Global coverage of infant Haemophilus influenzae type b (Hib) vaccination has increased considerably during the past decade, partly due to GAVI Alliance donations of the vaccine to low-income countries. In settings where large numbers of children receive only one or two vaccine doses rather than the recommended three doses, dose-specific efficacy estimates are needed to predict impact. The objective of this meta-analysis is to determine Hib vaccine efficacy against different clinical outcomes after receiving one, two or three doses of vaccine. Studies were eligible for inclusion if a prospective, controlled design had been used to evaluate commercially available Hib conjugate vaccines. Eight studies were included. Pooled vaccine efficacies against invasive Hib disease after one, two or three doses of vaccine were 59%, 92% and 93%, respectively. The meta-analysis provides robust estimates for use in decision-analytical models designed to predict the impact of Hib vaccine.

Throughout the African meningitis belt, meningococcal meningitis outbreaks occur only during the dry season. Measles in Niger exhibits similar seasonality, where increased population density during the dry season probably escalates measles transmission. Because meningococcal meningitis and measles are both directly transmitted, we propose that host aggregation also impacts the transmission of meningococcal meningitis. Although climate affects broad meningococcal meningitis seasonality, we focus on the less examined role of human density at a finer spatial scale. By analysing spatial patterns of suspected cases of meningococcal meningitis, we show fewer absences of suspected cases in districts along primary roads, similar to measles fadeouts in the same Nigerien metapopulation. We further show that, following periods during no suspected cases, districts with high reappearance rates of meningococcal meningitis also have high measles reintroduction rates. Despite many biological and epidemiological differences, similar seasonal and spatial patterns emerge from the dynamics of both diseases. This analysis enhances our understanding of spatial patterns and disease transmission and suggests hotspots for infection and potential target areas for meningococcal meningitis surveillance and intervention.

Environmental staphylococcal contamination was investigated by culture of 400 automated teller machines (ATMs). Isolates were characterized for antibiotic and antiseptic susceptibility, carriage of antiseptic resistance genes (QAC genes), and spa types. MRSA, which was similar to local clinical isolates, was present on two (0·5%) of the 62 (15·5%) ATMs that yielded Staphylococcus aureus. QAC genes were more common in coagulase-negative staphylococci (qacA/B 26·0%, smr 14%) than S. aureus (11·3% qacA/B, 1·6% smr). QAC-positive isolates had significantly higher minimum inhibitory concentrations/minimum bactericidal concentrations to benzalkonium chloride and chlorhexidine digluconate. QAC gene presence was significantly associated with methicillin and tetracycline resistance. Survival of staphylococci, including MRSA, on common access sites may be facilitated by low disinfectant concentrations, which select for disinfectant-tolerant strains, while co-selecting for antibiotic-resistance determinants. Disinfection procedures should be performed correctly to help prevent spread of resistant pathogens from reservoirs in the community.

Methicillin-resistant Staphylococcus aureus (MRSA) commonly causes infection in hospitalized patients. Resistance is due to the acquisition of mecA gene located on the chromosomal element SCCmec and to date 12 types have been identified. Specific epidemic clones of MRSA have emerged with enhanced ability to spread within and among hospitals and to cross national boundaries. We studied 30 isolates from patients with MRSA infections at two hospitals in Porto Alegre city from April to December, 2008 and determined their SCCmec type by PCR. Representative strains were typed by PFGE. Eighteen (60%) isolates carried SCCmec type III and had PFGE profiles clonally related to the previously characterized Brazilian epidemic clone, and 11 (36·7%) isolates with pulsotypes closely related to the Cordobes/Chilean clone harboured SCCmec type I. To the best of our knowledge, this is the first report of the appearance of Cordobes/Chilean clone involved in nosocomial infection in Brazil.

