In epidemiological studies of community-acquired pneumonia (CAP) that utilize administrative data, cases are typically defined by the presence of a pneumonia hospital discharge diagnosis code. However, not all such hospitalizations represent true CAP cases. We identified 3991 hospitalizations during 1997–2005 in a managed care organization, and validated them as CAP or not by reviewing medical records. To improve the accuracy of CAP identification, classification algorithms that incorporated additional administrative information associated with the hospitalization were developed using the classification and regression tree analysis. We found that a pneumonia code designated as the primary discharge diagnosis and duration of hospital stay improved the classification of CAP hospitalizations. Compared to the commonly used method that is based on the presence of a primary discharge diagnosis code of pneumonia alone, these algorithms had higher sensitivity (81–98%) and positive predictive values (82–84%) with only modest decreases in specificity (48–82%) and negative predictive values (75–90%).

In order to analyse the impact of vaccination against cytomegalovirus (CMV) on congenital infection incidence using current vaccines tested in phase II clinical trials, we simulated different scenarios by mathematical modelling, departing from the current vaccine characteristics, varying age at vaccination, immunity waning, vaccine efficacy and mixing patterns. Our results indicated that the optimal age for a single vaccination interval is from 2 to 6 months if there is no immunity waning. Congenital infection may increase if vaccine-induced immunity wanes before 20 years. Congenital disease should increase further when the mixing pattern includes transmission among children with a short duration of protection vaccine. Thus, the best vaccination strategy is a combined schedule: before age 1 year plus a second dose at 10–11 years. For CMV vaccines with low efficacy, such as the current ones, universal vaccination against CMV should be considered for infants and teenagers.

This study describes an outbreak of rabies in a flock of 110 sheep in Yangqu county, Shanxi province, China, in 2010. The flock, housed in a cave being used as a sheepfold, was attacked by a rabid dog, which resulted in 36 deaths over the following 2 days from the crushing and trampling caused by panic, and some 15 further deaths from rabies 2 weeks later. Rabies in the sheep was confirmed by the fluorescent antibody test (FAT) and RT–PCR. Rabies virus was isolated from the index dog brain and its N gene was partially sequenced (nucleotides 77-880). Results showed that the canine isolate (SXTYD01) was rabies virus with the N gene fragment 100% identical to that of the virus isolated from rabid sheep. This is the first confirmed sheep rabies outbreak in China. The clinical presentation of the disease is also described.

Medico-legal death investigation systems have the potential to play an important role in disease surveillance. While these systems are in place to serve a public function, the degree to which they are independent of central government can vary depending on jurisdiction. How these systems use this independence may present problems for public health initiatives, as it allows death investigators to decline to participate in government-led surveillance regardless of how critical the studies may be to public health and safety. A recent illustration of this problem in the UK is examined, as well as general lessons for removing impediments to death investigation systems participating in public health research.

Socioeconomic factors and the patterns of use of health services associated with influenza and pneumococcal vaccination were studied in people aged ⩾65 years admitted to three general hospitals in Spain between 2005 and 2007. The following data were collected: age, sex, risk of pneumonia, educational level, social class, type of household, physician visits, length of time with the same general practitioner, and influenza and pneumococcal vaccination (23vPPV). Associations between variables were assessed using multivariate logistic regression analysis. In total, 1702 patients were included; 59·9% had received 23vPPV and 65·6% influenza vaccine. Older age (OR 1·04, P<0·001), living with a partner (OR 1·72, P=0·003) and influenza vaccination during the last year (OR 6·64, P<0·001) were associated with 23vPPV. Male sex (OR 1·44, P=0·005), older age (OR 1·02, P=0·009), moderate risk of pneumonia (OR 1·58, P=0·001), living with a partner (OR 1·52, P=0·015) and frequent physician visits during the last year (1–6 annuals visits (OR 2·65, P<0·001); >6 visits (OR 3·83, P<0·001)) were associated with influenza vaccination. Coordination between public health and primary-care services may be necessary to improve vaccine uptake.

