Mycobacterium avium subsp. paratuberculosis in cow bulk tank milk in Cyprus detected by culture and quantitative IS900 and F57 real-time PCR

Isolation and identification of nontuberculous mycobacteria from raw milk and traditional cheese based on the 16S rRNA and hsp65 genes, Tehran, Iran

As an important source of human food, milk can be a carrier of human pathogenic bacteria, including tuberculous and nontuberculous mycobacteria (NTM), in its raw and unpasteurized state. In this research, 175 raw milk samples and 175 traditional cheese samples were collected from traditional dairy stores in 22 regions of Tehran in a 9- month period from August 2019 to May 2020. Samples were prepared and transferred to a specialized laboratory, where they were inoculated in Lowenstein-Jensen (LJ) medium containing glycerol or sodium pyruvate, as well as Herrold's egg-yolk with and without Mycobactin J. to determine the sample's identity of samples. The recommended 16S rRNA (1436 bp) and hsp65 (644 bp) gene fragments from the positive isolates identified in Ziehl-Neelsen (Z-N) staining were amplified and sequenced using PCR and compared with the sequences of the gene fragments of reference strains available in the global GenBank database. No mycobacterial species were isolated from traditional cheese samples in microbial culture. In case of raw milk samples, a total of four bacteria were collected, all of which were found in the genetic differential testing to be NTM, including n = 1 Mycobacterium heraklionense, n = 2 Mycolicibacterium fortuitum, and n = 1 Mycobacterium thermoresistibile. The analysis of the results obtained by isolate sequencing using the 16S rRNA gene showed higher discriminatory power and percentage similarities in the identification of the isolates than the hsp65 gene.

Prevalence of paratuberculosis in cattle in China: A systematic review and meta-analysis

Bovine paratuberculosis is a chronic infectious disease caused by Mycobacterium avium subspecies paratuberculosis (MAP). Here, a systematic literature review was conducted to investigate the bovine paratuberculosis distribution and associated risk factors in China before 2022. The databases CNKI, VIP, WanFang, PubMed, and ScienceDirect were used to search for articles. The random effect model of the "Meta" package of "R" software was used, and the Arcsine transformation was chosen for the rate conversion analysis. To reveal the factors that led to research heterogeneity, the research data were used for subgroup analysis and univariate meta-regression analysis. Among the 1238 identified articles, 54 met the eligibility criteria. Based on data obtained from the selected articles, the combined positive rate of bovine paratuberculosis was 6.95% in China. In the sampling year subgroup, the positive rate of bovine paratuberculosis before 2013 was 4.94%, which was lower than in other time periods. In the sampling season subgroup, the highest positive rate of bovine paratuberculosis in cattle was 14.60% in the autumn. Furthermore, in the detection method subgroup, the highest positive rate of bovine paratuberculosis was 7.21%, which was detected by using ELISA. In the age subgroup, the positive rate of bovine paratuberculosis was 17.47% in cattle > 12 months old, significantly higher than other age subgroups. The highest positive rate of bovine paratuberculosis was 11.35% for female cattle in the gender subgroup, while in the geographic region subgroup, the highest positive rate was 8.12% for East China, which was significantly higher than in other regions. The highest positive rate of bovine paratuberculosis was for dairy cattle (8.00%), and the highest positive rate by rearing method was 11.03% for non-scale farming. The effects of different geographical and climatic factors on the positive rate of bovine paratuberculosis were evaluated. In summary, we recommend focusing on screening cattle infected with MAP in warm and humid areas.

Improved DNA Amplification of the Hallmark IS900 Element in Mycobacterium avium subsp. paratuberculosis: a Reexamination Based on Whole-Genome Sequence Analysis

Amplification of the IS900 multicopy element is a hallmark nucleic acid-based diagnostic test for Mycobacterium avium subsp. paratuberculosis, which causes Johne's disease in ruminants. This assay is frequently used to determine the presence of the bacterium in feces of infected cattle and sheep. Two IS900 primer sets developed in the 1990s were widely used for decades, and their use has continued in current studies. However, these primers were developed prior to the availability of complete genome sequences. Recent sequence analysis of the binding locations for one primer pair (P90/P91) identified errors and binding inefficiencies that can be easily corrected to further increase detection sensitivity. The P90 primer is missing two nucleotides that should be present near the 3' end, and it does not bind all copies of IS900 due to 5' deletions at some IS900 loci. These IS900 primer pairs, along with newly developed primers, were tested by real-time PCR on purified genomic DNA to determine which primer set performed the best and how primer design errors affect amplification efficiencies. The newly designed PCR primer set (JB5) showed increased sensitivity by two to three quantification cycles using purified genomic DNA and was similar in efficiency to 150C/921. These tests were extended using DNA from feces and tissues of infected cows, which showed similar results. Finally, a 167-bp partial duplication of IS900 was found in type I strains. Although P90 and P91 primers successfully amplify M. avium subsp. paratuberculosis DNA, their use should be discontinued in favor of more efficient primer pairs in future studies. IMPORTANCE This study is an example of how applied genomic analysis can aid diagnostic test improvements. Detection of Mycobacterium avium subsp. paratuberculosis infection of livestock prior to the appearance of clinical disease signs is very difficult but essential for identifying animals shedding the bacterium to prevent transmission of Johne's disease. Total M. avium subsp. paratuberculosis quantity in the feces as determined by real-time PCR (qPCR) using the IS900 target indicates bacterial shedding status and potential for transmission of the pathogen. However, legacy primers designed prior to the availability of complete genome sequences that are used in these tests to detect M. avium subsp. paratuberculosis were based on data from only a single copy of IS900 and not considering all copies collectively as a group. This approach resulted in primer design errors which can be easily corrected to improve test sensitivities. We tested original primers that contain these errors and their corrected versions by qPCR and showed improved sensitivity on purified genomic DNA as well as fecal and tissue samples. These findings may help detect the organism from environmental samples on farms where sensitivity is currently lacking.

