Due to its substantially lower prevalence of bovine tuberculosis (bTB) relative to other areas of Great Britain, Scotland was designated as an officially (bovine) TB-free region in 2009. This paper investigates resultant possibilities for reducing surveillance by developing risk-based alternatives to current 4-year testing of eligible herds. A model of freedom of infection was used to develop strategies that specifically tested herds that are at risk of infection but would probably not be identified by slaughterhouse meat inspection. The performance of current testing is mimicked by testing all herds that slaughter fewer than 25% of their total stock per year and regularly import animals from high-incidence areas of England and Wales or from Ireland. This system offers a cost reduction by requiring 25% fewer herd and animal tests and 25% fewer false positives.

The study investigated the genetic diversity of human astroviruses (HAstVs) detected in children hospitalized with gastroenteritis in Italy in 2008–2009. A total of 1321 faecal samples were collected in Parma (northern Italy), Bari (southern Italy), and Palermo (Sicily) and screened for the presence of HAstVs. RT–PCR amplification of a portion at the 5′-end of ORF2 allowed the detection of HAstVs in 3·95% of the patients. Four different genotypes (HAstV-1, HAstV-2, HAstV-4, HAstV-5) were found to be circulating during the study period, with HAstV-1 being the predominant type. Interestingly, a novel lineage, proposed as HAstV-2d, was found to have emerged in Parma in 2009. Investigating the genetic variability of HAstVs will be important for understanding the epidemiological trends and evolution of these viruses.

A large outbreak of cholera reported during April–July 2009 in the Kendrapada district of Odisha, India was investigated. Forty-one rectal swabs and 41 water samples, collected from diarrhoeal patients and from different villages were bacteriologically analysed for the isolation of bacterial enteriopathogens, antibiogram profile and detection of various toxic genes. The bacteriological analysis of rectal swabs and environmental water samples revealed the presence of V. cholerae O1 Ogawa biotype El Tor. The V. cholerae strains were resistant to ciprofloxacin, co-trimoxazole, chloramphenicol, streptomycin, ampicillin, furazolidone and nalidixic acid. The multiplex polymerase chain reaction (PCR) assay on V. cholerae strains revealed the presence of ctxA and tcpA genes. The mismatch amplification of mutation assay (MAMA) PCR on clinical and environmental isolates of V. cholerae revealed that the strains were El Tor biotype, which harboured the ctxB gene of the classical strain. The random amplified polymorphic DNA PCR analysis and pulsed-field gel electrophoresis results indicated that the V. cholerae isolates belonged to the same clone. This investigation gives a warning that the El Tor variant of V. cholerae has spread to the coastal district causing a large outbreak that requires close monitoring and surveillance on diarrhoeal outbreaks in Odisha.

Cryptosporidium is a zoonotic protozoan parasite with public health importance worldwide. The objectives of this study were to (1) conduct a meta-analysis of published literature for oocyst shedding and diarrhoea outcomes, and (2) develop recommendations for standardization of experimental dose–response studies. Results showed that for the outcome of oocyst shedding in faeces, the covariates ‘experimental species’, ‘immunosuppression’, ‘oocyst dose’ and ‘oocyst dose’ × ‘age’ were all significant (P ⩽ 0·05). This study suggests that exposing mice, piglets, or ruminants, and using immunosuppressed experimental hosts, is more likely to result in oocyst shedding. For the outcome of diarrhoea in experimentally infected animal species, the key covariates ‘experimental species’, ‘age’ and ‘immunosuppression’ were significant (P ⩽ 0·2). Therefore, based on the results of this meta-analysis, these variables should be carefully reported and considered when designing experimental dose–response studies. Additionally, detection of possible publication bias highlights the need to publish additional studies that convey statistically non-significant as well as significant results in the future.

