Between October 1999 and May 2000, a total of 28 strains of influenza C virus were isolated in four Japanese prefectures: Yamagata, Miyagi, Saitama and Hiroshima. Antigenic analysis showed that the 28 isolates were divided into three distinct antigenic groups, and viruses belonging to different antigenic groups were co-circulating in each of the four prefectures. Phylogenetic analysis of the seven protein genes demonstrated that the viruses having a similar genome composition spread in various areas of Japan during the same period. Furthermore, phylogenetic analysis showed that most of the influenza C viruses isolated in various areas of the world between the 1970s and 1980s were closely related to the contemporary Japanese viruses in all gene segments. These observations suggest that the influenza C viruses cause epidemics in some communities during the same season and that antigenically and genetically similar influenza C viruses spread throughout Japan and may be circulating worldwide.

The study objective was to evaluate three methods of Salmonella enterica prevalence estimation in swine herds (faecal culture, culture of abattoir-collected samples, and serum ELISA). From each of six swine herds, we necropsied approximately 100 finishing pigs (>70 kg); one-half on farm and the other half at the abattoir, after transport and approximately 2·5 h holding. We collected the same samples for S. enterica culture at both locations (1 g faecal, 10 g caecal contents, ileocaecal lymph nodes, superficial inguinal lymph nodes, 25 g of gluteal muscle for serum ELISA). On farm, the 1 g faecal sample only detected 13·3% (2/15) of all positive pigs necropsied on farm. However, with abattoir and on-farm results combined, the faecal sample detected 57·4% (74/129) of positive pigs. Abattoir-collected samples provided prevalence estimates much higher than on-farm collected samples (39·9 vs. 5·3%; P<0·001). This study shows that faecal samples have a low sensitivity for detecting infected pigs and that abattoir-collected samples overestimate the on-farm S. enterica prevalence. For most herds, serology overestimated the on-farm culture prevalence.

The prevalence of colonization with the anaerobic intestinal spirochaetes Brachyspira aalborgi and Brachyspira pilosicoli was investigated in humans (n=316) and dogs (n=101) living on three tea estates in Assam, India. Colonization was detected using PCR on DNA from faeces. Nineteen (6%) human faecal samples contained B. aalborgi DNA, 80 (25·3%) contained B. pilosicoli DNA, and 10 (3·2%) contained DNA from both species. One canine sample contained DNA from B. pilosicoli. Significant factors for B. aalborgi colonization in logistic regression were: infection of family members with B. aalborgi (P<0·001), being a resident of Balipara (P=0·03), and use of water treatment (P=0·03). For B. pilosicoli, significant factors were: other family members being positive for B. pilosicoli (P<0·001), water obtained from a well (P=0·006), water treatment (P=0·03), and not having visited a doctor in the previous 12 months (P=0·03).

Faecal samples from 350 farm workers on 276 dairy farms and 50 abattoir employees from seven different operations were examined for the presence of Verocytotoxin-producing Escherichia coli O157 (VTEC O157) by an O157-specific enzyme-linked fluorescent assay followed by immuno-concentration. VTEC O157 was isolated from four (1·1%) of the farm workers. A second stool sample was obtained from the positive farm workers as well as from their household contacts. VTEC O157 was isolated from the wife of one of them. The strains from the same household shared the same Verocytotoxin genes profile, phage type and pulsed-field gel electrophoresis pattern. The VTEC O157-positive subjects had neither intestinal symptoms at the moment of sampling nor a history of bloody diarrhoea or renal failure. Our study seems to confirm the hypothesis that farm residents often develop immunity to VTEC O157 infection, possibly due to recurrent exposure to less virulent strains of VTEC.

Prevalence and incidence measures are the common way to describe epidemics. The reproduction number supplies information on the potential for growth or decline of an epidemic. We define an actual reproduction number for infectious disease transmission that has taken place. An estimator is suggested, based on the number of new infections observed in a given time-interval, the number of those infected at the start of the interval, and the length of the infectious period. That estimator is applied to HIV among men having sex with other men over the period, 1977–1995, in Scandinavia. The actual reproduction number was estimated with acceptable certainty from the period, 1981–1982, yielding a value of 15 secondary cases. A value of less than one secondary case was assessed for the period, 1988–1995, in Denmark and Sweden. The actual reproduction number gives us some additional understanding of the dynamics of epidemics, compared with prevalence and incidence curves.

