To estimate the prevalence and distribution of salmonellae, especially Salmonella enterica subsp. enterica serovar Enteritidis (S. Enteritidis), in Western Japan, an investigation was conducted of the chicken industry and environmental sources between 1995 and 1998. Salmonellae were isolated from 34 of 90 samples (37·8 %) of raw chicken parts, 34 of 98 faecal samples (34·7 %) at 35 broiler farms, 11 of 59 samples (18·6 %) of liquid eggs, and from 71 of 272 samples (26·1 %) of swab specimens from equipment and cracked or faecally soiled shell eggs at the processing facilities. Salmonellae, including S. Enteritidis, were also isolated from swab samples of henhouses associated with one of the shell-egg processing facilities (11 samples out of 55, 20 %). In the broiler meat production environment, S. Infantis was dominant. Twenty-two of 36 sewage samples (61·1 %) and 16 of 72 samples (22·2 %) taken from 5 rivers contained salmonellae including S. Enteritidis. S. Enteritidis isolates were analysed with pulsed-field gel electrophoresis using enzyme Bln I. Thirty-four isolates from shell-egg processing facilities and henhouses, obtained over several years, had the same pulsed-field profile as isolates obtained from four individual outbreaks that occurred in this location in 1997. One of the clonal lines of S. Enteritidis, among multiple serovars of salmonellae in the environment, was thought to have distributed in reservoirs, laying hens, for several years, and continued to cause outbreaks in this area.

On Friday, 22 November 1996, the microbiologist at a hospital in Lanarkshire, Scotland, identified presumptive Escherichia coli O157 in faecal specimens submitted by three patients with bloody diarrhoea, and confirmed its presence in one. Over the next 6 h, 12 more potential cases were identified. Investigations first indicated then confirmed a single food premises as the source of infection. Effective control measures were applied promptly. The outbreak was declared over on 20 January 1997, by which time 512 cases had been identified, and infection with the outbreak strain confirmed in 279. Twenty deaths occurred in cases during the outbreak and there were two more in cases during 1997. Seventeen of these deaths resulted from the outbreak. This paper describes the outbreak's epidemiological investigation, referring to other investigations, and control measures, where appropriate.

The aim of the study was to define the prevalence of verotoxin-producing Escherichia coli (VTEC) in cattle and pigs in a Hong Kong abattoir. Faecal and carcass samples collected from 986 cattle and 487 pigs from an abattoir were tested for verotoxin (VT) by PCR and cytotoxicity assays. VTEC was isolated from 41·5 and 1·8 % of cattle faecal and carcass samples and from 2·1 and 0·2 % of porcine faecal and carcass samples, respectively. Amongst 409 VTEC isolates from cattle, 9 were serotype O157:H7 and eaeA+. The most prevalent vt genotype among bovine VTEC was vt1+vt2+ (73·8 %) and in porcine VTEC was vt2e+ (30 %). None of the porcine VTEC isolates and 9·3 % of the bovine VTEC isolates was eaeA+. The non-O157 serogroup VTEC isolates carrying eaeA and EHEC-hlyA belonged to serogroups O172, O15, O84, O91, O110 and O121. The local dietary preference for pork or chicken (rather than beef ), the low VTEC carriage in pigs, the rarity of additional virulence factors (eaeA) in VTEC isolated from cattle may explain the apparently low incidence of human diarrhoeal disease associated with VTEC in Hong Kong hitherto. However, the presence of non-O157 VTEC strains carrying the eaeA virulence marker in cattle highlights the fact that sole reliance on sorbitol-MacConkey agar for screening human VTEC isolates may underestimate the human disease burden. The changing dietary habits of the population in Hong Kong reinforce the need for continued vigilance.

