Mycobacterium porcinum strains isolated from bovine bulk milk: Implications for Mycobacterium avium subsp. paratuberculosis detection by PCR and culture

Development and evaluation of genomics informed real-time PCR assays for the detection and strain typing of Mycobacterium avium subsp. paratuberculosis

AIMS

This study aimed to identify specific genomic targets for the detection and strain typing of Map and analyse their sensitivity and specificity, and detect Map directly from faeces.

METHODS AND RESULTS

A comparative genomics approach was used to identify specific genomic targets for the detection and strain typing of Map. A Map specific qPCR using the primer pair 7132 that targets a DNA segregation ATPase protein was able to detect all strains of Map and is more sensitive than the current Johne's disease PCR assays with a sensitivity of 0.0002 fg µl-1. A strain specific qPCR using the Atsa primer pair that targets the arylsulfase gene was able to differentiate between Type S and Type C strains of Map and was more sensitive than the IS1311 PCR and REA with a sensitivity of 40 fg µl-1 and was specific for Type S Map. Both assays successfully detected Map directly from faeces.

CONCLUSION

This study developed and validated two genomics informed qPCR assays, 7132B Map and Atsa Type S and found both assays to be highly specific and sensitive for the detection of Map from culture and directly from faeces. This is the first time that a probe-based qPCR has been designed and developed for Map strain typing, which will greatly improve the response time during outbreak investigations.

First serological diagnosis of Mycobacterium avium subsp. paratuberculosis infection in sheep in the state of Pernambuco, Brazil

This study aimed to diagnose Mycobacterium avium subsp. paratuberculosis (MAP) infections in sheep in the state of Pernambuco, Brazil. A total of 276 blood samples were analyzed using the enzyme-linked immunosorbent assay IDEXX Paratuberculosis Screening kit, and 261 fecal samples were submitted for bacterial culture and polymerase chain reaction tests. An animal-level sero-frequency of 0.72% (n = 2/276) and a farm-level sero-frequency of 20% (n = 2/10) were found. All fecal sample cultures were negative, and molecular analyses were also negative. To the best of our knowledge, this is the first study of MAP infection in sheep in the state of Pernambuco and one of the pioneers in the country. It is an asymptomatic disease that is difficult to diagnose in this species because the susceptibility of sheep to the organism is lower than that of other ruminant species. However, the sero-frequency found reveals that there is MAP exposure in sheep flocks in the region. In addition, serological monitoring can contribute to the observation of the organism's behavior in herds. Our results support the potential risk of MAP infection in sheep in the state of Pernambuco, Brazil.

A scoping review of the testing of bulk milk to detect infectious diseases of dairy cattle: Diseases caused by bacteria

Testing of bulk milk (BM) samples is a convenient, cost-effective strategy that can easily be implemented as part of disease surveillance programs on dairy farms. Here, we performed a scoping review to summarize the literature reporting on the testing of BM samples to detect infectious diseases of dairy cattle caused by bacteria. We also provide a non-exhaustive, albeit significant, list of diagnostic tests that are marketed for BM samples, as well as a list of disease surveillance activities that included testing of BM samples. A literature search was carried out in 5 databases, yielding 8,829 records from which 474 were retained. Overall, 575 eligible bacterial pathogens were screened for using BM samples, ranging from 1 to 6 individual pathogens per study. Staphylococcus aureus, including methicillin-resistant Staph. aureus, were the most studied bacteria (n = 179 studies), followed by Streptococcus agalactiae (86), Mycobacterium avium ssp. paratuberculosis (79), Coxiella burnetii (79), and Mycoplasma spp. (67). Overall, culture-based protocols, ELISA, real-time PCR, and PCR were the most commonly adopted methodologies to screen BM samples. Sensitivity of BM testing for bovine paratuberculosis was generally low and varied greatly according to the ELISA cut-offs adopted and herd-level definition of disease. In general, protocols had low to moderate sensitivities (<50%), which increased for herds with high within-herd seroprevalence. Specificity of BM testing for paratuberculosis was generally high. With respect to mastitis pathogens, BM testing demonstrated high sensitivity and specificity for Strep. agalactiae, in general. However, we observed inconsistency among studies with respect to the sensitivity of BM culture to detect infected herds, which was notably higher if enrolled herds were heavily infected or had history of clinical disease. Among Salmonella spp. pathogens, Salmonella Dublin was the most frequently studied bacterium for which BM testing has been validated. Specificity of BM ELISA was high, ranging from 89.0 to 99.4. In contrast, sensitivity varied greatly among studies, ranging from 50.6% to 100%. Our findings support that one of most important factors affecting sensitivity of BM ELISA for Salmonella Dublin is whether nonlactating cattle are considered in the definition of herd infection status. In general, protocols analyzed in this review suffered from very low sensitivities, which hardly justifies their use as part of disease surveillance as single testing. Nevertheless, test sensitivity can be increased by the adoption of more inclusive definitions of disease-free herds. Further, low-sensitivity and high-specificity methods can be valuable tools for surveillance when used repeatedly over time.

