Current understanding of the genetic diversity of Mycobacterium avium subsp. paratuberculosis

Development of visual dye-based loop-mediated isothermal amplification assays for Mycobacterium avium subsp. paratuberculosis detection in ruminants

IMPORTANCE

Mycobacterium avium subsp. paratuberculosis (MAP), the causative agent of Johne's disease (JD) in ruminants, is a potential zoogenic pathogen. At the asymptomatic subclinical stage, infected animals periodically shed the pathogen through feces and milk, serving as silent carriers for disease transmission. In Republic of Korea, where treatment for JD is not pursued and culling is the primary management strategy for infected animals, early detection is crucial for effective disease control.

OBJECTIVE

In this study, we aimed to develop a new primer set for the loop-mediated isothermal amplification (LAMP) method for facilitating visual-based detection of MAP.

METHODS

We designed LAMP primers for the MAP-specific gene IS1311 and optimized the reaction conditions to enhance diagnostic sensitivity and specificity. Practical application was evaluated using 170 field samples of feces and intestinal tissues from cattle and goats.

RESULTS

The LAMP method demonstrated sensitivity superior to that of the conventional polymerase chain reaction (PCR) method and equal to that of real-time-PCR targeting the F57 gene, detecting as low as 0.1 pg MAP DNA per reaction. Notably, we integrated a mixed dye composed of calcein and hydroxynaphthol blue at an optimal ratio, enabling clear visual distinction of results under natural light. In practical application, the LAMP assay demonstrated a true positive rate of 100% and true-negative rate of 92.22%.

CONCLUSIONS AND RELEVANCE

The developed mixed dye-LAMP method facilitates immediate, sensitive diagnosis by providing a user-friendly readout. By reducing diagnostic time and enhancing visual clarity without specialized equipment, it significantly improves JD control in the livestock industry.

MIRU-VNTR Typing of Atypical Mycobacteria Isolated from the Lymph Nodes of Slaughtered Pigs from Poland

No regulations currently require the excision of lymph nodes from pig carcasses or the thermal processing of pork before consumption. Therefore, the presence of anatomopathological lesions with signs of coagulation necrosis in lymph nodes from pigs during post-mortem inspection is concerning, as is the increasing incidence of mycobacteriosis in humans. Therefore, the aim of the present study is to verify whether mycobacteria can be isolated from tuberculous-like lesions in mandibular lymph nodes in slaughtered pigs, and whether further molecular analysis based on MIRU-VNRT, used to identify mycobacteria from the Mycobacterium avium complex, can indicate zoonotic potential. Forty of the fifty isolates from the lymph nodes with signs of coagulation necrosis were classified as Mycobacterium avium complex. MIRU-VNTR analysis allowed for the isolation of six strains, one of which was classified as M. avium subsp. paratuberculosis (MAP). Our findings confirm the presence of atypical mycobacteria in the lymph nodes of slaughtered pigs. While the isolated strains (other than MAP) do not pose a significant or direct health risk to consumers, further research and monitoring are necessary. Atypical mycobacteria can cause a wide range of diseases in children and compromised adults, and often show resistance to many classes of antibiotics, including those used to treat tuberculosis.

Serological and Molecular Characterization of Mycobacterium avium Subsp. paratuberculosis (MAP) from Sheep, Goats, Cattle and Camels in the Eastern Province, Saudi Arabia

Simple Summary

Mycobacterium avium subsp. paratuberculosis (MAP) is the causative agent of Johne’s disease, affecting small and large ruminants and causing chronic diarrhea and severe emaciation. MAP is prevalent in many countries, including Saudi Arabia. Serological and molecular characterization of MAP and determination of the prevalent strains are essential for the control strategies. The results obtained from 31 herds showed that the sheep type (S-type) was the most prevalent MAP type and the molecular characterization revealed different strain profiles distributed among the sheep, goat, cattle, and camel herds in Eastern Province, Saudi Arabia.