This is the first study to provide a comprehensive insight into the molecular epidemiology of endemic Clostridium difficile and particularly that associated with a recently recognized epidemic strain. We DNA fingerprinted all C. difficile isolates from the stools of patients with symptomatic antibiotic-associated diarrhoea and from repeated samples of the inanimate ward environment on two elderly medicine hospital wards over a 22-month period. Notably, C. difficile was not recoverable from either ward immediately before opening, but was found on both wards within 1–3 weeks of opening, and the level of environmental contamination rose markedly during the first 6 months of the study period. C. difficile infection (CDI) incidence data correlated significantly with the prevalence of environmental C. difficile on ward B (r = 0·76, P < 0·05) but not on ward A (r = 0·26, P > 0·05). We found that RAPD and RS–PCR typing had similar discriminatory power, although, despite fingerprinting over 200 C. difficile isolates, we identified only six distinct types. Only two distinct C. difficile strains were identified as causing both patient infection and ward contamination. Attempts to determine whether infected patients or contaminated environments are the prime source for cross-infection by C. difficile had limited success, as over 90% of C. difficile isolates were the UK epidemic clone. However, a non-epidemic strain caused a cluster of six cases of CDI, but was only isolated from the environment after the sixth patient became symptomatic. The initial absence of this strain from the environment implies patient-to-patient and/or staff-to-patient spread. In general, routine cleaning with detergent was unsuccessful at removing C. difficile from the environment. Understanding the epidemiology and virulence of prevalent strains is important if CDI is to be successfully controlled.

A total of 122 human and animal Salmonella Typhimurium DT104 isolates and 6 epidemiologically related DT104b isolates from human and animal products were analysed by pulsed-field gel electrophoresis (PFGE). Genomic DNA was subjected to macrorestriction with three enzymes, SpeI, SfiI and XbaI. A total of 14 restriction fragment length polymorphism (RFLP) profiles were identified when the PFGE patterns from the three enzymes were combined. The majority of isolates (81·2%) exhibited the same RFLP profile. Six animal DT104 isolates, susceptible to enrofloxacin and resistant to naladixic acid, were identified from the antibiotic susceptibility test. Four of these isolates had a different PFGE profile from the common RFLP. In addition, 4 of the 6 isolates were geographically clustered in one region. It was concluded that there was one predominant strain of S. Typhimurium DT104 in Ireland and that the potential and selection pressures for emergence of fluoroquinolone-resistant isolates were present.

Imprecise values arise when bacterial colonies are too numerous to be counted or when no colonies grow at a specific dilution. Our objective was to show the usefulness of multiple imputation in analysing data containing imprecise values. We also indicate that interval censored regression, which is faster computationally in situations where it applies, can be used, providing similar estimates to imputation. We used bacteriological data from a large epidemiological study in daycare centres to illustrate this method and compared it to a standard method which uses single exact values for the imprecise data. The data consisted of numbers of FC on children's and educators' hands, from sandboxes and from playareas. In general, we found that multiple imputation and interval censored regression provided more conservative intervals than the standard method. The discrepancy in the results highlights both the importance of using a method that best captures the uncertainty in the data and how different conclusions might be drawn. This can be crucial for both researchers and those who are involved in formulating and regulating standards for bacteriological contamination.

Resident and transient Escherichia coli strains from the colonic microflora of 13 Swedish schoolgirls were analysed for carriage of genes encoding a range of adhesins (P, type 1 and S fimbriae, Dr haemagglutinin and three varieties of the P fimbrial papG adhesin) and other virulence traits (K1 and K5 capsule, haemolysin and aerobactin) using multiplex PCR. Forty-four percent of the resident clones carried genes for P fimbriae, K1 or K5 capsule, and aerobactin, compared with only 3% of transient clones (P<0·0001). The P-fimbriated clones most often had the class II variety of the P-fimbrial adhesin gene papG and this adhesin was significantly associated with persistence of a strain. S fimbriae and type 1 fimbriae were equally common in resident and transient strains. The results indicate that not only P fimbriae, but also, certain capsules and the ability to produce the siderophore aerobactin might contribute to persistence of E. coli in the large intestine.

