For epidemiological investigations of the most common and non-host-adapted Salmonella serotypes, such as Typhimurium, highly discriminatory approaches are essential. In the present study, we evaluated three genotyping methods; amplified fragment length polymorphism (AFLP), pulsed-field gel electrophoresis (PFGE) and repetitive palindromic extragenic–PCR (Rep–PCR) using 40 isolates. AFLP showed the highest discriminatory index (0·939), resolution and throughput. To determine clonality of Salmonella Typhimurium isolates and epidemiological relatedness in different commercial pig production units, we employed AFLP in combination with antimicrobial resistance pattern and phage typing. Salmonella serovar Typhimurium isolates (n=196) obtained from a longitudinal study of 18 pig farms over a 3-year period were studied. Using this approach, 16 distinct clonal types were identified. We found two common multidrug- resistant patterns including AmCmStSuTe and AmKmStSuTe. Two commonly multidrug- resistant phage types that are of known public health importance, DT104 and DT193, were also common. AFLP differentiated distinct clones within DT104, a phage type previously reported to be clonal. Fourteen of the clonal types were unique to one of the two production systems, showing diversity between independent commercial pig production systems located in the same geographical area. Clonal types obtained from nursery farms and corresponding finishing units were, however, similar.

We conducted a case-control study to assess risk factors for typhoid fever in Diyarbakir, Turkey, a region where transmission of Salmonella typhi is endemic. We prospectively identified febrile patients from Diyarbakir and the surrounding area who were admitted to hospital. Cases were defined as patients who had S. typhi isolated from at least one blood culture. Sixty-four cases with blood culture-confirmed S. typhi were identified between May 2001 and May 2003. In total, 128 age- and sex-matched controls selected from neighbourhoods as cases were enrolled. We hypothesized that consumption of raw vegetables contaminated with sewage would be associated with an increased risk of typhoid fever. Conditional logistic regression modelling revealed that living in a crowded household (OR 3·31, 95% CI 1·58–6·92, P=0·002), eating cig kofte (a traditional raw food) (OR 5·29, 95% CI 2·20–12·69, P=0·000) and lettuce salad (OR 3·55, 95% CI 1·52–8·28, P=0·003) in the 15 days prior to symptoms onset was independently associated with typhoid fever. We conclude that living in a crowded household and consumption of raw vegetables outside the home increase the risk of typhoid fever in this region.

The study was designed to determine the contribution of standardized scored inspections implemented during the Athens 2004 Pre-Olympic and Olympic period, in assessing the presence of Legionella spp. in water sites. Inspection grading scores of 477 water supply systems, 127 cooling towers and 134 decorative fountains were associated with the corresponding microbiological test results of 2514 samples for Legionella spp. Nine violations of water supply systems and nine of cooling towers significantly associated with positive microbiological test results, and four violations of water supply systems and one of cooling towers were among those designated as ‘critical’ water safety hazards in the inspection reports. The study documents a strong correlation [water supply systems (RR 1·92), cooling towers (RR 1·94)] between unsatisfactory inspection scoring results and Legionella-positive microbiological test results (in excess of 10000 c.f.u./l) and suggests the utility of inspection scoring systems in predicting Legionella proliferation of water systems and in preventing Legionnaires' disease.

To investigate the emergence and current situation of terrestrial rabies in Cuba, a collection of rabies virus specimens was employed for genetic characterization. These data supported the monophyletic nature of all terrestrial rabies viruses presently circulating in Cuba but additionally delineated several distinct variants exhibiting limited spatial distribution which may reflect the history of rabies spread on the island. The strain of rabies currently circulating in Cuba, which emerged on the island in the early 20th century, has very close evolutionary ties to the Mexican dog type and is a member of the cosmopolitan lineage widely distributed during the colonial period. The Cuban rabies viruses, which circulate predominantly within the mongoose population, are phylogenetically distant from viruses circulating in mongooses in other parts of the world. These studies illustrate, at a global level, the adaptation of multiple strains of rabies to mongoose species which should be regarded as important wildlife hosts for rabies re-emergence. Given the recent emergence of human cases due to bat contact in Cuba, this study also included a single insectivorous bat specimen which was found to most closely resemble the rabies viruses known to circulate in Mexican vampire bats.