We followed up a cohort of 446 toxoplasma-infected pregnant women to determine the median and variability of the duration of positive toxoplasma–IgM (immunoglobulin M) results measured by an immunofluorescence test (IFT) and an immunosorbent agglutination assay (ISAGA). IgM antibodies were detected for longer using the ISAGA test [median 12·8 months, interquartile range (IQR) 6·9–24·9] than the IFT (median 10·4, IQR 7·1–14·4), but the variability between individuals in the duration of IgM positivity was greatest for the ISAGA test. IgM-positive results persisted beyond 2 years in a substantial minority of women (27·1% ISAGA, 9·1% IFT). Variation in the duration of the IgM response measured by ISAGA and IFT limit their usefulness for predicting the timing of infection in pregnant women. However, measurement of IgM and IgG antibodies in a cross-sectional serosurvey offers an efficient method for estimating the incidence of toxoplasma infection.

A year-long community-based study of diarrhoeal diseases was conducted in Canto Grande, a periurban community in Lima, Peru. In 109 (34%) houses out of 323 that were visited, at least one individual was detected with shigellosis. The frequency of the 161 shigella isolates obtained was as follows: 117 S. flexneri (73%), 21 S. boydii (13%), 15 S. dysenteriae (9%), and 8 S. sonnei (5%). Using a non-radioactive ipaH gene probe as a molecular epidemiological tool, a total of 41 S. flexneri strains were shown to be distributed in 25 intra-family comparisons by pairs (icp). Further subdivision, based on a comparison of the serotype, plasmid profile, antibiotic resistances and ipaH hybridization patterns indicated that Group I, with 11 icp (44%), had strains that were identical, Group II with 8 icp (32%), had strains that were different and Group III with 6 icp (24%), had strains with the same serotype and identical ipaH profiles but with differences in other markers. This data indicates that a diversity of shigella clones circulated in this community resulting from both clonal spread and horizontal transfer of genetic elements. Furthermore, ipaH profiling of isolates can be used not only to differentiate between closely related shigella strains but also with other parameters, help to understand the dynamics of the generation of new clones of pathogenic bacteria.

We attempted to predict epidemics of influenza B, focusing on B/Victoria/2/87-like (V) and B/Yamagata/16/88-like (Y) lineages, in Yamagata, Japan. We collected 9624 nasopharyngeal swabs for virus isolation from patients with respiratory infections between 1996 and 2003 and 237 sera for seroepidemiological analysis by haemagglutination–inhibition test in 2001. We isolated 424 V-lineage and 246 Y-lineage viruses during the study period. Three herald viruses in the 2000–2001 season enabled us to predict a V-lineage epidemic in the following season. However, another V-lineage epidemic occurred in the 2002–2003 season, although we caught four herald Y-lineage viruses, whose antigenic drift was suggested by seroepidemiological study, at the end of the previous season. Since the epidemiology of the two influenza B lineages remains unclear, a careful watch should be kept on these lineages in order to provide effective public-health strategies against future epidemics.

Campylobacter sp. is the most common cause of acute bacterial gastroenteritis in Sweden and the incidence has been increasing. Case-control studies to identify risk factors have been conducted in several countries, but much remains unexplained. The geographical distribution of campylobacter infections varies substantially, and many environmental factors may influence the observed pattern. Geographical Information Systems (GIS) offer an opportunity to use routinely available surveillance data to explore associations between potential environmental risk factors showing a geographical pattern and disease incidence, complementing traditional approaches for investigating risk factors for disease. We investigated associations between campylobacter incidence and environmental factors related to water and livestock in Sweden. Poisson regression was used to estimate the strength of the associations. Positive associations were found between campylobacter incidence and average water-pipe length per person, ruminant density, and a negative association with the percentage of the population receiving water from a public water supply. This indicates that drinking water and contamination from livestock may be important factors in explaining sporadic human campylobacteriosis in Sweden, and that contamination occurring in the water distribution system might be more important than previously considered.

Catheter-related bloodstream infection (CRBSI) caused by coagulase-negative staphylococci (CNS) is common in haematological patients with febrile neutropenia. As the clinical signs of CRBSI are usually scarce and it is difficult to differentiate from blood culture contamination, we tried to confirm CRBSI by molecular typing of CNS isolated from paired blood cultures (one from a peripheral vein and another from the central venous catheter hub). Blood cultures were positive in 59 (36%) out of 163 patients. CNS were isolated in 24 (40%) patients; in 14 from paired blood cultures (28 isolates) and in 10 from a single blood culture. CNS from paired blood cultures were identified as Staphylococcus epidermidis. Antimicrobial susceptibility was determined and bacteria were typed by pulsed-field gel electrophoresis (PFGE) of bacterial genomic DNA. In 13 patients, the antibiotic susceptibility of isolates was identical. The PFGE patterns from paired blood cultures were identical or closely related in 10 patients, thus confirming the presence of CRBSI. In the remaining four patients they were unrelated, and suggested a mixed infection or contamination. Since CNS isolates from three patients had identical PFGE patterns, they were probably nosocomially spread amongst them.