A prevalence survey of nasal methicillin-resistant Staphylococcus aureus (MRSA) carriage was undertaken on a random sample of adults (aged over 16) resident in the community in Birmingham, UK during 1998. Microbiological samples were taken from the anterior nares at the subjects' general practice or in their home. Information about risk factors for the acquisition of MRSA was obtained via a self-completed questionnaire. A 58% response rate (280/483) was achieved. The prevalence of nasal MRSA colonization was 1.5% [4/274, 95% confidence interval (CI) 0.03–2.9%]. Twenty-three per cent (63/274) of subjects were nasal carriers of S. aureus. Six per cent (4/63) of S. aureus isolates were MRSA and 2 of the 4 MRSA carriers reported previous contact with health facilities. The prevalence of MRSA colonization in the general adult population in Birmingham appears to be low.

The saliva-based H. pylori test, HeliSAL™, is insufficiently accurate for use in the clinical setting. However, its ease of use and non-invasiveness make it attractive for population-based studies of the epidemiology of H. pylori. We validated HeliSAL™, and comment here on its usefulness in prevalence surveys. One hundred and ninety-six patients receiving endoscopy at a clinic in New Zealand provided saliva samples for H. pylori assessment, which were compared to CLOtest (Delta West Pty Ltd, Western Australia) as a gold standard measure. Nineteen percent were truly H. pylori positive, 41 % were positive according to HeliSAL™. Test sensitivity was 74 % and specificity was 67 %. While HeliSAL™ is not well suited for the clinical diagnosis of H. pylori infection, it may be useful for large-scale prevalence surveys because, provided it is validated locally, mathematical adjustment can be made for misclassification. Being inexpensive, non-invasive, and easily stored and handled, HeliSAL™ may be a valuable tool for studies of the epidemiology of H. pylori.

Ninety-three clinical isolates of vancomycin-resistant enterococci (VRE) collected from nine hospitals in Taiwan were examined for the presence of vanA, vanB, vanC1, or vanC2/vanC3 genes by a multiplex PCR. Forty-seven of these VRE isolates were vanA positive, 1 contained both vanC1 and vanA, 40 harboured vanB, 2 were vanC1, and 3 were identified to be vanC2/vanC3. Twenty-four vanA isolates were sensitive to teicoplanin and thus did not have a typical VanA phenotype. Five isolates with the VanC phenotype harboured vanB. None of the 40 clinically isolated vancomycin-susceptible E. faecium or E. faecalis and the vancomycin-resistant Leuconostoc and Pediococcus isolates were positive for any of the van genes. While performing nosocomial surveillance, VRE were isolated from 47 of 467 rectal swabs by culture. Compared with the conventional culture method, the sensitivity and specificity of the multiplex PCR for detecting and identifying vancomycin-resistance genes in enterococci directly from culture-positive broth were 97·9% and 100%, respectively. The results suggest that genotypic characterization of vancomycin-resistance is necessary for all clinical VRE isolates and that the multiplex PCR assay can be an alternative method for this purpose.

The carriage rate of a range of virulence genes was compared between resident and transient Escherichia coli strains obtained from the rectal flora of 22 home-delivered Pakistani infants 0–6 months old. Genes for the following virulence factors were assessed using multiplex PCR: P, type 1 and S fimbriae, three P fimbrial adhesin varieties, Dr haemagglutinin, K1 and K5 capsule, haemolysin and aerobactin. The E. coli strains examined here differed from those previously obtained from hosts in Western Europe in a lower prevalence of genes for P, S and type 1 fimbriae, K1 capsule and haemolysin. Nevertheless, genes for P fimbriae, the class II variety of papG adhesin, and aerobactin were significantly more common among resident than transient strains, as previously observed in a Swedish study. The results suggest that P fimbriae and aerobactin, previously implicated as virulence factors for urinary tract infection, might contribute to persistence of E. coli in the normal intestinal microflora.

