The minimum inhibitory concentration (MIC) of five antibiotics and the presence of resistance genes was determined in 163 Haemophilus influenzae isolates collected over 13 years (1987–2000) in four two-yearly sampling periods from patients with respiratory tract infections. The prevalence of β-lactamase-negative ampicillin-susceptible strains was approximately 80% over the sampling period although fewer strains (65·9%) were recovered in the period 1995–1997. TEM-1 type β-lactamase-producing strains were less frequent starting at 15·6% and declining to 2·2% in the final sampling period. Low-β-lactamase-negative ampicillin-resistant (BLNAR) strains were uncommon in 1987–1989 (2·2%), peaked to 19·5% in 1995–1997, but fell back to 11·1% by 2000. Fully BLNAR strains were not detected until the last sampling period (6·7%). The MICs of ampicillin, levofloxacin, cefditoren and ceftriaxone remained stable but there was an eight-fold increase in the MIC of cefdinir over the sampling period. Pulsed-field gel electrophoresis of DNA digests showed that three representative BLNAR strains were genetically distinct and 11 DNA profiles were identified among 17 low-BLNAR strains. These data suggest that the number of genetically altered BLNAR and low-BLNAR strains are increasing in Japan.

A family outbreak of Escherichia coli O157 infection was microbiologically associated with consumption of dry-fermented salami made with pork meat only and produced in a local plant. E. coli O157 strains isolated from a wife and husband, both hospitalized with bloody diarrhoea, and from the salami carried vt1, vt2 and eae genes and shared the same PFGE pattern. The food vehicle implicated in this outbreak is unusual because of both the animal species from which it originates and the fermentation and drying steps of the manufacturing process. This could be the first report of an outbreak associated with a product containing pork meat only. Even though sources of contamination other than pork meat could not be excluded, pork products should not be neglected in E. coli O157 outbreak investigations.

We examined the association between socioeconomic status and the level of serum antibodies to selected faeco-orally transmitted pathogens among Israeli adolescents. Random samples of eighty volunteers aged 12–15 years from high (HSL), medium (MSL) and low (LSL) standard of living towns were included in the study. Serum samples were examined by radioimmunoassay for HAV and by in-house-developed ELISA systems for IgA and IgG antibody levels against Shigella sonnei, S. flexneri, E. coli O157[ratio ]H7 lipopolysacchride and Cryptosporidium parvum antigens. Seropositivity to HAV was highest (98·8%) in the LSL towns and lowest (25%) in the HSL towns, showing a statistically significant linear trend. Antibody levels to the other enteropathogens had gender variation, with higher titres in females. Significantly lower titres in the HSL towns were found for: IgA anti-S. sonnei in females (P<0·001); IgG anti-S. sonnei in females (P=0·024) and males (P=0·033); IgG anti-S. flexneri in females (P=0·016). Inverse linear association with socioeconomic status was found for IgA anti-C. parvum in females (P<0·001); IgA anti-E. coli O157[ratio ]H7 in females (P<0·001) and males (P=0·024). A statistically significant association between HAV seropositivity and higher titres of IgA anti-S. sonnei and E. coli O157[ratio ]H7 was shown. In conclusion, exposure to enteropathogens transmitted via the faecal–oral route in communities of lower socioeconomic status is reflected in a higher prevalence of lifelong lasting antibodies to HAV, and higher levels of antibodies to bacterial and protozoan enteropathogens. Among females, the levels of specific serum antibodies are higher and more strongly associated with low socioeconomic status.

For jurisdictions implementing measles elimination strategies, a minimum surveillance benchmark of 1/100 000 population per year measles-like illness (MLI) cases initially notified, but then rejected based on laboratory testing was proposed. We used this standard to assess the quality of the Victorian enhanced measles surveillance between 1998 and 2003. Victorian enhanced measles surveillance includes interviews with notified cases and confirmatory laboratory testing for notifications. We found 72% (918/1281) of measles notifications were discarded after testing. The median annual rate of discard was 2·9/100 000. The annual discard rate was inversely associated with the age of the notifications, and measles negative with no other diagnosis made was the most common laboratory outcome. The annual rates of discarded notifications in Victoria were consistently above the minimum recommended standard. The rate of discarded MLIs as a surveillance threshold should be useful in measles endemic regions, but may require modification where disease elimination has occurred.

