Risk factors for Salmonella Dublin on dairy farms in Ontario, Canada

Salmonella Dublin is an emerging pathogen on dairy farms in Canada. In Ontario, Salmonella Dublin has been increasingly isolated from diagnostic laboratory samples. The objective of this observational cross-sectional study was to identify management practices associated with herd positivity for Salmonella Dublin. A convenience sample of 100 dairy farms was visited in Ontario, Canada, from April to August 2022. Farms were visited once to collect blood samples from 20 heifers between 4 and 24 mo old, sample bulk tank milk, and administer an in-person questionnaire on management practices. An additional bulk tank milk sample was collected before the visit by milk transporters. All bulk tank and serum samples underwent ELISA testing to determine Salmonella Dublin positivity (≥35% positivity on ELISA). Of the 1,990 heifers sampled, 44 (2.2%) animals were seropositive for Salmonella Dublin. At least one seropositive heifer was identified on 24% of participating farms. Based on the bulk tank milk samples collected during both sampling periods, 4% of farms were positive for Salmonella Dublin. Overall, of the 100 farms visited, 25% were classified as Salmonella Dublin positive, meaning at least one serum or bulk tank sample was interpreted as positive. A multivariable logistic regression model identified 5 factors associated with herd-level positivity for Salmonella Dublin. Specifically, introducing purchased animals within the last 2 years increased the likelihood that farms were positive for Salmonella Dublin (odds ratio [OR] = 4.6). Farms that had at least one animal leave the premises for a cattle show, embryo collection center, or loan to another farm and return within the last 2 years were also at a higher risk for Salmonella Dublin (OR = 4.9). Farms that removed manure from the surface of bedding in calving pens twice per month or after every calving were at greater risk for Salmonella Dublin than farms that removed manure less frequently (OR = 8.5). Farms that added bedding material to calving areas once or twice weekly were at lower risk for Salmonella Dublin compared with farms that added bedding less than once weekly (OR = 0.1). In addition, farms that kept 3 cows or less per pen in the calving area were at lower risk for Salmonella Dublin. Test positivity for Salmonella Dublin among Ontario dairy farms sampled is high, and dairy producers should consider avoiding management practices that are associated with an increased risk of Salmonella Dublin infection.

Semi-Quantitative Biosecurity Assessment Framework Targeting Prevention of the Introduction and Establishment of Salmonella Dublin in Dairy Cattle Herds

An increasing average herd size and complexity in farm structures call for a higher level of biosecurity. It can reduce the risk of introducing and establishing pathogens with multiple-pathway and indirect spread mechanisms, such as Salmonella Dublin, a pathogen with an increasing occurrence in dairy cattle farms across different countries and continents. Therefore, this study aimed to use existing knowledge to develop a framework with a supporting tool allowing for a time-efficient, yet comprehensive, assessment of biosecurity measures that can help prevent the introduction and establishment of S. Dublin in dairy herds. Based on the literature review, a seven-step biosecurity assessment framework was developed and evaluated in collaboration with biosecurity experts. The resulting framework includes a weighted semi-quantitative assessment method with a scoring guide in an electronic supporting tool for 12 biosecurity sections assessed through on-farm observations and farmer interviews. The framework and tool provide a novel approach to comprehensively assess the overall (mainly external) on-farm biosecurity level by a trained biosecurity assessor. They can be used for systematic data collection in epidemiological studies on risk factors for the introduction and establishment of S. Dublin in dairy farms. Preliminary interrater reliability testing indicated moderate reliability between assessors with varying biosecurity skills.

Serological testing of an equal-volume milk sample - a new method to estimate the seroprevalence of small ruminant lentivirus infection?

BACKGROUND

In cattle attempts to evaluate within-herd prevalence of various infectious and parasitic diseases by bulk-tank milk (BTM) testing with ELISA have been made with moderate success. The fact that BTM is composed of variable and unknown volumes of milk from individual lactating animals weakens the relationship between numerical result of the ELISA and the within-herd prevalence. We carried out a laboratory experimental study to evaluate if a pooled milk sample created by mixing an equal volume of individual milk samples from seropositive and seronegative goats, henceforth referred to as an equal-volume milk sample (EVMS), would allow for accurate estimation of within-herd seroprevalence of caprine arthritis-encephalitis (CAE) using 3 different commercial ELISAs. By mixing randomly selected milk samples from seronegative and seropositive goats, 193 EVMS were created - 93 made of seronegative samples and 100 with the proportion of seropositive individual milk samples (EVMS_%POS) ranging from 1 to 100%. EVMS_%POS could be considered as a proxy for the within-herd seroprevalence. Then, OD of EVMS (OD_EVMS) of the 193 EVMS was measured using 3 commercial ELISAs for CAE - 2 indirect and 1 competitive.