The emergence of type 6B Streptococcus pneumoniae resistant to five antibiotics (penicillin, chloramphenicol, trimethoprim–sulphamethoxazole, erythromycin and tetracycline) in both the Northern Territory and Queensland prompted an investigation of the genetic relatedness and patterns of migration of the isolates. Pulsed field gel electrophoresis of genomic DNA of 74 multiple drug-resistant (MDR) isolates cultured in both regions between August 1988 and June 1997 showed that 100% of MDR isolates from the Northern Territory and 96% of MDR strains from Queensland were genetically indistinguishable or closely related to the index strain. None of a further 65 type 6B isolates that were resistant to one or two, or susceptible to all of the above antibiotics, were clonally related to the MDR pneumococci. The geographical distribution of the MDR type 6B clone increased over time. The index strain, first isolated in Darwin in August 1988, was identified in Brisbane, 2900km distant, less than 4 years later and subsequently in other Queensland centres. Surveillance programmes are important to monitor the emergence and spread of potentially invasive MDR pneumococcal clones in countries that are well serviced by air and road transport.

Aminoglycoside modifying enzymes (AMEs) are major factors which confer aminoglycoside resistance on bacteria. Distribution of genes encoding seven AMEs was investigated by multiplex PCR for 279 recent clinical isolates of enterococci derived from a university hospital in Japan. The aac(6′)-aph(2″), which is related to high level gentamicin resistance, was detected at higher frequency in Enterococcus faecalis (42·5 %) than in Enterococcus faecium (4·3 %). Almost half of E. faecalis and E. faecium isolates possessed ant(6)-Ia and aph(3′)-IIIa. The profile of AME gene(s) detected most frequently in individual strains of E. faecalis was aac(6′)-aph(2″)+ant(6)-Ia+aph(3′)-IIIa, and isolates with this profile showed high level resistance to both gentamicin and streptomycin. In contrast, AME gene profiles of aac(6′)-Ii+ant(6)-Ia+aph(3′)-IIIa, followed by aac(6′)-Ii alone, were predominant in E. faecium. Only one AME gene profile of ant(6)-Ia+aph(3′)-IIIa was found in Enterococcus avium. The ant(4′)-Ia and ant(9)-Ia, which have been known to be distributed mostly among Staphylococcus aureus strains, were detected in a few enterococcal strains. An AME gene aph(2″)-Ic was not detected in any isolates of the three enterococcal species. These findings indicated a variety of distribution profiles of AME genes among enterococci in our study site.

Acute poststreptococcal glomerulonephritis (APSGN) is an inflammatory kidney condition that can complicate Group A streptococcal infections. Two clusters of APSGN occurred recently in New South Wales (NSW), Australia; one in a rural town in December 1999 and the other in a Sydney suburb in January 2000. We interviewed carers of the affected children but found no common exposures except three of the Sydney cases were cousins in frequent contact. To assess the probability of these clusters occurring, we analysed hospital admissions for acute glomerulonephritis, as a proxy for APSGN in younger patients. The incidence of acute glomerulonephritis in NSW during 1989/90–1997/8 in residents aged under 20 years was 2·2/100000/year (95% CI 2·0–2·5). Incidence was highest in children aged 5–9 years, boys and Aboriginal children. We found no evidence for other clusters during that period. The recent clusters highlight the continued potential for unexpected future outbreaks of APSGN.