To monitor risk factors for illness, we conducted a case-control study of sporadic Shiga toxin-producing Escherichia coli O157 (STEC O157) infections in 1999–2000. Laboratory-confirmed cases of STEC O157 infection were identified through active laboratory surveillance in all or part of seven states. Patients and age-matched controls were interviewed by telephone using a standard questionnaire. Information was collected on demographics, clinical illness, and exposures to food, water, and animals in the 7 days before the patient's illness onset. During the 12-month study, 283 patients and 534 controls were enrolled. STEC O157 infection was associated with eating pink hamburgers, drinking untreated surface water, and contact with cattle. Eating produce was inversely associated with infection. Direct or indirect contact with cattle waste continues to be a leading identified source of sporadic STEC O157 infections.

In99, a possible ancestor of In100, is a class 1 integron associated with carbenicillinase (blaPSE) and aminoglycoside resistance genes [aac(6′)-Ib and aadA2]. In99 was present in 8 of 81 clinical isolates of Pseudomonas aeruginosa from unrelated patients collected in different years. The strains fell into two clonal groups and exhibited resistance to β-lactams and aminoglycosides.

Cases of ornithosis amongst workers on a rural duck abattoir and farm were notified from late 2003 to health authorities in Victoria, Australia. In May 2004 we conducted a serological survey to identify the extent of exposure to Chlamydophila psittaci amongst workers and a case control study to identify high-risk work areas for ornithosis-related pneumonia. Some workers in all occupational groups showed serological evidence of exposure, while those with pneumonia were more likely to have worked in the slaughtering area of the abattoir (adjusted odds ratio 16·7, 95% confidence interval 1·3–207). High exposure to blood and feathers from recently killed birds is likely to represent an occupational hazard to workers, but pneumonia did occur in workers without these exposures. We recommended respiratory protection for all abattoir workers and improvements to airflow and reduction of environmental contamination in high-risk work areas to prevent further cases.

Specimens of human faeces were tested by a rapid strategy for detection of Campylobacter jejuni lineages by the presence of specific single nucleotide polymorphisms (SNPs) based on the C. jejuni multi locus sequence typing (MLST) scheme. This strategy was derived from analysis of the MLST databases to identify clonal complex specific SNPs followed by the design of real-time PCR assays to enable identification of six major C. jejuni clonal complexes associated with cases of human infection. The objective was to use the MLST SNP-based assays for the direct detection of C. jejuni by clonal complex from specimens of human faeces, and then confirm the accuracy of the clonal complex designation from the SNP-based assays by performing MLST on the cultured faecal material, this targeted at determining the validity of direct molecular specimen identification. Results showed it was possible to identify 38% of the isolates to one of the six major MLST clonal complexes using a rapid DNA extraction method directly from faeces in under 3 h. This method provides a novel strategy for the use of real-time PCR for detection and characterization beyond species level, supplying real-time epidemiological data, which is comparable with MLST results.

Meningococci are regarded as being unlikely to survive outside of their human host although this has possibly been more assumed than demonstrated. Seven strains of meningococci were tested for their ability to survive on glass or plastic while retaining expression of their capsule and important outer membrane proteins. A known number of colony-forming units of each strain were dried onto glass and onto plastic and tested for viability over time. Survival on glass was significantly better than on plastic (P<0·0001). Isolates of the New Zealand epidemic strain, B:4:P1.7-2,4 survived better on glass than all other strains tested. Recovered isolates still expressed their capsules and outer membrane proteins. These findings raise the question of whether meningococci can be transferred from person to person via fomites contaminated with oropharyngeal secretions containing meningococci.

This study investigated 21 foodborne type-E botulism outbreaks, without antitoxin administration, from 1951 to 1965 in Hokkaido, Japan, to characterize the descriptive epidemiology and evaluate the relationship between case fatality and incubation period. The median (25–75% quartile) attack rate and case fatality, which were evaluated by outbreak, were 58·3% (38·0–73·2) and 25·7% (0·1–50·0) respectively. Individual records of 64 diagnoses, including 31 deaths, were also examined using logistic regression analysis, revealing that a shorter incubation period is likely to result in a significantly higher risk of death (P=0·01). The observed case fatality was more than 50% for those who developed symptoms within the first 18 h after exposure, possibly reflecting underlying dose-dependent mechanisms. In the event of intentional contamination of food with botulinum toxin, rapidly determining the incubation periods may be critical for guiding public health response efforts.

