The incidence, morbidity, and mortality associated with Clostridium difficile gastrointestinal infections has increased greatly over recent years, reaching epidemic proportions; a trend due, in part, to the emergence of hypervirulent and antibiotic-resistant strains. The need to identify alternative, non-antibiotic, treatment strategies is therefore urgent. The ability of bacteria in faecal matter transplanted from healthy individuals to displace pathogen populations is well recognized. Further, there is growing evidence that such faecal microbiota transplantation can be of benefit in a wide range of conditions associated with gut dysbiosis. Recent technical advances have greatly increased our ability to understand the processes that underpin the beneficial changes in bacterial community composition, as well as to characterize their extent and duration. However, while much of the research into faecal microbiota transplantation focuses currently on achieving clinical efficacy, the potential for such therapies to contribute to the transmission of infective agents also requires careful consideration.

Encephalitis is a clinical syndrome often associated with infectious agents. This study describes the epidemiology and disease burden associated with encephalitis in Canada and explores possible associations with arboviral causes. Encephalitis-associated hospitalizations, 1994–2008, were analysed according to aetiological category (based on ICD-9/ICD-10 codes) and other factors using multivariate logistic regression for grouped (blocked) data and negative binomial regression. A discrete Poisson model tested spatio-temporal clustering of hospitalizations associated with unclassified and arboviral encephalitis aetiologies. Encephalitis accounted for an estimated 24028 hospitalizations in Canada (5·2/100 000 population) and unknown aetiologies represented 50% of these hospitalizations. In 2003, clusters of unclassified encephalitis were identified in the summer and early autumn months signifying potential underlying arboviral aetiologies. Spatio-temporal patterns in encephalitis hospitalizations may help us to better understand the disease burden associated with arboviruses and other zoonotic pathogens in Canada and to develop appropriate surveillance systems.

The French epidemiology of infectious encephalitis has been described in a 2007 prospective study. We compared these results with available data (demographic features, causative agents, case-fatality ratio) obtained through the French national hospital discharge 2007 database (PMSI), in order to evaluate it as a surveillance tool for encephalitis. Causative agents were identified in 52% of cases in the study, and 38% in PMSI (P < 0·001). The incidence of encephalitis in France in 2007 was estimated as 2·6 cases/100 000 inhabitants. HSV and VZV were the most frequent aetiological agents in both databases with similar rates. Listeria monocytogenes and Mycobacterium tuberculosis were less frequent in PMSI than in the study (Listeria: 2% vs. 5%, P = 0·001; Mycobacterium: 2% vs. 8%, P < 0·001). The case-fatality ratios were similar, except for Listeria (46% in the study vs. 16%). Nevertheless, despite the absence of case definitions and a possible misclassification weakening PMSI data, we suggest that PMSI may be used as a basic surveillance tool at a limited cost.

A cross-sectional serological survey was conducted during January to August 2001 to determine the seroprevalence of Leptospira serovars in five species of livestock in Thailand and to identify associations between seropositivity and sex, age, species and geographical locations. Sera from 14188 livestock (9288 cattle, 1376 buffaloes, 1898 pigs, 1110 sheep, 516 goats) from 36 provinces were tested for antibodies against 24 Leptospira serovars with the microscopic agglutination test (MAT) for which the criterion for a positive result was set at a titre of ⩾1:50. A total of 1635 [11·5%, 95% confidence interval (CI) 11·0–12·0] animals were seropositive and the highest prevalence (30·4%, 95% CI 28·2–32·5) of evidence of infection was recorded in the northeast region followed by the central region (22·2%, 95% CI 20–24·6). Seroprevalences recorded for cattle, buffaloes, pigs, sheep and goats were 9·9% (95% CI 9·3–10·5), 30·5% (95% CI 28·1–32·9), 10·8% (95% CI 9·5–12·3), 4·7% (95% CI 3·6–6·1) and 7·9% (95% CI 5·8–10·5), respectively. Buffaloes were 3·1 (95% CI 2·8–3·4) times more likely than cattle to be seropositive. The most commonly detected antibodies were against L. interrogans serovars Ranarum, Sejroe, and Mini in cattle, Mini, Sejroe, and Bratislava in buffaloes, Ranarum, Pomona, and Bratislava in pigs and Mini, Shermani, and Ranarum in sheep and goats. Seroprevalences in cattle and buffaloes trended upwards with increasing age and there was no difference in the risk of seropositivity between males and females.