This report describes an outbreak of gastroenteritis of 5 months' duration in a farming family, associated with the consumption of unpasteurized cows' milk, where Campylobacter jejuni was implicated. A total of six individuals in the family acquired the illness, and two had several episodes of diarrhoea within the 5-month period. Identical PFGE genotypes of C. jejuni were isolated from human and bovine faeces, and bulk tank milk samples. Incompletely sealed rubber liners fitted to a milking machine shortly before the outbreak started was the probable reason, allowing faecal material to contaminate the milk over the period concerned.

The spatial and temporal distribution of hantavirus and arenavirus antibody-positive wild rodents in Trentino, Italy, was studied using immunofluorescence assays (IFA) in two long-term sites trapped in 2000–2003, and six other sites trapped in 2002. The overall hantavirus seroprevalence in the bank voles, Clethrionomys glareolus (n=229) screened for Puumala virus (PUUV) antibodies was 0·4%, and that for Apodemus flavicollis mice (n=1416) screened for Dobrava virus (DOBV) antibodies was 0·2%. Antibodies against lymphocytic choriomeningitis virus (LCMV) were found in 82 (5·6%) of the 1472 tested rodents; the seroprevalence being 6·1% in A. flavicollis (n=1181), 3·3% in C. glareolus (n=276), and 14·3% in Microtus arvalis (n=7). Of the serum samples of 488 forestry workers studied by IFA, 12 were LCMV-IgG positive (2·5%) and one DOBV-IgG positive (0·2%), however, the latter could not be confirmed DOBV-specific with a neutralization assay. Our results show a widespread distribution but low prevalence of DOBV in Trentino, and demonstrate that the arenavirus antibodies are a common finding in several other rodent species besides the house mouse.

The Wells–Riley equation for modelling airborne infection in indoor environments is incorporated into an SEIR epidemic model with a short incubation period to simulate the transmission dynamics of airborne infectious diseases in ventilated rooms. The model enables the effect of environmental factors such as the ventilation rate and the room occupancy to be examined, and allows the long-term impact of infection control measures to be assessed. A theoretical parametric study is carried out to demonstrate how changes to both the physical environment and infection control procedures may potentially limit the spread of short-incubation-period airborne infections in indoor environments such as hospitals.

We conducted a nested case-control study to determine potential risk factors for developing encephalitis from West Nile virus (WNV) infection. Retrospective medical chart reviews were completed for 172 confirmed WNV cases hospitalized in Houston between 2002 and 2004. Of these cases, 113 had encephalitis, including 17 deaths, 47 had meningitis, and 12 were fever cases; 67% were male. Homeless patients were more likely to be hospitalized from WNV compared to the general population. A multiple logistic regression model identified age [odds ratio (OR) 1·1, P<0·001], history of hypertension, including those cases taking hypertension-inducing drugs (OR 2·9, P=0·012), and history of cardiovascular disease (OR 3·5, P=0·061) as independent risk factors for developing encephalitis from WNV infection. After adjusting for age, race/ethnicity (being black) (OR 12·0, P<0·001), chronic renal disease (OR 10·6, P<0·001), hepatitis C virus (OR 23·1, P=0·0013), and immunosuppression (OR 3·9, P=0·033) were identified as risk factors for death from WNV infection.