Occurrence of Mycobacterium avium subsp. paratuberculosis in coalho cheese in the State of Pernambuco, Brazil

ABSTRACT Paratuberculosis is a chronic and incurable disease that affects ruminants and other domestic animals. It is caused by Mycobacterium avium subsp. paratuberculosis (MAP) that may also be involved in some human diseases such as Crohn's disease, type 1 diabetes, sarcoidosis, multiple sclerosis, and Hashimoto's thyroiditis. The objective of this study was to investigate the occurrence of MAP DNA in samples of artisanal coalho cheese purchased in the State of Pernambuco. Forty samples of coalho cheese submitted to the Real Time Polymerase Chain Reaction (qPCR) technique were analyzed for the detection of the MAP region IS900. 11 (27.5%) were positive with a mean of 195.9 MAP colony forming unit (CFU) per gram of each sample, with a minimum of 30.3 CFU/g and a maximum of 324.2 CFU/g. Thus, this type of cheese that is one of the most consumed in this region of Brazil constitutes a source of human exposure to MAP. Further research in this area should be performed to evaluate the viability of the bacteria in this cheese type.

Molecular epidemiology of mycobacteria among herds in Marajó Island, Brazil, reveals strains genetically related and potential zoonotic risk of clinical relevance

Mycobacterium bovis is the main causative agent of bovine tuberculosis (bTB) being among the animal-adapted Mycobacterium tuberculosis complex. Herds can also be infected with non-tuberculous mycobacteria (NTM) causing a negative effect on the economy and on animal and human health through zoonotic infections. Molecular tools are required for mycobacteria identification; thus, it is laborious to determine the epidemiological information of mycobacteria among herds. We aimed to describe the mycobacterial pathogens associated with cases of suspected bTB lesions in cattle/buffaloes slaughtered for consumption and to investigate bTB transmission. We evaluated 74 lesion samples from 48 animals (27 bovine/21 buffaloes) from 16 mapped farms. Positives samples from nested-PCR were cultured in Lowenstein-Jensen (LJ), 2% pyruvate (LJ + P), and 2% glycerol (LJ + G) media, followed by Ziehl-Neelsen (ZN) staining technique and partial gene sequencing (hsp65, rpoB, and 16S-rRNA). Spoligotyping and 24-MIRU-VNTR were performed. The LJ + P increased the chance of obtaining bacilli. The respiratory tract and the oral cavity were the most important infection route. In addition, the calcified part of the lesions suggested chronic bTB. Spoligotypes of M. bovis (SIT986/SB0885) differed from others found in South America, and the MIRU-VNTR 24 loci suggested that bTB was associated to highly related strains. The NTM species found are of clinical importance in humans.

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.

Estimation of Performance Characteristics of Analytical Methods for Mycobacterium avium subsp. paratuberculosis Detection in Dairy Products

