Hospital discharge reports have provided data for studies of methicillin-resistant Staphylococcus aureus (MRSA) skin and soft-tissue infection (SSTI) studies. This analysis determined the sensitivity and positive predictive value of International Classification of Diseases, Ninth Revision, Clinical Modification (ICD-9-CM) code combinations to calculate hospitalization incidence rates, representativeness of a set of three ICD-9-CM codes to define MRSA SSTI, and hospitalization incidence rate trends for paediatric MRSA SSTIs in Los Angeles County (LAC). Using 133 cases from 31 hospitals, we found that the set of three ICD-9-CM codes used to define laboratory-confirmed cases had one of the highest positive predictive values (49%). There was no difference in age and race between those categorized using three codes vs. other code combinations. A dramatic increase in paediatric MRSA SSTI cases occurred in LAC during 1998–2006. We conclude that this combination of codes may be used to determine the rise of MRSA SSTIs in paediatric populations.

Streptococcus pyogenes group A (GAS) is a primary human pathogen. We performed genetic emm sequence and serological T-antigen typing of 819 mostly invasive GAS isolates recovered in Israel during 1996–2005. Of the 72 emm types found, the six most prevalent types (1, 81, 89, 14, 28, 5) comprised 30·2% of all isolates, and emm-type changes were observed over the years. The predicted coverage of the 26-valent S. pyogenes vaccine formulated for usage in the USA was predicted to be only ~60%. On the basis of different emm–T antigen type associations, some Israeli strains are probably different clonal types than those found in USA. About 2% of GAS had emm types that were originally associated with S. dysgalactiae subsp. equisimilis emm genes. Therefore, routine emm typing allows meaningful GAS strain surveillance, and provides data relevant to better vaccine coverage.

In 2006 an outbreak of avian influenza A(H5N1) in Turkey caused 12 human infections, including four deaths. We conducted a serological survey to determine the extent of subclinical infection caused by the outbreak. Single serum samples were collected from five individuals with avian influenza whose nasopharyngeal swabs tested positive for H5 RNA by polymerase chain reaction, 28 family contacts of the cases, 95 poultry cullers, 75 individuals known to have had contact with diseased chickens and 81 individuals living in the region with no known contact with infected chickens and/or patients. Paired serum samples were collected from 97 healthcare workers. All sera were tested for the presence of neutralizing antibodies by enzyme-linked immunoassay, haemagglutination inhibition and microneutralization assays. Only one serum sample, from a parent of an avian influenza patient, tested positive for H5N1 by microneutralization assay. This survey shows that there was minimal subclinical H5N1 infection among contacts of human cases and infected poultry in Turkey in 2006. Further, the low rate of subclinical infection following contact with diseased poultry gave further support to the reported low infectivity of the virus.

A population-based telephone survey of acute gastroenteritis (AG) was conducted in Hong Kong from August 2006 to July 2007. Study subjects were recruited through random digit-dialling with recruitments evenly distributed weekly over the 1-year period. In total, 3743 completed questionnaires were obtained. An AG episode is defined as diarrhoea ⩾3 times or any vomiting in a 24-h period during the 4 weeks prior to interview, in the absence of known non-infectious causes. The prevalence of AG reporting was 7%. An overall rate of 0·91 (95% CI 0·81–1·01) episodes per person-year was observed with women having a slightly higher rate (0·94, 95% CI 0·79–1·08) than men (0·88, 95% CI 0·73–1·04). The mean duration of illness was 3·6 days (s.d.=5·52). Thirty-nine percent consulted a physician, 1·9% submitted a stool sample for testing, and 2·6% were admitted to hospital. Of the subjects aged ⩾15 years, significantly more of those with AG reported eating raw oysters (OR 2·4, 95% CI 1·3–4·4), buffet meals (OR 1·8, 95% CI 1·3–2·5), and partially cooked beef (OR 1·8, 95% CI 1·2–2·7) in the previous 4 weeks compared to the subjects who did not report AG. AG subjects were also more likely to have had hot pot, salad, partially cooked or raw egg or fish, sushi, sashimi, and ‘snacks bought at roadside’ in the previous 4 weeks. This first population-based study on the disease burden of AG in Asia showed that the prevalence of AG in Hong Kong is comparable to that experienced in the West. The study also revealed some ‘risky’ eating practices that are more prevalent in those affected with AG.

