Meningococcal serogroup W strains have been emerging throughout the current century with most of the isolates belonging to the sequence type (ST11)/electrophoretic type (ET37) clonal complex (ST11/E37 CC), particularly since the international outbreak following Hajj 2000. That outbreak appears to have triggered off that trend, contributing to the spread of W ST11/ET37 CC strains globally; however, local strains could be also responsible for increases in the percentage and/or incidence rates of this serogroup in some countries. More recently, unexpected increases in the percentage and incidence rate of W has been noticed in different countries located in the South Cone in Latin America, and W ST11/ET37 CC strains now appear as endemic in the region and an extensive immunization programme with tetravalent conjugate vaccine (covering serogroups A, C, Y and W) has been recently implemented in Chile. It is difficult to ascertain whether we are observing the emergence of W ST11 CC strains in different geographical areas or whether the Hajj 2000 strain is still spreading globally. Several aspects of the evolution of that situation are analysed in this paper, reviewing also the implications in immunization programmes. Closely related with the analysis of this potential evolution, it will be very interesting to monitor the evolution of serogroup W in the African meningitis belt after implementation of the extensive immunization programme with serogroup A conjugate vaccine that is currently underway. More data about carriers, transmission, clonal lineages, etc. are needed for taking decisions (target groups, outbreak control, defining the extent, etc.) to adapt the response strategy with potential interventions with broad coverage vaccines against the emergent serogroup W.

For decades, vaccination with the 23-valent polysaccharide pneumococcal vaccine (PPV23) has been available for risk groups aged ⩾2 years to prevent invasive pneumococcal disease (IPD). Recently, a 13-valent pneumococcal conjugated vaccine (PCV13) has been licensed for use in all age groups. PCV13 may induce better protection than PPV23 because of different immunogenic properties. This called for a revision of vaccine recommendations for risk groups. We therefore reviewed literature on risk groups for IPD, and effectiveness and safety of pneumococcal vaccines and supplemented that with information from public health institutes, expert consultations and data on IPD epidemiology. We included 187 articles. We discuss the implications of the heterogenic vulnerability for IPD within and between risk groups, large indirect effects of childhood immunization, and limited knowledge on additional clinical benefits of PCV13 in combination with PPV23 for the Norwegian recommendations. These are now step-wise and consider the need for vaccination, choice of pneumococcal vaccines, and re-vaccination interval by risk group.

Invasive meningococcal disease (IMD) reported to the Massachusetts Department of Public Health from 1988 to 2011 was reviewed. The average annual incidence of IMD/100 000 decreased from 1·57 [95% confidence interval (CI) 1·42–1·73] for 1988–1991 to 0·22 (95% CI 0·17–0·29) for 2008–2011. The pattern of decreasing incidence over time differed by age group. There was a decrease in IMD/100 000 in the 0–4 years age group after 1991 from 10·92 (95% CI 8·08–14·70) in 1991 to 5·76 (95% CI 3·78–8·72) in 1992. Incidence in the 0–4 years age group remained below 5/100 000 per year on average thereafter. A substantial reduction in incidence in all age groups was observed between 2000 and 2009, which began before the introduction of conjugate meningococcal vaccine in 2005. Marked reductions in incidence of IMD in Massachusetts, and elsewhere, deserve further investigation with respect to potential factors that go beyond the introduction and deployment of improved meningococcal vaccines.

We investigated whether straight-line distance from residential compounds to healthcare facilities influenced mortality, the incidence of pneumonia and vaccine efficacy against pneumonia in rural Gambia. Clinical surveillance for pneumonia was conducted on 6938 children living in the catchment areas of the two largest healthcare facilities. Deaths were monitored by three-monthly home visits. Children living >5 km from the two largest healthcare facilities had a 2·78 [95% confidence interval (CI) 1·74–4·43] times higher risk of all-cause mortality compared to children living within 2 km of these facilities. The observed rate of clinical and radiological pneumonia was lower in children living >5 km from these facilities compared to those living within 2 km [rate ratios 0·65 (95% CI 0·57–0·73) and 0·74 (95% CI 0·55–0·98), respectively]. There was no association between distance and estimated pneumococcal vaccine efficacy. Geographical access to healthcare services is an important determinant of survival and pneumonia in children in rural Gambia.