Vaccination coverage and seroprevalence of poliovirus antibodies were assessed in Argentinean children (aged 8–12 and 19–21 months) living in Cordoba City pre-/post-implementation of a DTwP-IPV-Hib vaccination programme, and compared to those of controls from neighbouring populations receiving a full oral poliovirus vaccine schedule. Vaccination coverage was higher in control areas pre-intervention; this increased post-intervention in Cordoba (>90%) but not in control areas. Poliovirus types 1 and 2 seroprotection rates were >97% in all groups pre-/post-intervention. Type 3 seroprotection rates were generally lower, but increased post-intervention in Cordoba becoming significantly higher than control rates. Anti-type 1 and 3 antibody titres increased twofold and sevenfold, respectively, post-intervention, whereas anti-type 2 antibody titres decreased ~40% in the 8–12 months group. All titres increased in the 19–21 months post-intervention group. The introduction of a three-dose primary DTwP-IPV-Hib schedule maintained protection against poliovirus types 1 and 2, and increased protection against type 3, while vaccine coverage in the study area increased.

We report a molecular epidemiological study of rabies virus (RABV) strains circulating in animal populations in Bhutan, and investigate potential origins of these viruses. Twenty-three RABV isolates originating from dogs and other domestic animals were characterized by sequencing the partial nucleoprotein (N) gene (395 bp). Phylogenetic analysis was conducted and the Bhutanese isolates were compared with rabies viruses originating from other parts of the world. Phylogenetic analysis showed that Bhutanese isolates were highly similar and were closely related to Indian strains and South Asian Arctic-like-1 viruses. Our study suggests that the rabies viruses spreading in southern parts of Bhutan have originated from a common ancestor, perhaps from the Indian virus strain.

In contrast to bacteraemic pneumococcal community-acquired pneumonia (CAP), there is a paucity of data on the clinical characteristics and outcomes of non-bacteraemic pneumococcal CAP. This retrospective study compared the outcome of hospitalized patients with bacteraemic and non-bacteraemic pneumococcal CAP treated at a medical centre from 2004 to 2008. Data on clinical outcomes including all-cause mortality, length of hospital stay, need for intensive-care unit admission and extrapulmonary involvement were analysed. In all, 221 patients with pneumococcal pneumonia (87 bacteraemic, 134 non-bacteraemic) were included. Patients with bacteraemic pneumococcal pneumonia (BPP) were older than those with non-BPP (46·2±30·7 years vs. 21·7±30·8 years, P<0·001) and were more likely to have underlying medical diseases (66·7% vs. 33·6%, P<0·001). The overall mortality rates at 7, 14, and 30 days were significantly higher in BPP than non-BPP patients (12·6% vs. 2·2%, 14·9% vs. 3·7%, 19·5% vs. 5·1%, all P<0·01). Multivariate logistic regression analysis showed that pneumococcal bacteraemia was correlated with extrapulmonary involvement (odds ratio 5·46, 95% confidence interval 1·97–15·16, P=0·001). In conclusion, S. pneumoniae bacteraemia increased the risk of mortality and extrapulmonary involvement in patients with pneumococcal CAP.

To determine the extent age, sex and co-infection affect morbidity in people infected with hepatitis C virus (HCV), we performed a population-based study linking HCV notifications in New South Wales, Australia with their hospital (July 2000 to June 2006), hepatitis B virus (HBV) and HIV notification, and death records. Poisson models were used to calculate hospitalization rate ratios (RRs) for all-cause, illicit drug and liver-related admissions. Co-infection RRs were used to estimate attributable risk (AR). The 86 501 people notified with HCV contributed 422 761 person-years of observation; 0·8% had HIV, 3·7% HBV, and 0·04% had both. RRs for males were equal to or lower than for females in younger ages, but higher in older ages (P for interaction ⩽0·013). HBV/HIV co-infection resulted in ARs of over 70% for liver disease and 30–60% otherwise. However, at the cohort level the impact was minimal (population ARs 1·3–8·7%). Our findings highlight the importance and success of public health measures, such as needle and syringe exchange programmes, which have helped to minimize the prevalence of co-infection in Australia. The findings also suggest that the age of study participants needs to be considered whenever the burden of HCV-related morbidity is reported by sex. The results are likely to be representative of patterns in hospital-related morbidity for the entire HCV-infected population in Australia and the ARs generalizable to other developed countries.

Large Q-fever outbreaks were reported in The Netherlands from May 2007 to 2009, with dairy-goat farms as the putative source. Since Q-fever outbreaks at such farms were first reported in 2005, we explored whether there was evidence of human outbreaks before May 2007. Space–time scan statistics were used to look for clusters of lower-respiratory infections (LRIs), hepatitis, and/or endocarditis in hospitalizations, 2005–2007. We assessed whether these were plausibly caused by Q fever, using patients' age, discharge diagnoses, indications for other causes, and overlap with reported Q fever in goats/humans. For seven detected LRI clusters and one hepatitis cluster, we considered Q fever a plausible cause. One of these clusters reflected the recognized May 2007 outbreak. Real-time syndromic surveillance would have detected four of the other clusters in 2007, one in 2006 and two in 2005, which might have resulted in detection of Q-fever outbreaks up to 2 years earlier.

