Methicillin-Resistant Staphylococcus aureus Strains in Swiss Pigs and Their Relation to Isolates from Farmers and Veterinarians.

Methicillin-resistant Staphylococcus aureus (MRSA) has emerged over the last few decades as a One Health problem with an increasing prevalence in various animal species. The most notable animals are pigs, as asymptomatic carriers, and horses, where there is often an association with infections. The current study looked at the course of MRSA prevalence in Swiss livestock since 2009, with a special focus on pigs, followed by screening of veterinarians and farmers. Livestock isolates were obtained from the Swiss monitoring program and then characterized by spa typing. Concentrating on the year 2017, we analyzed the prevalence of MRSA in Swiss veterinarians and farmers, followed by whole-genome sequencing of selected human and animal strains. The phylogeny was assessed by applying core-genome multilocus sequence typing (MLST) and single-nucleotide polymorphism (SNP) analyses, followed by screening for resistance genes and virulence factors. The prevalence of MRSA in Swiss pigs showed a dramatic increase from 2% in 2009 to 44% in 2017. Isolates typically belonged to clonal complex 398 (CC398), split between spa t011 and t034. The higher prevalence was mainly due to an increase in t011. spa t034 strains from farmers were found to be closely associated with porcine t034 strains. The same could be shown for spa t011 strains from horses and veterinarians. spa t034 strains had a high number of additional resistance genes, and two strains had acquired the immune evasion cluster. However, all but one of the pig spa t011 strains clustered in a separate group. Thus, the increase in pig spa t011 strains does not directly translate to humans.IMPORTANCE MRSA is an important human pathogen; thus, its increasing prevalence in livestock over the last decade has a potentially large impact on public health. Farmers and veterinarians are especially at risk due to their close contact with animals. Our work demonstrates a dramatic increase in MRSA prevalence in Swiss pigs, from 2% in 2009 to 44% in 2017. Whole-genome sequencing allowed us to show a close association between farmer and pig strains as well as veterinarian and horse strains, indicating that the respective animals are a likely source of human colonization. Furthermore, we could demonstrate that pig spa t011 strains cluster separately and are probably less likely to colonize humans than are pig spa t034 strains. This research may provide a basis for a more substantiated risk assessment and preventive measures.

Extrapolating Antibiotic Sales to Number of Treated Animals: Treatments in Pigs and Calves in Switzerland, 2011-2015.

To evaluate the contribution of antimicrobial use in human and veterinary medicine to the emergence and spread of resistant bacteria, the use of these substances has to be accurately monitored in each setting. Currently, various initiatives collect sales data of veterinary antimicrobials, thereby providing an overview of quantities on the market. However, sales data collected at the level of wholesalers or marketing authorization holders are of limited use to associate with the prevalence of bacterial resistances at species level. We converted sales data to the number of potential treatments of calves and pigs in Switzerland for the years 2011 to 2015 using animal course doses (ACD). For each authorized product, the number of potential therapies was derived from the sales at wholesaler's level and the ACD in mg per kg. For products registered for use in multiple species, a percentage of the sales was attributed to each authorized species according to their biomass distribution. We estimated a total of 5,914,349 therapies for pigs and 1,407,450 for calves in 2015. Using the number of slaughtered animals for that year as denominator, we calculated a treatment intensity of 2.15 therapies per pig and 5.96 per calf. Between 2011 and 2015, sales of veterinary antimicrobials decreased by 30%. The calculated number of potential therapies decreased by 30% for pigs and 15% for calves. An analysis of treatment intensity at antimicrobial class level showed a decrease of 64% for colistin used in pigs, and of 7% for macrolides used in both pigs and calves. Whereas the use of 3rd and 4th generation cephalosporins in calves decreased by 15.8%, usage of fluoroquinolones increased by 10.8% in the same period. Corresponding values for pigs were -16.4 and +0.7%. This is the first extrapolation of antimicrobial usage at product level for pigs and calves in Switzerland. It shows that calves were more frequently treated than pigs with a decreasing trend for both number of therapies and use of colistin, macrolides and cephalosporins 3rd and 4th generations. Nonetheless, we calculated an increase in the usage of fluoroquinolones. Altogether, this study's outcomes allow for trend analysis and can be used to assess the relationship between antimicrobial use and resistance at the national level.