The major evolutionary stresses on Streptococcus pneumoniae are thought to be the widespread use of antibiotics and the deployment of effective vaccines against the capsular polysaccharides. Our current knowledge of genetic lineages among pneumococcal isolates comes largely from investigations just before and after the introduction of the 7-valent pneumococcal conjugate vaccine (PCV7) introduced in 2000. We examined 66 serogroup 6 isolates from the 1970s, long before the introduction of PCV7 and before widespread penicillin resistance was common in Birmingham, Alabama, to look for ancestors of the clones that came into play around the introduction of the PCV7 vaccine. The hypothesis was that some clonal complexes, if not individual clones, would be stable enough to persist over this period of time. We compared the 1970s isolates with 122 isolates from the 1990s in US and worldwide collections. Genotyping with pulsed-field gel electrophoresis (PFGE) and multi-locus sequence typing (MLST) revealed that while some clones were probably localized to our area, others have persisted within groups that have expanded or diminished over the years.

This study reports clinico-epidemiological features and viral agents causing acute encephalitis syndrome (AES) in the eastern Indian region through hospital-based case enrolment during April 2011 to July 2012. Blood and CSF samples of 526 AES cases were investigated by serology and/or PCR. Viral aetiology was identified in 91 (17·2%) cases. Herpes simplex virus (HSV; types I or II) was most common (16·1%), followed by measles (2·6%), Japanese encephalitis virus (1·5%), dengue virus (0·57%), varicella zoster virus (0·38%) and enteroviruses (0·19%). Rash, paresis and cranial nerve palsies were significantly higher (P < 0·05) with viral AES. Case-fatality rates were 10·9% and 6·2% in AES cases with and without viral aetiology, respectively. Simultaneous infection of HSV I and measles was observed in seven cases. This report provides the first evidence on viral aetiology of AES viruses from eastern India showing dominance of HSV that will be useful in informing the public health system.

This paper examines the importance of environmental factors (mosquito pools and home foreclosures) in human West Nile virus (WNV) transmission in California and Colorado. The role of environmental factors is investigated by applying an instrumental variable technique to a spatial filtering random-effects negative binomial model to correct for both spatial autocorrelation and endogeneity. The results suggest that mosquito pools and home foreclosures are significant in explaining the prevalence of human WNV. An innovative aspect of this research is that it emphasizes the role of home foreclosures in WNV transmission and in the allocation of resources. Knowledge of the factors associated with WNV prevalence is crucial for abatement of future outbreaks. The results suggest that more resources should be allocated to areas that have a high number of home foreclosures and mosquito pools for surveillance and mitigation of the disease.

The study aimed to determine the geographical diversity in seasonality of major diarrhoeal pathogens among 21 138 patients enrolled between 2010 and 2012 in two urban and two rural sites in Bangladesh under the surveillance system of the International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b). Distinct patterns in seasonality were found for rotavirus diarrhoea which peaked in winter across the sites (December and January) and dipped during the rainy season (May) in urban Dhaka, August in Mirpur and July in Matlab, equated by time-series analysis using quasi-Poisson regression model. Significant seasonality for shigellosis was observed in Dhaka and rural Mirzapur. Cholera had robust seasonality in Dhaka and Matlab in the hot and rainy seasons. For enterotoxogenic Escherichia coli (ETEC) diarrhoea, clearly defined seasonality was observed in Dhaka (summer). Understanding the seasonality of such pathogens can improve case management with appropriate therapy, allowing policy-makers to identify periods of high disease burden.

The European wild boar populations are growing and spreading to new areas, which might constitute a threat to public health, since wild boar can harbour pathogens with the potential to cause serious illness in humans. Tonsils, ileocaecal lymph nodes and faecal samples were collected from 88 Swedish wild boars and analysed for the presence of the zoonotic pathogens Salmonella spp., Yersinia enterocolitica, Y. pseudotuberculosis and enterohaemorrhagic Escherichia coli O157:H7 (EHEC). A combination of cultivation and polymerase chain reaction (PCR) analysis was used and overall, 20% of sampled individuals tested positive for Y. enterocolitica, 20% for Y. pseudotuberculosis and 10% for Salmonella spp. A total of 41% of sampled individuals tested positive for one or more of these three pathogens. No EHEC were detected. Samples PCR-positive for Salmonella spp. were cultivated further and six isolates were obtained, belonging to Salmonella enterica subspecies enterica and subspecies diarizone. The pathogens were most commonly detected in tonsil samples.