Puumala virus (PUUV) is the causative agent of nephropathia epidemica, a mild form of haemorrhagic fever with renal syndrome. PUUV is transmitted to humans via aerosolized excreta of the infected bank vole (Clethrionomys glareolus). Current methods for screening of the PUUV prevalence among bank vole populations are laborious, combining sampling in the field and subsequent analyses in the laboratory. In order to facilitate animal testing, a new serological immunochromatographic rapid test was developed. The test uses PUUV nucleocapsid protein as antigen, and it detects anti-PUUV IgG antibodies in rodents. With fresh and undiluted bank-vole blood samples (n=105) the efficacy of the test was 100%, and with frozen and diluted samples (n=78) the efficacy was 91%. The test was also shown to detect related hantavirus infections in Norway lemmings and sibling voles (n=31) with 99% efficacy. The test provides an applicable tool for studying PUUV and related hantavirus infections in arvicoline rodents.

The majority of those infected and affected by HIV are younger adults. The ability of highly active antiretroviral therapies (HAART) to extend survival means that those infected when younger may reach older age, and future increases in numbers of older individuals living with HIV in England, Wales and Northern Ireland (E,W&NI) are expected. Evidence that older individuals engage in risky sexual behaviours suggests potential for HIV transmission. Data from national HIV/AIDS surveillance systems were reviewed (1997–2001). An older individual is defined as aged 45 years or over. Between 1997 and 2001, 2290 older individuals were diagnosed with HIV; 361 in 1997, rising to 648 in 2001. Heterosexual acquisition accounted for 1073 (47%) infections; 662 were male. Where reported, 666 (65%) older heterosexuals were probably infected in Africa, 144 (14%) in the United Kingdom and 113 (11%) in Asia. There were 1020 (45%) new diagnoses acquired homosexually; white (92%), infected in the United Kingdom (78%). Numbers of older individuals accessing HIV-related services more than doubled between 1997 (2488) and 2001 (5175). In 2001, 2270 (53%) were London residents. Between 1997 and 2001, among HIV-infected older individuals attending genitourinary medicine (GUM) clinics, the proportions previously undiagnosed were 60% and 82% in heterosexual males and females respectively, and for men who have sex with men (MSM), 42%. Numbers of older individuals newly diagnosed with HIV have increased in recent years. The increase in numbers of older individuals accessing HIV-related services were in excess of younger adults. A significant proportion of older HIV-infected female heterosexuals and MSM were undiagnosed. Awareness must be raised among clinicians, and an ‘aged response’ to HIV is required.

The number of patients with severe invasive group-G streptococcal (Streptococcus dysgalactiae subsp. equisimilis) infections has been increasing in Japan. The emm genotypes and SmaI-digested pulsed-field gel electrophoresis DNA profiles were variable among the strains isolated, suggesting there has not been clonal expansion of a specific subpopulation of strains. However, all strains carried scpA, ska, slo and sag genes, some of which may be involved in the pathogenesis of the disease.

This study aims to investigate Severe Acute Respiratory Syndrome (SARS)-related behaviours of travellers returning to Hong Kong by air. A total of 820 travellers returning to Hong Kong by air were interviewed about their SARS-related behaviours in April 2003. Three quarters of the respondents wore a mask most/all of the time on board, 15% did so in public places at the travel destination. Perceived susceptibility to SARS at the destination predicted mask-wearing in public places and avoidance of crowded places, and perceived efficacy was a predictor for mask-wearing during flight. Approximately 16% of the respondents stated that they would delay their medical consultation for flu-like symptoms until returning to Hong Kong. Nearly 18·2% stated that they would not wear a mask in public places at the destination if they had flu-like symptoms. Education programmes, special services and effective thermal screening are required to minimize the chance of the spread of SARS by air travellers.

Rabbit haemorrhagic disease virus (RHDV) has killed many millions of wild rabbits in Europe and Australia, but has had little impact in the United Kingdom, despite outbreaks having occurred since 1994. High seroprevalence detected in the absence of associated mortality had suggested the presence of an endemic non-pathogenic strain which may be ‘protecting’ UK populations. Following the first detailed field study of RHDV epidemiology in the United Kingdom, using mark–recapture with serum sampling, we report that RHDV caused highly prevalent persistent infection in seropositive rabbits in the absence of associated mortality. Furthermore the virus strains responsible could not be distinguished phylogenetically from known pathogenic isolates, and were clearly very different from the only previously identified non-pathogenic strain of RHDV. These findings suggest that many – perhaps most – strains of RHDV may be propagated through both ‘pathogenic’ and ‘non-pathogenic’ modes of behaviour. Transmission occurred predominantly during and just after the breeding season.