Since 1996 Salmonella Typhimurium DT104 salmonellosis has increased in The Netherlands. This prompted a case-control study of risk factors for salmonellosis to inform transmission routes for this phage type. Cases were laboratory-confirmed patients with a Salmonella infection and controls were selected from population registries by frequency matching for age, sex, degree of urbanization and season. Cases and controls received a questionnaire on risk factors. Of the 1171 cases, 573 (49%) responded: 245 S. Enteritidis and 232 S. Typhimurium cases (both DT104 and non-DT104), of which 58 were DT104. Of the 10250 controls, 3409 (33%) responded. Use of H2 antagonists [odds ratio (OR) 4·4, 95% CI 1·6–12·2] and proton pump inhibitors (OR 4·2, 95% CI 2·2–7·9), consumption of raw eggs (OR 3·1, 95% CI 1·3–7·4) and products containing raw eggs (OR 1·8, 95% CI 1·1–3·0) were associated with endemic S. Enteritidis infection. Risk factors for endemic S. Typhimurium infection were use of proton pump inhibitors (OR 8·3, 95% CI 4·3–15·9), occupational exposure to raw meat (OR 3·0, 95% CI 1·1–7·9), playing in a sandbox (for children aged 4–12 years) (OR 2·4, 95% CI 1·6–3·7), consumption of undercooked meat (OR 2·2, 95% CI 1·1–4·1) and use of antibiotics (OR 1·9, 95% CI 1·0–3·4). Use of proton pump inhibitors (OR 11·2, 95% CI 3·9–31·9) and playing in a sandbox (OR 4·4, 95% CI 1·8–10·7) were the only risk factors for S. Typhimurium DT104 salmonellosis. This study confirms known risk factors for salmonellosis. However, playing in a sandbox was a predominant new risk factor for S. Typhimurium salmonellosis in children [population attributable risk (PAR) 14%], and especially for S. Typhimurium DT104 (PAR 32%).

This study tested the hypothesis of airborne transmission of Salmonella Agona (Trial I) and Salmonella Typhimurium (Trial II) in weaned pigs. The trials were performed using stainless-steel/glass isolation cabinets connected by air ducts to permit an unidirectional airflow from cabinet 1 (two control pigs) to cabinet 3 (two sentinel pigs), passing through cabinet 2 (two inoculated pigs). Air samples, pooled faecal samples from the floor and rectal swabs were collected daily and assessed by culture and PCR. A fumigation chamber and rubber gloves coupled to the cabinets allowed sampling without opening the system. Trials I and II lasted 15 and 19 days respectively. The recovery of S. Agona and S. Typhimurium and detection of seroconversion in sentinel pigs indicate that airborne Salmonella transmission in weaned pigs over short distances is possible. Further studies on the role of aerosols in the epidemiology of Salmonella in intensive pig production should be performed.

Vaccination coverage in 595 adult patients undergoing total splenectomy in the Hospital Clinic of Barcelona during 1992–2002 was studied. The rates of cover for pneumococcal, Haemophilus influenzae type b and meningococcal vaccines were 63, 63 and 61% respectively, during 2000–2002; 32, 17 and 22% in 1997–1999; and 24, 9 and 8% in 1992–1996. Multivariate analysis showed a greater risk of no vaccination in splenectomies due to trauma, malignant neoplasms of solid organs and incidental splenectomy compared with both neoplastic and non-neoplastic haematological disease, and those patients undergoing splenectomy before 2001. Coverage ([ges ]1 vaccine) since 1997 in patients with haematological diseases was 83·5% (71/85), haematological neoplasias 69·2% (18/26), solid organ neoplasms 38·3% (36/94), incidental splenectomy 35·6% (16/45), and traumas 28·4% (21/74). Mandatory hospital admission of patients undergoing splenectomy offers a good opportunity for vaccination of these patients. Specific vaccination policies should be developed to take advantage of this circumstance.