The A(H1N1) influenza pandemic has been a challenge for public health surveillance systems in all countries. An objective evaluation has not been conducted, as yet, of the performance of those systems during the pandemic. This paper presents an algorithm based on Benford's Law and the mortality ratio in order to evaluate the quality of the data and the sensitivity of surveillance systems. It analyses records of confirmed cases reported to the Pan American Health Organization by its 35 member countries between epidemiological weeks 13 and 47 in 2009. Seventeen countries did not fulfil Benford's Law, and mortality exceeded the regional average in 40% of the countries. The results suggest uneven performance by surveillance systems in the different countries, with the most frequent problem being low diagnostic coverage. Benford's Law proved to be a useful tool for the evaluation of a public health surveillance system's performance.

Multi-locus sequence typing was performed on 1003 Campylobacter jejuni isolates collected in a 2-year longitudinal study of 15 dairy farms and four sheep farms in Lancashire, UK. There was considerable farm-level variation in occurrence and prevalence of clonal complexes (CC). Clonal complexes ST61, ST21, ST403 and ST45 were most prevalent in cattle while in sheep CC ST42, ST21, ST48 and ST52 were most prevalent. CC ST45, a complex previously shown to be more common in summer months in human cases, was more prevalent in summer in our ruminant samples. Gene flow analysis demonstrated a high level of genetic heterogeneity at the within-farm level. Sequence-type diversity was greater in cattle compared to sheep, in cattle at pasture vs. housed, and in isolates from farms on the Pennines compared to the Southern Fylde. Sequence-type diversity was greatest in isolates belonging to CC ST21, ST45 and ST206.

This study aimed to identify risk factors for intestinal colonization with multidrug-resistant (MDR) E. coli in dogs on admission to a veterinary teaching hospital. Exposures to potential risk factors, including prior treatments, hospitalizations and interventions during the 42 days prior to admission were assessed for 82 case admissions and 82 time-matched controls in a retrospective prevalence-based case-control study of 20 months duration. On multivariable analyses, risk of MDR E. coli colonization on admission was increased with prior hospitalization for 4–7 days and >7 days relative to shorter periods, and in dogs that had prior diagnostic imaging techniques. Univariable analyses indicated that risk was increased following prior treatment with several antimicrobial agents. However, on multivariable analysis, administration of fluoroquinolones was associated with increased risk but risk did not appear to increase following administration of other antimicrobials. These results can inform management of canine patients and infection control procedures to mitigate the risk of clinical disease due to MDR bacteria in hospitalized dogs.

We estimated the excess risk of in-patient hospitalization in a large cohort of persons diagnosed with hepatitis C virus (HCV) infection, controlling for social deprivation. A total of 20 749 individuals diagnosed with HCV in Scotland by 31 December 2006 were linked to the Scottish hospital discharge database, and indirectly standardized hospitalization rates, adjusting for sex, age, year and deprivation were calculated. We observed significant excess morbidity considering episodes for: any diagnosis [standardized morbidity ratio (SMR) 3·4, 95% CI 3·3–3·5]; liver-related diagnoses (SMR 41·3, 95% CI 39·6–43·0); and only non-liver-related diagnoses (SMR 2·14, 95% CI 2·08–2·19). Cox regression analyses of the 2000–2006 data indicated increased relative risks of hospitalization for males [hazard ratio (HR) 1·1, 95% CI 1·0–1·2], older age (per 10 years) (HR 1·55, 95% CI 1·5–1·6), and those testing HIV-positive (HR 1·6, 95% CI 1·3–1·8). This study has revealed substantial excess all-cause and liver-related morbidity in the Scottish HCV-diagnosed population, even after allowing for deprivation.

The objective of this study was to characterize empirically the association between vaccination coverage and the size and occurrence of measles epidemics in Germany. In order to achieve this we analysed data routinely collected by the Robert Koch Institute, which comprise the weekly number of reported measles cases at all ages as well as estimates of vaccination coverage at the average age of entry into the school system. Coverage levels within each federal state of Germany are incorporated into a multivariate time-series model for infectious disease counts, which captures occasional outbreaks by means of an autoregressive component. The observed incidence pattern of measles for all ages is best described by using the log proportion of unvaccinated school starters in the autoregressive component of the model.

