisting symptoms on discharge suggesting neuropsychological rehabilitation is an important issue for survivors.

Identification of covariates associated with disease is a key part of epidemiological research. Yet, while adjustment for imperfect diagnostic accuracy is well established when estimating disease prevalence, similar adjustment when estimating covariate effects is far less common, although of important practical relevance due to the sensitivity of such analyses to misclassification error. Case-study data exploring evidence for seasonal differences in Salmonella prevalence using serological testing is presented, in addition simulated data with known properties are analysed. It is demonstrated that: (i) adjusting for misclassification error in models comprising continuous covariates can have a very substantial impact on the resulting conclusions which can then be drawn from any analyses; and (ii) incorporating prior knowledge through Bayesian estimation can provide potentially more informative assessments of covariates while removing the assumption of perfect diagnostic accuracy. The method presented is widely applicable and easily generalized to many types of epidemiological studies.

We conducted an epidemic investigation to discover the route of transmission and the host factors of an outbreak of post-injection abscesses. Of the 2984 patients who visited a single clinic, 77 cases were identified and 208 age- and sex-matched controls were selected for analysis. Injected medications per se were not found to be responsible, and a deviation from safe injection practice suggested the likelihood of diluent contamination. Therefore the injected medications were classified according to whether there was a need for a diluent, and two medications showed a statistically significant association, i.e. injection with pheniramine [adjusted odds ratios (aOR) 5·93, 95% confidence interval (CI) 2·97–11·87] and ribostamycin (aOR 47·95, 95% CI 11·08–207·53). However, when considered concurrently, pheniramine lost statistical significance (aOR 8·71, 95% CI 0·44–171·61) suggesting that normal saline was the causative agent of this outbreak. Epidemiological evidence strongly suggested that this post-injection outbreak was caused by saline contaminated with Mycobacterium massiliense without direct microbiological evidence.

Campylobacter is the most common known source of human bacterial enteritis in the developed world and poultry is considered the main source. Broilers often become colonized with Campylobacter during rearing, and then contaminate the farm environment. The objective of this study was to identify Campylobacter-positive environmental reservoirs on farms, as these pose a risk to broiler flocks becoming colonized with Campylobacter. We considered the temporal aspects of exposure and colonization. A longitudinal study monitored six conventional rearing farms over 2 years. The broiler flocks, catchers' equipment, vehicles, shed surrounds, shed entrance, other equipment, farm entrance, other animals, puddles, dead birds, mains water and drinkers were systematically sampled 2–4 times per flock. A multivariable generalized estimating equation model was used to assess associations between contaminated environmental sites and colonized broiler flocks. The associations were adjusted for confounders and other known risk factors. To further assess temporality of contamination, the sequence of contamination of the different environmental sites and the flocks was established. Contaminated shed entrances and anterooms, contaminated drinkers and shedding of Campylobacter by other animals such as cattle, dogs, wildlife and rodents were significantly associated with positive flocks. The reservoir of ‘other animals’ was also the reservoir most commonly positive before the flock became colonized. The other sites usually became contaminated after the flock was colonized.

Global dissemination of imipenem-resistant (IR) clones of Acinetobacter baumannii–A. calcoaceticus complex (ABC) have been frequently reported but the molecular epidemiological features of IR-ABC in military treatment facilities (MTFs) have not been described. We characterized 46 IR-ABC strains from a dataset of 298 ABC isolates collected from US service members hospitalized in different US MTFs domestically and overseas during 2003–2008. All IR strains carried the blaOXA-51 gene and 40 also carried blaOXA-23 on plasmids and/or chromosome; one carried blaOXA-58 and four contained ISAbal located upstream of blaOXA-51. Strains tended to cluster by pulsed-field gel electrophoresis profiles in time and location. Strains from two major clusters were identified as international clone I by multilocus sequence typing.

The introduction and the widespread use of the varicella vaccine in Taiwan has led to a 75–80% decrease in the incidence of varicella in children. However the vaccine's long-term impact on the incidence of herpes zoster (HZ) has attracted attention. By controlling gender, underlying diseases, and age effects, a Poisson regression was applied on the 2000–2008 chart records of 240 000 randomly selected residents who enrolled in the Universal National Health Insurance. The results show that, as the vaccine coverage in children increases, the incidence of varicella decreases. However, the incidence of HZ increased even before the implementation of the free varicella vaccination programme in 2004, particularly in females. The increase in the incidence of HZ cannot be entirely and directly attributed to the widespread vaccination of children. Continuous monitoring is needed to understand the secular trends in HZ before and after varicella vaccination in Taiwan and in other countries.

Leptospirosis is one of the most widespread zoonoses in the world. A large outbreak of suspected human leptospirosis began in Sri Lanka during 2008. This study investigated spatial variables associated with suspected leptospirosis risk during endemic and outbreak periods. Data were obtained for monthly numbers of reported cases of suspected clinical leptospirosis for 2005–2009 for all of Sri Lanka. Space–time scan statistics were combined with regression modelling to test associations during endemic and outbreak periods. The cross-correlation function was used to test association between rainfall and leptospirosis at four locations. During the endemic period (2005–2007), leptospirosis risk was positively associated with shorter average distance to rivers and with higher percentage of agriculture made up of farms <0·20 hectares. Temporal correlation analysis of suspected leptospirosis cases and rainfall revealed a 2-month lag in rainfall-case association during the baseline period. Outbreak locations in 2008 were characterized by shorter distance to rivers and higher population density. The analysis suggests the possibility of household transmission in densely populated semi-urban villages as a defining characteristic of the outbreak. The role of rainfall in the outbreak remains to be investigated, although analysis here suggests a more complex relationship than simple correlation.

Independent outbreaks of dengue virus (DENV) infection and sporadic cases of chikungunya virus (CHIKV) have been recorded in the metropolitan city of Delhi on several occasions in the past. However, during a recent 2010 arboviral outbreak in Delhi many cases turned negative for DENV. This prompted us to use duplex reverse transcriptase–polymerase chain reaction (D-RT–PCR) to establish the aetiology of dengue/chikungunya through sequencing of CprM and E1 genes of dengue and chikungunya viruses. Interestingly, for the first time, both DENV and CHIKV co-circulated simultaneously and in equally dominant proportion during the post-monsoon period of 2010. DENV-1 genotype III and the East Central South African genotype of CHIKV were associated with post-monsoon spread of these viruses.

This study was performed to determine the prevalence, distribution of specimen sources, and antimicrobial susceptibility of the Acinetobacter calcoaceticus–Acinetobacter baumannii (Acb) species complex in Singapore. One hundred and ninety-three non-replicate Acb species complex clinical isolates were collected from six hospitals over a 1-month period in 2006. Of these, 152 (78·7%) were identified as A. baumannii, 18 (9·3%) as ‘Acinetobacter pittii’ [genomic species (gen. sp.) 3], and 23 (11·9%) as ‘Acinetobacter nosocomialis’ (gen. sp. 13TU). Carbapenem resistance was highest in A. baumannii (72·4%), followed by A. pittii (38·9%), and A. nosocomialis (34·8%). Most carbapenem-resistant A. baumannii and A. nosocomialis possessed the blaOXA-23-like gene whereas carbapenem-resistant A. pittii possessed the blaOXA-58-like gene. Two imipenem-resistant strains (A. baumannii and A. pittii) had the blaIMP-like gene. Representatives of carbapenem-resistant A. baumannii were related to European clones I and II.