The objective of this study was to determine the distribution of Shiga toxin-producing Escherichia coli (STEC) virulence markers (stx1, stx2, eae, ehxA) in E. coli strains isolated from young calves aged fewer than 7 days (bobby calves). In total, 299 recto-anal mucosal swabs were collected from animals at two slaughter plants and inoculated onto tryptone bile X-glucuronide and sorbitol MacConkey agar supplemented with cefixime and potassium tellurite. Isolates were analysed using multiplex polymerase chain reaction to detect stx1, stx2, eae and ehxA genes. The most common combination of virulence markers were eae, ehxA (n = 35) followed by eae (n = 9). In total, STEC and atypical enteropathogenic E. coli (aEPEC) were isolated from 8/299 (2·6%) and 37/299 (12·3%) calves, respectively. All the isolates could be assigned to 15 genotype clusters with >70% similarity cut-off using XbaI pulsed-field gel electrophoresis. It may be concluded that healthy calves from the dairy industry are asymptomatic carriers of a diverse population of STEC and aEPEC in New Zealand.

We describe a foodborne outbreak in Italy caused by enteroinvasive Escherichia coli (EIEC), an enteric pathogen uncommon in industrialized countries. On 14 April 2012 a number of employees of the city of Milan Fire Brigade (FB) were admitted to hospital with severe diarrhoea after attending their canteen. Thirty-two patients were hospitalized and a total of 109 cases were identified. A case-control study conducted on 83 cases and 32 controls attending the canteen without having symptoms identified cooked vegetables to be significantly associated with the disease. Stool samples collected from 62 subjects were screened for enteric pathogens using PCR-based commercial kits: 17 cases and two asymptomatic kitchen-workers were positive for the Shigella marker gene ipaH; an ipaH-positive EIEC strain O96:H19 was isolated from six cases. EIEC may cause serious dysentery-like outbreaks even in Western European countries. Microbiologists should be aware of microbiological procedures to detect EIEC, to be applied especially when no common enteric pathogens are identified.

In 2011, from August to November, the Monroe County Department of Public Health (MCDPH) investigated 47 salmonellosis cases. Geographical information software (GIS) was used to map the address locations of these cases. The resulting GIS analysis and culture information indicated that there were two distinct clusters of Salmonella that were geographically different. Pulsed-field gel electrophoresis (PFGE) testing was run at the New York State Department of Health Wadsworth Laboratory and identified S. Enteritidis (23 cases) and S. Typhimurium (10 cases). The epidemiological investigation identified Turkish pine nuts as the link between ill S. Enteritidis cases. Pine nut samples sent for laboratory testing were a PFGE match to human isolates with S. Enteritidis. A national recall of Turkish pine nuts ensued. A multistate outbreak was identified as a result of the initial investigation of MCDPH, in which 43 people were infected with the outbreak strain from five states. GIS software and shopper card data provided important tools in the epidemiological investigation.

In a first study from India, a diverse collection of 140 environmental and clinical non-O157 Shiga-toxigenic Escherichia coli strains from a large geographical area in north India was typed by multi-locus variable number tandem repeat analysis (MLVA). The distribution of major virulence genes stx1, stx2 and eae was found to be 78%, 70% and 10%, respectively; 15 isolates were enterohaemorrhagic E. coli (stx1 +/stx2 + and eae +). By MLVA analysis, 44 different alleles were obtained. Dendrogram analysis revealed 104 different genotypes and 19 MLVA-type complexes divided into two main lineages, i.e. mutton and animal stool. Human isolates presented a statistically significant greater odds ratio for clustering with mutton samples compared to animal stool isolates. Five human isolates clustered with animal stool strains suggesting that some of the human infections may be from cattle, perhaps through milk, contact or the environment. Further epidemiological studies are required to explore these sources in context with occurrence of human cases.

We provide an update on the epidemiology of shigellosis in Israel using data generated by a sentinel laboratory-based surveillance network for the period 1998–2012. The average annual incidence of culture-proven shigellosis was 97/100 000. We estimated that each case of shigellosis accounted for 25 cases in the community indicating the high burden of disease. Orthodox Jewish communities, living in highly crowded conditions and with a high number of children aged <5 years were the epicentre of country-wide biennial propagated epidemics of S. sonnei shigellosis. S. flexneri was the leading Shigella serogroup in Israeli Arabs. S. flexneri 2a and S. flexneri 6 alternated as the most common serotypes. Both S. sonnei and S. flexneri isolates showed high rates of resistance to ampicillin and trimethoprim/sulfamethoxazole and very low rates of resistance to quinolones and third-generation cephalosporins. Shigellosis due to S. sonnei conferred 81% (95% confidence interval 69–89) protection against the homologous Shigella serotype when epidemic exposure re-occurred 2 years later. These data are of value in the process of Shigella vaccine development.