RESULTS

The cut-off values of OD_EVMS indicating SRLV infection were determined. The regression functions were developed to link OD_EVMS with EVMS_%POS. A significant monotonic relationship between OD_EVMS measured with 2 commercial indirect ELISAs and EVMS_%POS was identified. Two regression models developed on this basis described approximately 90% of variability and allowed to estimate EVMS_%POS, when it was below 50%. High OD_EVMS indicated EVMS_%POS of > 50%.

CONCLUSION

Our study introduces the concept of serological testing of EVMS as a method of detecting SRLV-infected herds and estimating the proportion of strongly seropositive goats. Further field studies are warranted to assess practical benefits of EVMS serological testing.

Role of Infection and Immunity in Bovine Perinatal Mortality: Part 1. Causes and Current Diagnostic Approaches

While non-infectious causes are more commonly diagnosed in cases of bovine perinatal mortality (PM), the proportion caused by infections is highly variable between studies (~5-35%); the reasons for this variation, and possible underestimation, are discussed. The most important pathogen-specific infectious causes of PM are bacteria (in particular, Bacillus licheniformis and Leptospira spp.), viruses (in particular BVDv) and a parasite (Neospora caninum). However, co-infection may occur in a small proportion of cases and in many cases no single pathogen is detected but gross or microscopic lesions of an inflammatory response are identified. Diagnosis is complicated by the criteria required to establish exposure, infection and causation. Additionally, pathogens can be classified as primary or secondary though such differentiation can be arbitrary. The majority of infectious cases of PM are due to in utero infections but postnatal infections (0-2 days) can also cause PM. Diagnosis of infectious PM is based on a systematic investigation of the herd health history and dam and cohort sampling and examination of the perinate and its placenta. Gross and histopathologic examinations and maternal/herd and perinate serology form the basis of current infectious PM investigations.

Genomic Investigation of the Emergence of Invasive Multidrug-Resistant Salmonella enterica Serovar Dublin in Humans and Animals in Canada

Salmonella enterica subsp. enterica serovar Dublin is a zoonotic pathogen that often leads to invasive bloodstream infections in humans that are multidrug resistant. Described here are the results of Canadian national surveillance of S Dublin from 2003 to 2015 in humans and bovines, principally collected through the Canadian Integrated Program for Antibiotic Resistance Surveillance (CIPARS). An increase in human infections due to multidrug-resistant (MDR) S Dublin was observed in 2010, many of which were bloodstream infections. Phylogenomic analysis of human and bovine isolates revealed a closely related network that differed by only 0 to 17 single nucleotide variants (SNVs), suggesting some potential transmission between humans and bovines. Phylogenomic comparison of global publicly available sequences of S Dublin showed that Canadian isolates clustered closely with those from the United States. A high correlation between phenotypic and genotypic antimicrobial susceptibility was observed in Canadian isolates. IS26 replication was widespread among U.S. and Canadian isolates and caused the truncation and inactivation of the resistance genes strA and blaTEM-1B A hybrid virulence and MDR plasmid (pN13-01125) isolated from a Canadian S Dublin isolate was searched against NCBI SRA data of bacteria. The pN13-01125 coding sequences were found in 13 Salmonella serovars, but S Dublin appears to be a specific reservoir. In summary, we have observed the rise of invasive MDR S Dublin in humans in Canada and found that they are closely related to bovine isolates and to American isolates in their mobile and chromosomal contents.

INVITED REVIEW: Farm size and animal welfare

Critics of agricultural intensification have argued that the transition from smaller to larger farms has compromised animal welfare. To critically examine evidence relevant to this claim, we reviewed more than 150 publications that examined the relationship between farm size and at least one animal welfare indicator. Although much of this literature focuses on dairy cattle, we also reference other farmed species where appropriate. We found little evidence of any simple relationship, negative or positive, between farm size and animal welfare. Instead, the evidence suggests that larger farms provide some opportunities to improve animal welfare but may also create welfare risks. For example, larger farms permit more specialized and professional management of animal health but can make it more difficult to accommodate outdoor access that some view as integral to animal welfare. Future research should attempt to specify the underlying casual mechanisms by which statistical associations between farm size and indicators of welfare are believed to occur. We also suggest that policy and advocacy efforts aimed at reversing increases in farm size would be better directed toward improving welfare on farms of all sizes.

