Bayesian evaluation of temporal changes in sensitivity and specificity of three serological tests for multiple circulating strains of rabbit haemorrhagic disease virus.

Competition and indirect ELISAs are currently being used to monitor rabbit haemorrhagic disease viruses (RHDV1 and RHDV2) in rabbits worldwide. Temporal changes in the sensitivity (Se) and specificity (Sp) of RHDV1 competition-ELISA (cELISA1), RHDV2 competition-ELISA (cELISA2), and RHDV1 Immunoglobulin G (IgG1) ELISA, were investigated using Bayesian Latent Class models (BCLM) in the Australian wild rabbit population where both viruses circulate simultaneously and a long-term serological dataset exists. When cELISA1 was compared to IgG1 ELISA, the Se of cELISA1 improved while the Sp of IgG1 ELISA declined over the 2011-21. This corresponded with a decline in the true RHDV1 prevalence in 2018-21, suggesting that a large proportion of RHDV1 exposed rabbits survived the introduction and dominance of RHDV2 up to approximately 2017/2018, after which they died and were not replaced. The Se and Sp estimates for 2014-15 for both cELISA1 and IgG1 ELISA, and the true prevalence when analysing all three tests together were similar to those obtained from the analysis of cELISA1/IgG1 ELISA. The same was also true for the Se and Sp of cELISA2 and IgG1 ELISA estimates from 2018 onwards. This suggests that RHDV1 was the dominant infection type in 2014-15, but RHDV2 was the dominant infection type in 2018-21. Further, the increase in Se of cELISA2 and the low Sp of IgG1 ELISA in the cELISA2/IgG1 ELISA analysis, compared to the Se of cELISA2 and Sp of IgG1 ELISA when analysing all three tests together suggests that the underlying infection status was more influenced by RHDV2 and that the higher Se of IgG1 ELISA is due to cross-reaction of RHDV2 antibodies on IgG1 ELISA. The true prevalence data suggest that RHDV2 exposure peaked in 2017. Our findings show that test characteristics changed in response to the changing virus prevalences over time. IgG1 ELISA, currently having a high Se, should be used to monitor both viruses and will perform better than both cELISAs.

Comparative Efficacy in Challenge Dose Models of a Toxin Expressing Whole-Cell Vaccine against Eight Serovars of Actinobacillus pleuropneumoniae in Pigs.

Actinobacillus pleuropneumoniae is a major economically significant bacterial respiratory pig pathogen, and whole cell vaccines are used to prevent disease. However, there is little data available on multi-serovar whole cell vaccine protection. Therefore, we determined the protective efficacies of a whole-cell A. pleuropneumoniae serovar 1 and 2 vaccine comprising ApxI-III toxins (C-vaccine, Coglapix®, Ceva, France) against serovars 1, 2, 4, 5, 6, 7, 9/11, and 13. The infection doses used induced disease representative of endemic field conditions, and standard protocols were used for all studies. Protection against homologous serovars 1 and 2 significantly reduced lung lesion scores (LLS) compared to positive controls: p = 0.00007 and p = 0.00124, respectively. The protection against heterologous serovars 4, 5, 6, 7, 9/11, and 13 also significantly reduced LLS: range p = 2.9 × 10-10 to p = 0.00953. As adjudged by the estimated random effect, reproducibility between studies was high. A highly significant serovar-independent reduction of pathological lung lesions by the C-vaccine was found for all the serovars tested (1, 2, 4, 5, 6, 7, 9/11, and 13). We conclude that the C-vaccine gives high serovar-independent protection against disease and is suitable for this use in the field.

Dynamics of somatic cell count (SCC) and differential SCC during and following intramammary infections.