Recovery of Mycobacteria from Heavily Contaminated Environmental Matrices

For epidemiology studies, a decontamination method using a solution containing 4.0% NaOH and 0.5% tetradecyltrimethylammonium bromide (TDAB) represents a relatively simple and universal procedure for processing heavily microbially contaminated matrices together with increase of mycobacteria yield and elimination of gross contamination. A contamination rate only averaging 7.3% (2.4% in Cluster S; 6.9% in Cluster R and 12.6% in Cluster E) was found in 787 examined environmental samples. Mycobacteria were cultured from 28.5% of 274 soil and water sediments samples (Cluster S), 60.2% of 251 samples of raw and processed peat and other horticultural substrates (Cluster R), and 29.4% of 262 faecal samples along with other samples of animal origin (Cluster E). A total of 38 species of slow and rapidly growing mycobacteria were isolated. M. avium ssp. hominissuis, M. fortuitum and M. malmoense were the species most often isolated. The parameters for the quantitative detection of mycobacteria by PCR can be significantly refined by treating the sample suspension before DNA isolation with PMA (propidium monoazide) solution. This effectively eliminates DNA residue from both dead mycobacterial cells and potentially interfering DNA segments present from other microbial flora. In terms of human exposure risk assessment, the potential exposure to live non-tuberculous mycobacteria can be more accurately determined.

Diagnostic Sequences That Distinguish M. avium Subspecies Strains

Over a decade ago Mycobacterium avium subspecies paratuberculosis (Map) specific genes were initially identified in a whole genome context by comparing draft genome sequences of Map strain K-10 with Mycobacterium avium subspecies hominissuis (Mah) strain 104. This resulted in identification of 32 Map specific genes, not including repetitive elements, based on the two-genome comparison. The goal of this study was to define a more complete catalog of M. avium subspecies-specific genes. This is important for obtaining additional diagnostic targets for Johne's disease detection and for understanding the unique biology, evolution and niche adaptation of these organisms. There are now over 28 complete genome sequences representing three M. avium subspecies, including avium (Maa), Mah, and Map. We have conducted a comprehensive comparison of these genomes using two independent pan genomic comparison tools, PanOCT and Roary. This has led to the identification of more than 250 subspecies defining genes common to both analyses. The majority of these genes are arranged in clusters called genomic islands. We further reduced the number of diagnostic targets by excluding sequences having high BLAST similarity to other mycobacterial species recently added to the National Center for Biotechnology Information database. Genes identified as diagnostic following these bioinformatic approaches were further tested by DNA amplification PCR on an additional 20 M. avium subspecies strains. This combined approach confirmed 86 genes as Map-specific, seven as Maa-specific and three as Mah-specific. A single-tube PCR reaction was conducted as a proof of concept method to quickly distinguish M. avium subspecies strains. With these novel data, researchers can classify isolates in their freezers, quickly characterize clinical samples, and functionally analyze these unique genes.

Phage Amplification Assay for Detection of Mycobacterial Infection: A Review

An important prerequisite for the effective control, timely diagnosis, and successful treatment of mycobacterial infections in both humans and animals is a rapid, specific, and sensitive detection technique. Culture is still considered the gold standard in the detection of viable mycobacteria; however, mycobacteria are extremely fastidious and slow-growing microorganisms, and therefore cultivation requires a very long incubation period to obtain results. Polymerase Chain Reaction (PCR) methods are also frequently used in the diagnosis of mycobacterial infections, providing faster and more accurate results, but are unable to distinguish between a viable and non-viable microorganism, which results in an inability to determine the success of tuberculosis patient treatment or to differentiate between an active and passive infection of animals. One suitable technique that overcomes these shortcomings mentioned is the phage amplification assay (PA). PA specifically detects viable mycobacteria present in a sample within 48 h using a lytic bacteriophage isolated from the environment. Nowadays, an alternative approach to PA, a commercial kit called Actiphage™, is also employed, providing the result within 6–8 h. In this approach, the bacteriophage is used to lyse mycobacterial cells present in the sample, and the released DNA is subsequently detected by PCR. The objective of this review is to summarize information based on the PA used for detection of mycobacteria significant in both human and veterinary medicine from various kinds of matrices.

A novel one-day phage-based test for rapid detection and enumeration of viable Mycobacterium avium subsp. paratuberculosis in cows' milk

Abstract

Bacteriophage-based methods for the rapid detection of viable Mycobacterium avium subsp. paratuberculosis (MAP) in veterinary specimens are a recent addition to the Johne’s disease diagnostic toolbox. Here, we report the use of D29 mycobacteriophage-coated tosylactivated paramagnetic beads to capture and concentrate MAP cells from samples (termed phagomagnetic separation, PhMS) and then naturally lyse viable MAP cells (from the inside out) to provide DNA for IS900 qPCR purposes. Transmission electron microscopy confirmed that D29 phages had bound to beads in the correct orientation and that the phage-coated beads captured MAP cells from a suspension. During test optimization, conventional IS900 PCR results were used to subjectively assess the effect of different phage:bead coating ratios, differing amounts of coated beads during PhMS, optimal incubation time post-PhMS to obtain maximal MAP DNA, and the potential benefit of a brief heat shock (55 °C/1 min) prior to IS900 TaqMan qPCR. The limit of detection 50% (LOD_50%) of the optimised PhMS-qPCR assay was 10.00 MAP cells/50 ml milk (95% CI 1.20–82.83). Finally, in order to demonstrate the new assay’s ability to detect viable MAP in naturally contaminated milk, bulk tank milk samples from 100 dairy farms were tested. Forty-nine (49%) of these tested PhMS-qPCR-positive, with viable MAP numbers detected ranging from 3–126 MAP/50 ml. The novel PhMS-qPCR assay is a sensitive, specific and easy-to-apply phage-based assay for viable MAP, with potential application for milk surveillance or diagnosis of Johne’s disease.

Key points

• Phage-coated magnetic beads could capture, concentrate and lyse MAP cells from milk.

• PhMS-qPCR assay proved to be a rapid, sensitive and specific test for viable MAP.

• A potential application of PhMS-qPCR assay for milk surveillance was demonstrated.