Fasciolosis, caused by trematodes of the genus Fasciola, is an emerging disease of humans. One of the highest levels of human fasciolosis hepatica is found amongst the indigenous Aymaran people of the Northern Bolivian Altiplano. A meta-analysis of epidemiological surveys from 38 communities in the region demonstrates that fasciolosis has been endemic in the region since at least 1984 and is a zoonosis of rural communities. Human and bovine fasciolosis is associated with the communities lying in the plain from Lake Titicaca to La Paz, predominantly in the Los Andes province. In Los Andes incidences of up to 67% of population cohorts were found, and prevalence is age-related with the highest infection rate in children aged 8–11 years.

Antibiotic resistance data, made available from laboratory records during eight cholera outbreaks between 1990 and 2004 showed Vibrio cholerae serogroup O1 to have a low level of resistance (2–3%) to tetracycline during 1990–1991. Resistance increased for tetracycline (95%), chloramphenicol (78%), doxycycline (70%) and trimethoprim–sulphamethoxazole (97%) in subsequent outbreaks. A significant drop in resistance to tetracycline and chloramphenicol followed the adoption of a national policy to replace tetracycline with erythromycin for treating cholera. Sixty-nine strains from cholera outbreaks in Zambia between 1996 and 2004, were examined for antibiotic resistance and basic molecular traits. A 140 MDa conjugative, multidrug-resistant plasmid was found to encode tetracycline resistance in strains from 1996/1997 whereas strains from 2003/2004 were resistant to furazolidone, but susceptible to tetracycline, and lacked this plasmid. PCR revealed 25 of 27 strains from 1996/1997 harboured the intl1 class 1 integron but lacked SXT, a conjugative transposon element. Similar screening of 42 strains from 2003/2004 revealed all carried SXT but not the intl1 class 1 integron. All 69 strains, except two, one lacking ctxA and the other rstR and thus presumably truncated in the CTX prophage region, were positive for important epidemic markers namely rfbO1, ctxA, rstR2, and tcpA of El Tor biotype. Effective cholera management is dependent on updated reports on culture and sensitivity to inform the choice of antibiotic. Since the emergence of antibiotic resistance may significantly influence strategies for controlling cholera, continuous monitoring of epidemic strains is crucial.

Norway rats (Rattus norvegicus) carry several zoonotic pathogens and because rats and humans live in close proximity in urban environments, there exists potential for transmission. To identify zoonotic agents carried by rats in Baltimore, Maryland, USA, we live-trapped 201 rats during 2005–2006 and screened them for a panel of viruses, bacteria, and parasites. Antibodies against Seoul virus (57·7%), hepatitis E virus (HEV, 73·5%), Leptospira interrogans (65·3%), Bartonella elizabethae (34·1%), and Rickettsia typhi (7·0%) were detected in Norway rats. Endoparasites, including Calodium hepatica (87·9%) and Hymenolepis sp. (34·4%), and ectoparasites (13·9%, primarily Laelaps echidninus) also were present. The risk of human exposure to these pathogens is a significant public health concern. Because these pathogens cause non-specific and often self-limiting symptoms in humans, infection in human populations is probably underdiagnosed.

Enterotoxigenic F4+ Escherichia coli can colonize the intestine of pigs and cause diarrhoea. Our primary goal was to find a discriminant rule to discriminate between F4+ E. coli shedding profiles as this may reflect differences in the infectiousness of pigs. Our secondary goal was to find a discriminant rule to discriminate between diarrhoeic and non-diarrhoeic pigs. Repeated measurements (bacterial shedding and percentage dry matter of faeces) were taken of 74 weaned pigs that were infected experimentally with F4+ E. coli. These measurements were summarized into two new variables by means of a principal components analysis. Discriminant rules were derived based on these summary variables by fitting a mixture of normal distributions. Finally, the association between the classifications (as derived from the discriminant rules) and the occurrence in the pigs of the F4 receptor, an adhesion site for F4+ E. coli, was studied. We found that only the classification based on bacterial shedding allowed us to distinguish two significantly different groups of pigs (high and low shedders). Presence of the F4 receptor was associated strongly with pigs being high shedders.