Somatic cell count is frequently used as an indicator of intramammary infections (IMI) in dairy cattle worldwide. The newly introduced differential SCC (DSCC) can potentially contribute to detection of IMI. The purpose of this study was to investigate the dynamics of SCC and DSCC after IMI. We used a data set with monthly samples from 2 Danish dairy herds through 1 yr, using bacterial culture to identify IMI. The dynamics of SCC and DSCC with regard to IMI were assessed at quarter level following new IMI with each of 3 defined pathogen groups, major, minor, or "other" pathogens, using general additive models. Both SCC and DSCC increased after IMI, with a more pronounced increase if major or other pathogens were detected compared with minor pathogens. We found that DSCC increased after IMI with other pathogens in both herds and, in herd 2, after IMI caused by major and minor pathogens. We also estimated the duration of increased SCC and DSCC when they exceeded a threshold, done separately for each pathogen group. Major pathogens had the longest-lasting effect in both herds for both SCC and DSCC. We conclude that the magnitude and duration of response of SCC and DSCC to IMI differs between herds and causative pathogens.

Spatio-temporal variations in mortality during the seawater production phase of Atlantic salmon (Salmo salar) in Norway.

In a sustainable production of animals, monitoring and minimizing mortality must be a top priority. Systematic measuring of mortality over time can be used to evaluate the impact of changes in management and production strategies in Norway. To aid understanding of the potential for reducing mortality, we have used data from 2014 to 2018 to investigate the spatio-temporal patterns of mortality, by descriptive analyses and statistical modelling of possible determinants of mortality. The results show large differences in mortality across different production zones and between years. The areas with the highest density of farmed salmon are also the ones with highest mortality. The total cumulated mortality of farmed salmon increased from 32.3 million in 2014 to 35.2 million in 2018, corresponding to 14.3% and 15.8% of the standing stock. An initial higher mortality was observed during the first 3 months after stocking (mean: 1.5% [0.9%-8.6%] mortality/month). This was followed by a period of stability and lower mortality (mean: 0.8% [0.9%-3.1%] mortality/month), until month 10, when mortality started to increase again. The month of first stocking, the year of slaughter, production zone and number of months at sea were all found to be statistically significant determinants for mortality, with p-values < 1e-15.

Using Creativity as an Educational Tool in Veterinary Surgery: Students' Perceptions and Surgical Performance.

With the aim of improving students' ability to handle the complexity of surgery, we introduced a creative assignment in a veterinary surgical course. We hypothesized that by using this active, inductive educational method, reflection, creativity and self-efficacy in student novice surgeons could be improved. During a companion animal surgical course an intervention group was investigated against a control group. Twenty-nine fourth-year students were instructed in ovariohysterectomy by classical lectures, while 23 fourth-year students were provided with creative materials and assigned to consider and illustrate how to perform the procedure themselves. Surgical performance was assessed for both groups using a modified Objective Structured Assessment of Technical Skills (OSATS) while performing a simulated ovariohysterectomy. Furthermore, both groups were investigated with respect to how they would handle a specific hypothetical surgical complication. Semi-structured interviews were conducted with 17 intervention-group students and were analyzed using thematic analysis. The intervention group showed a significantly better performance and needed significantly less help with the surgical complication than the control group students. Data from interviews furthermore demonstrated that students believed the creative intervention produced increased reflection, more creative initiatives, and a feeling of security before surgery. Our study results thus indicate that an educational tool which stimulates creative thinking can promote reflection, creativity, and self-efficacy in novice surgeons without compromising surgical performance.

LA-MRSA CC398 in Dairy Cattle and Veal Calf Farms Indicates Spillover From Pig Production.