The development and use of Actiphage® to detect viable mycobacteria from bovine tuberculosis and Johne's disease-infected animals

Here, we describe the development of a method that exploits bacteriophage D29 as a lysis agent for efficient DNA extraction from low numbers of mycobacterial cells. This method (Actiphage® ) used in combination with PCR achieved rapid and sensitive (LOD ≤ 10 cell ml-1 ) detection and identification of viable, pathogenic mycobacteria in blood samples within 6 h. We demonstrate that mycobacteriophage D29 can be used to detect a range of mycobacteria from clinical blood samples including both Mycobacterium tuberculosis complex and Mycobacterium avium subsp. paratuberculosis without the need for culture and confirms our earlier observations that a low-level bacteraemia is associated with these infections in cattle. In a study of M. bovis-infected cattle (n = 41), the sensitivity of the Actiphage® method was 95 % (95 % CI; 0.84-0.99) and specificity was 100 % (95% CI; 0.92-1). We further used Actiphage® to demonstrate viable Mycobacterium avium subsp. paratuberculosis is present in the blood of Johne's infected cattle. This method provides a revolutionary new tool for the study of infections caused by these difficult to grow pathogens.

Flock sensitivity and specificity of pooled fecal qPCR and pooled serum ELISA for screening ovine paratuberculosis

The aim of our study was to evaluate the flock sensitivity and specificity of fecal qPCR and serum ELISA using pooled samples for screening paratuberculosis in French sheep.

Using individual feces with low or high qPCR Ct values from ewes sampled in 14 infected flocks, a total of 555 pools of size 5, 10 and 20 were created by diluting individual materials in negative feces and analysed using a commercial IS900 qPCR kit. The relative performances of pooled serum ELISA analysis were evaluated based on the analysis of 181 different pools of size 5 and 10, composed of individual serum samples of various individual S/P values. Results showed that for pools of size 5, 10 or 20, individual fecal samples with low Ct values were invariably detected. Conversely fecal samples with high Ct values were associated with a lower detection rate in both pools of size 5 (87.0% to 90.0%), 10 (63.0% to 70.7%) and 20 (46.7% to 60.0%). After lowering the decision threshold to 25% and 15% for serum pools of size 5 and 10 respectively, the pooled serum ELISA relative sensitivity ranged between 62.2% and 100.0% depending on the composition of the pools.

Finally, a simulation study was carried out to evaluate the performances of 16 screening strategies at flock level, with varying pool size (5 to 20) and number (5 to 60). The use of pooled serum ELISA led to very false positive detection rate ranging between 37.6% and 91.8% in paratuberculosis free flocks and prevents its further use in that context. For infection prevalence ≤ 5%, the flock sensitivity based on pooled fecal qPCR ranged between 39.0% (5 pools of size 10) and 99.9% (300 sampled individuals, with pools of size 5,10 or20), and was always above 93% when the infection prevalence was greater or equal to 15%. We conclude that pooled-fecal qPCR but not pooled-serum ELISA could be a useful tool to detect sheep flocks infected with paratuberculosis.

Management of Mycobacterium avium subsp. paratuberculosis in dairy farms: Selection and evaluation of different DNA extraction methods from bovine and buffaloes milk and colostrum for the establishment of a safe colostrum farm bank

The aim of this study was to develop and validate different innovative DNA extraction methods to detect Mycobacterium avium subsp. paratuberculosis (MAP) DNA from bovine and buffalo colostrum. Paratuberculosis is a chronic inflammatory infection of domestic and wild animals, especially ruminants, caused by MAP. The primary route of disease transmission is feces, but MAP can also be excreted in milk and colostrum. In 2015, the Italian Ministry of Health has issued a voluntary control plan of MAP in order to allow risk‐based certification of bovine and buffaloes farms. In addition to the annual diagnostic screening and to the clinical surveillance of animals the plan includes the adoption of biosecurity and management measures to progressively mitigate the incidence of MAP. To achieve this goal it is crucial to ensure the accuracy of the methods used to detect the presence of MAP in bovine and buffaloes milk and colostrum, in order to: (1) support a "safe colostrum farm‐bank" set‐up and thus prevent the main within‐farm MAP transmission route and (2) to allow the MAP‐free certification of milk products for export purposes. To achieve these goals, seven different DNA extraction protocols were identified from bibliography, out of which three methods were finally selected after the adoption of an evaluation procedure aimed at assessing the efficiency of extraction of DNA, the purity of DNA and the adaptability of the DNA amplification: NucleoSpin^® Food Kit (Macherey‐Nagel), NucleoSpin^® Food Kit (Macherey‐Nagel) combined with the magnetic beads, and QIAamp Cador Pathogen Mini kit (QIAGEN). In particular, the NucleoSpin^® Food Kit (Macherey‐Nagel) and the QIAamp Cador Pathogen Mini kit (QIAGEN) were tested on bovine and buffalo colostrum, showing a LOD between 4 × 10⁴ (2.6 × 10⁶ cfu/ml) and 4.08 (26.7 cfu/ml) IS900 target copies and a LOD between 5.3 × 10⁵ (4.1 × 10⁶ cfu/ml) and 53 (4.1 × 10³ cfu/ml) IS900 target copies, respectively.

ISMap02 element targeted nested polymerase chain in the detection of Mycobacterium avium subsp. paratuberculosis in fecal samples of cattle and buffaloes

Background and Aim

Johne's disease is chronic granulomatous enteritis which affects ruminants. There are many diagnostic approaches for the detection of Mycobacterium avium subsp. paratuberculosis (MAP) of which molecular detection methods using various elements are less time consuming and more accurate. The present study was conducted using ISMap02 element for nested polymerase chain reaction (nPCR) based detection of MAP in fecal samples. The aim was to test the sensitivity and specificity of the ISMap02 element and also to use this element for the detection of MAP in fecal samples of cattle and buffaloes.

Materials and Methods

A total of 211 fecal samples of cattle and buffaloes from different herds around Ludhiana aged between 2 and 13 years were collected, and DNA extraction was done from these samples. The nPCR was carried out for the detection of MAP in fecal samples.