During a 15-month period in Scotland a small but important number of human Campylobacter cases (3·2%) arose from 91 putative household outbreaks. Of the 26 outbreaks with known strain composition, 89% were composed of the same MLST which supports the potential use of MLST in public health epidemiology. The number of cases associated with household outbreaks is much larger than general outbreaks and there is some evidence to indicate that there may be secondary transmission, although this is relatively rare.

Pseudorabies virus (PrV) infections appear to be more widely distributed in the European wild boar (Sus scrofa) population than assumed. In Europe, attempts to isolate and characterize the causative agents have been limited so far. We therefore collected and examined a total of 35 PrV isolates obtained from wild boar or hunting dogs in Germany, France, Spain, Italy, Slovakia and Hungary between 1993 and 2008. Restriction enzyme analysis of genomic DNA using BamHI showed that all isolates, except one, belonged to genogroup I but different subtypes were evident. For further investigations of the phylogenetic relationships, a 732-bp fragment of the glycoprotein C (gC) gene was amplified by PCR. Sequence analysis revealed about 40 variant positions within this fragment. Comparison of the nucleotide sequences supported the separation into a clade containing isolates from North-Rhine Westphalia, Rhineland-Palatinate (Germany), France and Spain (clade B) and an apparently more variable clade comprising isolates from Brandenburg, Baden-Wurttemberg, Saxony, Saxony-Anhalt (Germany), Slovakia, Hungary, Italy and France (clade A).

In outbreaks of foodborne disease associated with retail outlets, the outlet often closes as a precaution before the specific food vehicle has been identified. Suspect food vehicles may be named as part of general control measures. A conventional case-control study cannot be performed because both cases and potential controls are likely to be aware of the hypothesis and therefore potentially biased. Modern sales recording systems in many food retail outlets may provide a basis for constructing a virtual cohort and allow a statistical inference to be made about various possible vehicles of infection. In 2007, an outbreak of E. coli O157 infection in Paisley, Scotland, was linked to cooked meat from a supermarket delicatessen using descriptive epidemiology. Construction of a virtual cohort allowed a relative risk and confidence interval to be estimated which supported the hypothesis of cooked beef topside being the vehicle of infection. This novel method could be valuable in the investigation of future outbreaks.

Few population-based studies have investigated the epidemiology of adult community-acquired pneumonia (CAP). We aimed to determine the incidence of CAP in a population at high-risk for pneumococcal disease and to evaluate a standardized method for interpreting chest radiographs adapted from the World Health Organization paediatric chest radiograph interpretation guidelines. We reviewed radiology records at the two healthcare facilities serving the White Mountain Apache tribe to identify possible pneumonia cases ⩾40 years of age. We categorized patients with clinical criteria and a physician diagnosis of pneumonia as clinical CAP and those with clinical criteria and an acute infiltrate as radiographic CAP. We identified 100 (27/1000 person-years) and 60 (16/1000 person-years) episodes of clinical and radiographic CAP, respectively. The incidence of CAP increased with age. Both radiographic and clinical CAP were serious illnesses with more than half of patients hospitalized. Our case definitions and methods may be useful for comparing data across studies and conducting vaccine trials.

Although the involvement of common childhood infections in the aetiology of acute appendicitis has long been conjectured, supporting evidence is largely restricted to a disparate set of clinical case reports. A systematic population-based analysis of the implied comorbid associations is lacking in the literature. Drawing on a classic epidemiological dataset, assembled by the School Epidemics Committee of the United Kingdom's Medical Research Council (MRC) in the 1930s, this paper presents a historical analysis of the association between termly outbreaks of each of six common childhood infections (chickenpox, measles, mumps, rubella, scarlet fever and whooping cough) and operated cases of acute appendicitis in 27 English public boarding schools. When controlled for the potential confounding effects of school, year and season, multivariate negative binomial regression revealed a positive association between the level of appendicitis activity and the recorded rate of mumps (β=0·15, 95% CI 0·07–0·24, P<0·001). Non-significant associations were identified between appendicitis and the other sample infectious diseases. Subject to data caveats, our findings suggest that further studies are required to determine whether the comorbid association between mumps and appendicitis is causal.

During a recent large tularemia outbreak in Bulgaria we found several cases that were remote from the main focus. One case had an unusual mode of transmission. A hunter acquired tularemia through a nail scratch from a buzzard (Buteo buteo) and consequently developed a typical ulceroglandular form of the disease. The diagnosis was confirmed by serological methods and successful cultivation. Comparative strain typing was performed by high-resolution multi-locus variable-number tandem repeat analysis (MLVA). The isolated strain was identical to one of the outbreak genotypes. We consider that this case represents a bird-to-human transmission of F. tularensis.

