Detection of Mycobacterium avium subspecies paratuberculosis in environmental samples by faecal culture and real-time PCR in relation to apparent within-herd prevalence as determined by individual faecal culture

High-Impact Risk Factors for Mycobacterium avium ssp. paratuberculosis in Dairy Herds in Germany

In a cross-sectional study, it was identified that three regions in Germany differed with respect to their herd-level prevalence for paratuberculosis in dairy cattle. In the study presented here, the same farms were analyzed to identify those components of biosecurity and farm management with the highest impact on Mycobacterium avium ssp. paratuberculosis (MAP) introduction and establishment in a farm. Hence, the data analyzes included 183, 170 and 104 herds from the study regions north, east and south, respectively. A herd was considered MAP-positive if at least one fecal environmental sample was positive. Twenty-six different possible risk factors from five different components of biosecurity and farm management were analyzed. We show that the average management of calf feeding increased the odds for a MAP-positive farm by 5.22 times (95% confidence interval (CI) = 1.25-21.83). With every 100-cow increase in farm size, the risk for a farm to test MAP-positive increased by 1.94 times (CI = 1.15-3.27), 1.14 times (CI = 1.02-1.27) and 5.53 times (CI = 0.44-68.97) in the north, east and south study regions, respectively. Furthermore, the purchase of cattle with an unknown MAP status increased the risk for a farm testing MAP-positive by 2.86-fold (CI = 1.45-5.67). Our results demonstrate that herd size, unknown MAP status of the purchased cattle and different aspects of calf feeding play an important role in the MAP status of a farm and should be in focus in regions with different MAP between-herd prevalence. Additionally, farm individual risk patterns should be identified during (veterinary) biosecurity consultancy.

Detection of Low MAP Shedder Prevalence in Large Free-Stall Dairy Herds by Repeated Testing of Environmental Samples and Pooled Milk Samples

Simple Summary

Paratuberculosis is a disease which affects ruminants worldwide. Many countries have implemented certification and monitoring systems to control the disease, particularly in dairy herds. Monitoring herds certified as paratuberculosis non-suspect is an important component of paratuberculosis herd certification programs. The challenge is to detect the introduction or reintroduction of the infectious agent as early as possible with reasonable efforts but high certainty. In our study, we evaluated different low-cost testing schemes in herds where the share of infected animals was low, resulting in a low within-herd prevalence of animals shedding the bacteria that causes paratuberculosis in their feces. The test methods used were repeated pooled milk samples and fecal samples from the barn environment. Our study showed that numerous repetitions of different samples are necessary to monitor such herds with sufficiently high certainty. In the case of herds with a very low prevalence, our study showed that a combination of different sampling approaches is required.

Abstract

An easy-to-use and affordable surveillance system is crucial for paratuberculosis control. The use of environmental samples and milk pools has been proven to be effective for the detection of Mycobacterium avium subsp. paratuberculosis (MAP)-infected herds, but not for monitoring dairy herds certified as MAP non-suspect. We aimed to evaluate methods for the repeated testing of large dairy herds with a very low prevalence of MAP shedders, using different sets of environmental samples or pooled milk samples, collected monthly over a period of one year in 36 herds with known MAP shedder prevalence. Environmental samples were analyzed by bacterial culture and fecal PCR, and pools of 25 and 50 individual milk samples were analyzed by ELISA for MAP-specific antibodies. We estimated the cumulative sensitivity and specificity for up to twelve sampling events by adapting a Bayesian latent class model and taking into account the between- and within-test correlation. Our study revealed that at least seven repeated samplings of feces from the barn environment are necessary to achieve a sensitivity of 95% in herds with a within-herd shedder prevalence of at least 2%. The detection of herds with a prevalence of less than 2% is more challenging and, in addition to numerous repetitions, requires a combination of different samples.