In recent years, human leptospirosis has been reported in Jinping and Liping counties, Guizhou province, but the leptospires have never been isolated. To track the source of infection and understand the aetiological characteristics, we performed surveillance for field mice carriage of leptospirosis in 2011. Four strains of leptospire were isolated from Apodemus agrarius. PCR confirmed the four isolates as pathogenic. Multiple-locus variable-number tandem repeat analysis (MLVA) showed that the four strains were closely related to serovar Lai strain 56601 belonging to serogroup Icterohaemorrhagiae, which is consistent with the antibody detection results from local patients. Furthermore, the diversity of leptospiral isolates from different hosts and regions was demonstrated with MLVA. Our results suggest that A. agrarius may be the main carrier of Leptospira in Jinping and Liping counties, and the serogroup Icterohaemorrhagiae serovar may be the epidemic serogroup of Leptospira. This will contribute to the control and prevention of leptospirosis in these localities.

This study was conducted to determine the seroprevalence of anti-Neospora caninum antibodies and to investigate the risk factors related to seroprevalence in dogs from urban and rural areas with distinct economic activities (milk and coffee production) in Minas Gerais state, Brazil. For this purpose, blood samples from 703 dogs were collected and questionnaires addressing epidemiological aspects were completed by dog-owners. The sera were analysed for anti-N. caninum antibodies by indirect fluorescent antibody tests (IFAT ⩾ 1:50). Association between epidemiological aspects and seropositivity in dogs was evaluated with multivariate logistic regression models. A total of 80 (11·4%) dogs tested positive for N. caninum. In the multivariate logistic regression models, dogs aged >4 years, dogs used as guard dogs, dogs that spontaneously hunt, and history of bovine abortion were found to be greater risk factors for canine N. caninum infection. When we considered only dogs from rural areas, an association with seroprevalence was seen for milk farms, dogs not fed with commercial food, dogs that hunt, and dogs used as guard dogs.

Enteric commensal bacteria of food animals may serve as a reservoir of genes encoding antimicrobial resistance (AMR). The genes are often plasmidic. Different aspects of bacterial ecology can be targeted by interventions to control plasmid-mediated AMR. The field efficacy of interventions remains unclear. We developed a deterministic mathematical model of commensal Escherichia coli in its animate and non-animate habitats within a beef feedlot's pen, with some E. coli having plasmid-mediated resistance to the cephalosporin ceftiofur. We evaluated relative potential efficacy of within- or outside-host biological interventions delivered throughout rearing depending on the targeted parameter of bacterial ecology. Most instrumental in reducing the fraction of resistant enteric E. coli at steer slaughter age were interventions acting on the enteric E. coli and capable of either ‘plasmid curing’ E. coli, or lowering maximum E. coli numbers or the rate of plasmid transfer in this habitat. Also efficient was to increase the regular replacement of enteric E. coli. Lowering replication rate of resistant E. coli alone was not an efficient intervention target.

West Nile virus (WNV) strains belonging to lineage 2 were detected and isolated from the tissues of a goshawk and two carrion crows in Sardinia in August 2012. According to NS3 sequence analysis, the Sardinian isolates shared a high level of similarity with those of Italian lineage 2 strains which circulated in 2011 and with the homologous sequence of the 2004 Hungarian isolate. Following the human fatality reported in 2011 in Olbia, this study is the first to report the spread and enzootic circulation of WNV lineage 2 in Sardinia.