Most of the multiplex PCR (mPCR) used to identify Shigella do not discriminate between Shigella species or serotypes. We designed a mPCR to differentiate between S. flexneri and S. sonnei strains based on the detection of markers associated with the she pathogenicity island described in Shigella. In addition, specific primers were included to detect the Shigella virulence determinants ShET-1 and ShET-2 enterotoxin genes. The analysis of 304 Shigella strains from Chile and 79 Shigella strains from other geographic locations indicated that the mPCR described here detected all Shigella species and specifically differentiated S. flexneri and S. sonnei. The technique was sensitive, reproducible, specific and simple to perform, providing a new tool with the potential to be employed for epidemiological and diagnostic purposes.

In 2005, a serological study was carried out on horses in five ecologically contrasted zones of the Senegal River basin (Senegal) to assess West Nile virus (WNV) transmission and investigate underlying environmental risk factors. In each study zone, horses were randomly selected and blood samples taken. A land-cover map of the five study areas was built using two satellite ETM+ images. Blood samples were screened by ELISA for anti-WNV IgM and IgG and positive samples were confirmed by seroneutralization. Environmental data were analysed using a principal components analysis. The overall IgG seroprevalence rate was 85% (n=367; 95% CI 0·81–0·89). The proximity to sea water, flooded banks and salted mudflats were identified as protective factors. These environmental components are unfavourable to the presence of Culex mosquitoes suggesting that in Senegal, the distribution of the vector species is more limiting for WNV transmission than for the hosts' distribution.

In late 2002, health professionals from the ministries of health and academia of Jordan, the Palestinian Authority and Israel formed the Middle East Consortium on Infectious Disease Surveillance (MECIDS) to facilitate trans-border cooperation in response to infectious disease outbreaks. The first mission of MECIDS was to establish a regional, laboratory-based surveillance network on foodborne diseases. The development of harmonized methodologies and laboratory capacities, the establishment of a common platform of communication, data sharing and analysis and coordination of intervention steps when needed were agreed upon. Each of the three parties selected the microbiological laboratories that would form the network of sentinel laboratories and cover the different districts of each country and also designated one laboratory as the National Reference Laboratory (NRL). Data analysis units have been established to manage the data and serve as a central point of contact in each country. The MECIDS also selected a regional data analysis unit, the Cooperative Monitoring Centre (CMC) located in Amman, Jordan, and established a mechanism for sharing data from the national systems. Joint training courses were held on interventional epidemiology and laboratory technologies. Data collection started in July 2005 with surveillance of salmonellosis as the first target. This network of collaboration and communication established in an area of continuous dispute represents an important step towards assessing the burden of foodborne diseases in the region and is expected to be fundamental for coordination of public health interventions and prevention strategies.

Statins reduce cardiovascular mortality and related risks associated with pneumonia suggesting potentially beneficial use in influenza pandemics. We investigated the effect of current statin use on acute respiratory infections in primary care. Data from anonymized electronic medical records of persons aged ⩾45 years were examined for statin use, chronic morbidity, respiratory diagnoses, vaccination procedures, and immune suppression. Logistic regression models were used to calculate odds ratios (ORs) for statin users vs. non-users in respiratory infection outcomes. A total of 329 881 person-year observations included 18% statin users and 46% influenza vaccinees. Adjusted ORs for statin users vs. non-users were: influenza-like illness, 1·05 (95% CI 0·92–1·20); acute bronchitis, 1·08 (95% CI 1·01–1·15); pneumonia, 0·91 (95% CI 0·73–1·13); all acute respiratory infections, 1·03 (95% CI 0·98–1·07); and urinary tract infections, 0·91 (95% CI 0·85–0·98). We found no benefit in respiratory infection outcomes attributable to statin use, although uniformly higher ORs in non-vaccinated statin users might suggest synergism between statins and influenza vaccination.

Knowledge on the relative importance of alternative sources of human campylobacteriosis is important in order to implement effective disease prevention measures. The objective of this study was to assess the relative importance of three key exposure pathways (travelling abroad, poultry meat, pet contact) for different patient age groups in Switzerland. With a stochastic exposure model data on Campylobacter incidence for the years 2002–2007 were linked with data for the three exposure pathways and the results of a case-control study. Mean values for the population attributable fractions (PAF) over all age groups and years were 27% (95% CI 17–39) for poultry consumption, 27% (95% CI 22–32) for travelling abroad, 8% (95% CI 6–9) for pet contact and 39% (95% CI 25–50) for other risk factors. This model provided robust results when using data available for Switzerland, but the uncertainties remained high. The output of the model could be improved if more accurate input data are available to estimate the infection rate per exposure. In particular, the relatively high proportion of cases attributed to ‘other risk factors’ requires further attention.