Health risks in the effluents of seven swine abattoirs and of seven poultry abattoirs were evaluated with regard to environment degradation and to dissemination of pathogenic microorganisms during the rainy and dry seasons. Supply-water samples from affluents and effluents of the treatment systems at different sites within the abattoir processing system were analysed. Similarly, water samples from the three recipient sites (emission point, 100 m upstream, 100 m downstream) were also analysed. Temperature, free residual chlorine (FRC), total coliform bacteria, Escherichia coli, enterococci, identification and serotyping of salmonellae were assessed. Scalding is the most significant stage in the slaughtering chain (P<0·05) when temperature is taken into account. Temperatures at effluents and at the sampled sites in the water bodies accorded to state and federal legislation standards. Supply waters did not meet the standards for FRC and microbial count standards according to the Ministry of Health and within limits imposed by the Industrial and Sanitary Inspection Regulations for Animal Products. Feather plucking and evisceration in poultry slaughter and the cleansing of carcasses and facilities in poultry and swine slaughtering had the highest contamination impact. The three loci at the water bodies were above the microbiological standards for classes II and III sites, in conformity with Law 8468 of the state of São Paulo, Brazil and Conama. Salmonella was found at several sites during slaughter, at both types of abattoirs, including in the effluent treatment system. This showed that these sites were the dissemination sources of the microorganism.

Vaginal complaints compel an evaluation of bacterial vaginosis (BV), however, many cases of BV are asymptomatic. We evaluated the sensitivity and specificity of vaginal symptoms in the diagnosis of BV and examined the utility of creating a BV screening tool using clinical, behavioural and demographic characteristics. A total of 1916 pregnant women were included in this analysis. In total, 757 women screened positive for BV and over one third of BV-positive women presented without any lower genital tract symptoms (39·4%). African American race, abnormal vaginal odour, and smoking were independently related to BV positivity. A BV screening tool including these three factors was fairly predictive of BV status with the area under the ROC curve equal to 0·669. This three-item prediction rule may be useful in identifying high- risk pregnant women in need of BV screening and, given the high specificity, accurately identify the group of BV-negative pregnant women.

Wild boars are important disease reservoirs. It is well known that abundance estimates are needed in wildlife epidemiology, but the expense and effort required to obtain them is prohibitive. We evaluated a simple method based on the frequency of faecal droppings found on transects (FBII), and developed a spatial aggregation index, based on the runs test statistic. Estimates were compared with hunting data, and with porcine circovirus and Aujeszky's disease virus seroprevalences and Mycobacterium tuberculosis complex and Metastrongylus spp. prevalence. The FBII and the aggregation index were correlated with the hunting index, but both of the former estimates correlated better than the latter with the disease prevalences. Hence, at least in habitats with high wild boar densities, the FBII combined with the aggregation index constitutes a cheap and reliable alternative for wild boar abundance estimation that can be used for epidemiological risk assessment, even outside the hunting season and in areas with no available data on hunting activities.

Two variants of Listeria monocytogenes were isolated from blood cultures from each of two patients with listeriosis. Each variant displayed a two-band difference in DNA profile from the other by pulsed-field gel electrophoresis. Although this difference in profile is insufficient to distinguish clearly between the variants, the possibility of co-infection with different strains of L. monocytogenes needs to be considered. We suggest that more than one colony should be selected for molecular typing to aid interpretation during investigation of the sources and routes of Listeria infection.

During a group A streptococcus (GAS) outbreak 21 abattoir workers developed skin infections. The unusual outbreak strain (emm 108.1) was cultured from five workers and four persons in the community with links to the abattoir. The attack rate was 26% in the lamb line. Communal nailbrushes were neither routinely disinfected nor changed, and had high bacterial counts. A cohort study found a higher risk from working in the gutting area and getting cuts on hands more than weekly. Despite high bacterial counts daily nailbrush use had a lower risk, as did always wearing disposable gloves. Working in the gutting area (OR 11·44) and nailbrush use at least once a day (OR 0·04) were significant in the multivariate model. Transmission of infection is likely to have occurred on carcasses. GAS infection among abattoir workers was once common. Simple hygiene measures, such as nailbrush use, may reduce the impact of future outbreaks.

Clostridium difficile (C. diff) is a major nosocomial problem. Epidemiological surveillance of the disease can be accomplished by microbiological or administrative data. Microbiological tracking is problematic since it does not always translate into clinical disease, and it is not always available. Tracking by administrative data is attractive, but ICD-9 code accuracy for C. diff is unknown. By using a large administrative database of hospitalized patients with C. diff (by ICD-9 code or cytotoxic assay), this study found that the sensitivity, specificity, positive, and negative predictive values of ICD-9 coding were 71%, 99%, 87%, and 96% respectively (using micro data as the gold standard). When only using symptomatic patients the sensitivity increased to 82% and when only using symptomatic patients whose test results were available at discharge, the sensitivity increased to 88%. C. diff ICD-9 codes closely approximate true C. diff infection, especially in symptomatic patients whose test results are available at the time of discharge, and can therefore be used as a reasonable alternative to microbiological data for tracking purposes.