In sub-Saharan Africa, many nomadic pastoralists have begun to settle in permanent communities as a result of long-term water, food, and civil insecurity. Little is known about the epidemiology of cholera in these emerging semi-nomadic populations. We report the results of a case-control study conducted during a cholera outbreak among semi-nomadic pastoralists in the Karamoja sub-region of northeastern Uganda in 2010. Data from 99 cases and 99 controls were analysed. In multivariate analyses, risk factors identified were: residing in the same household as another cholera case [adjusted odds ratio (aOR) 6·67, 95% confidence interval (CI) 2·83–15·70], eating roadside food (aOR 2·91, 95% CI 1·24–6·81), not disposing of children's faeces in a latrine (aOR 15·76, 95% CI 1·54–161·25), not treating drinking water with chlorine (aOR 3·86, 95% CI 1·63–9·14), female gender (aOR 2·43, 95% CI 1·09–5·43), and childhood age (10–17 years) (aOR 7·14, 95% CI 1·97–25·83). This is the first epidemiological study of cholera reported from a setting of semi-nomadic pastoralism in sub-Saharan Africa. Public health interventions among semi-nomadic pastoralists should include a two-faceted approach to cholera prevention: intensive health education programmes to address behaviours inherited from insecure nomadic lifestyles, as well as improvements in water and sanitation infrastructure. The utilization of community-based village health teams provides an important method of implementing such activities.

A total of 111 clinical and environmental O1, O139 and non-O1/O139 Vibrio cholerae strains isolated between 1978 and 2008 from different geographical areas were typed using a combination of methods: antibiotic susceptibility, biochemical test, serogroup, serotype, biotype, sequences containing variable numbers of tandem repeats (VNTRs) and virulence genes ctxA and tcpA amplification. As a result of the performed typing work, the strains were organized into four clusters: cluster A1 included clinical O1 Ogawa and O139 serogroup strains (ctxA+ and tcpA+); cluster A2 included clinical non-O1/O139 strains (ctxA− and tcpA−), as well as environmental O1 Inaba and non-O1/O139 strains (ctxA− and tcpA−/tcpA+); cluster B1 contained two clinical O1 strains and environmental non-O1/O139 strains (ctxA− and tcpA+/tcpA−); cluster B2 contained clinical O1 Inaba and Ogawa strains (ctxA+ and tcpA+). The results of this work illustrate the advantage of combining several typing methods to discriminate between clinical and environmental V. cholerae strains.

In the summer of 2009, an outbreak of verocytotoxigenic Escherichia coli O157 (VTEC O157) was identified in visitors to a large petting farm in South East England. The peak attack rate was 6/1000 visitors, and highest in those aged <2 years (16/1000). We conducted a case-control study with associated microbiological investigations, on human, animal and environmental samples. We identified 93 cases; 65 primary, 13 secondary and 15 asymptomatic. Cases were more likely to have visited a specific barn, stayed for prolonged periods and be infrequent farm visitors. The causative organism was identified as VTEC O157 PT21/28 with the same VNTR profile as that isolated in faecal specimens from farm animals and the physical environment, mostly in the same barn. Contact with farm livestock, especially ruminants, should be urgently reviewed at the earliest suspicion of a farm-related VTEC O157 outbreak and appropriate risk management procedures implemented without delay.

E. coli O157 can be transmitted to humans by three primary (foodborne, environmental, waterborne) and one secondary (person-to-person transmission) pathways. A regression model and quantitative microbiological risk assessments (QMRAs) were applied to determine the relative importance of the primary transmission pathways in NE Scotland. Both approaches indicated that waterborne infection was the least important but it was unclear whether food or the environment was the main source of infection. The QMRAs over-predicted the number of cases by a factor of 30 and this could be because all E. coli O157 strains may not be equally infective and/or the level of infectivity in the dose–response model was too high. The efficacy of potential risk mitigation strategies to reduce human exposure to E. coli O157 using QMRAs was simulated. Risk mitigation strategies focusing on food and environment are likely to have the biggest impact on infection figures.

We determined characteristics of Escherichia coli O157:H7 pulsed-field gel electrophoresis clusters that predict their being solved (i.e. that result in identification of a confirmed outbreak). Clusters were investigated by the Minnesota Department of Health (MDH) using a dynamic iterative model. During 2000–2008, 19 (23%) of 84 clusters were solved. Clusters of ⩾3 isolates were more likely to be solved than clusters of two isolates. Clusters in which the first two case isolates were received at MDH on the same day were more likely to be solved than were clusters in which the first two case isolates were received over ⩾8 days. Investigation of clusters of ⩾3 E. coli O157:H7 cases increased the success of cluster investigations.