The concomitant occurrence of a case of haemolytic–uraemic syndrome (HUS) and 62 cases of mild gastroenteritis in schools of a small rural community in southern Italy induced the health authorities to suspect a foodborne outbreak of shiga-toxin-producing Escherichia coli (STEC) infection. The schools were closed and the catering service involved was investigated. However, STEC were not isolated from the HUS case or from the 56 cases of gastroenteritis examined, and the HUS case and the outbreak of gastroenteritis were probably just coincidental. A retrospective cohort study failed to show any correlation with consumption of school meals and suggested that the outbreak probably started outside the school setting and then spread within the schools by person-to-person transmission. All the cases examined were negative for common enteric pathogens and the responsible agent for the cases of gastroenteritis was not identified. The concern raised in the small community by the occurrence of a severe case of HUS and the lack of a rapid epidemiological assessment excluding the occurrence of a STEC outbreak, turned an epidemic episode of mild gastroenteritis into a public health emergency with relevant socioeconomic consequences. Prompt intervention in outbreaks following timely and effective risk communication are crucial for taking the most appropriate control measures and avoiding the spread of fear and panic in the community.

A micro-epidemic of hantavirus infections occurred in Lower Bavaria, South-East Germany, starting in April 2004. While only three cases were registered from 2001 to 2003, a dramatically increased number of clinically apparent human hantavirus infections (n=38) was observed in 2004, plus seven additional cases by June 2005. To determine the reservoir responsible for the infections, a total of 43 rodents were trapped in Lower Bavaria. Serological and genetic investigations revealed that Puumala virus (PUUV) is dominant in the local population of bank voles. Partial PUUV S segment nucleotide sequences originating from bank voles at four different trapping sites in Lower Bavaria showed a low divergence (up to 3·1%). This is contrasted by a nucleotide sequence divergence of 14–16% to PUUV strains detected in Belgium, France, Slovakia or North-Western Germany. PUUV sequences from bank voles in Lower Bavaria represent a new PUUV subtype which seems to be responsible for the observed increase of human hantavirus infections in 2004–2005.

This study examined the prevalence of the intestinal spirochaetes Brachyspira aalborgi and Brachyspira pilosicoli in different Western Australian (WA) populations. Faecal samples included 287 from rural patients with gastrointestinal symptoms, comprising 142 from non-Aboriginal and 145 from Aboriginal people; 227 from recent healthy migrants to WA from developing countries; and 90 from healthy non-Aboriginal individuals living in Perth, WA. DNA was extracted from faeces, and subjected to PCR assays for both species. B. pilosicoli-positive individuals were confined to the rural Aboriginal (14·5%) and migrant (15·0%) groups. B. aalborgi was detected at a lower but similar prevalence in all four groups: rural non-Aboriginals, 5·6%; rural Aboriginals, 6·9%; migrants, 7·9%; controls, 5·6%. In migrants and Aborigines, the presence of B. pilosicoli and B. aalborgi was associated (P<0·001), suggesting that colonization by B. pilosicoli may be facilitated by colonization with B. aalborgi. Amongst the Aboriginal patients, logistic regression identified both spirochaete species as being associated with chronic diarrhoea, failure to thrive and being underweight. Both species may have pathogenic potential, but B. aalborgi appears more host-adapted than the opportunistic B. pilosicoli.

Mathematical models are used to quantify the effect of border control measures in reducing the international spread of SARS. Border screening is shown to play a relatively minor role in reducing disease spread. Assuming detection rates similar to those reported for arrival screening in Australia, screening can detect up to 10% (95% CI 3–23) of infected travellers, and reduce the probability of a large outbreak by up to 7% (95% CI 2–17). Rapid reductions in the time to diagnosis and effective facilities for the isolation of cases are essential to ensure that there will not be a large outbreak, and each week of delay in responding to imported infection approximately doubles the total number of cases. While the control response is being developed in a currently uninfected region, border screening can provide up to one week's additional time in which to improve methods for early isolation of cases.

