The purpose of our retrospective 3-year study was to analyse and compare clinical and epidemiological characteristics in hospitalized patients older than 6 years with community-acquired pneumonia (CAP) caused by Chlamydia pneumoniae (87 patients) and Mycoplasma pneumoniae (147 patients). C. pneumoniae and M. pneumoniae infection was confirmed by serology. C. pneumoniae patients were older (42·12 vs. 24·64 years), and were less likely to have a cough, rhinitis, and hoarseness (P<0·001). C. pneumoniae patients had higher levels of C-reactive protein (CRP), and aspartate aminotransferase (AST) than M. pneumoniae patients (P<0·001). Pleural effusion was recorded more frequently in patients with M. pneumoniae (8·84 vs. 3·37%). There were no characteristic epidemiological and clinical findings that would distinguish CAP caused by M. pneumoniae from C. pneumoniae. However, some factors are indicative for C. pneumoniae such as older age, lack of cough, rhinitis, hoarseness, and higher value of CRP, and AST.

Sepsis continues to have a substantial mortality and morbidity despite advances in the diagnosis and management of this condition. We retrospectively analysed hospital charts of patients diagnosed to have sepsis between January 2002 and June 2003. Demographic characteristics of patients, microbiological findings and predictors of survival were evaluated. Sixty-nine sepsis episodes that occurred in 63 patients were analysed. The most common underlying diseases were hypertension, malignancies and diabetes mellitus. Renal insufficiency, respiratory distress and disseminated intravascular coagulation developed in 52·2, 30·4 and 30·4% of the episodes respectively; 47·7% of the blood cultures yielded an organism. Gram-negative bacteria were the predominant microorganisms (65·9%). Fifty-five patients (87·3%) died. Mechanical ventilation and underlying renal disease were significant determinants of mortality. In conclusion, Gram-negative bacteria remain the major pathogens in sepsis. The mortality remains very high, and a change in the clinical approach to the septic patient should be employed to improve the outcome.

The subtypes of Campylobacter isolates from human infections in two Danish counties were compared to isolates from retail food samples and faecal samples from chickens, pigs and cattle. During a 1-year period, 1285 Campylobacter isolates from these sources were typed by two methods: ‘Penner’ heat-stable serotyping and automated ribotyping (RiboPrinting). C. jejuni was the dominating species, but C. coli was more prevalent among food and chicken isolates (16%) compared to human isolates (4%). In total, 356 different combined sero-ribotypes (subtypes) were found. A large subtype overlap was seen between human isolates and isolates from food (66%), chickens (59%) and cattle (83%). This was verified by PFGE typing of 212 isolates representing selected subtypes. All frequent (n>3) subtypes found in food were also present in humans. Sixty-one per cent of the isolates from domestically acquired infections had subtypes that were also found in food as opposed to 31% of travel-associated infections. The results showed differences in the various Campylobacter populations, e.g. the Danish population as reflected in the domestically acquired infections and the Danish-produced food was more uniform than the isolates originating from outside the country. The study shows that most C. jejuni subtypes found in poultry food samples, broiler chickens, and cattle were represented in the domestically acquired cases, indicating that C. jejuni from these reservoirs are likely sources of human infections in Denmark.

To estimate the frequency of infectious gastroenteritis across Australia, and to identify risk factors, we conducted a national telephone survey of 6087 randomly selected respondents in 2001–2002. The case definition was three or more loose stools and/or two or more vomits in a 24-hour period in the last 4 weeks, with adjustment to exclude non-infectious causes and symptoms secondary to a respiratory infection. Frequency data were weighted to the Australian population. Multivariate logistic regression was used to assess potential risk factors including season, region, demographic and socioeconomic status. Among contacted individuals, 67% responded. The case definition applied to 7% of respondents (450/6087) which extrapolates to 17·2 million (95% CI 14·5–19·9 million) cases of gastroenteritis in Australia in one year, or 0·92 (95% CI 0·77–1·06) cases/person per year. In the multivariate model, the odds of having gastroenteritis were increased in summer and in the warmest state, in young children, females, those with higher socioeconomic status and those without health insurance.