Results

The ISMap02 element was specific for the detection of MAP only and showed a sensitivity of detection of 7.6 fg/µL of the standard genomic DNA. Among the 211 fecal samples of cattle and buffaloes tested for the ISMap02 element, 18 samples (8.5%) were positive for MAP.

Conclusion

The ISMap02 element is specific and sensitive for the detection of MAP in various samples, and when used in nPCR format, it can increase the sensitivity of detection.

Exploring the potential hazard of Mycobacterium avium subspecies paratuberculosis as a cause for Crohn's disease

Background:

Mycobacterium avium subspecies paratuberculosis (MAP) is the causative agent of Johne’s disease (JD), or paratuberculosis in ruminants has been suspected to be implicated in the pathogenesis of Crohn’s disease (CD) in humans with chronic inflammatory intestinal changes. As the hypothesis is now fast being recognized that MAP could possibly be the etiological agent of CD which is found to be excreted in milk of dairy animals subclinically or terminally ill with JD.

Aim:

The present study was aimed to detect MAP in milk by polymerase chain reaction (PCR) targeting IS900 and to describe the excretion pattern of MAP in milk from asymptomatic lactating cows and does with relevance to the public health significance.

Materials and Methods:

A total of 77 milk samples were collected randomly from lactating animals which include cows (45) and does (32). All the 77 milk samples were processed to identify the presence of MAP by employing the direct IS900 PCR as per the standard protocol.

Results:

Out of 77 milk samples from asymptomatic lactating animals, 12 (15.58%) were showed positivity for IS900 PCR in which 5 (11.11%) were from lactating cows and 7 (21.87%) were from lactating does.

Conclusion:

In our study, 15.58% of milk samples showed IS900 positivity which indicates the presence of subclinical MAP infection in lactating animals. Hence, there is a possibility for excretion of MAP through milk which can be a potential threat for CD in humans by raw milk consumption. Therefore, the prevention of MAP in the food chain need to be assured by sourcing raw products from animal herds free of MAP infection.

Investigation of Mycobacterium avium complex (MAC) in Australian commercial milk using qPCR

This technical research communication describes the first study to use quantitative polymerase chain reaction (qPCR) to investigate the presence of Mycobacterium avium complex (MAC) in Australian pasteurised milk. MAC is the most common NTM responsible for human illnesses and includes M. avium subspecies paratuberculosis (MAP). MAC is a causative agent of lymphadenitis in children, with contaminated food and water considered as a likely source. As such the presence of MAC in milk would have public health significance. MAP has been linked to Crohn's disease and is also the causative agent of Johne's disease in cattle. Previous studies have detected MAP in pasteurised milk from Brazil, India, Czech Republic, USA, Argentina, UK, Iran, Ireland and the United Kingdom. This study investigated a total of 180 commercially available Australian pasteurised milk samples which were tested for MAC DNA in triplicate using PCR. All samples were negative for MAC DNA. An additional 14 milk samples were tested, incubated for 3 weeks at 37 °C to potentially increase the concentration of any viable MAC that may be present and then retested. All samples were again negative for MAC DNA. This could be due to concentrations below the limit of detection, limited sample size or could be reflective of the Australian biosecurity control protocols and surveillance of Johne's disease in ruminant animals.

Detection of Mycobacterium avium subsp. paratuberculosis in bovine milk from the state of Pernambuco, Brazil

The aim of this study was to detect the IS900 region of Mycobacterium avium subsp. paratuberculosis (MAP) in bovine milk samples using real-time polymerase chain reaction (qPCR) and conventional PCR, and to study the agreement between these tests. A total of 121 bovine milk samples were collected from herds considered positive for MAP, from the State of Pernambuco, Brazil. MAP DNA was detected in 20 samples (16.5%) using conventional PCR and in 34 samples (28.1%) using qPCR. MAP DNA was detected in all of the 6 animal farms studied. Moderate agreement was found between qPCR and conventional PCR results, where the sensitivity and specificity of conventional PCR in relation to qPCR were 50% and 96.6%, respectively. Thus, the IS900 region of MAP was found in bovine milk samples from the State of Pernambuco. To the best of our knowledge, this is the first report of MAP DNA found in bovine milk in Northeast Brazil. We also demonstrated the qPCR technique is more sensitive than conventional PCR with respect to detection of MAP in milk samples.

Comparative risk assessment for new cow-level Mycobacterium avium ssp. paratuberculosis infections between 3 dairy production types: Organic, conventional, and conventional-grazing systems

Johne's disease, a granulomatous enteritis of ruminant animals, is a hidden threat on dairy farms, adversely affecting animal welfare as well as herd productivity. Control programs in the United States advocate for specific management practices to temper the spread of the causal organism (Mycobacterium avium ssp. paratuberculosis, MAP), such as improving calving area hygiene and limiting introduction of replacement stock with unknown infection status. A need remains for direct exploration of Johne's disease prevention strategies in the United States with respect to production type. Alongside the growing demand for organic products, the safety of organic dairy practices with respect to MAP control is warranted. Further, conventional herds for which organic practices such as pasture grazing are used should be situated within the risk spectrum. We developed a risk assessment model using the US Voluntary Bovine Johne's Disease Control Program as a framework, with the goal of evaluating the risk of new cow-level MAP infections. A total of 292 organic and conventional farms in 3 states were surveyed on management practices, and an overall analysis was conducted in which each farm was first scored on individual practices using a range of "no risk" to "high risk," according to the literature. The sum of all risk factors was then analyzed to quantify and compare the risk burden for each production type. Organic herds received higher overall risk scores compared with both conventional grazing and nongrazing subtypes. To identify which factors contributed to the overall increased risk for organic herds, the management practices were categorized and evaluated by logistic regression. We determined that the increased risk incurred by organic herds was predominantly due to decisions made in the calving area and preweaned calf group. However, although certain individual risk factors related to calf management are commonly involved in prevention strategies (e.g., cow/calf separation) and were thus included in the overall risk assessment, empirical evidence linking them to the spread of MAP is lacking. Instead, these factors are problematic when executed with other management decisions, leading to a hypothesized synergism of transmission risk. To this end, we developed a set of compound risk factors, which were also evaluated as outcomes in logistic regression models, with production type serving as the predictor of interest. Organic farms in our study were more susceptible to risks associated with the synergism of study variables. Notably, organic producers were most likely to allow calves to spend extended time with the dam, while also lacking a dedicated calving area. Additionally, calves in organic herds were more often permitted to nurse even with poor udder hygiene on farm. A heightened vigilance toward calving area hygiene is therefore indicated for these herds.