The possible spillover from pigs into other production animals incites concern for unresolved reservoirs of human exposure. The present investigation was therefore initiated, to elucidate if Danish veal and dairy farms constitute a reservoir of livestock-associated methicillin-resistant Staphylococcus aureus (LA-MRSA) CC398 and to potentially identify the source of introduction. We collected nasal swab samples from 17 Danish veal farms, 2 slaughterhouses, and received bulk tank milk samples from 286 dairy farms. All samples were analyzed by culturing and screening on MRSA selective plates and presumed MRSA was verified by MALDI-TOF and PCR. MRSA isolates were subjected to spa typing and whole-genome sequencing. LA-MRSA was found on two veal farms in one and three calves, respectively, with subsequent follow-up samples found negative. Eight of 286 dairy farms (2.8%) were found LA-MRSA positive and follow-up samples, from five farms showed intermittent detection of LA-MRSA. The spa types, t034 and t011, were the most common while a single isolate from a dairy farm belonged to spa type t843 associated to mecC-MRSA CC130 and is the first report of mecC-MRSA in the Danish dairy production. A phylogenetic analysis showed that some of the isolates grouped within or close to the dominant Danish pig clusters, suggesting spillover into cattle farms. Other isolates clustered outside the dominant pig clusters suggesting that other routes of introduction cannot be excluded. Results of the investigation indicated a contamination of veal farms while some dairy farms seemed to be a permanent reservoir. Thus, Danish cattle represent a low prevalence reservoir of LA-MRSA CC398, which at present, is not of major human health concern.

Evaluation of the performance of register data as indicators for dairy herds with high lameness prevalence.

BACKGROUND: The modern dairy industry routinely generates data on production and disease. Therefore, the use of these cheap and at times even "free" data to predict a given state of welfare in a cost-effective manner is evaluated in the present study. Such register data could potentially be used in the identification of herds at risk of having animal welfare problems. The present study evaluated the diagnostic performance of four routinely registered indicators for identifying herds with high lameness prevalence among 40 Danish dairy herds. Indicators were extracted as within-herd annual means for a one-year period for cow mortality, bulk milk somatic cell count, proportion of lean cows at slaughter and the standard deviation (SD) of age at first calving. The target condition "high lameness prevalence" was defined as a within-herd prevalence of lame cows of ≥ 16% (third quartile). Diagnostic performance was evaluated by constructing and analysing Receiver Operating Characteristic curves and their area under the curve (AUC) for single indicators and indicator combinations. Sensitivity (Se) and specificity (Sp) of the indicators were assessed at the optimal cut-off based on data and compared to a set of predefined cut-off levels (national annual means or 90-percentile). RESULTS: Cow mortality had the highest AUC (0.76), while adding the three other indicators to the model did not yield significant increase in AUC. Cow mortality and SD of age at first calving had highest Se (100%, 95% confidence interval (CI): 72-100%), while highest Sp was found for the proportion of lean cows at slaughter (83%, 95% CI: 66-93%). The highest differential positive rate (DPR = 0.53) optimizing both Se and Sp was found for cow mortality. Optimal cut-off points were lower than the presently used pre-defined cut-offs. CONCLUSIONS: The selected register-based indicators proved to be able to identify herds with high lameness prevalences. Optimized cut-offs improved the predictive ability and should therefore be preferred in official control schemes.

Risk-based eradication as a control measure to limit the spread of LA-MRSA among Danish pig herds - a simulation study.

A national screening in 2016 identified 88% of Danish pig herds positive for livestock-associated Methicillin-resistant Staphylococcus aureus (LA-MRSA). This highlights the importance of evaluating potential control measures that could reduce the prevalence of LA-MRSA among Danish pig herds. In addition to describing the effects of (1) reduced within-herd transmission, (2) increased biosecurity, and (3) movement restrictions, the eradication of LA-MRSA as a potential control measure was investigated using a simulation model mimicking the spread of LA-MRSA among pig herds between 2006 and 2015. The latter strategy was simulated either as eradication of a random selection of herds for surveillance or as a risk-based selection of herds based on their potential to spread LA-MRSA via pig movements in four different scenarios: low- vs. high-prevalence scenarios with control measures starting in 2007 and in 2010. Almost all control measures showed the potential to reduce the spread of LA-MRSA among pig herds, especially when implemented intensively and when control measures were combined. Risk-based selection of herds for eradication led to a greater relative reduction compared to random selection. In the high-prevalence scenario in particular, combinations including risk-based eradication led to the greatest relative reduction.

Continuing occurrence of vancomycin resistance determinants in Danish pig farms 20 years after removing exposure to avoparcin.