This paper originated in a project to develop a practical, generic tool for the economic evaluation of surveillance for farm animal diseases at national level by a state veterinary service. Fundamental to that process is integration of epidemiological and economic perspectives. Using a generalized example of epidemic disease, we show that an epidemic curve maps into its economic equivalent, a disease mitigation function, that traces the relationship between value losses avoided and mitigation resources expended. Crucially, elementary economic principles show that mitigation, defined as loss reduction achieved by surveillance and intervention, must be explicitly conceptualized as a three-variable process, and the relative contributions of surveillance and intervention resources investigated with regard to the substitution possibilities between them. Modelling the resultant mitigation surfaces for different diseases should become a standard approach to animal health policy analysis for economic efficiency, a contribution to the evolving agenda for animal health economics research.

To examine the prevalence of human pathogens carried by rats in urban areas in Hanoi and Hai Phong, Vietnam, we live-trapped 100 rats in January 2011 and screened them for a panel of bacteria and viruses. Antibodies against Leptospira interrogans (22·0%), Seoul virus (14·0%) and rat hepatitis E virus (23·0%) were detected in rats, but antibodies against Yersinia pestis were not detected. Antibodies against L. interrogans and Seoul virus were found only in adult rats. In contrast, antibodies to rat hepatitis E virus were also found in juvenile and sub-adult rats, indicating that the transmission mode of rat hepatitis E virus is different from that of L. interrogans and Seoul virus. Moreover, phylogenetic analyses of the S and M segments of Seoul viruses found in Rattus norvegicus showed that Seoul viruses from Hai Phong and Hanoi formed different clades. Human exposure to these pathogens has become a significant public health concern.

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.

Statistical models of epidemiology in wildlife populations usually consider diseased individuals as a single class, despite knowledge that infections progress through states of severity. Bovine tuberculosis (bTB) is a serious zoonotic disease threatening the UK livestock industry, but we have limited understanding of key epidemiological processes in its wildlife reservoirs. We estimated differential survival, force of infection and progression in disease states in a population of Eurasian badgers (Meles meles), naturally infected with bTB. Our state-dependent models overturn prevailing categorizations of badger disease states, and find novel evidence for early onset of disease-induced mortality in male but not female badgers. Males also have higher risk of infection and more rapid disease progression which, coupled with state-dependent increases in mortality, could promote sex biases in the risk of transmission to cattle. Our results reveal hidden complexities in wildlife disease epidemiology, with implications for the management of TB and other zoonotic diseases.

In India, rotavirus infections cause the death of 98621 children each year. In urban neighbourhoods in Delhi, children were followed up for 1 year to estimate the incidence of rotavirus gastroenteritis and common genotypes. Infants aged ⩽1 week were enrolled in cohort 1 and infants aged 12 months (up to +14 days) in cohort 2. Fourteen percent (30/210) gastroenteritis episodes were positive for rotavirus. Incidence rates of rotavirus gastroenteritis episodes in the first and second year were 0·18 [95% confidence interval (CI) 0·10–0·27] and 0·14 (95% CI 0·07–0·21) episodes/child-year, respectively. The incidence rate of severe rotavirus gastroenteritis in the first year of life was 0·05 (95% CI 0·01–0·10) episodes/child-year. There were no cases in the second year. The common genotypes detected were G1P[8] (27%) and G9P[4] (23%). That severe rotavirus gastroenteritis is common in the first year of life is relevant for planning efficacy trials.

Surgical site infection (SSI) after vascular surgery is a serious complication increasing morbidity, mortality, and costs for healthcare systems. A 4-year retrospective cohort study was performed in a university hospital with patients who had undergone arterial vascular surgery below the aortic arch. Investigated variables included demographics and clinical data. Forty-four of 756 patients experienced SSI, 29 of which were superficial, five were deep, and 10 had organ/space infections. Coagulase-negative staphylococci (22%), enterococci (20%), and Staphylococcus aureus (18%) were the most common pathogens. Independent risk factors for SSIs were femoral grafting [odds ratio (OR) 6·7], peripheral atherosclerotic disease, Fontaine stages III–IV (OR 4·1), postoperative drainage >5 days (OR 3·6), immunosuppression (OR 2·8), duration of operation >214 min (OR 2·8), and body mass index >29 (OR 2·6). The application of perioperative antibiotic prophylaxis was an independent protective factor (OR 0·2). Patients with certain risk factors for SSIs warrant special attention for infection prevention.