A study on the prevalence of the faecal carriage of Escherichia coli O157 in lambs was performed in the major slaughterhouse in Rome, central Italy, during 2002. A total of 643 animals, consisting of 378 weaned and 265 suckling lambs, were assayed for the presence of E. coli O157. Five O157-agglutinating E. coli strains were isolated (0·8%, 95% CI 0·3–1·9). Only one was positive to PCR specific for the eae gene and produced verocytotoxin VT2, with a VTEC O157 overall prevalence of 0·2% (95% CI 0·0–1·0), whereas one strain possessed the eae gene only. All the other isolates were negative for the presence of all the virulence genes considered. The animals were either from local farms or imported from Eastern Europe. The results suggest an age-specific difference since the microorganism was isolated only from 0·3% (95% CI 0·0–1·7) of weaned lambs, while all samples from suckling lambs tested negative. From this study, the overall risk of human exposure to pathogenic E. coli O157 from lamb meat consumption derived from the major slaughterhouse in Rome can be considered reasonably low, particularly when suckling lamb meat is considered.

We estimated the number of deaths in France for the year 2000 in HIV-infected adults using three sources. The sources were (1) the ‘Mortalité 2000’ survey (M2000): 964 deaths were documented by 185 hospital wards involved in HIV management; (2) 1288 death certificates with a mention of HIV infection (INSERM-CepiDc) and (3) the French hospital database on HIV infection (FHDH) identified 654 deaths. The capture–recapture method was used with log-linear modelling. Overall 1559 deaths were observed. Estimation of the number of deaths in France was 1699 (95% CI 1671–1727). The completeness of M2000, CepiDc and FHDH were 55%, 76% and 38% respectively. Diversification of diseases and of causes of death in HIV-infected adults may explain: (1) the diversification of physicians involved in their management and incomplete coverage of M2000 and FHDH, and (2) why HIV infection was not mentioned in all death certificates.

In 2001, two residents of a nursing home in Lower Saxony, Germany, were diagnosed with acute hepatitis B virus (HBV) infection. A systematic contact investigation of 188 residents yielded 19 confirmed or probable cases of acute or recent HBV infection and three persistent asymptomatic HBsAg carriers. Sequence analysis revealed that one carrier had high viraemia (109 genomes/ml), HBV genotype A2, and the same S gene and/or X gene sequence as 16 acutely infected persons. An unmatched case-control study was conducted with the 17 cases that had sequence identity together with 26 controls. The strongest association was found for treatment by a particular general practitioner (GP) (OR>11, P<0·001) and blood sampling for glucose monitoring on a particular day by the GP's staff (OR 13·6, P<0·001, adjusted OR 8·5, P=0·017). Control measures were implemented. Serological controls after 6 and 18 months revealed that the outbreak was brought under control.

The current WHO policy during measles outbreaks focuses on case management rather than reactive vaccination campaigns in urban areas of resource-poor countries having low vaccine coverage. Vaccination campaigns may be costly, or not timely enough to impact significantly on morbidity and mortality. We explored the time available for intervention during two recent epidemics. Our analysis suggests that the spread of measles in African urban settings may not be as fast as expected. Examining measles epidemic spread in Kinshasa (DRC), and Niamey (Niger) reveals a progression of smaller epidemics. Intervening with a mass campaign or in areas where cases have not yet been reported could slow the epidemic spread. The results of this preliminary analysis illustrate the importance of revisiting outbreak response plans.

During a period of 3 years, 1998–2000, 1047 faecal swabs from Black-headed gulls were sampled at one location in Southern Sweden. Salmonella spp. was found in 28 individuals (2·7%) and the dominating serotype found was S. Typhimurium (83%). Twenty-five per cent of the Salmonella-infected gulls were later recaptured and re-sampled. We found that Salmonella infection in Black-headed gulls was of short duration, and that infection in this bird species was predominantly expressed as carriage without disease manifestations. All S. Typhimurium isolates were subjected to antibiotic resistance profiling and molecular characterization by pulsed-field gel electrophoresis and IS200 polymerase chain reaction. The S. Typhimurium gull isolates were compared to human and domestic animal isolates of the same serotype and phage type. We found genetic relatedness of S. Typhimurium DT195 isolates from gulls, domestic animals and humans, indicating that Black-headed gulls might play a role in the spread of S. Typhimurium in Sweden.