Campylobacter is the most prevalent cause of bacterial gastroenteritis worldwide and it represents a significant public health risk of increasing severity due to its escalating resistance to clinically important quinolone and macrolide antibiotics. As a zoonotic pathogen Campylobacter is transmitted along the food chain and naturally cycles from environmental waters, feedstuff, animals and food to humans. We determined antibiotic resistance profiles, as well as multilocus sequence types and flaA-SVR types for 52 C. jejuni isolated in Slovenia from human, animal, raw and cured chicken meat and water samples. Twenty-eight different sequence types, arranged in ten clonal complexes, three new allele types and five new sequence types were identified, indicating the relatively high diversity in a small group of strains. The assignment of strains from different sources to the same clonal complexes indicates their transmission along the food supply chain. The most prevalent clonal complex was CC21, which was also the genetic group with 95% of quinolone-resistant strains. Based on the genetic relatedness of these quinolone-resistant strains identified by polymerase chain reaction with a mismatch amplification mutation assay and sequencing of the quinolone resistance-determining region of the gyrA gene, we conclude that the high resistance prevalence observed indicates the local clonal spread of quinolone resistance with CC21.

Epidemiological and virological studies indicate that noroviruses-contaminated groundwater was the primary source of four acute gastroenteritis outbreaks in South Korea between 2008 and 2012. Furthermore, cabbage kimchi was first identified as the vehicle of transmission between groundwater and infected patients in an outbreak in 2011. The proper treatment of groundwater sources prior to use for drinking or in food preparation is necessary to prevent further outbreaks.

American Samoa does not have a hepatitis B vaccination policy for healthcare personnel (HCP). Consequently, hepatitis B has remained a health threat to HCP. In this study, we performed a cross-sectional study and examined demographic and risk information and hepatitis B vaccination, testing, and serostatus in hospital employees in American Samoa. Of 604 hospital employees, 231 (38·2%) participated, and of these, 158 (68·4%) were HCP. Of HCP participants, 1·9% had chronic hepatitis B infection, 36·1% were susceptible, and 60·8% were immune. Nearly half of HCP participants reported history of needlestick injury. Overall, participants' knowledge of their hepatitis B infection and vaccination status was low. These data support the adoption of a hepatitis B vaccination policy for HCP by American Samoa, as currently recommended by the World Health Organization and the US Centers for Disease Control and Prevention. Adherence to the policy could be monitored as a way to measure protection.

We studied hepatitis C virus (HCV) prevalence and risk factors for HCV infection in a sample of Brazilian HIV-positive patients. A cross-sectional study was conducted with 580 HIV-positive patients from a specialized HIV/AIDS diagnosis and treatment centre in southern Brazil. All patients were interviewed for socio-demographic and risk factors and tested for HCV antibodies and HCV-RNA detection. A multivariate analysis was performed to identify risk factors for HCV infection. A total of 138 (24%) patients had past or chronic hepatitis C. The following risk factors were associated with HCV infection for each gender: alcohol misuse and injecting drug use in women (P < 0·001) and low educational level, smoking drug use, and injecting drug use in men (P < 0·01). These results suggest that alcohol misuse, low educational level, smoking drug use, and injecting drug use are probable risk factors for HCV infection in HIV-positive patients. This information contributes to an understanding of the epidemiology of HIV/HCV co-infection in Brazil.

Genotypes are associated with the natural course of hepatitis C virus (HCV) infection and response to antiviral therapy for HCV. HCV genotype 1b has been the dominant genotype in Japan, where the prevention of HCV transmission through blood transfusion or nosocomial infection has been established since 1990. The distribution of HCV genotype was investigated based on patient's birth year in 5515 HCV-infected Japanese individuals at three institutions from different areas of Japan. At all three institutions, the proportion of HCV genotype 1b decreased and was <50% in individuals born after 1970. By contrast, the percentage of HCV genotype 2b increased in subsequent birth cohorts after 1920–1929. Significant changes in HCV genotype distribution were observed across Japan regardless of area.

The aim of this study was to monitor the spatio-temporal spread of influenza incidence in Spain during the 2009 pandemic and the following two influenza seasons 2010–2011 and 2011–2012 using a Bayesian Poisson mixed regression model; and implement this model of geographical analysis in the Spanish Influenza Surveillance System to obtain maps of influenza incidence for every week. In the pandemic wave the maps showed influenza activity spreading from west to east. The 2010–2011 influenza epidemic wave plotted a north-west/south-east pattern of spread. During the 2011–2012 season the spread of influenza was geographically heterogeneous. The most important source of variability in the model is the temporal term. The model of spatio-temporal spread of influenza incidence is a supplementary tool of influenza surveillance in Spain.