Campylobacter is the most common bacterial cause of gastroenteritis in England and Wales, with 45 000 cases reported annually. Campylobacter incidence is highly seasonal; the consistent peak in late spring suggests a role for meteorological factors in the epidemiology of this organism. We investigated the relationship between ambient temperature and Campylobacter enteritis using time-series analysis to study short-term associations between temperature and number of Campylobacter reports adjusted for longer-term trend and seasonal patterns. We found a linear relationship between mean weekly temperature and reported Campylobacter enteritis, with a 1°C rise corresponding to a 5% increase in the number of reports up to a threshold of 14°C. There was no relationship outside this temperature range. Our findings provide evidence that ambient temperature influences Campylobacter incidence, and suggest that its effect is likely to be indirect, acting through other intermediate pathways.

The prevalence of Neisseria meningitidis carriage is highest in teenagers and lowest in young children. In contrast, invasive meningococcal disease is most common in young children with a smaller secondary peak in teenagers. Data on carriage and disease were analysed to quantify the risks of infection and disease by age and serogroup. The forces of infection for serogroups B, C, other meningococci and Neisseria lactamica were modelled together with the risk of disease given infection for serogroups B and C, using maximum likelihood to fit the models to the available data. The risk of meningococcal disease given infection declines steeply through childhood and is higher for serogroup C than for serogroup B. The secondary peak in disease in teenagers appears to be explained mostly by increased transmission although there is a suggestion that other factors may also contribute. These analyses provide important insights and may be used to guide further data collection and modelling studies.

In order to identify subtyping methods able to contribute to the surveillance or investigation of Australian Campylobacter infection, six genotypic and three phenotypic subtyping methods were evaluated on a collection of 84 clinical isolates collected over a 30-month period from one region in Australia. The aim was to compare the logistics of various subtyping methods and examine their ability to assist in finding outbreaks or common sources of sporadic infection. The genotypic subtyping methods used were sequencing of the short variable region of the flaA gene, two methods using restriction fragment length polymorphism (RFLP) of the flaA gene using either DdeI or EcoRI with PstI, automated ribotyping, pulsed field gel electrophoresis and multilocus sequence typing. The phenotypic methods employed included Laboratory of Enteric Pathogens serotyping, Lior biotyping and antibiotic resistotyping. The level of agreement between subtyping results was determined. Phenotypic methods showed little agreement whereas genotypic typing methods showed a high level of agreement. Using the premise that five of the six genotypic typing methods were in agreement 15 genotypic groupings were identified. Sequencing of the short variable region of the flaA gene, RFLP of the flaA gene or automated ribotyping in conjunction with multilocus sequence typing best identified genotypic groupings. An alternative combination of RFLP of the flaA gene followed by ribotyping was equally satisfactory. RFLP of the flaA gene appeared to be suitable as a preliminary typing method based on ease of operation, equipment availability and cost.

A cluster of 10 cases of tuberculosis disease (one of them extrapulmonary) occurred from July 2001 until November 2003 in a health district in Southern Austria. Eight patients were culture confirmed and shared an identical strain. One of these eight cases was identified as outbreak-related by molecular strain typing only. Due to public pressure, a further 600 persons received chest X-ray and clinical examinations. Apart from one case which could be excluded from the outbreak because of a different strain pattern, no outbreak-related case of active tuberculosis was detected by this non-targeted procedure. Tuberculin skin testing, not part of the Austrian routine protocol of contact investigation in adults, was initiated after diagnosis of case 8. Forty-nine latently infected contacts were detected. Population-based genotyping of all isolates, prioritization of contact investigations and early use of targeted tuberculin skin testing are critical for effective tuberculosis control in low-incidence countries.

Ninety-seven isolates of Shigella flexneri from children seeking medical care from three sites in Egypt were characterized. Overall, 46·4% of children (median age 17 months) were febrile or reported blood in their stools, 25·8% were dehydrated and 16·5% were admitted to hospital. Serotypes 2a (37·1%), 1b (18·6%), 1c (17·5%), and 6 (15·5%) comprised over 88·7% of the total isolates. We observed marked resistance to ampicillin (87·6%), tetracycline (84·5%) and trimethoprim–sulfamethoxazole (63·9%). Pulsed-field electrophoresis grouped the majority of isolates within a serotype together, separately from isolates of an alternative serotype. The set gene was present in all serogroup 2a isolates, however, the sen gene was detected in every isolate. Our results show S. flexneri 1c has emerged as a dominant S. flexneri serotype in Egypt. Development and application of a Shigella vaccine should consider the diversity of Shigella serotypes within a geographical region prior to administration.