Geographical BSE risk assessment and its impact on disease detection and dissemination.

Bovine Spongiform Encephalopathy (BSE) rapidly evolved into an issue of major public concern particularly when, in 1996, evidence was provided that this disease had crossed the species barrier and infected humans in the UK with what has become known as "variant Creutzfeldt Jakob Disease" (vCJD). The aim of this paper is to describe the European Geographical BSE risk assessment (GBR) that was successfully used for assessing the qualitative likelihood that BSE could be present in a country where it was not yet officially recognized. It also discusses how this can lead to risk-based and therefore preventive management of BSE at national and international levels. The basic assumption of the GBR method is that the BSE agent is initially introduced into a country's domestic cattle production system through the importation of contaminated feedstuffs or live cattle. This is referred to as an "external challenge". The ability of the system to cope with such a challenge is, in turn, referred to as its "stability": a stable system will not allow the BSE agent to propagate and amplify following its introduction, while an unstable system will. The BSE-status of a country assessed by this system was used by the European Commission as the basis for trade legislation rules for cattle and their products. The GBR was an invaluable tool in evaluating the potential global spread of BSE as it demonstrated how a disease could be transferred through international trade. This was shown to be a critical factor to address in reducing the spread and amplification of BSE throughout the world. Furthermore, GBR resulted in the implementation of additional measures and management activities both to improve surveillance and to prevent transmission within the cattle population.

Bovine viral diarrhea (BVD) eradication in Switzerland--experiences of the first two years.

A national eradication programme was designed with the aim of achieving total freedom from bovine viral diarrhea virus (BVDV) infection in the Swiss cattle population. The eradication programme consisted of testing every Swiss bovine for antigen, culling virus-positive animals and applying movement restrictions. Starting in 2008, the campaign achieved the goal of reducing the proportion of newborn calves that were virus-positive from 1.8% to under 0.2% within two years (situation in September 2010). Both good data flow between the parties involved as well as speed and efficiency (e.g. concerning the application of tests, movement restrictions and slaughter) are central to the success of the programme. Since the beginning of the programme 2.85 million cattle have been tested for bovine viral diarrhea virus (BVDV). The BVD-prevalence in cattle at the individual and herd levels following the implementation of the eradication programme was assessed. Using data collected during this campaign a risk factor analysis was conducted in order to identify factors associated with the appearance of virus positive newborn calves in herds where BVD had not previously been detected; these risk factors would allow targeting of future surveillance. Herd size, early death rate (i.e. the number of animals that either die before 15 days of age or are stillborn per number of newborns per year), buying in stock, using communal summer grazing, production type, age structure and management strategy were factors associated with the appearance of new cases of infection. Testing of newborn calves for antigen will continue to be conducted until the end of 2011, this is combined with outbreak investigation of newly infected herds (consisting of re-testing dams of virus-positive calves and if necessary all cattle on or that recently left the farm). This process is done to identify infected animals that may have been missed during prior testing (false negatives), it also serves to identify other factors that may be responsible for the introduction of BVDV onto the farm. Since October 2009, testing of calves for antigen combined with outbreak investigation has led to the detection of 55 infected animals that had tested negative (presumably false negative) during previous rounds of testing.

Atypical transmissible spongiform encephalopathies in ruminants: a challenge for disease surveillance and control.

Since 1987, when bovine spongiform encephalopathy (BSE) emerged as a novel disease in cattle, enormous efforts were undertaken to monitor and control the disease in ruminants worldwide. The driving force was its high economic impact, which resulted from trade restrictions and the loss of consumer confidence in beef products, the latter because BSE turned out to be a fatal zoonosis, causing variant Creutzfeldt-Jakob disease in human beings. The ban on meat and bone meal in livestock feed and the removal of specified risk materials from the food chain were the main measures to successfully prevent infection in cattle and to protect human beings from BSE exposure. However, although BSE is now under control, previously unknown, so-called atypical transmissible spongiform encephalopathies (TSEs) in cattle and small ruminants have been identified by enhanced disease surveillance. This report briefly reviews and summarizes the current level of knowledge on the spectrum of TSEs in cattle and small ruminants and addresses the question of the extent to which such atypical TSEs have an effect on disease surveillance and control strategies.