Faecal specimens collected from 2101 patients with acute gastroenteritis from three cities (Pune, Alappuzha, Belgaum) in India during 1994–1995 and 2004–2010 were tested for group B rotavirus (RVB) by amplification of the NSP2 gene using RT–PCR. Seventy-five (3·6%) specimens were shown to contain RVB RNA. The positivity rate in Pune, Alappuzha and Belgaum was 4·1%, 7·3% and 4·1%, respectively, in the 2000s which was not significantly different from the detection rate in the 1990s in Pune (2·5%, P>0·05). RVB infections prevailed in adolescents and adults (62/1082, 5·7%) compared to children (13/1019, 1·3%, P<0·001) and were detected throughout the year. Phylogenetically, all strains clustered in an NSP2 lineage together with Indian-Bangladeshi RVB strains belonging to VP7 genotype G2. The study confirmed the occurrence of RVB infections in western India and reported for the first time circulation of RVB strains in southern India, suggesting that an increased awareness and monitoring for RVB infections is necessary in India.

Influenza surveillance in Danish intensive care units (ICUs) was performed during the 2009/10 and 2010/11 influenza seasons to monitor the burden on ICUs. All 44 Danish ICUs reported aggregate data for incidence and point prevalence, and case-based demographical and clinical parameters. Additional data on microbiological testing, vaccination and death were obtained from national registers. Ninety-six patients with influenza A(H1N1)pdm09 were recorded in 2009/10; 106 with influenza A and 42 with influenza B in 2010/11. The mean age of influenza A patients was higher in 2010/11 than in 2009/10, 53 vs. 44 years (P = 0·004). No differences in other demographic and clinical parameters were detected between influenza A and B patients. In conclusion, the number of patients with severe influenza was higher in Denmark during the 2010/11 than the 2009/10 season with a shift towards older age groups in influenza A patients. Influenza B caused severe illness and needs consideration in clinical and public health policy.

The objective of this study was to characterize Listeria monocytogenes isolated from farmed Atlantic salmon (Salmo salar) and the processing environment in three different Norwegian factories, and compare these to clinical isolates by multiple-locus variable-number tandem repeat analysis (MLVA). The 65 L. monocytogenes isolates obtained gave 15 distinct MLVA profiles. There was great heterogeneity in the distribution of MLVA profiles in factories and within each factory. Nine of the 15 MLVA profiles found in the fish-associated isolates were found to match human profiles. The MLVA profile 07-07-09-10-06 was the most common strain in Norwegian listeriosis patients. L. monocytogenes with this profile has previously been associated with at least two known listeriosis outbreaks in Norway, neither determined to be due to fish consumption. However, since this profile was also found in fish and in the processing environment, fish should be considered as a possible food vehicle during sporadic cases and outbreaks of listeriosis.

The aim of this study was to compare the responses of colistin treatment alone vs. a combination of colistin and rifampicin in the treatment of ventilator-associated pneumonia (VAP) caused by a carbapenem-resistant A. baumannii strain. Forty-three patients were randomly assigned to one of two treatment groups. Although clinical (P = 0·654), laboratory (P = 0·645), radiological (P = 0·290) and microbiological (P = 0·597) response rates were better in the combination group, these differences were not significant. However, time to microbiological clearance (3·1 ± 0·5 days, P = 0·029) was significantly shorter in the combination group. The VAP-related mortality rates were 63·6% (14/22) and 38·1% (8/21) for the colistin and the combination groups (P = 0·171), respectively. Our results suggest that the combination of colistin with rifampicin may improve clinical and microbiological outcomes of VAP patients infected with A. baumannii.

A total of 207 wild rodents were caught on nine pig farms, five chicken farms and five non-farm locations in Sweden and surveyed for a selection of bacteria, parasites and viruses. Lawsonia intracellularia and pathogenic Yersinia enterocolitica were only detected in rodents on pig farms (9% and 8% prevalence, respectively) which indicate that these agents are more likely to be transmitted to rodents from pigs or the environment on infected farms. Brachyspira hyodysenteriae (1%), Brachyspira intermedia (2%), Campylobacter jejuni (4%), Campylobacter upsaliensis (2%), leptospires (7%) and encephalomyocarditis virus (9%) were also detected from rodents not in contact with farm animals. Giardia and Cryptosporidium spp. were common, although no zoonotic types were verified, and Salmonella enterica was isolated from 1/11 mice on one farm but not detected by PCR from any of the rodents. Trichinella spp. and Toxoplasma gondii were not detected.