Settings of fingerprint-type analysing computer software were optimized for analysis of enterohaemorrhagic Escherichia coli (EHEC) pulsed-field gel electrophoresis (PFGE) patterns. Under the lowest values of parameters, maximum value of similarities calculated using the Dice coefficient were obtained between PFGE patterns from one EHEC strain on the same gel when reference lanes for calibration of distortions during electrophoresis were set to every fourth lane. PFGE patterns of 15 EHEC strains on different gels were investigated. Similarity values calculated using the Pearson product-moment correlation coefficient (Pearson correlation) were significantly higher than those using the Dice coefficient with optimal values of parameters determined by the program (P<0·01). When PFGE patterns of 45 EHEC strains were analysed by the computer program, EHEC strains from one mass outbreak and three intra-family outbreaks were each clustered and the similarity values within the clusters were >90% using Pearson correlation.

We examined the epidemiology of community-acquired bacterial meningitis among adults in England and Wales between 1991 and 2002. Among 3169 cases, meningococcal infection was predominant among young adults and pneumococcal meningitis among older adults. Whilst infection due to most causes decreased, the incidence of tuberculous (TB) meningitis doubled over the 12 years. The mortality rate among meningococcal and pneumococcal infections fell from 0·45/105 to 0·31/105 (P=0·0001). This study demonstrates important changes in the epidemiology of bacterial meningitis among UK adults. Improvements in clinical management, childhood vaccination programmes and the re-emergence of tuberculosis are likely to be drivers of these changes.

Vibrio parahaemolyticus and Vibrio vulnificus were isolated from faecal samples of wild aquatic birds in winter. Although V. parahaemolyticus and V. vulnificus were present in low numbers in seawater in the area where the faecal samples of the birds were collected, the pathogens were isolated from the faeces of the birds. This study demonstrates that wild aquatic birds are a vehicle for V. parahaemolyticus and V. vulnificus to survive in winter.

The relationship of Mycobacterium tuberculosis Beijing genotype with tuberculosis relapse was examined. Beijing strains were detected from 32 out of 45 (71%) relapsed cases and 148 out of 290 (51%) non-relapsed cases. Multivariate logistic regression analysis revealed that Beijing genotype was significantly associated with tuberculosis relapse (OR 2·64, 95% CI 1·30–5·34, P=0·005).

A total of 113 strains of Shigella dysenteriae type 2 isolated from patients attending the Dhaka diarrhoea treatment centre of ICDDR,B: Centre for Health and Population Research during the period 1999–2004 were studied. Serotype of the isolates was confirmed using commercially available antisera. Except for arabinose fermentation, all the strains had similar biochemical reactions. More than 60% of the strains were sensitive to commonly used antibiotics; only 6% (n=7) of the strains were resistant to nalidixic acid, and none of the strains were resistant to mecillinam and ciprofloxacin. All strains were invasive as demonstrated by the presence of a 140 MDa plasmid, ial, sen and ipaH genes, Congo Red absorption ability and by the Sereny test performed on representative strains. Plasmid patterns were heterogeneous but more than 50% of strains were confined to a single pattern. All strains possessed a 1·6 MDa plasmid and 87% of the strains contained a 4 MDa plasmid. Middle-range plasmids (90 MDa to 30 MDa) present in 36% of the strains were not associated with antibiotic resistance. All the strains were clustered within a single type with four subtypes by pulsed-field gel electrophoresis while ribotyping patterns of all the strains were identical.

To clarify whether prevalence or special pathogenicity is more important in determining urinary tract infection (UTI) causation, we compared the biotype, phylogenetic group, and virulence genes of Escherichia coli urine strains from 11 women with acute lower UTI with those of the host's dominant intestinal E. coli strain(s). Twenty-one unique E. coli clones were identified. For three women, the single faecal clone identified was also the host's urine clone, whereas for eight women faecal samples yielded 1 or 2 distinct non-urine clones (total, n=10), either with (n=3) or without (n=5) the concurrent urine clone. The eight urine clones from the latter eight women exhibited significantly greater inferred virulence, according to virulence gene content and phylogenetic background, than did the hosts' 10 corresponding ‘faecal only’ clones. In contrast, the three urine clones that were detected as the host's sole faecal clone exhibited significantly lower inferred virulence than the other eight urine clones, and were statistically indistinguishable from the 10 ‘faecal only’ clones. In conclusion, special pathogenicity is an important determinant of UTI pathogenesis in women, although prevalence may occasionally allow less virulent strains to cause UTI.