A survey of the seroprevalence of pertussis antibodies in a representative sample of the population from Catalonia was carried out. Ninety-seven municipalities and 30 schools were randomly selected to recruit the 2126 subjects who participated in the study. A serum sample was obtained from all individuals participating in the study in order to determine levels of pertussis toxin (PT) and filamentous hemagglutinin (FHA) antibodies by ELISA test. Sociodemographic data were collected for all subjects. The prevalence of PT antibodies was 75 % and that of FHA antibodies 89 %. Significant increments were observed with age, both in the prevalence of PT (P < 0·0001) and of FHA (P = 0·018). Of the sociodemographic variables studied, only urban habitat was significantly associated to PT antibodies. The agreement observed among the two types of antibodies studied was weak (κ = 0·264). Routine revaccination with the acellular vaccine in children over 7 years of age, in adolescents and adults seems a reasonable strategy to prevent the appearance of cases of pertussis in the community.

The Northern Territory of Australia has had historically very high incidence rates of invasive Haemophilus influenzae type b disease in children less than 5 years of age, with the burden of disease greatest among Aboriginal infants less than 12 months. This study documents the impact of conjugate Hib vaccines introduced in 1993. Immunization rates were monitored using an existing immunization register, and case finding was done retrospectively using hospital and laboratory records. Following the vaccine introduction, the incidence fell abruptly to a seventh of its pre-vaccination level, in both Aboriginal and non-Aboriginal children. The effectiveness of PRP-OMPC (PedvaxHIBTM) was 97·5% and the overall effectiveness of the vaccination programme was 86·3%. The study shows Hib immunization as an effective intervention while discussing continuing needs for Hib control in high risk populations. It also illustrates the benefit of immunization registers in the evaluation of immunization programmes and assessment of vaccine effectiveness.

Several epidemics of gonococcal conjunctivitis have occurred in Aboriginal populations in Central Australia. In 1997, the first outbreak in the Kimberley region of Western Australia occurred, spreading to Central Australia with a total of 447 cases. A genotyping method was applied directly to DNA extracted from patient samples to characterize the gonococcus causing the epidemic and to compare it with contemporaneous genital isolates. Those positive conjunctival specimens from Kimberley and Central Australia that could be genotyped were all indistinguishable, but were distinct from the genital gonococci, even when they shared the same auxotype and serotype. This suggested that the outbreak was due to a single genotype of Neisseria gonorrhoeae that had probably been carried between communities by infected individuals. We did not find evidence to support the existence of a genital reservoir of the types causing epidemic gonococcal conjunctivitis.

More than 36000 individuals living in rural Malawi were skin tested with antigens derived from 12 different species of environmental mycobacteria. Most were simultaneously tested with RT23 tuberculin, and all were followed up for both tuberculosis and leprosy incidence. Skin test results indicated widespread sensitivity to the environmental antigens, in particular to Mycobacterium scrofulaceum, M. intracellulare and one strain of M. fortuitum. Individuals with evidence of exposure to ‘fast growers’ (i.e. with induration to antigens from fast growers which exceeded their sensitivity to tuberculin), but not those exposed to ‘slow growers’, were at reduced risk of contracting both tuberculosis and leprosy, compared to individuals whose indurations to the environmental antigen were less than that to tuberculin. This evidence for cross protection from natural exposure to certain environmental mycobacteria may explain geographic distributions of mycobacterial disease and has important implications for the mechanisms and measurement of protection by mycobacterial vaccines.

A retrospective ecological study was undertaken to identify social and environmental factors associated with increased incidence of meningococcal disease in university halls of residence. A standardized questionnaire was sent to UK universities and colleges of higher education outside London, for distribution to halls containing at least 50 students. Incidence rate ratios of invasive meningococcal disease were obtained for a range of social and environmental variables. Multi-variable Poisson regression analysis identified 3 factors as having a strong association: a high proportion of first year undergraduate residents (P = 0·0008), decreasing smokiness of the hall bar (P < 0·0001), and opening of hall bar before 1990 (P = 0·0001). The inverse relationship between disease incidence and smokiness of bars was an unexpected finding, and may be due to confounding factors. Universities should continue to promote awareness of meningococcal disease, encourage vaccination of first year students against serogroup C disease, and where appropriate, take measures to reduce overcrowding.