Vancomycin-resistant Enterococcus spp. is a major health problem worldwide and livestock have been implicated in constituting a reservoir for the transmission of vancomycin resistance to zoonotic pathogens. Vancomycin resistance determinants can be situated on mobile genetic elements and transferred between bacterial species The livestock reservoir must therefore be included in a risk assessment of the vancomycin resistance burden. Avoparcin, a vancomycin analogue, has not been used in Danish pig production for over 20 years and vancomycin has never been used. The objective of this study was to screen faecal samples from Danish pig farms for nine selected vancomycin resistance determinants. We found at least four different vancomycin resistance determinants in all screened Danish pig farms (665 finisher farms and 78 sow farms). The vancomycin resistance determinants present in vanB or vanG clusters were found at significantly different levels in sow and finisher farms. However, vanA was not detected in any of the farms. In conclusion, vancomycin resistance determinants are still present in Danish pig production 25 years after the ban on avoparcin use.

Outcomes From Using Mortality, Antimicrobial Consumption, and Vaccine Use Data for Monitoring Endemic Diseases in Danish Swine Herds.

The aim of this study was to assess the potential of using multiple data sources currently available in Denmark for monitoring swine diseases. The study included farms that, based on serology, changed from "negative" to "positive" status for Porcine Reproductive and Respiratory Syndrome (PRRS), enzootic pneumonia (Mycoplasma hyopneumonia), and porcine pleuropneumonia (Actinobacillus pluropneumoniae) between January 2014 and September 2017. These corresponded to 45 swine farms working as individual operation units (i.e., their disease status is independent from other farms) and 81 farms that were part of joint operation units (i.e., 2 or more farms considered to be an epidemiological unit, having swine and personnel are transferred among them, that have the same disease status). Additionally, a total of 95 farms with a negative status for these three diseases during the study period were also included in the study. Changes in mortality data, antimicrobial consumption, and vaccine use at herd level were monitored using Shewhart control charts prior to, during, and after these farms were found positive for the three diseases. The analysis was run separately for the different age groups-weaners (up to 30 kg), sows and finishers herds-within each farm. Briefly, the highest percentage of herds generating alarms was generated up to 3 months before they changed their disease status based on mortality (30%) and 1 month after based on antimicrobial use for respiratory diseases (100%). Porcine pleuropneumonia showed to be the disease with the highest impact on these data at herd level; alarms based on the three data streams were generated in the same month that herds changed their status to porcine pleuropneumonia-positive, as well as the following months. Alarms based on vaccine use generally occurred within the same month or after changes in disease status. False alarms were found in 2% (median value) of the herds for the different age groups based on mortality and antimicrobial use for respiratory diseases in healthy farms. Monitoring changes in mortality data, antimicrobial consumption, and vaccine use showed changes (i.e., warnings) at herd level prior to confirmation from diagnostic tests.

Effects of control measures on the spread of LA-MRSA among Danish pig herds between 2006 and 2015 - a simulation study.

There has been a rapid increase in Danish pig herds testing positive for livestock-associated Methicillin-resistant Staphylococcus aureus (LA-MRSA) since the first screening in 2008. Despite a national action plan to control LA-MRSA in the Danish pig population, 88% of pig herds tested positive in a 2016 cross-sectional study of 57 herds. The national action plan was initiated in April 2015 and aimed to reduce the spread of LA-MRSA among pig herds. However, its success is uncertain. We used a simulation model mimicking the spread of LA-MRSA among pig herds between 2006 and 2015 to evaluate the impact of control strategies if these had these been implemented in 2007 or 2010. The strategies were combinations of the following control measures: (1) a reduced number of herds using high-risk antibiotics, (2) a reduced probability of indirect transmission among herds via humans, (3) movement restrictions, and (4) voluntary eradication in 5-7.5% of the herds. Almost all tested control strategies simulated a reduction in the spread of LA-MRSA. The combination of two, three or four intervention strategies showed additive effects and led to larger reductions in the predicted herd prevalence. In addition, the prevalence of LA-MRSA-positive herds at the time when control measures were initiated influenced the effects of the control strategies. Combining the simulated control measures can be considered in future action plans to control LA-MRSA.