Mycobacterium avium ssp. paratuberculosis detection in animals, food, water and other sources or vehicles of human exposure: A scoping review of the existing evidence

Mycobacterium avium ssp. paratuberculosis is the etiologic agent of Johne's disease in ruminants and is hypothesized to be an infectious cause of Crohn's disease, as well as some other human diseases. Due to key knowledge gaps, the potential public health impact of M. paratuberculosis is unknown. This scoping review aims to identify and characterised the evidence on potential sources and vehicles of M. paratuberculosis exposure for humans to better understand how exposure is likely to occur. Evidence from 255 primary research papers is summarized; most examined the prevalence or concentration of M. paratuberculosis in animals (farmed domestic, pets and wildlife) (n=148), food for human consumption (62) (milk, dairy, meat, infant formula) or water (drinking and recreational) and the environment (farm, pasture and areas affected by runoff water) (20). The majority of this research has been published since 2000 (Figure- abstract). Nine case-control studies examining risk factors for Crohn's disease highlighted significant associations with the consumption of processed meats and cheese, while direct contact with ruminants, high risk occupations (farmer, veterinarian), milk consumption and water source were factors not associated with the disease and/or M. paratuberculosis exposure status. Molecular epidemiology studies demonstrated strain-sharing between species. Produce and seafood were the only previously suggested sources of human exposure for which there was no supporting evidence identified in this scoping review. The results of this review indicate that ruminant populations from around the globe are infected with M. paratuberculosis and many non-ruminant species have also been found to carry or be infected with M. paratuberculosis. Several potential sources for human exposure to M. paratuberculosis were identified; however there remain important gaps in quantitative information on the prevalence and concentration of M. paratuberculosis in contaminated sources of exposure. This information is critical to understanding the risk of exposure, opportunities for risk mitigation interventions and modelling exposures to distill the importance of various sources of human exposure to M. paratuberculosis including direct contact with animals and the environment as well as consumption of contaminated foods and water. Results of this study may be used to prioritize future research and to support evidence-informed decision-making on the M. paratuberculosis issue.

Estimation of Mycobacterium avium subsp. paratuberculosis load in raw bulk tank milk in Emilia-Romagna Region (Italy) by qPCR

Consumption of milk and dairy products is considered one of the main routes of human exposure to Mycobacterium avium subsp. paratuberculosis (MAP). Quantitative data on MAP load in raw cows' milk are essential starting point for exposure assessment. Our study provides this information on a regional scale, estimating the load of MAP in bulk tank milk (BTM) produced in Emilia-Romagna region (Italy). The survey was carried out on 2934 BTM samples (88.6% of the farms herein present) using two different target sequences for qPCR (f57 and IS900). Data about the performances of both qPCRs are also reported, highlighting the superior sensitivity of IS900-qPCR. Seven hundred and eighty-nine samples tested MAP-positive (apparent prevalence 26.9%) by IS900 qPCR. However, only 90 of these samples were quantifiable by qPCR. The quantifiable samples contained a median load of 32.4 MAP cells mL(-1) (and maximum load of 1424 MAP cells mL(-1) ). This study has shown that a small proportion (3.1%) of BTM samples from Emilia-Romagna region contained MAP in excess of the limit of detection (1.5 × 10(1) MAP cells mL(-1) ), indicating low potential exposure for consumers if the milk subsequently undergoes pasteurization or if it is destined to typical hard cheese production.

PCR-based detection of Mycobacterium avium subsp. paratuberculosis infection in cattle in South Korea using fecal samples

Mycobacterium avium subsp. paratuberculosis (MAP) is the causative agent of bovine paratuberculosis (PTB). The first step in the control of PTB is the identification and isolation of sub-clinical fecal shedders from the herd. In the current study, real-time and nested PCR targeting MAP-specific genetic elements (IS900 and ISMAP02) DNA isolated from fecal samples were used to detect MAP infection in cattle. Of the 1,562 fecal samples obtained from 37 herds, regardless of diarrhea, 35 samples tested positive in both IS900-targeted real-time and ISMAP02-targeted nested PCR. At the herd level, 12 of the 37 herds were found to be positive for MAP. Detection rates of the PCR tests were similar to those reported for ELISA-based methods. These results suggest that PCR can be used to detect sub-clinical fecal shedders of MAP.

Mycobacterium avium Subspecies paratuberculosis and Bovine Leukemia Virus Seroprevalence and Associated Risk Factors in Commercial Dairy and Beef Cattle in Northern and Northeastern China

Mycobacterium avium subspecies paratuberculosis (MAP) and bovine leukemia virus (BLV) are important pathogens, commonly responsible for economical loss to cattle farms all over the world, yet their epidemiology in commercial dairy and beef cattle in China is still unknown. Thus, from September 2013 to December 2014, a large-scale seroprevalence study was conducted to determine the seroprevalence and identify herd-level risk factors associated with MAP and BLV infection. The source sample was 3674 cattle from 113 herds in northern and northeastern China. Antibodies against MAP and BLV were detected using ELISA tests. At animal-level, the seroprevalence of antibodies against MAP and BLV was 11.79% (433/3674) and 18.29% (672/3674), respectively. At herd-level, the seroprevalence of antibodies against MAP and BLV was 20.35% and 21.24% (24/113), respectively. Herd size was identified to be associated with MAP infection while herd size and presence of cattle introduced from other farms were significantly associated with BLV infection. Further research is needed to confirm these findings and improve the knowledge of the epidemiology of these two pathogens in these regions and elsewhere in China.

