This study assessed changes in prevalence and distribution of HIV-1 non-subtype B viruses in Italian and immigrant patients over two decades in a province in Italy. All HIV-positive patients who underwent genotypic resistance testing were selected. Prevalence of non-subtype B viruses in 3-year periods was calculated. All sequences of non-subtype B and those provided by REGA as unassigned were analysed for phylogenetic relationships. In total, 250/1563 (16%) individuals were infected with a non-subtype B virus. Prevalence increased over time, reaching a peak (31·5%) in 2004–2006. In Italian patients, the most frequent subtypes were B (92·5%) and F1 (4%). F1 subtype was also prevalent in patients from South America (13·6%); in patients of African origin, CRF02_AG (54·9%) and G (12·3%) were the most frequent. HIV-1 non-subtype B infections in Italians were mostly found in patients who acquired HIV sexually. A phylogenetic relationship between F subtypes in Italian and representative HIV-1 sequences from Brazil was found. C subtypes in Italians were phylogenetically related to subtypes circulating in Brazil. Inter-subtype recombinants were also found in the latest years. The HIV-1 epidemic in Brescia province evolved to the point where about 1/3 patients recently diagnosed harboured non-B HIV subtypes. The distribution of HIV-1 non-B subtypes in Italian patients resembled that in South American patients and phylogenetic relatedness between some Italian and South American HIV-1 strains was found. The possible epidemiological link between these two populations would have been missed by looking only at risk factors for HIV acquisition declared by patients. The evidence of inter-subtype recombinants points to significant genetic assortment. Overall our results support phylogenetic analysis as a tool for epidemiological investigation in order to guide targeted prevention strategies.

Because syndromic surveillance systems use pre-diagnostic data for early detection of disease outbreaks, it is important to know how the earliest signs and symptoms of a disease might appear in these systems. The available medical literature describing the sequence of signs and symptoms of pneumonic plague reveals that, during the earliest stages, patients will most likely present with certain gastrointestinal and minimal, if any, respiratory signs. Without this knowledge, early evidence of pneumonic plague in syndromic surveillance systems may be missed until the respiratory signs become prevalent. Because plague is a zoonotic disease, new syndromic surveillance systems that use animal data from park rangers and veterinarians may provide useful evidence. This paper shows how a review of both human and animal literature can be used to design queries for syndromic surveillance systems.

Influenza viruses circulate around the world every year. From time to time new strains emerge and cause global pandemics. Many national and international health agencies recommended the use of face masks during the 2009 influenza A (H1N1) pandemic. We reviewed the English-language literature on this subject to inform public health preparedness. There is some evidence to support the wearing of masks or respirators during illness to protect others, and public health emphasis on mask wearing during illness may help to reduce influenza virus transmission. There are fewer data to support the use of masks or respirators to prevent becoming infected. Further studies in controlled settings and studies of natural infections in healthcare and community settings are required to better define the effectiveness of face masks and respirators in preventing influenza virus transmission.

Five major human toxic syndromes caused by the consumption of shellfish contaminated by algal toxins are presented. The increased risks to humans of shellfish toxicity from the prevalence of harmful algal blooms (HABs) may be a consequence of large-scale ecological changes from anthropogenic activities, especially increased eutrophication, marine transport and aquaculture, and global climate change. Improvements in toxin detection methods and increased toxin surveillance programmes are positive developments in limiting human exposure to shellfish toxins.

Turkey is the only country in Europe where urban dog-mediated rabies persists. Control measures in recent decades have reduced the burden of rabies to relatively low levels but foci of disease still persist, particularly in urban areas. Occasional human cases result from this persistence although the source of these appears to be both dog and wildlife reservoirs. This review considers the current state of rabies in Turkey including current control measures, the varying epidemiology of the disease throughout this country and the prospects for rabies elimination.