Most lyssaviruses appear to have bat species as reservoir hosts. In Europe, of around 800 reported cases in bats, most were of European bat lyssavirus type 1 (EBLV-1) in Eptesicus serotinus (where the bat species was identified). About 20 cases of EBLV-2 were recorded, and these were in Myotis daubentonii and M. dasycneme. Through a passive surveillance scheme, Britain reports about one case a year of EBLV-2, but no cases of the more prevalent EBLV-1. An analysis of E. serotinus and M. daubentonii bat genetics in Britain reveals more structure in the former population than in the latter. Here we briefly review these differences, ask if this correlates with dispersal and movement patterns and use the results to suggest an hypothesis that EBLV-2 is more common than EBLV-1 in the UK, as genetic data suggest greater movement and regular immigration from Europe of M. daubentonii. We further suggest that this genetic approach is useful to anticipate the spread of exotic diseases in bats in any region of the world.

We sought to systematically review the published literature describing the epidemiological aspects of the first wave of pandemic A(H1N1) 2009 influenza in the Southern Hemisphere. Fifteen studies were included in this review, originating from South America, Australia or New Zealand, and Africa. Across the different studies, 16·8–45·3% of the laboratory-confirmed cases were admitted to hospital, and 7·5–26·0% of these cases were admitted to intensive care units (ICUs). The fatality rate was 0·5–1·5% for laboratory-confirmed cases in 6/8 studies reporting specific relevant data, and 14·3–22·2% for cases admitted to ICUs in 5/7 studies, respectively. In 4/5 studies the majority of laboratory-confirmed cases were observed in young and middle-aged adults, the percentage of older adults increased the higher the level of healthcare the cases received (e.g. laboratory confirmation, hospitalization or ICU admission) or for fatal cases. Many of the cases had no prior comorbidity, including conditions identified as risk factors for seasonal influenza. Pregnant women represented 7·4–9·1% and 7·1–9·1% of unselected laboratory-confirmed cases and of those admitted to ICUs, respectively. Obesity and morbid obesity were more commonly reported as the level of healthcare increased.

Genetic polymorphisms of the LMP/TAP gene coded by the HLA-II region may be associated with outcomes of HBV infection. We conducted a case-control study to test the hypothesis, including a persistent group of 155 patients with chronic hepatitis B and 36 healthy carriers, a recovered group of 165 individuals spontaneously recovered from HBV infection, and an uninfected group of 278 healthy normal controls. Genotypes of eight polymorphisms of the LMP/TAP gene were analysed by PCR–RFLP. A logistic regression model was used to analyse statistical differences in polymorphisms or haplotypes in different groups. Of the eight polymorphisms, two (TAP1 codon 637 and LMP7 codon 145) were observed to have statistically significant association with outcomes of HBV infection (P<0·05). The two-locus haplotype constructed with two such polymorphisms was analysed. The frequencies of haplotypes B (Asp-Lys), C (Gly-Gln), and D (Gly-Lys) were found to be increased significantly in the persistent group, compared to healthy controls (OR 2·26, 95% CI 1·62–3·15, P<0·001; OR 2·37, 95% CI 1·69–3·32, P<0·001; OR 4·38, 95% CI 1·78–10·77, P=0·001, respectively). The prevalence of haplotypes B (Asp-Lys), C (Gly-Gln), and D (Gly-Lys) were also significantly higher in the persistent infectious group than in the recovered group (OR 2·68, 95% CI 1·81–3·98, P<0·001; OR 2·40, 95% CI 1·62–3·55, P<0·001; OR 3·03, 95% CI 1·22–7·55, P=0·017, respectively). These findings indicated that genetic polymorphisms of the LMP/TAP gene might be an important factor in determining the outcome of HBV infection.

Reducing the burden of Salmonella in broiler flocks presents a challenge for public health. Worldwide, grow-out broilers are routinely vaccinated to prevent or lessen clinical manifestation of other infections. In this exploratory analysis we tested if details of a routine vaccination programme delivered to conventional grow-out broilers were associated with the burden of Salmonella in the flock as it progressed through its production cycle. None of the flocks studied were vaccinated against Salmonella or received a competitive exclusion product. The flocks were reared on conventional grow-out farms in southeastern USA, and sampled in a prospective field observational study. We observed significant associations between the content and design of a grow-out vaccination programme targeting other infections and the probability of detecting Salmonella in the broiler flock at different time points throughout the production cycle. To the best of the authors' knowledge, this is the first field report of such associations.