Influence of Stress Connected with Moving to a New Farm on Potentially MAP-Infected Mouflons

There is no European legislation concerning paratuberculosis that requires that imported animals be kept in quarantine and commonly they are directly released into areas with other animals. In this study, detection of latent infection of paratuberculosis in healthy mouflons previously diagnosed as paratuberculosis-free, but originating from a real time quantitative PCR- (qPCR-) positive herd, occurred after their transport to a new farm. During a twelve-day quarantine period, all mouflons irregularly shed Mycobacterium avium subsp. paratuberculosis (MAP) in faeces, and in a small number of cases also in milk. After the animals were released from quarantine, MAP was detected for a further two days, after which, testing was negative, except in one case. Therefore, the stress connected with transport, novel environment, dietary change, or limited area with high density of animals might have contributed to the induction of paratuberculosis and the shedding of MAP from the animals, previously diagnosed as MAP-negative. According to these results, the keeping of imported animals in quarantine and their examination for MAP presence not only before the transport but also afterwards should be recommended. The designation of a particular area of a farm as a quarantine enclosure could help to mitigate the impact of stress caused by a confined space with a high density of animals.

Detection of Mycobacterium avium subsp. paratuberculosis in bulk tank milk by combined phage-PCR assay: evidence that plaque number is a good predictor of MAP

Conventional culture and a rapid phage-PCR method were used to detect Mycobacterium avium subsp. paratuberculosis (MAP) in bulk tank milk (BTM) samples. Only two of 225 samples (0.9%) were found to contain MAP by culture whereas 50 (22%) MAP-positive samples were identified using the phage-PCR assay, including both samples that were MAP-culture positive. Results using the phage-based method for independently tested duplicate samples indicated that the assay is very reproducible (r(2)=0.897), especially when low levels of mycobacteria are present. A relationship was established between plaque number and the presence of MAP in a sample. A cut-off value was determined allowing identification of MAP-positive samples based on plaque number alone (90% sensitivity, 99% specificity; area under the curve=0.976). These results indicate that the assay is a robust method for screening BTM, providing results within 24 h.

Optimization of hexadecylpyridinium chloride decontamination for culture of Mycobacterium avium subsp. paratuberculosis from milk

A protocol was optimized for the isolation of Mycobacterium avium subsp. paratuberculosis (MAP) from milk and colostrum, with parameters including chemical decontamination, antibiotics, and different culture media. This study demonstrates that the efficiency of MAP recovery from milk is highly dependent upon the culturing protocol, and such protocols should be optimized to ensure that low concentrations of MAP in milk can be detected.

Paratuberculose em ruminantes no Brasil

A paratuberculose ou doença de Johne é uma enterite granulomatosa causada por Mycobacterium avium subsp. paratuberculosis (Map) e comumente afeta ruminantes domésticos, no entanto, pode infectar várias espécies de mamíferos. Está presente nos cinco continentes e é considerada endêmica em algumas regiões pela Organização Internacional de Epizootias (OIE). Pertence à lista de enfermidades notificáveis, que compreende as doenças transmissíveis de importância sócio-econômica e/ou em saúde-pública, cujo controle é necessário para o comércio internacional de animais e alimentos de origem animal. A importância da doença de Johne não se restringe somente aos prejuízos econômicos causados à indústria animal, mas também na possível participação do Map na íleocolite granulomatosa que afeta seres humanos, conhecida como doença de Crohn. No Brasil, a paratuberculose já foi descrita em diversas espécies de ruminantes e em vários estados. Embora os relatos naturais da enfermidade sejam pontuais, acredita-se na possibilidade da transmissão interespecífica e na disseminação do agente através da compra e venda de animais infectados. O objetivo deste artigo foi reunir as informações disponíveis referentes aos aspectos epidemiológicos, clínico-patológicos e laboratoriais da paratuberculose em bovinos, bubalinos, caprinos e ovinos no Brasil, e salientar a necessidade de implementação de medidas de controle sanitário da enfermidade no país, o que possibilitaria a melhoria da qualidade e valorização dos produtos de origem animal no mercado internacional.

Recent research on bovine paratuberculosis in South Korea

Bovine paratuberculosis (Johne's disease), a chronic and debilitating disease of ruminants caused by Mycobacterium avium subspecies paratuberculosis (MAP), is a major cause of chronic ruminant enteritis. A national eradication program has been in place in South Korea since the first report of the disease in 1967; however, only limited data on bovine paratuberculosis in South Korea are available. Some research, such as investigations of the reactivity of animal sera against MAP antigens, has been done in localized areas and in limited animal species. Compared with the worldwide situation, the development of diagnostic methods in South Korea has shown similar results even though some data were obtained from international collaborative studies. MAP is considered by some to be zoonotic, noting an association with Crohn's disease, although this issue is still controversial; however, research into this association is limited. Decisions based on disease priorities have hampered active progress in research on the disease. In this paper, we reviewed the available results generated from South Korea compared with global research. Finally, we propose a theme for future research.

Paratuberculose em caprinos e ovinos no Estado da Paraíba

Mediante o teste de ELISA foi determinada a presença de anticorpos para Mycobacterium avium subsp. paratuberculosis (map) em amostras de soro de 734 caprinos e 392 ovinos, sem sinais clìnicos aparentes, provenientes de 14 Municipios do semiárido Paraibano. Em caprinos, a frequência média de anticorpos de 44,86± 22,91% e em ovinos foi de 52,96±31,49. Das 46 propriedades estudadas, 44 (95,65%) apresentaram pelo menos um animal soropositivo. Nos 14 municípios avaliados houve presença de animais sorologicamente positivos, variando de 20% a 70%. Em caprinos sem raça definida e mestiços a frequência (48,56%) foi significativamente inferior (P<0,0270) que a de caprinos de raças puras (57,24%). Em ovinos com escore de 1 a 3 a frequência (59,39%) foi significativamente maior (P=0,0034) que a frequência em ovinos com escore superior a 3 (42,42%). Não houve diferença significativa nas frequências em caprinos e ovinos de diferentes idades, em caprinos com diferente escore corporal e em ovinos de diferentes raças. No exame microbiológico, em cultivos em meio HEYM com micobactina J, foram observadas colônias semelhantes às do Map em 9 (6,58%) das 180 amostras de fezes, sendo uma de caprinos e 8 de ovinos. Na coloração de Ziehl Nieelsen as bactérias apresentavam características morfo-tintorias de Map. Os resultados obtidos indicam alta frequência de caprinos e ovinos infectados com Map no semiárido da Paraíba, tornando-se necessário desenvolver pesquisas sobre a epidemiologia e forma de controle da doença nas condições de criação da região.