A systematic review of outbreak and non-outbreak studies of infections caused by extraintestinal pathogenic Escherichia coli (ExPEC) was conducted. This review examines the epidemiology, seasonality, source or mode of transmission, and temporal changes, based on E. coli serogroup, in ExPEC causing sporadic vs. outbreak-associated infections. Twelve outbreak and 28 non-outbreak studies were identified. The existence of ExPEC outbreaks was well supported. Three of four outbreak reports indicated peak periods during the winter months. Serogroups associated with outbreak infections ranged from 1% to 26% (average 11·4%) vs. (range 1–15%, average 3·5%) for serogroups associated with sporadic infections; the distribution of serogroups also differed for outbreak and non-outbreak infections. Study authors indicated that the outbreaks may have resulted from foodborne transmission, but direct evidence was unavailable. This review provides evidence that the epidemiology of endemic vs. epidemic ExPEC infections differs; however, study reporting quality limited epidemiological inferences.

Defining the causal relationship between a microbe and encephalitis is complex. Over 100 different infectious agents may cause encephalitis, often as one of the rarer manifestations of infection. The gold-standard techniques to detect causative infectious agents in encephalitis in life depend on the study of brain biopsy material; however, in most cases this is not possible. We present the UK perspective on aetiological case definitions for acute encephalitis and extend them to include immune-mediated causes. Expert opinion was primarily used and was supplemented by literature-based methods. Wide usage of these definitions will facilitate comparison between studies and result in a better understanding of the causes of this devastating condition. They provide a framework for regular review and updating as the knowledge base increases both clinically and through improvements in diagnostic methods. The importance of new and emerging pathogens as causes of encephalitis can be assessed against the principles laid out here.

In New Zealand Campylobacter infection rates have increased steadily since 1980, reaching a peak in 2003 (396/100 000 population). Compared to other nations, disease rates are unfavourably high (e.g. Australia 117/100 000 population, UK 85/100 000 population, USA 13/100 000 population). This ecological study investigated spatial variations in Campylobacter infection rates across New Zealand's Territorial Local Authorities (TLAs, n=73) for the period 1997–2005. Applying multiple linear regression, we examined whether geographical factors such as socio-demographic characteristics, climate, land use, water and the food environment were associated with local differences in the occurrence of Campylobacter infection rates. The results suggested significant variations in campylobacteriosis across TLAs (average annual rates ranging from 97 to 526/100 000 population), with higher rates in the South Island. Disease rates were associated with lower socio-economic deprivation (P<0·01), the proportion of the population aged 25–44 years (P<0·01) and fresh food outlet density (P<0·76). The results underline the role of area-level characteristics in explaining the spatial distribution of campylobacteriosis in New Zealand. In particular, the findings draw attention to the relatively unexplored role of fresh food outlets as a potential risk factor for increased Campylobacter notifications.

Hand, foot and mouth disease (HFMD) is generally a benign febrile exanthematous childhood disease caused by human enteroviruses. The route of transmission is postulated to be faeco-oral in developing areas but attributed more to respiratory droplet in developed areas. Transmission is facilitated by the prolonged environmental survival of these viruses and their greater resistance to biocides. Serious outbreaks with neurological and cardiopulmonary complications caused by human enterovirus 71 (HEV-71) seem to be commoner in the Asian Pacific region than elsewhere in the world. This geographical predilection is unexplained but could be related to the frequency of intra- and inter-typic genetic recombinations of the virus, the host populations' genetic predisposition, environmental hygiene, and standard of healthcare. Vaccine development could be hampered by the general mildness of the illness and rapid genetic evolution of the virus. Antivirals are not readily available; the role of intravenous immunoglobulin in the treatment of serious complications should be investigated. Monitoring of this disease and its epidemiology in the densely populated Asia Pacific epicentre is important for the detection of emerging epidemics due to enteroviruses.

Diphtheria is an uncommon disease in the UK due to an effective immunization programme; consequently when cases do arise, there can be delays in diagnosis and case-fatality rates remain high. We reviewed 102 patients with infections caused by toxigenic corynebacteria (an average of four per year) reported in the UK between 1986 and 2008: 42 Corynebacterium diphtheriae, 59 C. ulcerans and one C. pseudotuberculosis, as well as 23 asymptomatic carriers. Five fatalities were reported, all in unvaccinated patients. The major risk factor for C. diphtheriae infection continued to be travel to an endemic country. C. ulcerans infections became more common than C. diphtheriae infections in the UK; they were associated with contact with companion animals. The occurrence of indigenous severe C. ulcerans infections and imported C. diphtheriae cases highlights the need to maintain UK routine vaccination coverage at the 95% level in the UK, as recommended by the World Health Organization.