Low accuracy of Bayesian latent class analysis for estimation of herd-level true prevalence under certain disease characteristics-An analysis using simulated data.

Estimation of the true prevalence of infected individuals involves the application of a diagnostic test to a population and adjusting according to test performance, sensitivity and specificity. Bayesian latent class analysis for the estimation of herd and animal-level true prevalence, has become increasingly used in veterinary epidemiology and is particularly useful in incorporating uncertainty and variability into analyses in a flexible framework. However, the approach has not yet been evaluated using simulated data where the true prevalence is known. Furthermore, using this approach, the within-herd true prevalence is often assumed to follow a beta distribution, the parameters of which may be modelled using hyperpriors to incorporate both uncertainty and variability associated with this parameter. Recently however, the authors of the current study highlighted a potential issue with this approach, in particular, with fitting the distributions and a tendency for the resulting distribution to invert and become clustered at zero. Therefore, the objective of the present study was to evaluate commonly specified models using simulated datasets where the herd-level true prevalence was known. The specific purpose was to compare findings from models using hyperpriors to those using a simple beta distribution to model within-herd prevalence. A second objective was to investigate sources of error by varying characteristics of the simulated dataset. Mycobacterium avium subspecies paratuberculosis infection was used as an example for the baseline dataset. Data were simulated for 1000 herds across a range of herd-level true prevalence scenarios, and models were fitted using priors from recently published studies. The results demonstrated poor performance of these latent class models for diseases characterised by poor diagnostic test sensitivity and low within-herd true prevalence. All variations of the model appeared to be sensitive to the prior and tended to overestimate herd-level true prevalence. Estimates were substantially improved in different infection scenarios by increasing test sensitivity and within-herd true prevalence. The results of this study raise questions about the accuracy of published estimates for the herd-level true prevalence of paratuberculosis based on serological testing, using latent class analysis. This study highlights the importance of conducting more rigorous sensitivity analyses than have been carried out in previous analyses published to date.

Drivers for Livestock-Associated Methicillin-Resistant Staphylococcus Aureus Spread Among Danish Pig Herds - A Simulation Study.

To gain insight into the rapid increase in the number of livestock-associated Methicillin-resistant Staphylococcus aureus (LA-MRSA)-positive herds in Denmark, we developed an individual-based Monte Carlo simulation model. We aimed to assess whether transmission of LA-MRSA via pig movements could explain the observed increase in the number of positive herds in Denmark, and to evaluate the effect of other between-herd transmission mechanisms. Pig movements alone were not sufficient to mimic the observed increase in LA-MRSA-positive herds in Denmark in any of the modelled scenarios. The model identified three factors that played important roles in the between-herd spread of LA-MRSA: (1) the within-herd dynamics, (2) the frequency and effectiveness of indirect transmissions, and (3) unexplainable introduction of LA-MRSA to swine herds. These factors can act as starting points for the development of LA-MRSA control programs in pig herds in order to limit the risk of its transmission to humans.

Risk factors for the occurrence of livestock-associated methicillin-resistant Staphylococcus aureus (LA-MRSA) in Danish pig herds.

Livestock-associated methicillin-resistant Staphylococcus aureus (LA-MRSA) is widespread in many European countries including Denmark, where 88% of randomly selected production herds tested positive in 2016. In the present study, we investigated herd-level risk factors for farms being classified as LA-MRSA positive (study 1), in addition to herd-level risk factors for farms changing status from LA-MRSA negative to LA-MRSA positive during a 2-year period (study 2). Risk factors previously identified in other studies were confirmed in study 1: large herd size, herd type (lower risk in herds with sows) and number of pig suppliers. Due to the effect of herd type, data from sow herds (N = 41) and herds without sows (N = 166) were analysed separately. A univariable analysis found that the variables significantly associated with LA-MRSA status for sow herds were: use of wet feed in the sow units; higher weights of piglets at weaning; availability of a delivery room on the farm; cleaning of aisles after pigs were moved; number of pigs per weaner section; number of pigs purchased in the past year, and factors related to rodent control and human traffic in the herd. In herds without sows, the univariable analysis showed that the presence of other species of animal on the farm; negative pressure ventilation; full sectioning; frequent visits from the veterinarian; peroral use of tetracyclines for weaners; number of pigs purchased in the past year, and factors related to rodent control and human traffic in the herd were significantly associated with LA-MRSA status. For herds that changed from LA-MRSA negative to positive (study 2), having a company contract for mouse control, having more than one pig supplier and using group medication in the drinking water were the variables associated with LA-MRSA status in the univariable analysis. We did not succeed in building a biologically meaningful multivariable model based on any of the datasets and, as observed in similar studies, many of the risk factors identified in the univariable analysis were related to herd size. It was therefore not possible to determine whether it was the size of the herd or related factors that were the causal risk factors for being LA-MRSA positive.