Evaluation of the Thuringian Bovine Johne’s Disease Control Program—A Case Study

The Thuringian Johne’s Disease (JD) Control Program provides a voluntary approach to JD control in Thuringia, a federal state of Germany. The program has three objectives: reduce the level of infection when present; reduce the spread of JD to uninfected herds; and facilitate the certification and protection of herds that are non-suspect with respect to JD. The program offers pathways for the management of affected herds and for certification of herds with continuing negative tests. After the control stage (CS), a certification stage of at least 3 consecutive years with continuing negative results in the annual whole-herd test has to be passed until a herd can be certified as ‘non-suspect’ with respect to JD. This study focused on calf mortality in relation to JD herd status. In a longitudinal study, the association of annual calf mortality rate of a total of 93 dairy herds (13 ‘non-suspect’; 26 in control stage; 54 not enrolled) over 10 consecutive years with JD herd status was investigated using a generalized mixed linear model with repeated measures. Non-suspect herds had a lower calf mortality rate compared with other farms. We conclude that establishing JD control measures lowers the calf mortality rate.

Detection of Mycobacterium avium Subspecies Paratuberculosis in Pooled Fecal Samples by Fecal Culture and Real-Time PCR in Relation to Bacterial Density

Simple Summary

Paratuberculosis is a worldwide disease causing serious impacts to the dairy industry. Within the context of paratuberculosis control programs, dairy herds have to be classified as either paratuberculosis-positive or paratuberculosis-free with minimum effort but with sufficient reliability. We aimed to estimate the detection rate of positive herds using a combination of random sampling and pooling of five or ten fecal samples. The pooled samples were analyzed with two different laboratory methods (bacterial culture and polymerase chain reaction). Pools of size 10 can be used without significant decrease of detection probability compared with pools of size 5. Analyzing randomly sampled and pooled fecal samples allows the detection of paratuberculosis-positive herds, but the detection probability in herds with only few infected animals (<5.0%) is not high enough to recommend this approach for one-time testing in such herds.

Abstract

Within paratuberculosis control programs Mycobacterium avium subsp. paratuberculosis (MAP)-infected herds have to be detected with minimum effort but with sufficient reliability. We aimed to evaluate a combination of random sampling (RS) and pooling for the detection of MAP-infected herds, simulating repeated RS in imitated dairy herds (within-herd prevalence 1.0%, 2.0%, 4.3%). Each RS consisted of taking 80 out of 300 pretested fecal samples, and five or ten samples were repeatedly and randomly pooled. All pools containing at least one MAP-positive sample were analyzed by culture and real-time quantitative PCR (qPCR). The pool detection probability was 47.0% or 45.9% for pools of size 5 or 10 applying qPCR and slightly lower using culture. Combining these methods increased the pool detection probability. A positive association between bacterial density in pools and pool detection probability was identified by logistic regression. The herd-level detection probability ranged from 67.3% to 84.8% for pools of size 10 analyzed by both qPCR and culture. Pools of size 10 can be used without significant loss of sensitivity compared with pools of size 5. Analyzing randomly sampled and pooled fecal samples allows the detection of MAP-infected herds, but is not recommended for one-time testing in low prevalence herds.

A pilot study using environmental screening to determine the prevalence of Mycobacterium avium subspecies paratuberculosis (MAP) and antimicrobial resistance (AMR) in Irish cattle herds

Background

Dairy and beef cattle can be reservoirs of many pathogens, including Salmonella and Mycobacterium avium subsp. paratuberculosis (MAP), the causative agent of Johne’s disease (JD). Farm environments may provide potential entry points for the transmission of infectious agents into the food chain. Antibiotics are used to treat a wide variety of infections on farms, and administration of antimicrobial agents to cattle is considered to be a driving factor for antimicrobial resistance (AMR). Control of JD and AMR are priority for animal health initiatives in Ireland. A national JD pilot programme was introduced by Animal Health Ireland in 2014, while the national action plan launched by Department of Health and Department of Agriculture, Food and Marine introduced in 2017 aims to improve the surveillance of AMR. The current investigation was undertaken as a pilot study to determine the proportion of herds positive for MAP, Salmonella species (Salmonella spp), commensal Escherichia coli (E. coli), Extended-spectrum beta-lactamase (ESBL) AmpC β-lactamase and carbapenemase-producing E. coli from 157 environmental faecal samples in Irish farms.