A register-based study of the antimicrobial usage in Danish veal calves and young bulls

High antimicrobial usage and multidrug resistance have been reported in veal calves in Europe. This may be attributed to a high risk of disease as veal calves are often purchased from numerous dairy herds, exposed to stress related to the transport and commingling of new animals, and fed a new ration. In this study, we used national register data to characterize the use of antimicrobials registered for large Danish veal calf and young bull producing herds in 2014.

A total of 325 herds with veal calf and potentially young bull production were identified from the Danish Cattle database. According to the national Danish database on drugs for veterinary use (VetStat), a total of 537,399 Animal Daily Doses (ADD₂₀₀) were registered for these 325 herds during 2014. The amount of antimicrobials registered in 2014 varied throughout the year, with the highest amounts registered in autumn and winter. Antimicrobials were registered for respiratory disorders (79%), joints/limbs/CNS disorders (17%), gastrointestinal disorders (3.7%) and other disorders (0.3%). Of the registered antimicrobials, 15% were for oral and 85% for parenteral administration. Long-acting formulations with a therapeutic effect of more than 48 h covered 58% of the drugs for parenteral use. Standardized at the herd-level, as ADD₂₀₀/100 calves/day, antimicrobial use distributed as median [CI_95%] for starter herds (n = 22): 2.14 [0.19;7.58], finisher herds (n = 24): 0.48 [0.00;1.48], full-line herds (n = 183): 0.78 [0.05;2.20] and herds with an inconsistent pattern of movements (n = 96): 0.62 [0.00;2.24]. Full-line herds are herds, which purchase calves directly from a dairy herd and raise them to slaughter.

Furthermore, we performed a risk factor analysis on the 183 herds with a full-line production. Here, we investigated, whether the number of suppliers, the number of calves purchased, the frequency of purchase, the average age at introduction, the average time in the herd and vaccination influenced the amount of antimicrobials used in the herds. The final multivariable regression analysis revealed that the number of calves introduced was positively associated with the antimicrobial use in the herd.

A multidisciplinary approach to determine factors associated with calf rearing practices and calf mortality in dairy herds

In the Netherlands, an increase in ear-tagged calf mortality (3 days to 1 year of age) in dairy farms was observed. The aim was to determine why calf mortality increased and how to reduce calf mortality in herds with structural high rates. A multi-disciplinary approach was chosen to study this phenomenon. First analysis of census data revealed that the majority of the calves died in the first month of life. In addition, a panel of 236 farmers indicated that the increase in calf mortality might be related to priority, time management and the mind-set of farmers. For that reason a questionnaire was carried out to detect risk factors for mortality among young calves (<1 month) in 100 dairy farms with increased calf mortality compared to 100 dairy farms with stable and below average calf mortality. The results showed that, besides management factors such as IBR and BVDV control, and purchase of cattle, also the answers to statements giving an indication on the farmers' mind-set, were associated with calf mortality. Therefore, a qualitative sociological study on the farmers' identity was conducted by performing in-depth interviews among 30 farmers with structurally high calf mortality rates. Afterwards, the results were communicated with a veterinary advisor who visited the farmers and gave tailored advice. Most of the interviewed farmers believed to have sufficient knowledge and skills regarding calf rearing. The farmers did not share their calf rearing problems with colleagues and advisors but they mentioned to be open to receive advice if not communicated in a reproaching or pedantic way. The sociologist distinguished three different phases of awareness concerning calf mortality among the farmers: (1) farmers who were only partly, or not at all, aware of high calf mortality; (2) farmers who felt powerless because of their inability to find a solution to their problems; and (3) farmers who knew they can be inaccurate when it comes to rearing calves, but were reluctant to change this. With the background information of the farmers' identity it was easier for the veterinary advisor to provide tailored advice resulting in a higher probability of following up. A first evaluation in which calf mortality rates in the six months after providing the advice were monitored, indicated that the advice resulted in reduced mortality. The combination of census data, epidemiological and qualitative sociological research revealed that advisors should be aware of the attitude and mind-set of the farmer and adapt their approach and advice accordingly.