Data on the dynamics of malaria incidence, admissions and mortality and their best possible description are very important to better forecast and assess the implementation of programmes to register, monitor (e.g. by remote sensing) and control the disease, especially in endemic zones. Semi-annual and seasonal cycles in malaria rates have been observed in various countries and close similarity with cycles in the natural environment (temperature, heliogeophysical activity, etc.), host immunity and/or virulence of the parasite suggested. This study aimed at confirming previous results on malaria cyclicity by exploring whether trans-year and/or multiannual cycles might exist. The exploration of underlying chronomes (time structures) was done with raw data (without smoothing) by linear and nonlinear parametric regression models, autocorrelation, spectral (Fourier) and periodogram regression analysis. The strongest cyclical patterns of detrended malaria admissions were (i) annual period of 1·0 year (12 months or seasonality); (ii) quasi-biennial cycle of about 2·25 years; and (iii) infrannual, circadecennial cycle of about 10·3 years. The seasonal maximum occurred in May with the minimum in September. Notably, these cycles corresponded to similar cyclic components of heliogeophysical activity such as sunspot seasonality and solar activity cyclicities and well-known climate/weather oscillations. Further analyses are thus warranted to investigate such similarities. In conclusion, multicomponent cyclical dynamics of cerebral malaria admissions in Papua New Guinea were observed thus allowing more specific analyses and modelling as well as correlations with environmental factors of similar cyclicity to be explored. Such further results might also contribute to and provide more precise estimates for the forecasting and prevention, as well as the better understanding, of the dynamics and aetiology of this vector-borne disease.

Sensitive surveillance systems are crucial for effective control of infectious disease outbreaks, and regional surveillance could provide valuable data to supplement global systems, improve sensitivity and timeliness of reporting, or capture otherwise undetected outbreaks. In New Zealand (NZ), there are no endemic arboviral diseases in humans, and the majority of dengue cases are imported from neighbouring Pacific Islands where comprehensive surveillance systems are under development. From 1997 to 2009, 679 cases of dengue were reported in NZ (74·2% acquired from the Pacific Islands), and the patterns of reported incidence of dengue acquired from different islands closely reflected local reported incidence in those areas. NZ is therefore in a unique position to provide early alerts on dengue outbreaks in the Pacific Islands. Such a strategy would reduce disease burden in both the Pacific Islands and NZ, and provide a model for transnational collaboration in disease surveillance with regional as well as global benefits.

Animal losses due to abortion and malformed offspring during the lambing period 2011/2012 amounted to 50% in ruminants in Europe. A new arthropod-borne virus, called Schmallenberg virus (SBV), was identified as the cause of these losses. Blood samples were obtained from 40 goat flocks and tested for antibodies against SBV by ELISA, with 95% being seropositive. The calculated intra-herd seroprevalence (median 36·7%, min-max 0–93·3%) was smaller than in cattle or sheep flocks. Only 25% of the farmers reported malformations in kids. Statistical analysis revealed a significantly lower risk of goats housed indoors all year-round to be infected by SBV than for goats kept outside day and night. The low intra-herd seroprevalence demonstrates that German goat flocks are still at risk of SBV infection. Therefore, they must be protected during the next lambing seasons by rescheduling the mating period, implementing indoor housing, and continuous treatment with repellents or vaccination.

Societal and technological changes render traditional study designs less feasible for investigation of outbreaks. We compared results obtained from case-case and case-control designs during the investigation of a Salmonella Enteritidis PT14b (SE14b) outbreak in Britain to provide support for validation of this approach. Exposures of cases were compared to concurrent non-Enteritidis Salmonella cases and population controls recruited through systematic digit phone dialling. Infection with SE14b was associated with eating in oriental restaurants [odds ratio (OR) 35·8, 95% confidence interval (CI) 4·4–290·9] and consuming eggs away from home (OR 13·8, 95% CI 1·5–124·5) in the case-case study and was confirmed through a concurrent case-control study with similar effect estimates and microbiological findings of SE14b in eggs from a specific chicken flock on a Spanish farm. We found that the case-case design was feasible, quick and inexpensive, potentially minimized recall bias and made use of already interviewed cases with subtyping results. This approach has potential for use in future investigations.