Paratuberculosis is a chronic enteric infection, caused by Mycobacterium avium subsp. paratuberculosis (MAP), affecting virtually all ruminants as well as other animals. MAP is also suspected to be involved in the etiology of some human diseases, like Crohn's disease and others. In surveillance studies, different analytical methodologies were employed to detect MAP, showing different results and incidence in dairy products. The aim of this study was to evaluate the performance characteristics of three analytical methods [culture, quantitative PCR (qPCR) and peptide-mediated magnetic separation (PMS) phage-based assay] for MAP detection in raw, heat-treated and powdered milk. The methods were evaluated according to performance characteristics defined for qualitative methods in ISO 16140-2:2016. To estimate sensitivity (including trueness) and LOD, 720, and 900 test portions, respectively, were blind tested by two laboratories. Considering all matrices, different sensitivities, expressed as the percentage of positives from the total of true positive test portions, were obtained for IS900 qPCR (94%), f57 qPCR (76%), culture (83%), and PMS-phage (40%). Trueness, expressed as results correctly assigned (including positive and negative) to the reference value, was 93% for the IS900 qPCR method, 89% for culture and 49% for the PMS-phage. The LODs obtained in this study were similar to the LODs previously published for cultural and qPCR methods. However, for the PMS-phage method, the obtained results showed higher LOD values compared to the limited data available in the scientific literature. Our results highlight that while the PMS-phage assay is workable in pure liquid culture for estimation of MAP counts, its usage for surveillance of dairy matrices should be treated with a lot of caution as performance characteristics obtained were lower than for the two other methods tested. qPCR and culture are the most appropriate methods to detect MAP in milk-based matrices according to ISO 16140 methodology. Cultural techniques are considered the gold standard for detection of viable MAP, but qPCR, which is widely used in analytical and surveillance studies, can be considered a suitable and recommendable alternative to cultural methods for screening, if confirmation of MAP's viability is not requested.

First molecular epidemiological study of Mycobacterium avium subsp. paratuberculosis in cattle and buffalo from different regions of Brazil

Paratuberculosis is an incurable disease in ruminants with great worldwide economic impact, caused by Mycobacterium avium subsp. paratuberculosis (MAP). The objective of this study was to carry out a study of the molecular epidemiology of the MAP using the restriction enzyme analysis (REA) technique of IS1311 MAP region in biological samples of feces, intestinal tissue, and mesenteric lymph nodes of cattle and buffaloes from six Brazilian states. In total, 109 samples of feces and tissues of cattle and buffaloes were collected from animal paratuberculosis suspected. Twenty-five samples were positive in the detection of the DNA of the IS900 region of MAP and it was possible to type 18 strains in the analysis of the region IS1311, being 100% of them identified as belonging to subtype Bison MAP strain. This is the first epidemiological molecular study of MAP in Brazil. The results indicate that paratuberculosis is widespread in cattle and in buffaloes in several regions of Brazil, and the subtype Bison MAP strain was the only one identified in the samples analyzed in this study, demonstrating the similarity between the strains from different states tested. These results provide the necessary support for the implementation of paratuberculosis control strategies in cattle and buffaloes in Brazil.

Draft Genome Sequence of Mycobacterium porcinum CSURP1564

Mycobacterium porcinum is a rapidly growing environmental mycobacterium responsible for opportunistic infections. The 7,025,616-bp draft genome of M. porcinum strain CSURP1564 exhibits a 66.71% G+C content, 6,687 protein-coding genes, and 65 predicted RNA genes. In silico DNA-DNA hybridization confirms its assignment to the Mycobacterium fortuitum complex.

Survival of Mycobacterium avium subsp. paratuberculosis in the intermediate and final digestion products of biogas plants

AIMS

To evaluate the survival of Mycobacterium avium subsp. paratuberculosis (MAP) during anaerobic digestion (AD), we studied two different biogas plants loaded with manure and slurry from paratuberculosis-infected dairy herds.

METHODS AND RESULTS

Both plants were operating under mesophilic conditions, the first with a single digester and the second with a double digester. Mycobacterium avium subsp. paratuberculosis detection was performed by sampling each stage of the process, specifically the prefermenter, fermenter, liquid digestate and solid digestate stages, for 11 months. In both plants, MAP was isolated from the prefermenter stage. Only the final products, the solid and liquid digestates, of the one-stage plant showed viable MAP, while no viable MAP was detected in the digestates of the two-stage plant.

CONCLUSIONS

Mycobacterium avium subsp. paratuberculosis showed a significant decrease during subsequent steps of the AD process, particularly in the two-stage plant. We suggest that the second digester maintained the digestate under anaerobic conditions for a longer period of time, thus reducing MAP survival and MAP load under the culture detection limit.