Send more data: a systematic review of mathematical models of antimicrobial resistance.

Background: Antimicrobial resistance is a global health problem that demands all possible means to control it. Mathematical modelling is a valuable tool for understanding the mechanisms of AMR development and spread, and can help us to investigate and propose novel control strategies. However, it is of vital importance that mathematical models have a broad utility, which can be assured if good modelling practice is followed. Objective: The objective of this study was to provide a comprehensive systematic review of published models of AMR development and spread. Furthermore, the study aimed to identify gaps in the knowledge required to develop useful models. Methods: The review comprised a comprehensive literature search with 38 selected studies. Information was extracted from the selected papers using an adaptation of previously published frameworks, and was evaluated using the TRACE good modelling practice guidelines. Results: None of the selected papers fulfilled the TRACE guidelines. We recommend that future mathematical models should: a) model the biological processes mechanistically, b) incorporate uncertainty and variability in the system using stochastic modelling, c) include a sensitivity analysis and model external and internal validation. Conclusion: Many mathematical models of AMR development and spread exist. There is still a lack of knowledge about antimicrobial resistance, which restricts the development of useful mathematical models.

Building the foundation for veterinary register-based epidemiology: A systematic approach to data quality assessment and validation.

Epidemiological studies often use data from registers. Data quality is of vital importance for the quality of the research. The aim of this study was to suggest a structured workflow to assess the quality of veterinary national registers. As an example of how to use the workflow, the quality of the following three registers was assessed: the Central Husbandry Register (CHR), the database for movement of pigs (DMP) and the national Danish register of drugs for veterinary use (VetStat). A systematic quantitative assessment was performed, with calculation the proportion of farms and observations with "poor quality" of data. "Poor" quality was defined for each measure (variable) either as a mismatch between and/or within registers, registrations of numbers outside the expected range, or unbalanced in- and outgoing movements. Interviews were conducted to make a complementary qualitative assessment. The proportion of farms and observations within each quality measure varied. This study highlights the importance of systematic quality assessment of register data and suggests a systematic approach for such assessments and validations without the use of primary data.

Author Correction: Methods for estimating disease transmission rates: Evaluating the precision of Poisson regression and two novel methods.

A correction to this article has been published and is linked from the HTML and PDF versions of this paper. The error has been fixed in the paper.

Evaluation of a multiplex immunoassay for bovine respiratory syncytial virus and bovine coronavirus antibodies in bulk tank milk against two indirect ELISAs using latent class analysis.