In order to characterize the association between county-level risk factors and the incidence of Cryptosporidium in the 2007 Iowa outbreak, we used generalized linear mixed models with the number of Cryptosporidium cases per county as the dependent variable. We employed a spatial power covariance structure, which assumed that the correlation between the numbers of cases in any two counties decreases as the distance between them increases. County population size was included in the model to adjust for population differences. Independent variables included the number of pools in specific pool categories (large, small, spa, wading, waterslide) and pool-owner classes (apartment, camp, country club or health club, hotel, municipal, school, other) as well as the proportion of residents aged <5 years. We found that increases in the number of bigger pools, pools with more heterogeneous mixing (municipal pools vs. country club or apartment pools), and pools catering to young children (wading pools) are associated with more cases at the county level.

The aim of the present study was to assess the recent trends in the epidemiology of non-typhoid Salmonella in Israel using a sentinel laboratory-based surveillance network. Between 1999 and 2009, 8758 Salmonella stool isolates were reported by five sentinel laboratories. There was a significant decrease in the incidence rate of Salmonella isolates from 70·5/100 000 in 1999 to 21·6/100 000 in 2005 followed by a slight increase to 30·3/100 000 in 2009. Of all Salmonella, 64·3% were isolated from children in the 0–4 years age group. Up to 2008, S. Enteritidis was the most prevalent serotype and in 2009 S. Infantis emerged as the most common Salmonella serotype. The decrease in the incidence of S. Enteritidis and S. Typhimurium and increase in S. Infantis among humans were associated with a similar trend among breeding flocks, which followed significant preventive interventions conducted against S. Enteritidis and S. Typhimurium infections in poultry. Tight surveillance and education of food handlers and consumers should be enhanced to reduce the foodborne transmission of Salmonella in Israel.

This study aimed to investigate the relationship between hepatitis B virus (HBV) covalently closed circular DNA (cccDNA) in the ovary and vertical transmission of HBV. HBV DNA and HBV cccDNA were assayed in the ovaries of 33 pregnant women who were positive for HBV DNA. The HBVM (HBV markers, including HBsAg, HBsAb, HBeAg, HBeAb, HBcAb) level and the HBV DNA content in peripheral blood of infants were measured. The overall positive rate of HBV DNA and HBV cccDNA in samples was 51·52% (17/33). The intrauterine infection rate of the infants was 12·12% (4/33). When HBV DNA and HBV cccDNA were both positive, the intrauterine infection rate of infants was significantly higher than when they were both negative (P<0·05). Levels of HBV cccDNA and the rate of positive samples were significantly higher in mothers with infants with intrauterine infection than in those without (P<0·01 and P<0·05, respectively). HBV can infect the human ovary and may transmit to the filial generation via the ovum.

Information on the burden of hepatitis C virus (HCV) disease is needed to inform policy decisions on primary and secondary prevention. Specimen-based laboratory data (1989–2004) were converted to person-based data and combined with notification data (2004–2009) to describe the burden of HCV infection in Ireland. More than 10 000 people were confirmed as HCV infected in 1989–2004, with the numbers peaking in 2000. The predominant genotypes were 1 (55%) and 3 (39%). Drug use was the most likely risk factor in 80%, with receipt of blood or blood products in 16%. It is estimated that 20 000–50 000 people in Ireland are chronically infected with HCV, a population prevalence of 0·5–1·2%, which is similar to other countries in Northern Europe. This is the first published estimate of the number of chronic HCV infections in Ireland. These data will be of value in health service planning and will contribute to the understanding of HCV infection in Europe.