Occurrence of Mycobacterium avium subsp. paratuberculosis in milk at dairy cattle farms: a systematic review and meta-analysis

Presence of Mycobacterium avium subsp. paratuberculosis (MAP) in milk for human consumption is a concern due to its possible relationship with Crohn's disease in humans. Pasteurization effectively reduces the MAP load by four to five logs, but the efficacy depends on the MAP concentration, which depends on the prevalence among contributing herds and individuals. Considerable variation of MAP in bulk tank milk (BTM) and individual cow's milk (IM) is reported, but factors associated with MAP occurrence in milk at farm level have not been described. This study systematically reviewed published studies aiming at estimating the occurrence of MAP in on-farm BTM and IM by meta-analysis. A total of 692 articles were identified through electronic databases and initially screened using title and abstract. The quality of the 61 potentially relevant articles was assessed using full text and 31 articles were eventually included in the meta-analysis. The apparent prevalence (AP) of MAP in BTM and IM on farm were summarized in relation to strata defined by the test used to identify MAP and the infection status of the herds/animals. There was considerable inconsistency in the reporting, resulting in missing information potentially explaining the dispersion in the estimated AP. The overall AP and 95% confidence intervals based on PCR and culture of MAP were summarized to 0.10 (0.04-0.22) in BTM and 0.20 (0.12-0.32) in IM. Quantifying the MAP load in test-positive milk samples was not possible because very few articles provided quantitative information on individual samples.

Molecular approaches to analysing the microbial composition of raw milk and raw milk cheese

The availability and application of culture-independent tools that enable a detailed investigation of the microbiota and microbial biodiversity of food systems has had a major impact on food microbiology. This review focuses on the application of DNA-based technologies, such as denaturing gradient gel electrophoresis (DGGE), temporal temperature gradient gel electrophoresis (TTGE), single stranded conformation polymorphisms (SSCP), the polymerase chain reaction (PCR) and others, to investigate the diversity, dynamics and identity of microbes in dairy products from raw milk. Here, we will highlight the benefits associated with culture-independent methods which include enhanced sensitivity, rapidity and the detection of microorganisms not previously associated with such products.

Modeling the occurrence of Mycobacterium avium subsp. paratuberculosis in bulk raw milk and the impact of management options for exposure mitigation

Mycobacterium avium subsp. paratuberculosis (MAP) is the causal agent of paratuberculosis (Johne's disease) in cattle and other farm ruminants. The potential role of MAP in Crohn's disease in humans and the contribution of dairy products to human exposure to MAP continue to be the subject of scientific debate. The occurrence of MAP in bulk raw milk from dairy herds was assessed using a stochastic modeling approach. Raw milk samples were collected from bulk tanks in dairy plants and tested for the presence of MAP. Results from this analytical screening were used in a Bayesian network to update the model prediction. Of the 83 raw milk samples tested, 4 were positive for MAP by culture and PCR. We estimated that the level of MAP in bulk tanks ranged from 0 CFU/ml for the 2.5th percentile to 65 CFU/ml for the 97.5th percentile, with 95% credibility intervals of [0, 0] and [16, 326], respectively. The model was used to evaluate the effect of measures aimed at reducing the occurrence of MAP in raw milk. Reducing the prevalence of paratuberculosis has less of an effect on the occurrence of MAP in bulk raw milk than does managing clinically infected animals through good farming practices.

Highly specific and quick detection of Mycobacterium avium subsp. paratuberculosis in feces and gut tissue of cattle and humans by multiple real-time PCR assays

Mycobacterium avium subsp. paratuberculosis is the causative agent of Johne's disease (JD) in cattle and may be associated with Crohn's disease (CD) in humans. It is the slowest growing of the cultivable mycobacteria, and culture from clinical, veterinary, food, or environmental specimens can take 4 months or even longer. Currently, the insertion element IS900 is used to detect M. avium subsp. paratuberculosis DNA. However, closely related IS900 elements are also present in other mycobacteria, thus limiting its specificity as a target. Here we describe the use of novel primer sets derived from the sequences of two highly specific single copy genes, MAP2765c and MAP0865, for the quantitative detection of M. avium subsp. paratuberculosis within 6 h by using real-time PCR. Specificity of the target was established using 40 M. avium subsp. paratuberculosis isolates, 67 different bacterial species, and two intestinal parasites. Using the probes and methods described, we detected 27 (2.09%) M. avium subsp. paratuberculosis-positive stool specimens from 1,293 individual stool samples by the use of either IS900 or probes deriving from the MAP2765c and MAP0865 genes described here. In general, bacterial load due to M. avium subsp. paratuberculosis was uniformly low in these samples and we estimated 500 to 5,000 M. avium subsp. paratuberculosis bacteria per gram of stool in assay-positive samples. Thus, the methods described here are useful for rapid and specific detection of M. avium subsp. paratuberculosis in clinical samples.

Application of a peptide-mediated magnetic separation-phage assay for detection of viable Mycobacterium avium subsp. paratuberculosis to bovine bulk tank milk and feces samples

Naturally contaminated bovine bulk tank milk (n = 44) and feces (n = 39) were tested for the presence of viable Mycobacterium avium subsp. paratuberculosis by a novel peptide-mediated magnetic separation-phage (PMS-phage) assay. Counts of viable M. avium subsp. paratuberculosis cells ranging from 1 to 110 PFU/50 ml of milk and 6 to 41,111 PFU/g of feces were indicated by the PMS-phage assay.