Surveillance and simulation of bovine spongiform encephalopathy and scrapie in small ruminants in Switzerland.

BACKGROUND: After bovine spongiform encephalopathy (BSE) emerged in European cattle livestock in 1986 a fundamental question was whether the agent established also in the small ruminants' population. In Switzerland transmissible spongiform encephalopathies (TSEs) in small ruminants have been monitored since 1990. While in the most recent TSE cases a BSE infection could be excluded, for historical cases techniques to discriminate scrapie from BSE had not been available at the time of diagnosis and thus their status remained unclear. We herein applied state-of-the-art techniques to retrospectively classify these animals and to re-analyze the affected flocks for secondary cases. These results were the basis for models, simulating the course of TSEs over a period of 70 years. The aim was to come to a statistically based overall assessment of the TSE situation in the domestic small ruminant population in Switzerland. RESULTS: In sum 16 TSE cases were identified in small ruminants in Switzerland since 1981, of which eight were atypical and six were classical scrapie. In two animals retrospective analysis did not allow any further classification due to the lack of appropriate tissue samples. We found no evidence for an infection with the BSE agent in the cases under investigation. In none of the affected flocks, secondary cases were identified. A Bayesian prevalence calculation resulted in most likely estimates of one case of BSE, five cases of classical scrapie and 21 cases of atypical scrapie per 100'000 small ruminants. According to our models none of the TSEs is considered to cause a broader epidemic in Switzerland. In a closed population, they are rather expected to fade out in the next decades or, in case of a sporadic origin, may remain at a very low level. CONCLUSIONS: In summary, these data indicate that despite a significant epidemic of BSE in cattle, there is no evidence that BSE established in the small ruminant population in Switzerland. Classical and atypical scrapie both occur at a very low level and are not expected to escalate into an epidemic. In this situation the extent of TSE surveillance in small ruminants requires reevaluation based on cost-benefit analysis.

Field performance of two rapid screening tests in active surveillance of transmissible spongiform encephalopathies in small ruminants.

Recently, screening tests for monitoring the prevalence of transmissible spongiform encephalopathies specifically in sheep and goats became available. Although most countries require comprehensive test validation prior to approval, little is known about their performance under normal operating conditions. Switzerland was one of the first countries to implement 2 of these tests, an enzyme-linked immunosorbent assay (ELISA) and a Western blot, in a 1-year active surveillance program. Slaughtered animals (n = 32,777) were analyzed in either of the 2 tests with immunohistochemistry for confirmation of initial reactive results, and fallen stock samples (n = 3,193) were subjected to both screening tests and immunohistochemistry in parallel. Initial reactive and false-positive rates were recorded over time. Both tests revealed an excellent diagnostic specificity (>99.5%). However, initial reactive rates were elevated at the beginning of the program but dropped to levels below 1% with routine and enhanced staff training. Only those in the ELISA increased again in the second half of the program and correlated with the degree of tissue autolysis in the fallen stock samples. It is noteworthy that the Western blot missed 1 of the 3 atypical scrapie cases in the fallen stock, indicating potential differences in the diagnostic sensitivities between the 2 screening tests. However, an estimation of the diagnostic sensitivity for both tests on field samples remained difficult due to the low disease prevalence. Taken together, these results highlight the importance of staff training, sample quality, and interlaboratory comparison trials when such screening tests are implemented in the field.

Neuropathological survey of fallen stock: active surveillance reveals high prevalence of encephalitic listeriosis in small ruminants.

This paper describes the prevalence of brain lesions in the Swiss fallen stock population of small ruminants. 3075 whole brains (75% sheep, 25% goats) were collected as part of a year-long active survey of transmissible spongiform encephalopathies (TSEs) in small ruminants conducted by the Swiss authorities between July 2004 and July 2005. All fallen stock brains were systematically examined by histopathology to obtain reliable data on histologically identifiable brain lesions. Lesions were found in an unexpectedly high number of animals (8.1% of all examined brains). A wide spectrum of diseases was detected showing that this approach provides an excellent opportunity to screen for the prevalence of neurological diseases. Encephalitic listeriosis was by far the most frequent cause of CNS lesions in both species and its prevalence was unexpectedly high when compared to notified confirmed cases. In conclusion, the prevalence of listeriosis as estimated by passive surveillance based on the notification of clinical suspects has been underestimated in the past.