SIGNIFICANCE AND IMPACT OF THE STUDY

Our data are unable to exclude the presence of MAP in the final products of the biogas plants, particularly those products from the single digester; therefore, the use of digestates as fertilizers is a real concern related to the possible environmental contamination with MAP.

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.

High-throughput direct fecal PCR assay for detection of Mycobacterium avium subsp. paratuberculosis in sheep and cattle

Johne's disease (JD) is a chronic enteric disease caused by Mycobacterium avium subsp. paratuberculosis that affects ruminants. Transmission occurs by the fecal-oral route. A commonly used antemortem diagnostic test for the detection of M. avium subsp. paratuberculosis in feces is liquid culture; however, a major constraint is the 2- to 3-month incubation period needed for this method. Rapid methods for the detection of M. avium subsp. paratuberculosis based on PCR have been reported, but comprehensive validation data are lacking. We describe here a new test, the high-throughput-Johnes (HT-J), to detect M. avium subsp. paratuberculosis in feces. Its diagnostic accuracy was compared with that of liquid radiometric (Bactec) fecal culture using samples from cattle (1,330 samples from 23 herds) and sheep (596 samples from 16 flocks). The multistage protocol involves the recovery of M. avium subsp. paratuberculosis cells from a fecal suspension, cell rupture by bead beating, extraction of DNA using magnetic beads, and IS900 quantitative PCR. The limit of detection of the assay was 0.0005 pg, and the limit of quantification was 0.005 pg M. avium subsp. paratuberculosis genomic DNA. Only M. avium subsp. paratuberculosis was detected from a panel of 51 mycobacterial isolates, including 10 with IS900-like sequences. Of the 549 culture-negative fecal samples from unexposed herds and flocks, 99% were negative in the HT-J test, while 60% of the bovine- and 84% of the ovine-culture-positive samples were positive in the HT-J test. As similar total numbers of samples from M. avium subsp. paratuberculosis-exposed animals were positive in culture and HT-J tests in both species, and as the results of a McNemar's test were not significant, these methods probably have similar sensitivities, but the true diagnostic sensitivities of these tests are unknown. These validation data meet the consensus-based reporting standards for diagnostic test accuracy studies for paratuberculosis and the Minimum Information for Publication of Quantitative Real-Time PCR Experiments (MIQE) guidelines (S. A. Bustin et al., Clin. Chem. 55:611-622, 2009, doi:10.1373/clinchem.2008.112797). The HT-J assay has been approved for use in JD control programs in Australia and New Zealand.

Rapid and sensitive method to identify Mycobacterium avium subsp. paratuberculosis in cow's milk by DNA methylase genotyping

Paratuberculosis is an infectious, chronic, and incurable disease that affects ruminants, caused by Mycobacterium avium subsp. paratuberculosis. This bacterium is shed primarily through feces of infected cows but can be also excreted in colostrum and milk and might survive pasteurization. Since an association of genomic sequences of M. avium subsp. paratuberculosis in patients with Crohn's disease has been described; it is of interest to rapidly detect M. avium subsp. paratuberculosis in milk for human consumption. IS900 insertion is used as a target for PCR amplification to identify the presence of M. avium subsp. paratuberculosis in biological samples. Two target sequences were selected: IS1 (155 bp) and IS2 (94 bp). These fragments have a 100% identity among all M. avium subsp. paratuberculosis strains sequenced. M. avium subsp. paratuberculosis was specifically concentrated from milk samples by immunomagnetic separation prior to performing PCR. The amplicons were characterized using DNA methylase Genotyping, i.e., the amplicons were methylated with 6-methyl-adenine and digested with restriction enzymes to confirm their identity. The methylated amplicons from 100 CFU of M. avium subsp. paratuberculosis can be visualized in a Western blot format using an anti-6-methyl-adenine monoclonal antibody. The use of DNA methyltransferase genotyping coupled to a scintillation proximity assay allows for the detection of up to 10 CFU of M. avium subsp. paratuberculosis per ml of milk. This test is rapid and sensitive and allows for automation and thus multiple samples can be tested at the same time.