In this study comprising isolates from 2001 to 2003, resistance was considerably more widespread among Campylobacter jejuni from humans infected abroad than infected within Norway. The discrepancy was particularly notable for fluoroquinolone resistance (67·4% vs. 6·5%). This is probably a reflection of a low resistance prevalence in Norwegian broiler isolates (1·2% fluoroquinolone resistant).

Paediatric cases of epiglottitis declined markedly in England following the introduction of safe effective immunization against Haemophilus influenzae type b (Hib). With the recently described resurgence in Hib infections, a corresponding rise in the number of presentations of clinical epiglottitis in children was observed, although numbers were still well below those reported prior to vaccine availability. This was seen both in microbiology reports and hospital admissions data for England. In keeping with the more diverse aetiology of epiglottitis in adults, Hib vaccination had minimal impact on hospital presentations with upper airway infections in those aged 15 years and over, which showed an overall increasing trend over 10 years. The need for a high index of suspicion to allow early diagnosis of this life-threatening clinical presentation is reinforced.

The prevalence of Escherichia coli O157 displays striking variability across the Scottish cattle population. On 78% of farms, in a cross-sectional survey of 952, no shedding of E. coli O157 was detected, but on a small proportion, ∼2%, very high prevalences of infection were found (with 90–100% of pats sampled being positive). We ask whether this variation arises from the inherent stochasticity in transmission dynamics or whether it is a signature of underlying heterogeneities in the cattle population. A novel approach is taken whereby the cross-sectional data are viewed as providing independent snapshots of a dynamic process. Using maximum-likelihood methods to fit time-dependent epidemiological models to the data we obtain estimates for the rates of immigration and transmission of E. coli O157 infection – parameters which have not been previously quantified in the literature. A comparison of alternative model fits reveals that the variation in the prevalence data is best explained when a proportion of the cattle are assumed to transmit infection at much higher levels than the rest – the so-called super-shedders. Analysis of a second dataset, comprising samples taken from 32 farms at monthly intervals over a period of 1 year, additionally yields an estimate for the rate of recovery from infection. The pattern of prevalence displayed in the second dataset also strongly supports the super-shedder hypothesis.

Outbreaks of enteric disease associated with exposure to live animals on exhibit have occurred with increasing frequency in recent years. Possibly the most important pathogen causing such outbreaks is Escherichia coli O157:H7, because of the serious illness it can cause. Hand hygiene is consistently protective against disease among persons exposed to animals implicated in these outbreaks. Livestock barns have limited hand-washing facilities, therefore a waterless hand-sanitizing gel would be a potentially preventive measure readily available to visitors and animal exhibitors. This study compared the reduction of bacterial counts on hands of animal exhibitors when soap and water was used or when an ethanol-based hand gel was used after animal handling. Participants were youth and adults involved with showing livestock. The sanitation methods were similar in reducing the total bacteria and coliform counts on the hands of the participants (Wilcoxon rank sum test P values 0·12 and 0·69 respectively).

Salmonella Mississippi infections are very common in Australia's island state – Tasmania – with an annual rate of 17 cases/100000 population. A case-control study conducted during 2001–2002 found single variable associations with indirect exposure to many native animal species, untreated drinking water, travelling within the state, hand–mouth behaviours and contact with pet faeces. No associations were detected with farm animal or pet species or with any food. Indirect contact with native birds, untreated drinking water and travel within the state remained significant predictors of infection in the final model with population attributable fractions of 0·57 and 0·54 for native animals and untreated drinking water respectively. In Tasmania, Australian wildlife species are the likely reservoir for S. Mississippi, contaminating land and water environments. To decrease infection rates requires treatment of water supplies, particularly private rainwater collection systems and advising people to wash their hands after being outdoors and prior to eating.