Results

MAP was detected in 10.2% of samples collected; on culture in 4 (4.9%) of the dairy herds and from 1 (1.3%) of the beef/suckler herds, and by PCR in 10 (12.3%) and 6 (7.9%) of these herds respectively. All culture positive herds were also positive by PCR. An additional 11 herds were positive by PCR only. Salmonella was not detected, while commensal E. coli were isolated from 70.7% of the samples (111/157) with 101 of these isolates shown to be fully susceptible to all antimicrobials tested. Of the 27 presumptive ESBL AmpC β-lactamase producing E. coli detected, one isolate was resistant to ten antimicrobials, nine isolates were resistant to nine antimicrobials, and four isolates were resistant to eight antimicrobials. Carbapenemase-producing E. coli were not isolated.

Conclusions

The results highlight the importance of monitoring farm environments for Johne’s disease. This disease is a growing concern for dairy and beef producers in Ireland, and sampling the farm environment may offer a useful means to rapidly screen for the presence of MAP. Non-pathogenic common enteric commensal and multiple-drug-resistant E. coli may contribute to AMR acting as a reservoir and transferring resistance to other species/pathogens in the environment.

Prevalence of Mycobacterium avium subsp. paratuberculosis infection in dairy herds in Northern Antioquia (Colombia) and associated risk factors using environmental sampling

This cross-sectional study aimed to determine Mycobacterium avium subsp. paratuberculosis (MAP) herd-level prevalence using a quantitative real-time PCR method (qPCR), performed on environmental samples. Secondly, the study aimed to explore herd-level risk factors associated with the presence of MAP in dairy herds with in-paddock milking facilities of the Northern region of the Province of Antioquia (Colombia). Study herds (n = 292) located in 61 different districts from six municipalities were randomly selected amongst 7794 dairies registered in the foot-and-mouth disease vaccination records from 2015. The sampling strategy considered a proportional allocation, both at municipality and district level. Participant herds were visited once between June and October 2016 to collect one composite environmental sample and to complete a risk assessment questionnaire. Each composite environmental sample contained material from six different sites of concentration of adult cattle and/or high traffic areas (e.g. areas surrounding waterers and feeders, areas surrounding the current mobile milking-unit places). Identification of MAP was achieved using a duplex qPCR (Bactotype MAP PCR Kit^®, Qiagen). A herd was considered as MAP infected if the environmental sample was positive in the qPCR. Information about the general characteristics of the herd, management practices, and knowledge about the disease was collected using the risk-assessment questionnaire. The information on risk factors was analyzed using a multivariable logistic regression model. The apparent herd-level prevalence was 4.1% (12/292; 95% CI: 1.8-6.4). Herds with a history of mixed farming of cattle with other ruminants had higher odds of being MAP infected than herds without (OR = 3.9; 95% CI: 1.2-13.2). Our study demonstrates the MAP prevalence in dairy herds from Antioquia, Colombia and the possible relationship between MAP environmental positivity with the history of mixed farming of cattle with other susceptible ruminants.

Prevalence of Mycobacterium avium ssp. paratuberculosis infections in Canadian dairy herds

Johne's disease is a progressive, chronic disease with inflammation of the small intestine of ruminants caused by Mycobacterium avium ssp. paratuberculosis (MAP). Accurately estimating prevalence of MAP infections is important when controlling spread of infection or monitoring effectiveness of control programs. In the absence of a consistent test method used in prevalence studies across Canada, prevalence estimates among regions and programs cannot be compared. The aim of the current study was to estimate and compare prevalence of MAP infection in Western Canada, Ontario, Québec, and the Atlantic provinces, as well as among varying herd sizes and housing types. On 362 dairy farms located in all 10 provinces of Canada, environmental samples were collected and cultured for detection of MAP. For each herd, 1 sample was collected from the lactating cow area and manure storage. An additional environmental sample was collected from the area where breeding-age heifers were housed. Using prior distributions from previous research, diagnostic sensitivity and specificity were calculated to assess the ability of only 2 environmental samples (manure storage and lactating cow area) to identify MAP-positive farms, resulting in a sensitivity and specificity of 38 and 100%, respectively. We found no difference in sensitivity and specificity when including breeding-age heifers environmental samples. Test characteristics were applied to environmental culture results from the 362 participating farms in all 4 regions, resulting in true prevalence estimates of 66% for farms in Western Canada, 54% in Ontario, 24% in Québec, and 47% in Atlantic Canada. Herds housed in tiestalls had lower prevalence than freestall-housed herds, and herds with 101-150 and >151 cows had higher prevalence than herds with ≤100 cows. This was the first time MAP prevalence was determined using 1 detection method, performed in 1 laboratory, and within a single year across Canada, enabling direct comparisons of prevalence among regions, housing types, and herd sizes.