To clarify the determinants of vaccine trial power for non-typable Haemophilus influenzae, we constructed stochastic SIS models of infection transmission in small units (e.g. day-care centres) to calculate the equilibrium distribution of the number infected. We investigated how unit size, contact rate (modelled as a function of the unit size), external force of infection and infection duration affected the statistical power for detection of vaccine effects on susceptibility or infectiousness. Given a frequency-dependent contact rate, the prevalence, proportion of infections generated internally and the power to detect vaccine effects each increased slightly with unit size. Under a density-dependent model, unit size had much stronger effects. To maximize information allowing inference from vaccine trials, contact functions should be empirically evaluated by studying units of differing size and molecular methods should be used to help distinguish internal vs. external transmission.

Blood, donated by asymptomatic donors, may contain and transmit parvovirus B19. To investigate the dynamics of parvovirus viraemia in asymptomatic blood donors, we studied the amounts of parvovirus DNA in pools of donor plasma, the prevalence of parvovirus antibodies among blood donors in relation to age, and the seasonal and year-to-year variation of the incidence of parvovirus infection in The Netherlands. The incidence of parvovirus infection follows a seasonal cycle and a cycle of several years. Among Dutch blood donors the incidence was estimated to be 0·56% per year. Forty seven out of 100 pools of 5000 plasma donations tested positive for parvovirus DNA. We inferred that the course of viraemia in asymptomatic donors shows a short peak (>109 copies parvovirus DNA/ml), followed by viraemia below 106 copies/ml for about 2 weeks.

To investigate potential risk factors associated with Helicobacter pylori (Hp) infection, we performed a case-control study in 167 consecutively selected hospitalized children in Salvador, Brazil. Hp infection was identified by the presence of IgG against Hp in serum samples. Data were gathered using a structured questionnaire, 38·3% children were found to be seropositive and classified as cases, and 61·7% were seronegative controls. After multivariate analysis, independent variables associated with Hp infection included: the educational attainment of the child's provider [ges ]11 years (OR 0·1, 95% CI 0·01–0·9), poor garbage disposal service (OR 2·2, 95% CI 1·0–4·9), thumb sucking (OR 4·6, 95% CI 1·1–19·8), brushing teeth more than once a day (OR 5·6, 95% CI 1·8–17·7), having a pet dog (OR 2·5, 95% CI 1·0–6·1), and a history of chronic urticaria (OR 4·0, 95% CI 1·5–10·8). The risk factors identified are consistent with some, but not all, previous studies supporting either oral–oral or faecal–oral transmission of Hp. Our data suggested that a higher educational attainment might play an important role in preventing Hp infection.

From July 1995 to August 1998, mycobacterial blood cultures were obtained from 1032 HIV-infected patients seen at the Centro de Referência e Treinamento de AIDS (CRTA), Hospital São Paulo (HSP), and Centro de Referência de AIDS de Santos (CRAS). Overall, 179 episodes of mycobacteraemia were detected: 111 (62·0%) at CRTA, 50 (27·9%) at HSP, and 18 (10·1%) at CRAS. The frequency of positive cultures declined sharply from 22·6% in 1995 to 6·9% in 1998, consistent with the decrease in opportunistic infections following the publicly funded distribution of highly active antiretroviral therapy. In 1995, mycobacteraemia was more frequently due to Mycobacterium avium complex (59·2%) than Mycobacterium tuberculosis (28·6%), whereas in 1998 the relative frequencies were reversed (28·6 vs. 64·3% respectively), probably justified by the increased virulence of M. tuberculosis and the greater risk of invasive infection in less-immunocompromised patients, including patients unaware they are infected with HIV.

In July 2001, an outbreak of gastroenteritis occurred in Helsinki among children and adults after bathing in an outdoor wading pool. The epidemiological survey revealed that at least 242 persons were affected. Microbiological testing of both patient stool samples and of the pool water revealed the presence of two different gastroenteritis viruses: a norovirus (NV) and an astrovirus. Amplicon sequencing of the NV samples showed nucleotide sequence identity between the virus from patients and the water. After changing the pool water and the sand at the bottom of the pool followed by shock chlorination, no virus could be detected in the water. However, NV was continuously detected in the water outlet well as much as 8 months after the incident. Here we show how molecular methods aided in tracing the source of the epidemic and in finding the causative pathogens both in patients and in the environment.