The aim of this study was to retrospectively assess the value of whole genome sequencing (WGS) compared to conventional typing methods in the investigation and control of an outbreak of Shigella sonnei in the Orthodox Jewish (OJ) community in the UK. The genome sequence analysis showed that the strains implicated in the outbreak formed three phylogenetically distinct clusters. One cluster represented cases associated with recent exposure to a single strain, whereas the other two clusters represented related but distinct strains of S. sonnei circulating in the OJ community across the UK. The WGS data challenged the conclusions drawn during the initial outbreak investigation and allowed cases of dysentery to be implicated or ruled out of the outbreak that were previously misclassified. This study showed that the resolution achieved using WGS would have clearly defined the outbreak, thus facilitating the promotion of infection control measures within local schools and the dissemination of a stronger public health message to the community.

A cohort study was performed to investigate cryptosporidial prevalence and species distribution in 13 organic and 13 conventional dairy herds. Faecal samples were collected from 221 calves and 259 cows. Management routines were recorded at farm inspection and through a questionnaire. Samples were concentrated using sodium chloride flotation and cryptosporidial oocysts were detected by epifluorescence microscopy. Molecular analysis was used to determine species and subtypes. A multivariable model for factors associated with calves being Cryptosporidium spp. positive was built. Cryptosporidium spp.-positive animals were identified in all herds. Prevalences were similar in organic and conventional calves (44·7% vs. 52·3%), as well as in cows (3·1% vs. 3·8%), P > 0·05. Cryptosporidium bovis, C. ryanae and C. parvum were identified. C. ryanae was identified in a calf younger than the described prepatent period. The multivariable model included four significant variables; calf age, cleanliness of bedding, cleaning routines for group pens and farmers' attitudes towards biosecurity.

The European badger (Meles meles) has been identified as a wildlife reservoir of bovine tuberculosis and a source of transmission to cattle in Britain and Ireland. Both behavioural ecology and statistical ecological modelling have indicated the long-term persistence of the disease in some badger communities, and this is postulated to account for the high incidence of bovine tuberculosis in cattle across large tracts of England and Wales. This paper questions this consensus by using historical cartographic evidence to show that tuberculosis in cattle had a very different spatial distribution before 1960 to the present day. Since few of the badgers collected in road traffic accidents between 1972 and 1990 had tuberculosis in counties such as Cheshire, where the disease had until shortly before that been rife in the cattle population, the role of badgers as reservoirs in spreading disease in similar counties outside the south-west of England has to be questioned.

This study investigates neighbourhood variation in rates of pneumococcal bacteraemia and community-level factors associated with neighbourhood heterogeneity in disease risk. We analysed data from 1416 adult and paediatric cases of pneumococcal bacteraemia collected during 2005–2008 from a population-based hospital surveillance network in metropolitan Philadelphia. Cases were geocoded using residential address to measure disease incidence by neighbourhood and identify potential neighbourhood-level risk factors. Overall incidence of pneumococcal bacteraemia was 36·8 cases/100 000 population and varied significantly (0–67·8 cases/100 000 population) in 281 neighbourhoods. Increased disease incidence was associated with higher population density [incidence rate ratio (IRR) 1·10/10 000 people per mile2, 95% confidence interval (CI) 1·0–1·19], higher percent black population (per 10% increase) (IRR 1·07, 95% CI 1·04–1·09), population aged ⩽5 years (IRR 3·49, CI 1·8–5·18) and population aged ⩾65 years (IRR 1·19, CI 1·00–1·38). After adjusting for these characteristics, there was no significant difference in neighbourhood disease rates. This study demonstrates substantial small-area variation in pneumococcal bacteraemia risk that appears to be explained by neighbourhood sociodemographic characteristics. Identifying neighbourhoods with increased disease risk may provide valuable information to optimize implementation of prevention strategies.