Time-to-event analysis of predictors for recovery from Salmonella Dublin infection in Danish dairy herds between 2002 and 2012

Salmonella Dublin infections reduce gross margins and compromise animal health and welfare in dairy cattle herds. Despite on-going control efforts in several countries the duration and risk factors of a persistent infection have been difficult to study due to a lack of suitable data. This study utilised the unique opportunity to extract systematically collected repeated bulk-tank milk antibody measurements from all the Danish dairy herds during a 10-year period to perform a time-to-event analysis of the factors that affect the duration of test-positivity and the hazards of recovery from S. Dublin at herd level. Recovery was defined as a shift from test-positive to test-negative between two year-quarters followed by at least three more test-negative year-quarters. The average duration of infection was approximately 2 years. Predictors of recovery were tested in a multivariable Cox proportional hazard model allowing herds to recover from infection multiple times over the 10-year surveillance period. The model results were based on 36,429 observations with data on all the predictors, representing 3563 herds with a total of 3246 recoveries. Sixty-seven herds (2.4%) remained test-positive throughout the study period. The rest of the 317 herds that did not have any recoveries were censored, mainly due to a cessation of milk production. Prior recovery from test-positivity turned out not to be a significant predictor of recovery in the model. The effect of the duration of infection on the conditional probability of recovery (i.e. the hazard) was time-dependent: early in the study period, long durations of infection were predictive of a low hazard of recovery. Later in the control programme the effect of duration of infection was reduced indicating a desired effect of an intensified control programme. There was an increasing tendency towards longer durations and lower hazard of recovery with: (i) increasing herd sizes, (ii) increasing bulk-tank milk somatic cell counts, (iii) increasing local prevalence within a 5 km radius, (iv) organic farming and (v) recent purchase of cattle from test-positive herds. Participation in a voluntary paratuberculosis control programme reduced the duration of infection, and there were indications that recovery from S. Dublin infection was stimulated by a centrally organised and targeted control campaign. This is the first large-scale study that investigated duration of infection and predictors of recovery from S. Dublin in cattle herds over an extended period of time. The results provide useful knowledge for the design of control programmes for S. Dublin.

Within-herd prevalence ofSalmonellaDublin in endemically infected dairy herds

In this study within-herd prevalence ofSalmonellaDublin was investigated in three age groups (calves, young stock, adult cows) during five herd visits at 3-month intervals of 14 endemically infected dairy herds. A total of 10162 paired faecal cultures and antibody measurements were used to calculate the age and temporal dynamics of seroprevalence and prevalence of positive faecal cultures. Faecal culture-positive prevalence was generally low. It was highest (5·4%) in calves during December to February. Seroprevalence varied from 0% to 70% between herds, but was generally more stable in young stock and adult cows than in calves. Hierarchical mixed-model results showed that seroprevalence was associated with the bacteriological status in calves and cows, but not in young stock. These results can be used to develop and validate theoretical infection dynamics models and to design effective control programmes forSalmonellaDublin in dairy herds.

Salmonella Dublin faecal excretion probabilities in cattle with different temporal antibody profiles in 14 endemically infected dairy herds

This longitudinal field study investigated the hypothesis that persistently high antibody levels indicate a high risk of Salmonella Dublin shedding in animals in 14 endemically infected dairy herds. A hierarchical multivariable logistic regression was used to analyse 6614 paired faecal cultures and four types of temporal antibody profiles from cattle aged ≥180 days. Age and repeated measurements on animals nested within herds were taken into account. Overall, the prevalence of faecal shedders was low (0·3% and 2·8% in the lowest and highest risk groups, respectively). An important predictor of faecal shedding was young age. There was a significant, but modest increase in risk in cattle with persistently high or recently increased antibody levels, but no difference between these two groups. Contrary to previous recommendations, the detection of carriers by the use of repeated antibody testing is not likely to be a plausible control option in most Salmonella Dublin-infected dairy herds.

A new real-time PCR method for the identification of Salmonella Dublin

AIMS

Development of a real-time PCR method for the specific detection of Salmonella Dublin.

METHODS AND RESULTS

The method was directed towards a Salm. Dublin-specific sequence of the vagC gene on the Salmonella virulence plasmid (pSDV) and towards Salmonella genus-specific sequence of the invA gene, serving as an internal amplification control. The method showed 100% inclusivity and exclusivity when tested on a strain collection containing 50 serotyped S . Dublin strains, 20 strains of other Salmonella serotypes and 10 non- Salmonella strains. The method also showed 100% inclusivity and 99% exclusivity in a collaborative study comprising eight laboratories, where each laboratory received ten different S . Dublin strains and 10 other Salmonella serotypes.

CONCLUSIONS

The method showed excellent performance both when validated in the laboratory and in the collaborative study.

SIGNIFICANCE AND IMPACT OF THE STUDY

Application of the present method in food control, for example at slaughterhouses, can improve the contamination control of this veterinary and clinically important Salmonella serotype.