Increasing numbers of non-travel-associated hepatitis E virus (HEV) infections have been reported in Europe in recent years. Our objective was to review the evidence on risk factors and transmission routes of autochthonous HEV infection and hepatitis E in Europe in order to develop recommendations for future research, prevention and control. A systematic literature review was performed to identify all primary reports and studies published during 1998–2008 on hepatitis E in humans and animals in Europe by searching Pubmed, reference lists of major articles and international conference proceedings. Each of the 106 included studies was categorized into one of three evidence levels (EL) based on study design and diagnostic methodology. The evidence was generally weak (73 were assigned to EL1, two to both EL1 and EL2, and 30 to EL2), further compounded by the use of poorly validated serological assays in some studies. Only one case-control study was assigned to EL3. Persons with autochthonous hepatitis E infection were on average older than the general population and predominantly male. There was no evidence for one main transmission route of HEV infection or risk factor for hepatitis E. However, zoonotic transmission seemed likely and person-to-person transmission too inefficient to cause clinical disease. Multiple routes of transmission probably exist and should be further investigated through analytical studies and reliable diagnostic kits. Based on current evidence that points to zoonotic transmission from pigs, thorough cooking of all porcine products, prevention of cross-contamination in the kitchen and improved education for occupationally exposed people (e.g. pig farmers, veterinarians and sewage workers) may help prevent HEV infection. Although evidence for parenteral transmission is limited, it is recommended that a risk assessment is undertaken.

This article reviews the literature on the epidemiology of methicillin-resistant Staphylococcus aureus (MRSA) in dogs, cats and horses. Over the past 10 years, MRSA has emerged as an important pathogen in veterinary medicine, especially in countries with a high MRSA burden in human hospitals. During the same period, community-associated MRSA (CA-MRSA) infections in humans without apparent links to healthcare facilities have increased dramatically. Although animal infections occur outside human hospitals, significant epidemiological, clinical and genetic differences exist between CA-MRSA in humans and the majority of MRSA infections in the different animal species. The recognition of MRSA in animals has raised concern over their role as potential reservoirs or vectors for human MRSA infection in the community. However, available data on MRSA transmission between humans and companion animals are limited and the public health impact of such transmission needs to be the subject of more detailed epidemiological studies.

We utilized Medline to perform a systematic review of the literature to quantify the aetiology of cellulitis with intact skin. Of 808 patients with cellulitis, 127–129 (15·7–16·0%) patients had positive needle aspiration and/or punch biopsy cultures from intact skin. Of the patients with positive cultures, 65 (50·4–51·2%) had cultures positive for Staphylococcus aureus, 35 (27·1–27·6%) for group A streptococcus, and 35–37 (27·1–29·1%) for other pathogens. The most common aetiology of cellulitis with intact skin, when it can be determined, is S. aureus, outnumbering group A streptococcus by a ratio of nearly 2:1. Given the increasing incidence of community-associated methicillin-resistant S. aureus infections, our findings may have critical therapeutic implications.

Some studies have suggested that chronic hepatitis C virus (HCV) infection may induce an accelerated decline of forced expiratory volume in 1 second (FEV1). We performed a cross-sectional study to determine the prevalence of HCV infection in a sample of chronic obstructive pulmonary disease (COPD) patients and in a control group of blood donors. The clinical characteristics of HCV-positive and HCV-negative patients were compared. Anti-HCV antibody was determined and confirmed by HCV-RNA. The prevalence of HCV infection in COPD patients was 7·5% (95% CI 6·52–8·48) and in blood donors was 0·41% (95% CI 0·40–0·42). The HCV-positive patients had a lower FEV1 (34·7±8·6%) and a higher BODE index (median=6) than HCV-negative patients (42·7±16·5%, median=4, respectively) (P=0·011 and 0·027, respectively). Our results suggest a high prevalence of chronic HCV infection in patients with COPD in comparison with the blood donors. HCV-positive patients have a more severe disease.