Abstract

The objectives of the present study were to characterize Mycobacterium avium subsp. paratuberculosis (MAP) infection using serological and molecular tools and investigate the distribution and molecular characterization of MAP strains (cattle (C) and sheep (S) types) in sheep, goat, cattle, and camel herds in Eastern Province, Saudi Arabia. Serum and fecal samples were collected from all animals aged >2 years old in 31 herds (sheep = 8, goats = 6, cattle = 8 and camels = 9) from January to December 2019. Serum samples were tested by ELISA for the detection of MAP antibodies. Fecal samples were tested by PCR for the detection of MAP IS900 gene and the identification of MAP strains. MAP antibodies were detected in 19 (61.3%) herds. At the animal level, antibodies against MAP were detected in 43 (19.5%) sheep, 21 (17.1%) goats, 13 (19.7%) cattle and 22 (9.1%) camels. The IS900 gene of MAP was detected in 23 (74.2%) herds and was directly amplified from fecal samples of 59 (26.8%) sheep, 34 (27.6%) goats, 20 (30.3%) cattle and 36 (15.0%) camels. The S-type was the most prevalent MAP type identified in 15 herds, and all were identified as type-I, while the C-type was identified in only 8 herds. The IS900 sequences revealed genetic differences among the MAP isolates recovered from sheep, goats, cattle and camels. Results from the present study show that MAP was prevalent and confirm the distribution of different MAP strains in sheep, goat, cattle and camel herds in Eastern Province, Saudi Arabia.

Mammalian cell entry operons; novel and major subset candidates for diagnostics with special reference to Mycobacterium avium subspecies paratuberculosis infection

Mammalian cell entry (mce) genes are the components of the mce operon and play a vital role in the entry of Mycobacteria into the mammalian cell and their survival within phagocytes and epithelial cells. Mce operons are present in the DNA of Mycobacteria and translate proteins associated with the invasion and long-term existence of these pathogens in macrophages. The exact mechanism of action of mce genes and their functions are not clear yet. However, with the loss of these genes Mycobacteria lose their pathogenicity. Mycobacterium avium subspecies paratuberculosis (MAP), the etiological agent of Johne’s disease, is the cause of chronic enteritis of animals and significantly affects economic impact on the livestock industry. Since MAP is not inactivated during pasteurization, human population is continuously at the risk of getting exposed to MAP infection through consumption of dairy products. There is need for new candidate genes and/or proteins for developing improved diagnostic assays for the diagnosis of MAP infection and for the control of disease. Increasing evidences showed that expression of mce genes is important for the virulence of MAP. Whole-genome DNA microarray representing MAP revealed that there are 14 large sequence polymorphisms with LSPP12 being the most widely conserved MAP-specific region that included a cluster of six homologs of mce-family involved in lipid metabolism. On the other hand, LSP11 comprising part of mce2 operon was absent in MAP isolates. This review summarizes the advancement of research on mce genes of Mycobacteria with special reference to the MAP infection.

Ecological drivers of Mycobacterium avium subsp. paratuberculosis detection in mongoose (Herpestes ichneumon) using IS900 as proxy

Mycobacterium avium subsp. paratuberculosis (MAP) is the etiological agent of Johne’s disease or paratuberculosis, a chronic infection affecting domestic ruminants worldwide. Despite sporadic reports of MAP occurrence in non-ruminants, information on the risk factors predisposing for infection is still scarce and evidence of transmission paths linking the livestock-wildlife-environment interfaces also remains lacking. In this study, we predicted that environmental, host-related, land use and human driven disturbance factors would modulate carnivore exposure to MAP. To test these hypotheses, we performed a retrospective survey, based on microbiological and molecular methods, in mainland Portugal including five sympatric species from the Herpestidae, Canidae, Viverridae, and Mustelidae families (n = 202) and examined 16 variables as putative predictors of MAP occurrence. Molecular evidence of MAP using IS900 as proxy was demonstrated in 7.43% (95%CI: 4.55–11.9) of surveyed carnivores, the highest proportions being registered for red fox (Vulpes vulpes) (10%; 95%CI: 4.0–23) and Egyptian mongoose (Herpestes ichneumon) (6.0%; 95%CI: 3.2–11). We demonstrate that important species of the Mediterranean carnivore guild, such as stone marten (Martes foina) and common genet (Genetta genetta), may also be exposed to MAP, being this the first time that occurrence in genet is reported. The high proportion of DNA-positive specimens, concurrent with the apparent lack of gastro-enteric lesions and molecular confirmation of IS900 in feces, argue for the presence of subclinical carriers that occasionally shed bacteria, potentially aiding as source of infection to susceptible species and possibly contributing for environmental contamination. Achievement of MAP isolation would prove beyond any doubt that MAP is present in this wildlife population. Ecological modelling results suggested that the probability of MAP infection using IS900 as proxy in mongoose is positively associated with higher altitude and temperature stability, as well as with lower annual rainfall. Density of livestock farms was found not to be a significant predictor, which may indicate that the livestock-wildlife interface is probably not important as an infection route for mongoose.