Environmental sample characteristics and herd size associated with decreased herd-level prevalence of Mycobacterium avium ssp. paratuberculosis

Environmental sampling is an effective method for estimating regional dairy herd-level prevalence of infection with Mycobacterium avium ssp. paratuberculosis (MAP). However, factors affecting prevalence estimates based on environmental samples are not known. The objective was to determine whether odds of environmental samples collected on farm changed culture status over 2 sampling times and if changes were specific for location and type of housing (freestall, tiestall, or loose housing), the sample collected (i.e., manure of lactating, dry, or sick cows; namely, cow group), and effects of herd size. In 2012-2013 [sampling 1 (S1)] and 2015-2017 [sampling 2 (S2)], 6 environmental samples were collected and cultured for MAP from all 167 (99%) and 160 (95%) farms, respectively, in the province of Saskatchewan, Canada. Only the 148 dairy farms sampled at both sampling periods were included in the analysis. A mixed effects logistic regression was used to determine whether differences between sampling periods were associated with herd size and sample characteristics (cow group contributing to environmental sample, type of housing, and location). In S1 and S2, 55 and 34%, respectively, of farms had at least 1 MAP-positive environmental sample. Correcting for sensitivity of environmental sampling, estimated true prevalence in S1 and S2 was 79 and 48%, respectively. Herds with >200 cows were more often MAP-positive than herds with <51 cows in both S1 and S2. The percentage of positive samples was lower in S2 compared with S1 for all sampled areas, cow groups contributing to samples, types of housing where samples were collected, and herd size categories. However, samples collected from dry cow areas had the largest decrease in MAP-positive samples in S2 compared with all other cow group samples. Herds that were MAP-negative in S1 with a herd size 51 to 100 or 101 to 150 were more likely to stay MAP-negative, whereas MAP-positive herds with >200 cows more frequently stayed MAP-positive. No difference was observed in the odds of a sample being MAP-positive among housing types or location of sample collection in both sample periods. Of all farms sampled, 104 (70%) did not change status from S1 to S2. In conclusion, when herd-level MAP prevalence decreased over the 3-yr interval, the change in prevalence differed among herd size categories and was larger in samples from dry cow areas. It was, however, not specific to other characteristics of environmental samples collected.

Evaluation of different diagnostic methods for the detection of Mycobacterium avium subsp. paratuberculosis in boot swabs and liquid manure samples

Background

Environmental sampling based on boot swabs and/or liquid manure samples is an upcoming strategy for the identification of paratuberculosis (paraTB) positive herds, but only limited data are available regarding the diagnostic performance of molecular detection methods (qPCR) versus faecal culture (FC) for this purpose. In the present study, the test characteristics of two different qPCR protocols (A and B) and a standardized FC protocol, for the detection of Mycobacterium avium subsp. paratuberculosis in boot swabs and liquid manure samples were evaluated.

Results

In 19 paraTB unsuspicious and 58 paraTB positive herds boot swabs and liquid manure were sampled simultaneously and analyzed in three different diagnostic laboratories. Using boot swabs and liquid manure, a substantial to excellent accordance was found between both qPCRs, for boot swabs also with culture, while for liquid manure the detection rate of culture was decreased after prolonged storage at −20 °C. The quantitative results of both qPCR methods correlated well for the same sample and also for boot swabs and liquid manure from the same herd. When cut-off threshold cycle (C_T-)-values were applied as recommended by the manufacturers, herd level specificity (Sp) of qPCR B was below 100% for boot swabs and for both qPCRs for liquid manure. A decreased herd level sensitivity was encountered after adjustment of Sp to 100% and re-calculation of the cut-off C_T-values.

Conclusions

qPCR is equally suitable as bacterial culture for the detection of Mycobacterium avium subsp. paratuberculosis in boot swabs and liquid manure samples. Both matrices represent easily accessible composite environmental samples which can be tested with reliable results. The data encourage qPCR testing of composite environmental samples for paraTB herd diagnosis.