Mycobacterium avium subsp. paratuberculosis in dairy products, meat, and drinking water

Mycobacterium avium subsp. paratuberculosis (Map) is the cause of Johne's disease, a chronic infection of the gut, in ruminant animals that provide milk and/or meat for human consumption. Map also may be involved in Crohn's disease and type 1 diabetes in humans. Although the role of Map in human diseases has not been established, minimizing the exposure of humans to the organism is considered desirable as a precautionary measure. Infected animals can shed Map in feces and milk, and the organism can become disseminated in tissues remote from the gut and its associated lymph nodes. The presence of at least some Map in raw milk and meat and in natural waters is likely, but the numbers of Map in those foods and waters should be reduced through cooking or purification. The available information relating to Map in milk and dairy products, meats, and drinking water is reviewed here for assessment of the risks of exposure to Map from consumption of such foods and water.

How accurately can we detect Mycobacterium avium subsp. paratuberculosis infection?

Mycobacteria have thwarted detection by scientists for centuries. Mycobacterium paratuberculosis is one of the most fastidious of the Mycobacteriaceae, and has been implicated in both animal and human diseases. In domestic livestock, M. paratuberculosis has been associated with Johne's disease, which given its increasing incidence, is currently a cause for concern, due to the potential for M. paratuberculosis to enter our food chain. In addition, a tenuous link has been reported between M. paratuberculosis and Crohn's disease, however evidence to support this link is hampered by the lack of accurate methodologies for detection of M. paratuberculosis in humans. This review compares the sensitivity and specificity of traditional and more recent techniques to the culture and molecular detection of M. paratuberculosis. While serology and culture are popular choices for the livestock industry they have not produced useful data for human infection. Although the advent of molecular biology has enabled faster diagnosis of M. paratuberculosis in human infection, there is currently no gold standard such as culture on which to validate these findings. Even with DNA/RNA detection methods, there is the ever present issue of the genetic relatedness of M. paratuberculosis to other mycobacteria of the Mycobacterium avium complex, some of which also infect humans with very different pathological outcomes. Recent developments in this field include more rapid methods of M. paratuberculosis culture as well as the development of more accurate and sensitive PCR assays. The application of these techniques should offer a greater insight as to the role of M. paratuberculosis in human gastrointestinal diseases.

A novel real-time PCR assay for specific detection and quantification of Mycobacterium avium subsp. paratuberculosis in milk with the inherent possibility of differentiation between viable and dead cells

Background

Mycobacterium avium subsp. paratuberculosis (MAP) is the etiological agent of paratuberculosis (Johne's disease) in ruminants and is suggested to be one of the etiologic factors in Crohn's disease in humans. Contaminated milk might expose humans to that pathogen. The aim of the present study was to develop a novel real-time PCR assay providing the additional possibility to detect viable Mycobacterium avium subsp. paratuberculosis (MAP) based on the MAP-specific Mptb52.16 target. The design included an internal amplification control to identify false negative results.

Findings

Inclusivity and exclusivity tested on 10 MAP strains, 22 non-MAP mycobacteria, and 16 raw milk microflora strains achieved 100%. The detection limit in artificially contaminated raw milk was 2.42 × 10¹ MAP cells/ml milk. In a survey of naturally contaminated samples obtained from dairy herds with a known history of paratuberculosis, 47.8% pre-milk and 51.9% main milk samples tested positive. Real-time PCR-derived MAP-specific bacterial cell equivalents (bce) ranged from 1 × 10⁰ to 5.1 × 10² bce/51 ml; the majority of samples had less than one bce per ml milk. Expression of the chosen target was detected in artificially contaminated raw milk as well as inoculated Dubos broth, thus confirming the real-time PCR assay's potential to detect viable MAP cells.

Conclusions

Concentrating the DNA of a large sample volume in combination with the newly developed real-time PCR assay permitted quantification of low levels of MAP cells in raw milk and pasteurized milk. The selected target - Mptb52.16 - is promising with regard to the detection of viable MAP. Future studies integrating quantitative DNA- and RNA-based data might provide important information for risk assessment concerning the presence of MAP in raw milk and pasteurized milk.

Paratuberculose em caprinos e ovinos no Brasil

Este trabalho relata, pela primeira vez no Brasil, no Estado da Paraíba, paratuberculose em dois rebanhos com criação conjunta de caprinos e ovinos. Na Fazenda 1, de um rebanho de 33 caprinos e 13 ovinos, uma cabra adulta apresentou emagrecimento progressivo por aproximadamente um ano e fezes pastosas um mês antes da morte. Todos os animais do rebanho foram tuberculinizados com a prova comparativa. Um ovino (2,2%) teve resultado positivo à tuberculina aviar e em dois o teste foi inconclusivo. Na Fazenda 2, com 200 ovinos e 80 caprinos, foi afetada uma ovelha adulta que apresentou emagrecimento progressivo por aproximadamente um ano e fezes pastosas por aproximadamente 20 dias. Todos os ovinos com mais de 4 meses de idade e 23 caprinos foram tuberculinizados com tuberculina aviar; em 47 (25,4%) o resultado foi positivo, em 115 (61,5%) inconclusivo e em 25 (13,4%) negativo. Entre as cabras não houve nenhuma positiva à tuberculina aviar, mas em 11 (47,8%) o teste foi inconclusivo e em 12 (52,2%) foi negativo. Na necropsia dos dois animais com sinais clínicos os linfonodos mesentéricos estavam aumentados de tamanho e edemaciados. O ovino afetado da Fazenda 2, apresentou espessamento e enrugamento da mucosa do intestino, principalmente no íleo e válvula íleo-cecal. Microscopicamente o caprino e o ovino com sinais clínicos apresentaram lesões semelhantes, caracterizadas por granulomas com predominância de macrófagos espumosos, na lâmina própria e submucosa do intestino e linfonodos mesentéricos. O ovino positivo à tuberculina e um caprino negativo na Fazenda 1 foram eutanasiados e apresentaram discreto espessamento da mucosa do íleo. Na histologia foi observado infiltrado preferentemente linfocítico. Em todos os casos dentro de macrófagos e linfócitos havia bacilos ácool-ácidos resistentes, positivos na imunohistoquímica para Mycobacterium spp. Sugere-se a necessidade de estudar a prevalência de paratuberculose em rebanhos de caprinos e ovinos no Brasil, determinar medidas de controle e avaliar a possibilidade de transmissão para humanos.