Evaluation of combined high-efficiency DNA extraction and real-time PCR for detection of Mycobacterium avium subsp. paratuberculosis in subclinically infected dairy cattle: comparison with faecal culture, milk real-time PCR and milk ELISA

Background

Johne’s disease is caused by Mycobacterium avium subsp. paratuberculosis (Map) and it is one of the most important diseases in cattle worldwide. Several laboratory tests for Map detection are available; however, these are limited by inadequate sensitivity and specificity when used in subclinically infected populations. To identify Map shedders in subclinically infected cattle, we used a new, high-yield method for DNA-extraction from Map in faeces combined with quantitative real-time PCR (qPCR) for amplification of the insertion sequence IS900 of Map (HYDEqPCR). Evaluation of HYDEqPCR was carried out in comparison with faecal culture, milk qPCR, and milk enzyme-linked immunosorbent assay (ELISA), on 141 faecal and 91 milk samples, from 141 subclinically infected dairy cattle.

Results

The qPCR proved to be highly sensitive, with a detection limit of 2 IS900 DNA copies/μl in 67 % of the reactions. It also showed 100 % specificity, as determined from 50 Map and non-Map strains, and by the sequencing of qPCR amplicons. The detection limit of HYDEqPCR was 90 Map/g Map-spiked faeces, which corresponds to 2.4 colony forming units/g Map-spiked faeces, with an estimated efficiency of 85 % (±21 %). When tested on the field samples, HYDEqPCR showed 89 % of the samples as positive for Map, whereas faecal culture, milk qPCR, and milk ELISA detected 19 %, 36 % and 1 %, respectively. Fisher’s exact tests only show statistical significance (p ≤0.05) for the correlation between HYDEqPCR and faecal culture. The agreement between HYDEqPCR and milk qPCR and milk ELISA was poor, slight, and non-significant.

Conclusions

This study highlights the advantages of HYDEqPCR for detection of Map in subclinically infected populations, in comparison with faecal culture, milk qPCR and milk ELISA. HYDEqPCR can detect low-level Map shedders that go undetected using these other methods, which will thus underestimate the proportions of Map-shedders in herds. Identification of these shedding animals is extremely important for prevention of the spread of Map infection in an animal population. Due to the relatively high sensitivity and specificity of HYDEqPCR, it can be applied to test for Map at the herd or individual level, regardless of animal age or production stage. HYDEqPCR will allow early detection and control of Map in any population at risk.

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.

Effectiveness of combination of Mini-and Microsatellite loci to sub-type Mycobacterium avium subsp. paratuberculosis Italian type C isolates

Background

Mycobacterium avium subsp. paratuberculosis (Map) is the etiological agent of paratuberculosis. The aim of our study was to combine Mini-and Microsatellite loci analysis in order to explore the effectiveness of this sub-typing method in a group of Map isolates. For this purpose, 84 Italian Type C Map isolates, each from a different cattle herd, were submitted to MIRU-Variable-Number Tandem-Repeats (VNTRs) typing and Short Sequence repeats (SSRs) sequencing. Moreover, the method was used to analyse the variability inside 10 herds (from three to 50 isolates per herd).

Results

The molecular sub-typing, carried out using three SSR and 10 MIRU-VNTR loci, differentiated the 84 isolates into 33 clusters, reaching a Simpson's Discriminatory Index (SID) value of 0.952 (0.933 to 0.972, 95% confidence intervals). Among all considered loci, six (SSR2, MIRU2, SSR1, SSR8, VNTR3527 and VNTR1067) showed relevant allelic variability. Thirty-eight% of the isolates were clustered into four genotypes, differing from each other for the SSR2 locus. The other isolates, characterised by differences in two or more loci, were spread among the rest of the clusters. The intra-herd analysis revealed more than one genotype in most herds with a similar distribution of clusters.

Conclusions

Our results revealed the advantage of using both Mini-and Microsatellite approaches for successfully discriminating among Map Type C isolates from the same geographic area, host species and herd. These data suggest that the combination of loci here proposed could be a useful molecular tool for regional epidemiological studies.