The aim was to analyse variation in incidence of sporadic Legionnaires' disease in a geographical information system in three time periods (1990–2005) by the application of a grid model and to assess the model's validity by analysing variation according to grid position. Coordinates of the addresses at time of disease of 606 confirmed cases with Legionnaires' disease were obtained. The incidence was calculated in cells of 10×10 km in 25 different grids superimposed on a map of Denmark. A 95% and 99% threshold was applied to identify cells with excess incidence representing potential clusters. Four cells had excess incidence in all three time periods. The analysis in 25 different grid positions indicated a low risk of overlooking cells with excess incidence in a random grid. The coefficient of variation ranged from 0·08 to 0·11 independent of the threshold. By application of a random grid model we demonstrated that it was possible to detect small areas with excess incidence that were not detected in the present surveillance system.

Hepatitis B virus (HBV) infections are endemic in Korea. The aims of this study were to determine the prevalence of HBsAg positivity in Korea and to evaluate the changes in intrafamilial transmission after introduction of HBV vaccination in 1983. This study was based on the 2001 Korea National Health and Nutrition Examination Survey. A total of 2512 study subjects, aged 10–29 years, were selected from across Korea using a stratified multi-stage probability sampling design. To identify the changes in intrafamilial transmission after the introduction of the HBV vaccination programme, 1850 subjects with parental serological markers were selected. These subjects were then grouped into two birth cohorts (cohort 1: born before 1983; cohort 2: born after 1983). Appropriate sampling weights were used for all analyses. The weighted age-specific prevalence of HBsAg was 4·9% in participants in their 20s and 1·9% in adolescents; the combined weighted prevalence was 3·2%. Of subjects with HBsAg positivity in either parent, 17·5% were HBsAg-seropositive. Of subjects with two HBsAg-negative parents, 1·5% were HBsAg-seropositive. The HBsAg positivity rate of offspring with HBsAg-positive mothers was higher than those with HBsAg-positive fathers (27·3% vs. 4·8%, P<0·001). The weighted HBsAg positivity rate of offspring with HBsAg-negative mothers was 2·3% for cohort 1 and 0·4% for cohort 2 (P<0·01), and for those offspring with HBsAg-positive mothers it was also significantly decreased compared to cohorts 1 and 2 (40·2% vs. 16·4%, P<0·01). However, the weighted HBsAg positivity rate of offspring with HBsAg-positive mothers was still high. Our results showed that introduction of HBV vaccination has resulted in a decline in the overall HBsAg positivity rate and a reduction in intrafamilial transmission in Korea, but further preventive measures for maternal intrafamilial transmission are needed.

We examined the impact of one-dose vs. two-dose vaccination strategies on the epidemiology of varicella zoster virus (VZV) in Australia, using a mathematical model. Strategies were assessed in terms of varicella (natural and breakthrough) and zoster incidence, morbidity, average age of infection and vaccine effectiveness (VE). Our modelling results suggest that compared to a one-dose vaccination strategy (Australia's current vaccination schedule), a two-dose strategy is expected to not only produce less natural varicella cases (5% vs. 13% of pre-vaccination state, respectively) but also considerably fewer breakthrough varicella cases (only 11·4% of one-dose strategy). Therefore a two-dose infant vaccination programme would be a better long-term strategy for Australia.

The UK was one of few European countries to document a substantial wave of pandemic (H1N1) 2009 influenza in summer 2009. The First Few Hundred (FF100) project ran from April–June 2009 gathering information on early laboratory-confirmed cases across the UK. In total, 392 confirmed cases were followed up. Children were predominantly affected (median age 15 years, IQR 10–27). Symptoms were mild and similar to seasonal influenza, with the exception of diarrhoea, which was reported by 27%. Eleven per cent of all cases had an underlying medical condition, similar to the general population. The majority (92%) were treated with antiviral drugs with 12% reporting adverse effects, mainly nausea and other gastrointestinal complaints. Duration of illness was significantly shorter when antivirals were given within 48 h of onset (median 5 vs. 9 days, P=0·01). No patients died, although 14 were hospitalized, of whom three required mechanical ventilation. The FF100 identified key clinical and epidemiological characteristics of infection with this novel virus in near real-time.