Elucidating Transmission Patterns of Endemic Mycobacterium avium subsp. paratuberculosis Using Molecular Epidemiology

Mycobacterial diseases are persistent and characterized by lengthy latent periods. Thus, epidemiological models require careful delineation of transmission routes. Understanding transmission routes will improve the quality and success of control programs. We aimed to study the infection dynamics of Mycobacterium avium subsp. paratuberculosis (MAP), the causal agent of ruminant Johne’s disease, and to distinguish within-host mutation from individual transmission events in a longitudinally MAP-defined dairy herd in upstate New York. To this end, semi-annual fecal samples were obtained from a single dairy herd over the course of seven years, in addition to tissue samples from a selection of culled animals. All samples were cultured for MAP, and multi-locus short-sequence repeat (MLSSR) typing was used to determine MAP SSR types. We concluded from these precise MAP infection data that, when the tissue burden remains low, the majority of MAP infections are not detectable by routine fecal culture but will be identified when tissue culture is performed after slaughter. Additionally, we determined that in this herd vertical infection played only a minor role in MAP transmission. By means of extensive and precise longitudinal data from a single dairy herd, we have come to new insights regarding MAP co-infections and within-host evolution.

Genotyping methods and molecular epidemiology of Mycobacterium avium subsp. paratuberculosis (MAP)

Mycobacterium avium subsp. paratuberculosis (MAP) is the causative agent of Johne’s disease (JD) which affects mainly ruminants and is characterized by chronic diarrhea and emaciation. Johne’s disease is highly prevalent in many countries around the world and leads to high economic losses associated with decreased production. Genotyping of the involved pathogen could be used in the study of population genetics, pathogenesis and molecular epidemiology including disease surveillance and outbreak investigation. Principally, researchers have first assumed the presence of two different MAP strains that are associated with the animal host species (cattle and sheep). However, nowadays MAP characterization depends mainly upon genetic testing using genetic markers such as insertion elements, repetitive sequences and single nucleotide polymorphisms. This work aims to provide an overview of the advances in molecular biological tools used for MAP typing in the last two decades, discuss how these methods have been used to address interesting epidemiological questions, and explore the future prospects of MAP molecular epidemiology given the ever decreasing costs of the high throughput sequencing technology.

A synthesis of the patho-physiology of Mycobacterium avium subspecies paratuberculosis infection in sheep to inform mathematical modelling of ovine paratuberculosis

This literature review of exposure to Mycobacterium avium subsp. paratuberculosis (MAP) in sheep enabled a synthesis of the patho-physiology of ovine paratuberculosis (PTB). These results could be used to inform subsequent modelling of ovine PTB. We reviewed studies of both experimental and natural exposure. They were generally comparable. Possible outcomes following exposure were latent infection, i.e. mere colonization without lesions; active infection, with inflammatory histopathology in the intestinal tissues resulting in mild disease and low faecal shedding; and affection, with severe intestinal pathology, reduced production, clinical signs and high faecal shedding. Latent infection was an uninformative outcome for modelling. By contrast, histological lesions and their grade appeared to be a good marker of active infection and progression stages to clinical disease. The two possible pathways following infection are non-progression leading to recovery and progression to clinical disease, causing death. These pathways are mediated by different immune mechanisms. This synthesis suggested that host-related characteristics such as age at exposure and breed, combined with pathogen-related factors such as MAP dose, strain and inoculum type for experimental infection, have a strong influence on the outcome of exposure. The material reviewed consisted of disparate studies often with low numbers of sheep and study-level confounders. Hence comparisons between and across studies was difficult and this precluded quantitative model parameter estimation. Nevertheless, it allowed a robust synthesis of the current understanding of patho-physiology of ovine PTB, which can inform mathematical modelling of this disease.