Campylobacteriosis is the commonest cause of bacterial enteritis in England yet the epidemiology of apparently sporadic cases is not well understood. Here we evaluated the feasibility of applying a space-time cluster detection method to routine laboratory surveillance data in the North East of England by simulating prospective weekly space-time cluster detection using SaTScan as if it had been performed for 2008–2011. From the 209 simulated weekly runs using a circular window, 20 distinct clusters were found which contained a median of 30 cases (interquartile range 15–66) from a median population of ∼134 000 persons. This corresponds to detection of a new cluster every 10 weeks. We found significant differences in age, sex and deprivation score distributions between areas within clusters compared to those without. The results of this study suggest that space-time detection of Campylobacter clusters could be used to find groups of cases amenable to epidemiological investigation.

Population-based estimates of incidence and risk factors for acute gastrointestinal illness (AGI) are important for infectious disease surveillance and healthcare planning. We conducted a nationwide representative cross-sectional telephone survey of 21 262 adults over a 12-month period during 2008–2009 in Germany. Participants were asked if they had either AGI-related diarrhoea or vomiting in a 4-week recall period. We estimated 0·95 episodes/person per year (95% confidence interval 0·90–0·99), corresponding to 64·9 million episodes of AGI annually in adults, which results in 24·5 million outpatient visits, 19·9 million hospital days and 63·2 million days of work lost. We observed an overall declining trend of AGI with increasing age. Diarrhoea was more often reported than vomiting. The mean duration of illness was 3·8 days and did not differ between age groups. Social factors seemed to be weak predictors compared to state of health and health behaviour characteristics. This study allows international comparisons and contributes to the estimation of the global burden of AGI.

Methicillin-resistant Staphylococcus aureus (MRSA) bacteraemia cause significant morbidity and mortality in hospitalized patients. Using a nested case-control design, 204 MRSA bacteraemia cases were compared to 301 unmatched methicillin-susceptible Staphylococcus aureus (MSSA) bacteraemia controls and were matched 1:2 with non-infected controls. The independent risk factors for MRSA bacteraemia compared to MSSA bacteraemia were older age (P = 0·048), major organ transplant during current hospital stay (P = 0·016) and quinolone use (P = 0·016). Cases were more likely than non-infected controls to have renal failure (P = 0·003), cirrhosis (P = 0·013), and a central venous catheter (P = 0·003) after controlling for other risk factors. This large case-control study made it possible to assess risk factors for MRSA bacteraemia using two sets of controls and showed that risk factors differed greatly depending on the control group chosen. These results confirm the need for careful selection of appropriate control groups and the need to carefully adjust for underlying severity of illness.

The prevalence of natural carriage and molecular epidemiology of methicillin-resistant Staphylococcus aureus (MRSA) and methicillin-resistant coagulase-negative staphylococci (MR-CoNS) isolates in a Jordanian community were investigated. The MRSA nasal carriage rate in 227 healthy volunteers was 7·5% and the majority (81%) of MRSA harboured the resistance element SCCmec type IVe and were of a novel spa type t9519 (76%); other significant spa gene types were t223 (14·7%) and t044 (5·9%). All MRSA isolates were susceptible to other classes of antibiotics, and tested positive for at least three virulence factor encoding genes, but only two harboured the pvl gene. MR-CoNS carriage was 54·2% and these isolates were characterized by single, double and untypable SCCmec elements, with Staphylococcus epidermidis SCCmec type IVa predominating. Of eight subjects with nasal co-colonization of MR-CoNS + MRSA, three shared SCCmec type IV in both groups of organisms. This is the first report of methicillin-resistant staphylococci carriage in a Jordanian community and its findings are important for epidemiological study and infection control measures of these organisms.