Campylobacter jejuni is a leading cause of human bacterial gastroenteritis throughout the industrialized world. We investigated whether or not differences in gene complement at the lipooligosaccharide (LOS) biosynthesis locus can identify epidemiologically useful binary genomotypes in 87 C. jejuni isolates from poultry-associated multilocus sequence types (STs) collected during the course of a sentinel surveillance study. Using a PCR-based approach, we correlated assignment of both isolate LOS locus class and binary genomotype with ST. We found that isolates within STs 45, 190, 354 and 474 displayed mosaicism in gene complement at the intra-ST level. For example, based upon their binary genomotypes, we assigned individual ST-45 isolates from human clinical cases as probably originating from either a poultry or wild-bird source. However, intra-ST mosaicism in gene complement was observed alongside broader patterns of congruence in LOS locus class and gene complement that distinguished between isolates from different STs.

We identified eight consecutive patients who presented with a skin or soft tissue infection due to MRSA. Of seven household members of these cases, three were colonized with MRSA. The mean duration of MRSA colonization in index cases was 33 days (range 14–104), while mean duration of colonization in household cases was 54 days (range 12–95). There was a borderline significant association between having a concurrent colonized household member and a longer duration of colonization (mean 44 days vs. 26 days, P=0·08).

Invasive pneumococcal disease (IPD) is of concern in Japan, where the heptavalent pneumococcal conjugate vaccine (PCV7) is unavailable. We determined serotypes, genotypes indicating β-lactam resistance, and antibiotic susceptibilities of 496 isolates from normally sterile sites in patients (193 children, 303 adults) from 186 institutions between August 2006 and July 2007. Disease presentations included sepsis (46·2%), pneumonia (31·5%), and meningitis (17·5%). Mortality was 1·4% in children and 22·1% in adults, many of whom had underlying diseases. In children, serotype 6B (22·5%) was followed by 19F (14·1%), and 14 (13·1%); potential coverages of PCV7 and PCV13 were 75·4% and 93·7%, respectively. In adults, serotype 12F (14·3%) was followed by 3 (11·3%), and 6B (10·3%); 23-valent polysaccharide vaccine (PPV23) coverage was 85·4%. Most serotype 12F strains were gPISP, with pbp2b gene alteration; carbapenem had an excellent MIC90. PCV7 is recommended for children and PPV23 for adults to increase prevention against IPD.

Antimicrobial resistance is a priority emerging public health threat, and the ability to detect promptly outbreaks caused by resistant pathogens is critical for resistance containment and disease control efforts. We describe and evaluate the use of an electronic laboratory data system (WHONET) and a space–time permutation scan statistic for semi-automated disease outbreak detection. In collaboration with WHONET-Argentina, the national network for surveillance of antimicrobial resistance, we applied the system to the detection of local and regional outbreaks of Shigella spp. We searched for clusters on the basis of genus, species, and resistance phenotype and identified 19 statistical ‘events’ in a 12-month period. Of the six known outbreaks reported to the Ministry of Health, four had good or suggestive agreement with SaTScan-detected events. The most discriminating analyses were those involving resistance phenotypes. Electronic laboratory-based disease surveillance incorporating statistical cluster detection methods can enhance infectious disease outbreak detection and response.

Although multiple combinations of weather variability may contribute to an increased incidence of infectious gastrointestinal disease, few studies have investigated the association between weather variability and cases of infectious gastroenteritis. We acquired data for infectious gastroenteritis cases and weather variability in Fukuoka, Japan, from 1999 to 2007 and used time-series analysis to assess the effects of weather variability on infectious gastroenteritis cases, adjusting for confounding factors. In total, 422 176 infectious gastroenteritis cases were reported during the 9-year study period. The weekly number of infectious gastroenteritis cases increased by 7·7% (95% CI 4·6–10·8) for every 1°C increase in the average temperature and by 2·3% (95% CI 1·4–3·1) for every 1% decrease in relative humidity. From 1999 to 2007, infectious gastroenteritis cases increased significantly with increased average temperature and decreased relative humidity in Fukuoka, Japan.