We aimed to assess differences in the prevalence of hepatitis B virus (HBV) infection in The Netherlands between 1996 and 2007, and to identify risk factors for HBV infection in 2007. Representative samples of the Dutch population in 1996 and 2007 were tested for antibodies to hepatitis B core antigen (anti-HBc), hepatitis B surface antigen (HBsAg) and HBV-DNA. In 2007, the weighted anti-HBc prevalence was 3·5% (95% CI 2·2–5·5) and the HBsAg prevalence was 0·2% (95% CI 0·1–0·4). In indigenous Dutch participants, the anti-HBc prevalence was lower in 2007 than in 1996 (P=0·06). First-generation migrants (FGMs) had a 13-fold greater risk of being HBsAg- and/or HBV-DNA-positive than indigenous Dutch participants. In indigenous Dutch participants, risk factors for anti-HBc positivity were older age and having received a blood product before 1990. In FGMs, being of Asian origin was a risk factor. In second-generation migrants, having a foreign-born partner and injecting drug use were risk factors. FGMs are the main target group for secondary HBV prevention in The Netherlands.

This study evaluated the spatio-temporal variation of Legionella spp. in New Zealand using notification and laboratory surveillance data from 1979 to 2009 and analysed the epidemiological trends. To achieve this we focused on changing incidence rates and occurrence of different species over this time. We also examined whether demographic characteristics such as ethnicity may be related to incidence. The annual incidence rate for laboratory-proven cases was 2·5/100 000 and 1·4/100 000 for notified cases. Incidence was highest in the European population and showed large geographical variations between 21 District Health Boards. An important finding of this study is that the predominant Legionella species causing disease in New Zealand differs from that found in other developed countries, with about 30–50% of cases due to L. longbeachae and a similar percentage due to L. pneumophila for any given year. The environmental risk exposure was identified in 420 (52%) cases, of which 58% were attributed to contact with compost; travel was much less significant as a risk factor (6·5%). This suggests that legionellosis has a distinctive epidemiological pattern in New Zealand.

We examined pertussis hospitalizations among infants aged <1 year between 2006 and 2008 using the nationwide inpatient database in Japan. A total of 660 infants hospitalized for pertussis were identified. Peak incidence occurred at age 1 month and infants aged 0–2 months (too young for pertussis vaccination) and ⩾3 months (eligible for at least one dose of vaccination) accounted for 44·5% and 55·5% of hospitalizations, respectively. Complications related to pertussis were found in 165 (25·0%) cases, including one death; the age at admission did not differ significantly between patients with and those without complications (mean age 4·1 vs. 4·5 months, P=0·12). Seventeen patients required mechanical ventilation. Of the 17 cases, 14 infants were aged <3 months and three infants were aged ⩾3 months. Our findings highlight that the vaccination schedule against pertussis may often be delayed in Japan.

The aim of this study was to investigate the optimal pertussis booster vaccination strategy for The Netherlands. A realistic age-structured deterministic model was designed. Assuming a steady-state situation and correcting for underreporting, the model was calibrated using notification data from the period 1996–2000. Several sensitivity analyses were performed to explore the impact of different assumptions for parameters surrounded by uncertainty (e.g. duration of protection after natural infection, underreporting factors, and transmission probabilities). The optimal age of an additional booster dose is in the range of 10–15 years, and implementation of this booster dose will reduce both symptomatic and asymptomatic infections, although the incidence of symptomatic infections in older age groups will increase. The impact of the different assumptions used in the model was in general limited. We conclude that over a wide range of assumptions, an additional booster dose can reduce the incidence of pertussis in the population.

Identification of covariates associated with disease is a key part of epidemiological research. Yet, while adjustment for imperfect diagnostic accuracy is well established when estimating disease prevalence, similar adjustment when estimating covariate effects is far less common, although of important practical relevance due to the sensitivity of such analyses to misclassification error. Case-study data exploring evidence for seasonal differences in Salmonella prevalence using serological testing is presented, in addition simulated data with known properties are analysed. It is demonstrated that: (i) adjusting for misclassification error in models comprising continuous covariates can have a very substantial impact on the resulting conclusions which can then be drawn from any analyses; and (ii) incorporating prior knowledge through Bayesian estimation can provide potentially more informative assessments of covariates while removing the assumption of perfect diagnostic accuracy. The method presented is widely applicable and easily generalized to many types of epidemiological studies.