Occurrence of Mycobacterium avium subsp. paratuberculosis in raw water and water treatment operations for the production of potable water

Mycobacterium avium subsp. paratuberculosis (Map) causes Johne's disease of cattle and is implicated as a cause of Crohn's disease in humans. The organism is excreted in animal faeces and can contaminate water catchment areas. This coupled with Map's survival in the environment means that water destined for domestic use may be a source of exposure. This work was designed to determine the occurrence of Map in Lough Neagh (the largest freshwater lake in the British Isles), used as a reservoir, and in two water treatment works (WTW1 and WTW2) which abstract from the lough and which have slow sand filtration (SSF) and dissolved air flotation respectively as their principal treatment regimes. The organism was not detected in lough water samples by culture (n=70) but 29% (20/70) were positive by PCR. In the raw water to WTW1 and WTW2 no culture positives were detected but 54% (13/24) and 58% (14/24) respectively were PCR positive. In WTW1 there were no culture positives at the SSF or final water but 31% (8/26) and 45% (9/20) respectively were PCR positive. In WTW2 similar results were obtained with 26% (6/23) and 48% (11/23) in the floccules and final water respectively. At WTW2 however one culture positive was detected in the final water. This latter finding is of concern. The inability to reach definitive conclusions indicates the need for further research, particularly in the detection methods for viable Map.

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.

Detection of Mycobacterium avium ssp. paratuberculosis in cheese, milk powder and milk using IS900 and f57-based qPCR assays

AIMS

To develop a quantitative PCR assay for sensitive and specific detection of Mycobacterium avium ssp. paratuberculosis (Map) in a range of dairy products.

METHODS AND RESULTS

TaqMan(®) assays were designed to target the IS900 and f57 genetic elements of Map. Both real-time PCR assays were integrated with the Adiapure(®) Map DNA extraction kit and assessed separately for the detection/quantification of Map in spiked milk, Cheddar cheese and milk powder. Assays were validated against Cheddar cheese samples containing known concentrations of Map. The IS900 qPCR assay was significantly more sensitive than the assay based on the f57 primer/probe. At a threshold cycle value of 38, limits of detection (LOD) for the IS900 qPCR assay were 0·6 CFU ml(-1), 2·8 CFU g(-1) and 30 CFU g(-1) for artificially contaminated pasteurized milk, whole milk powder and Cheddar cheese, respectively. The respective LOD's for the f57 assay were 6·2 CFU ml(-1), 26·7 CFU g(-1) and 316 CFU g(-1).

CONCLUSION

The integrated Adiapure(®) extraction - IS900 real time assay described is a sensitive, quantitative method for the detection of Map in dairy products. This is the first study to consider qPCR as a quantitative estimation of Map-DNA in cheese and whole milk powder.

SIGNIFICANCE AND IMPACT OF THE STUDY

The assay developed allows sensitive detection and quantification of Map DNA in a range of dairy products which is valuable for the screening and surveillance of this potential zoonotic organism.

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.

Ocorrência de paratuberculose em búfalos (Bubalus bubalis) em Pernambuco

A paratuberculose (doença de Johne) é uma das doenças de maior importância econômica para ruminantes em vários países e pode representar uma ameaça ao desenvolvimento da pecuária brasileira. É uma doença infecto-contagiosa que provoca enterocolite granulomatosa crônica, incurável e de difícil controle, cujo agente é o Mycobacterium avium subsp. paratuberculosis (MAP). Descreve-se a ocorrência de paratuberculose em um rebanho de búfalos no Estado de Pernambuco, Brasil. Não foi encontrado registro, na literatura, da ocorrência de paratuberculose em búfalos no país. De 100 búfalos, cinco mostravam sinais clínicos característicos da doença. À necropsia de dois animais as lesões estavam restritas ao intestino delgado com evidente espessamento da mucosa, aumento de linfonodos mesentéricos e vasos linfáticos proeminentes e dilatados. À microscopia, observaram-se na mucosa do intestino, infiltrado inflamatório granulomatoso com numerosos macrófagos epitelióides e células gigantes de Langhans, além de bacilos álcool-ácido resistentes (BAAR) visualizados através da coloração de Ziehl-Neelsen (ZN). Nos linfonodos mesentéricos, havia espessamento da cápsula e marcada inflamação granulomatosa. O exame direto pela técnica de ZN para pesquisa do bacilo em esfregaços de fezes, raspado de mucosa intestinal e imprint de linfonodos mesentéricos resultou positivo. A PCR IS900 específico de linfonodo mesentérico e mucosa intestinal revelou amplificação de um fragmento de aproximadamente 110pb, confirmada pela comparação com outras sequências de M. avium subsp. paratuberculosis disponíveis no GenBank.