Bovine respiratory syncytial virus (BRSV) and bovine coronavirus (BCV) are responsible for respiratory disease and diarrhea in cattle worldwide. The Norwegian control program against these infections is based on herd-level diagnosis using a new multiplex immunoassay. The objective of this study was to estimate sensitivity and specificity across different cut-off values for the MVD-Enferplex BCV/BRSV multiplex, by comparing them to a commercially available ELISA, the SVANOVIR® BCV-Ab and SVANOVIR® BRSV-Ab, respectively. We analyzed bulk tank milk samples from 360 herds in a low- and 360 herds in a high-prevalence area. As none of the tests were considered perfect, estimation of test characteristics was performed using Bayesian latent class models. At the manufacturers' recommended cut-off values, the median sensitivity for the BRSV multiplex and the BRSV ELISA was 94.4 [89.8-98.7 95% Posterior Credibility Interval (PCI)] and 99.8 [98.7-100 95% PCI], respectively. The median specificity for the BRSV multiplex was 90.6 [85.5-94.4 95% PCI], but only 57.4 [50.5-64.4 95% PCI] for the BRSV ELISA. However, increasing the cut-off of the BRSV ELISA increased specificity without compromising sensitivity. For the BCV multiplex we found that by using only one of the three antigens included in the test, the specificity increased, without concurrent loss in sensitivity. At the recommended cut-off this resulted in a sensitivity of 99.9 [99.3-100 95% PCI] and specificity of 93.7 [88.8-97.8 95% PCI] for the multiplex and a sensitivity of 99.5 [98.1-100 95% PCI] and a specificity of 99.6 [97.6-100 95% PCI] for the BCV ELISA.

Latent class analysis of real time qPCR and bacteriological culturing for the diagnosis of Streptococcus agalactiae in cow composite milk samples.

Streptococcus agalactiae (S. agalactiae) has re-emerged as a mastitis pathogen among Norwegian dairy cows. The Norwegian cattle health services recommend that infected herds implement measures to eradicate S. agalactiae, this includes a screening of milk samples from all lactating cows. The performance of the qPCR-test currently in use for this purpose has not been evaluated under field conditions. The objective of this study was to estimate the sensitivity and specificity of the real-time qPCR assay in use in Norway (Mastitis 4 qPCR, DNA Diagnostics A/S, Risskov, Denmark) and compare it to conventional bacteriological culturing for detection of S. agalactiae in milk samples. Because none of these tests are considered a perfect reference test, the evaluation was performed using latent class models in a Bayesian analysis. Aseptically collected cow-composite milk samples from 578 cows belonging to 6 herds were cultured and tested by qPCR. While 37 (6.4%) samples were positive for S. agalactiae by bacteriological culture, 66 (11.4%) samples were positive by qPCR. The within-herd prevalence in the six herds, as estimated by the latent class models ranged from 7.7 to 50.8%. At the recommended cut-off (cycle threshold 37), the sensitivity of the qPCR was significantly higher at 95.3 (95% posterior probability interval [PPI] [84.2; 99.6]) than that of bacteriological culture at 58.2 (95% PPI [43.8; 74.4]). However, bacterial culture had a higher specificity of 99.7 (95% PPI [98.5; 100.0]) compared to the qPCR at 98.5 (95% PPI [94.6; 99.9]). The median estimated negative predictive values of qPCR was consistently higher than those of the BC at all estimated prevalences, and the superiority of the qPCR increased with increasing within-herd prevalence. The median positive predictive values of BC was in general higher than the estimates for the qPCR, however, at the highest prevalence the predictive ability of both tests were similar.

Persistence of antimicrobial resistance genes from sows to finisher pigs.

Antimicrobial resistance in pigs has been under scrutiny for many years. However, many questions remain unanswered, including whether the initial antimicrobial resistance level of a pig will influence the antimicrobial resistance found at slaughter. Faecal samples from finishers pigs from 681 farms and from sows from 82 farms were collected, and levels of seven antimicrobial resistance genes, ermB, ermF, sulI, sulII, tet(M), tet(O), and tet(W), were quantified by high-capacity qPCR. There were 40 pairs of observations where the finishers were born in the farms of the sows. The objective of this study was to evaluate whether the levels of AMR genes found in finisher pigs at slaughter were associated with the levels in the farm where the finishers were born, and whether the levels of the AMR genes were equal in the sow and finisher pig populations. We found a significant positive correlation between the levels of AMR genes in finishers and the sows in the farms where the pigs were born for some of the genes (ermB (ρ=0.47, p-value=0.002), ermF (ρ=0.41, p-value=0.03), and tet(O) (ρ=0.33, p-value=0.04)). Furthermore, there were significant differences between AMR gene levels for the sow and finisher populations for ermB, ermF, sulI, sulII, tet(O), and tet(W), though not for tet(M).