We describe trends in incidence rates of methicillin-resistant Staphylococcus aureus (MRSA) in HIV-infected and HIV-uninfected patients enrolled in a large northern California Health Plan, and the ratio of MRSA to methicillin-susceptible S. aureus (MSSA) case counts. Between 1995 and 2010, 1549 MRSA infections were diagnosed in 14060 HIV-infected patients (11·0%) compared to 89546 MRSA infections in 6597396 HIV-uninfected patients (1·4%) (P = 0·00). A steady rise in MRSA infection rates began in 1995 in HIV-uninfected patients, peaking at 396·5 infections/100000 person-years in 2007. A more rapid rise in MRSA infection rates occurred in the HIV-infected group after 2000, peaking at 3592·8 infections/100000 in 2005. A declining trend in MRSA rates may have begun in 2008–2009. Comparing the ratio of MRSA to MSSA case counts, we observed that HIV-infected patients shouldered a greater burden of MRSA infection during most years of study follow-up compared to HIV-uninfected patients.

We studied seasonal patterns of swine hepatitis E virus (HEV) infection in China. From 2008 to 2011, 4200 swine bile specimens were collected for the detection of HEV RNA. A total of 92/2400 (3·83%) specimens in eastern China and 47/1800 (2·61%) specimens in southwestern China were positive for HEV. Seasonal patterns differing by geographical area were suggested. In eastern China, the major peak of HEV RNA prevalence was during March–April, with a minor peak during September–October, and a dip during July–August. In southwestern China, the peak was during September–October and the dip during March–April. The majority of subtype 4a cases (63/82, 76·83%) were detected in the first half of the year, while the majority of subtype 4b cases (26/29, 89·66%) were concentrated in the second half of the year, suggesting that different subtypes contribute to different peaks. Our results indicate that the distribution of HEV subtypes is associated with seasonal patterns.

The prevalence and epidemiological traits of human immunodeficiency virus (HIV)/hepatitis B virus (HBV) infections in high-risk populations (HRPs) remained unclarified in Japan. We determined the prevalence of HIV, HBV and Treponema pallidum (TP) and the viral genotypes in HRPs who attended primary sexually transmitted infection (STI) clinics in Osaka province during 2006–2011. Of 7898 specimens, 133 (1·7%) were HIV positive, which was significantly higher than the figures reported by Japanese Red Cross (0·0019%) and public health centres (0·27%) in Japan. The frequency of HIV-1 subtype B was 88·7%, followed by CRF01_AE (2·3%) and C (0·8%), which were almost identical to the national trend. HBV seroprevalence was surprisingly high in the HIV-positive group (63·2%), which was significantly higher than that in the HIV-negative group (25·6%). By contrast, there was no statistical correlation between HIV and TP infection. Interestingly, the distinct HBV genotypes Ae and G were prevalent in the HIV-positive population (60·0% and 20·0%, respectively), although both were rarely detected during nationwide surveillance. The transmission of HIV and HBV appeared to occur largely within a closed community early in life. Of note, about one-quarter of HIV-positive cases would have remained untested if health professionals had not motivated individuals to undergo HIV testing. This is the first evidence-based assessment of HIV positivity and HIV/HBV co-infection in HRPs at primary STIs in Japan and the effect of the involvement of health professionals in the diagnosis of HIV infections in asymptomatic carriers. The genotyping of HBV provided valuable information for understanding HIV epidemical traits.

The aim of this study was to characterize updated HIV subtypes in Yunnan to determine their origins and distribution within the population. RT–PCR of both the gag and env genes were sequenced from Yunnan province inhabitants newly diagnosed with HIV-1. Sequence data from 290 samples were used for statistical analysis of subtype distribution and phylogenetic tree construction. Distribution data were adjusted to account for different geographical distributions of HIV-1 subtypes in the population. Phylogenetic analysis revealed six HIV-1 subtypes in Yunnan, including eight types of unique recombination forms (URFs). The most prevalent subtypes in this province, CRF07_BC (18·9%), CRF08_BC (39·1%), CRF01_AE (22·4%), and URFs (subtype C, 5·9% and subtype B, 4·5%), were all recombinants. We found significant differences in the distribution of these HIV-1 subtypes not only geographically, but also between various ethnic groups and with respect to transmission routes. Our findings indicate a complex population of HIV-1 subtypes, URFs, and recombinant subtypes in Yunnan province. This diversity could make the prevention and control of HIV infection in Yunnan more difficult due to the possibility of virus recombination or infection by multiple subtypes.