Review on the epidemiology and dynamics of BSE epidemics.

The paper describes how the comprehensive surveillance of bovine spongiform encephalopathy (BSE) and studies carried out on these data has enhanced our knowledge of the epidemiology of BSE. Around 7, 000 BSE cases were detected through the screening of about 50 million cattle with rapid tests in Europe. It confirmed that the clinical surveillance had a poor capacity to detect cases, and also showed the discrepancy of this passive surveillance efficiency between regions and production types (dairy/beef). Other risk factors for BSE were being in a dairy herd (three times more than beef), having a young age at first calving (for dairy cattle), being autumn-born (dairy and beef), and being in a herd with a very high milk yield. These findings focus the risk on the feeding regimen of calves/heifers. Several epidemiological studies across countries suggest that the feedborne source related to meat and bone meal (MBM) is the only substantiated route of infection - even after the feed ban -, while it is not possible to exclude maternal transmission or milk replacers as a source of some infections. In most European countries, the average age of the cases is increasing over time and the prevalence decreasing, which reflects the effectiveness of control measures. Consistent results on the trend of the epidemic were obtained using back-calculation modelling, the R(0) approach and Age-Period-Cohort models. Furthermore, active surveillance also resulted in the finding of atypical cases. These are distinct from previously found BSE and classified in two different forms based on biochemical characteristics; their prevalence is very low (36 cases up to 1st September 2007), affected animals were old and some of them displayed clinical signs. The origin and possibility of natural transmission is unknown.

Comparison of the historic recycling risk for BSE in three European countries by calculating the basic reproduction ratio R0.

A deterministic model of BSE transmission is used to calculate the R(0) values for specific years of the BSE epidemics in the United Kingdom (UK), the Netherlands (NL), and Switzerland (CH). In all three countries, the R(0) values decreased below 1 after the introduction of a ban on feeding meat and bone meal (MBM) to ruminants around the 1990s. A variety of additional measures against BSE led to further decrease of R(0) to about 0.06 in the years around 1998. The calculated R(0) values were consistent with the observations made on the surveillance results for UK, but were partially conflicting with the surveillance results for NL and CH. There was evidence for a dependency of the BSE epidemic in NL and CH from an infection source not considered in the deterministic transmission model. Imports of MBM and feed components can be an explanation for this discrepancy, and the importance of imports for these observations is discussed.

Diversity in neuroanatomical distribution of abnormal prion protein in atypical scrapie.

Scrapie is a transmissible spongiform encephalopathy (TSE) in sheep and goats. In recent years, atypical scrapie cases were identified that differed from classical scrapie in the molecular characteristics of the disease-associated pathological prion protein (PrP(sc)). In this study, we analyze the molecular and neuropathological phenotype of nine Swiss TSE cases in sheep and goats. One sheep was identified as classical scrapie, whereas six sheep, as well as two goats, were classified as atypical scrapie. The latter revealed a uniform electrophoretic mobility pattern of the proteinase K-resistant core fragment of PrP(sc) distinct from classical scrapie regardless of the genotype, the species, and the neuroanatomical structure. Remarkably different types of neuroanatomical PrP(sc) distribution were observed in atypical scrapie cases by both western immunoblotting and immunohistochemistry. Our findings indicate that the biodiversity in atypical scrapie is larger than expected and thus impacts on current sampling and testing strategies in small ruminant TSE surveillance.

Evaluation of the effectiveness of selected measures against bovine spongiform encephalopathy (BSE) in Switzerland by use of the basic reproduction ratio R0.

The effectiveness of two measures against Bovine Spongiform Encephalopathy (BSE), the compulsory processing of animal by products to meat and bone meal (MBM) at 133 degrees C under 3 bars of pressure for 20 minutes in February 1993 and the exclusion of fallen stock, heads with eyes and spinal cord of cattle older than 30 month from MBM production in April 1996, was evaluated in a process model. The transmission of BSE by calculation of the basic reproduction ratio R0 was modelled. The results were verified by use of a cohort model, based on observed surveillance data. Prior to 1990, before the ban of feeding MBM to ruminants, R0, as calculated in the process model, was above 1, coherent with a slowly progressing BSE epidemic. Since 1991, values of R0 were low at 0.06. The corresponding R0 values derived from the cohort model were higher, the lowest value 0.13 calculated for 1996. Given such low R0 values, the epidemic should have died out. Additionally, no influence of the two measures was obvious at that time given the low level of R0. The discrepancy between the results of the two models is evidence for a dependency of the BSE epidemic from an infection source not considered in the process model. This infection source is most likely importation of feed ingredients and MBM.