PCR Inhibition of a Quantitative PCR for Detection of Mycobacterium avium Subspecies Paratuberculosis DNA in Feces: Diagnostic Implications and Potential Solutions

Molecular tests such as polymerase chain reaction (PCR) are increasingly being applied for the diagnosis of Johne's disease, a chronic intestinal infection of ruminants caused by Mycobacterium avium subspecies paratuberculosis (MAP). Feces, as the primary test sample, presents challenges in terms of effective DNA isolation, with potential for PCR inhibition and ultimately for reduced analytical and diagnostic sensitivity. However, limited evidence is available regarding the magnitude and diagnostic implications of PCR inhibition for the detection of MAP in feces. This study aimed to investigate the presence and diagnostic implications of PCR inhibition in a quantitative PCR assay for MAP (High-throughput Johne's test) to investigate the characteristics of samples prone to inhibition and to identify measures that can be taken to overcome this. In a study of fecal samples derived from a high prevalence, endemically infected cattle herd, 19.94% of fecal DNA extracts showed some evidence of inhibition. Relief of inhibition by a five-fold dilution of the DNA extract led to an average increase in quantification of DNA by 3.3-fold that consequently increased test sensitivity of the qPCR from 55 to 80% compared to fecal culture. DNA extracts with higher DNA and protein content had 19.33 and 10.94 times higher odds of showing inhibition, respectively. The results suggest that the current test protocol is sensitive for herd level diagnosis of Johne's disease but that test sensitivity and individual level diagnosis could be enhanced by relief of PCR inhibition, achieved by five-fold dilution of the DNA extract. Furthermore, qualitative and quantitative parameters derived from absorbance measures of DNA extracts could be useful for prediction of inhibitory fecal samples.

Johne's disease: reliability of environmental sampling to characterize Mycobacterium avium subspecies paratuberculosis (MAP) infection in beef cow-calf herds

Environmental samples are considered to be a cost-effective method of identifying Mycobacterium avium subsp. paratuberculosis (MAP)-positive dairy herds, but evidence for beef cow-calf herds is weak. This study aims at evaluating this approach in a total of 20 German herds that were characterized by individual faecal samples (n = 2545) of all cows. For 14 MAP-positive herds having at least one MAP-positive animal, the within-herd prevalence was calculated from concurrent individual faecal culture-based testing. Six herds certified as 'MAP free' based on the negative results of previous years served as MAP-negative controls. On average, six environmental samples were taken at the end of winter from areas with high cow traffic and tested for MAP by faecal culture. According to the environmental samples, nine (64·3%) out of the 14 MAP-positive cow-calf herds were infected. The percentage of positive environmental samples and the apparent within-herd prevalence (Spearman's P = 0·73, P < 0·001) as well as the herd-level test results (positive and negative) and the herd's status based on individual testing (Fisher's exact test, P = 0·014) showed a positive association. Considering limitations in low-prevalence herds, MAP-positive beef cow-calf herds are detectable by environmental samples in temperate climate zones.

Within-herd prevalence thresholds for the detection of Mycobacterium avium subspecies paratuberculosis-positive dairy herds using boot swabs and liquid manure samples

The control of Johne's disease requires the identification of Mycobacterium avium ssp. paratuberculosis (MAP)-positive herds. Boot swabs and liquid manure samples have been suggested as an easy-to-use alternative to sampling individual animals in order to diagnose subclinical Johne's disease at the herd level, but there is a need to evaluate performance of this approach in the field. Using a logistic regression model, this study aimed to calculate the threshold level of the apparent within-herd prevalence as determined by individual faecal culture, thus allowing the detection of whether a herd is MAP positive. A total of 77 boot swabs and 75 liquid manure samples were taken from 19 certified negative and 58 positive dairy herds. Faecal culture, three different polymerase chain reaction (PCR) methods and the combination of faecal culture with PCR were applied in order to detect MAP. For 50% probability of detection, a within-herd prevalence threshold of 1·5% was calculated for testing both matrices simultaneously by faecal culture and PCR, with the threshold increased to 4·0% for 90% probability of detection. The results encourage the use of boot swabs or liquid manure samples, or a combination both, for identifying MAP-positive herds and, to a certain extent, for monitoring certified Johne's disease-negative cattle herds.