Survival analysis of factors affecting incidence risk of Salmonella Dublin in Danish dairy herds during a 7-year surveillance period

A national surveillance programme for Salmonella Dublin, based on regular bulk-tank milk antibody screening and movements of cattle, was initiated in Denmark in 2002. From 2002 to end of 2009 the prevalence of test-positive dairy herds was reduced from 26% to 10%. However, new infections and spread of S. Dublin between herds continued to occur. The objective of this study was to investigate factors affecting incidence risk of S. Dublin infection in Danish dairy herds between 2003 and 2009. Herds were considered at risk when they had been test-negative for at least four consecutive year-quarters (YQs), either at the start of the study period or after recovery from infection. Survival analysis was performed on a dataset including 6931 dairy herds with 118,969 YQs at risk, in which 1523 failures (new infection events) occurred. Predictors obtained from register data were tested in a multivariable, proportional hazard model allowing for recurrence within herds. During October to December the hazard of failures was higher (hazard ratio HR=3.4, P=0.0005) than the rest of the year. Accounting for the delay in bulk-tank milk antibody responses to S. Dublin infection, this indicates that introduction of bacteria was most frequent between July and October. Purchase from test-positive cattle herds within the previous 6 months was associated with higher hazard of failures (HR=2.5, P<0.0001) compared to no purchase and purchase from test-negative herds. Increasing local prevalence, herd size and bulk-tank milk somatic cell counts were also associated with increasing hazard of failures. The effect of prior infection was time-dependent; the hazard of failures was reduced following a logarithmic decline with increasing time at risk. The hazard was markedly higher in herds with prior infections the first year after becoming at risk again, and then approached the hazard in herds without known prior infections 2-3 years after becoming test-negative. This showed that herds with prior infections need to maintain a high level of biosecurity for at least 3 years after becoming test-negative for S. Dublin to prevent recurrence. Furthermore, general recommendations for dairy herds wishing to protect their herds against S. Dublin include avoidance of purchase from and contact to test-positive herds. Large herds, herds with test-positive neighbours and herds with high somatic cell counts need to obtain and maintain a high level of biosecurity.

Spatial patterns in surveillance data during control of Salmonella Dublin in bovine dairy herds in Jutland, Denmark 2003-2009

Salmonella Dublin is the most commonly isolated Salmonella serotype in Danish cattle and leads to economic and welfare losses in infected herds. Furthermore, it leads to high mortality in human cases. A national surveillance program for Salmonella Dublin was initiated in Denmark in October 2002. This study aimed at modelling the progress and spatial patterns during the control of Salmonella Dublin in dairy herds in the Jutland peninsula in Denmark, especially differences between regions and years. A total of 6331 dairy herds were included during 2003-2009. Antibody measurements of bulk-tank milk samples were used for testing herd-level Salmonella status in these dairy herds. Risk maps were estimated as prevalence intensity maps. Spatial clustering was analysed using scan statistics and SMR was estimated. In 2003, the prevalence of Salmonella Dublin test-positive dairy herds was 24%. It decreased to 12% in 2009. Prevalence intensity maps showed large differences in the reduction of Salmonella Dublin test-positive herds. The number of clusters reduced during the study period. However, throughout the study period two clusters remained significant. Differences were seen in the progress of the control between regions over the years. The implementation and effectiveness of the control program was different between regions. The progress of control was seen to vary not only between regions, but also over time influencing infection dynamics. Thus, recommendations and regionally targeted efforts during control campaigns are needed.

Prevalence and risk factors for Salmonella in veal calves at Danish cattle abattoirs

The study's objectives were to determine herd- and animal-level prevalence and herd-level risk factors for Salmonella in dairy-bred veal calves at slaughter in Denmark. In total, 1296 faecal samples were collected at five cattle abattoirs in Denmark during 2007–2008. The animals came from 71 randomly selected specialized veal-calf producers that delivered more than 100 animals to slaughter per year. Salmonella Dublin bacteria were isolated from 19 samples from 12 herds and Salmonella Typhimurium was isolated from one sample. The apparent prevalence of herds delivering Salmonella-shedding animals to slaughter was 18% (95% CI 9–27). The overall estimated true prevalence of shedding calves at slaughter was 1·3%. Veal-calf herds that purchased animals from herds not classified as low risk in the Danish Salmonella surveillance programme had significantly (P=0·03) higher risk of delivering Salmonella-shedding calves to slaughter. The results emphasize the importance of efforts in the dairy industry to ensure food safety for consumers.