BSE, feed and cattle in Switzerland: is there a spatial relation?

Cross-contamination of cattle feed with meat and bone meal (MBM) allowed in feed for other species is regarded as the current hypothesis for the infection pathway of Bovine Spongiform Encephalopathy (BSE) cases occurring after the implementation of a ban on feeding MBM to cattle. This study was aimed at establishing a spatial relation between BSE cases in Switzerland and the findings of MBM in cattle feed. A cluster analysis and a cohort study were performed. Two hundred sixteen BSE cases born after December 1990 and detected until August 1st 2005, screening data of 504 feed producers between 1996 and 2001 and population data from the Swiss 2001 cattle census were included. The cluster analysis showed feed producer, positive for MBM contaminations in cattle feed, as possible cluster centres for BSE cases. In the cohort study, farms within a radius of 2 and 10 km around positive feed producers showed significantly higher odds to have a BSE case than the control group. The odds ratio and its 95% confidence interval were 2.23 (1.26-3.93) for the 2 km radius and 1.38 (1-1.9) for the 10 km radius. The results provide evidence for a spatial relation between cross-contamination and BSE occurrence. These findings support the hypothesis of cross-contamination to be an important route for BSE transmission after a feed ban.

Atypical scrapie in a Swiss goat and implications for transmissible spongiform encephalopathy surveillance.

Different types of transmissible spongiform encephalopathies (TSEs) affect sheep and goats. In addition to the classical form of scrapie, both species are susceptible to experimental infections with the bovine spongiform encephalopathy (BSE) agent, and in recent years atypical scrapie cases have been reported in sheep from different European countries. Atypical scrapie in sheep is characterized by distinct histopathologic lesions and molecular characteristics of the abnormal scrapie prion protein (PrP(sc)). Characteristics of atypical scrapie have not yet been described in detail in goats. A goat presenting features of atypical scrapie was identified in Switzerland. Although there was no difference between the molecular characteristics of PrP(sc) in this animal and those of atypical scrapie in sheep, differences in the distribution of histopathologic lesions and PrP(sc) deposition were observed. In particular the cerebellar cortex, a major site of PrP(sc) deposition in atypical scrapie in sheep, was found to be virtually unaffected in this goat. In contrast, severe lesions and PrP(sc) deposition were detected in more rostral brain structures, such as thalamus and midbrain. Two TSE screening tests and PrP(sc) immunohistochemistry were either negative or barely positive when applied to cerebellum and obex tissues, the target samples for TSE surveillance in sheep and goats. These findings suggest that such cases may have been missed in the past and could be overlooked in the future if sampling and testing procedures are not adapted. The epidemiological and veterinary public health implications of these atypical cases, however, are not yet known.

Spongiform encephalopathy in a miniature zebu.

The first case of spongiform encephalopathy in a zebu (Bos indicus) was identified in a zoo in Switzerland. Although histopathologic and immunohistochemical analyses of the central nervous system indicated a diagnosis of bovine spongiform encephalopathy (BSE), molecular typing showed some features different from those of BSE in cattle (B. taurus).

Age-period-cohort analysis of the Bovine Spongiform Encephalopathy (BSE) epidemic in Switzerland.

Cattle born after animal-feed control measures were implemented in 1990 have become BSE cases in Switzerland, indicating sub-optimal effectiveness of these measures. To evaluate these measures, the incidence of BSE cases in Switzerland recorded through clinical case reporting from January 1991 to June 2000 (categorized into age groups and birth cohorts of 6-month duration) was analyzed by Poisson log-linear regression using an age-period-cohort model. The incidence was maximum in the cattle cohort born from October 1989 to March 1990, and dropped to zero in the cohort born from April to September 1991. A second peak was observed in a cohort born from April to September 1994. The first drop of incidence is interpreted as a result of initial implementation of the feed ban in 1990. The second peak might be related to exposure of cattle to feed intended for pigs and poultry.