Pathogens of Food Animals: Sources, Characteristics, Human Risk, and Methods of Detection

Pathogens associated with food production (livestock) animals come in many forms causing a multitude of disease for humans. For the purpose of this review, these infectious agents can be divided into three broad categories: those that are associated with bacterial disease, those that are associated with viruses, and those that are parasitic in nature. The goal of this chapter is to provide the reader with an overview of the most common pathogens that cause disease in humans through exposure via the food chain and the consequence of this exposure as well as risk and detection methods. We have also included a collection of unusual pathogens that although rare have still caused disease, and their recognition is warranted in light of emerging and reemerging diseases. These provide the reader an understanding of where the next big outbreak could occur. The influence of the global economy, the movement of people, and food makes understanding production animal-associated disease paramount to being able to address new diseases as they arise.

Genetic diversity ofMycobacterium aviumcomplex strains isolated in Argentina by MIRU-VNTR

Mycobacterium aviumsp.avium(MAA),M. aviumsp.hominissuis(MAH), andM. aviumsp.paratuberculosis(MAP) are the main members of theM. aviumcomplex (MAC) causing diseases in several hosts. The aim of this study was to describe the genetic diversity of MAC isolated from different hosts. Twenty-six MAH and 61 MAP isolates were recovered from humans and cattle, respectively. GenoType CM®and IS1311-PCR were used to identifyMycobacteriumspecies. The IS901-PCR was used to differentiate between MAH and MAA, while IS900-PCR was used to identify MAP. Genotyping was performed using a mycobacterial interspersed repetitive-unit-variable-number tandem-repeat (MIRU-VNTR) scheme (loci: 292, X3, 25, 47, 3, 7, 10, 32) and patterns (INMV) were assigned according to the MAC-INMV database (http://mac-inmv.tours.inra.fr/). Twenty-two (22/26, 84·6%) MAH isolates were genotyped and 16 were grouped into the following, INMV 92, INMV 121, INMV 97, INMV 103, INMV 50, and INMV 40. The loci X3 and 25 showed the largest diversity (D: 0·5844), and the global discriminatory index (Hunter and Gaston discriminatory index, HGDI) was 0·9300. MAP (100%) isolates were grouped into INMV 1, INMV 2, INMV 11, INMV 8, and INMV 5. The HGDI was 0·6984 and loci 292 and 7 had the largestD(0·6980 and 0·5050). MAH presented a higherDwhen compared with MAP. The MIRU-VNTR was a useful tool to describe the genetic diversity of both MAH and MAP as well as to identify six new MAH patterns that were conveniently reported to the MAC-INMV database. It was also demonstrated that, in the geographical region studied, human MAC cases were produced by MAH as there was no MAA found among the human clinical samples.

Exploring MALDI-TOF MS approach for a rapid identification of Mycobacterium avium ssp. paratuberculosis field isolates

AIMS

The aim of the study was to explore the suitability of matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry (MALDI-TOF MS) for a rapid and correct identification of Mycobacterium avium ssp. paratuberculosis (MAP) field isolates.

METHODS AND RESULTS

MALDI-TOF MS approach is becoming one of the most popular tests for the identification of intact bacterial cells which has been shown to be fast and reliable. For this purpose, 36 MAP field isolates were analysed through MALDI-TOF MS and the spectra compared with two different databases: one provided by the vendor of the system employed (Biotyper ver. 3·0; Bruker Daltonics) and a homemade database containing spectra from both tuberculous and nontuberculous Mycobacteria. Moreover, principal component analysis procedure was employed to confirm the ability of MALDI-TOF MS to discriminate between very closely related subspecies. Our results suggest MAP can be differentiated from other Mycobacterium species, both when the species are very close (M. intracellulare) and when belonging to different subspecies (M. avium ssp. avium and M. avium ssp. silvaticum).

CONCLUSIONS

The procedure applied is fast, easy to perform, and achieves an earlier accurate species identification of MAP and nontuberculous Mycobacteria in comparison to other procedures.

SIGNIFICANCE AND IMPACT OF THE STUDY

The gold standard test for the diagnosis of paratuberculosis is still isolation of MAP by cultural methods, but additional assays, such as qPCR and subculturing for determination of mycobactin dependency are required to confirm its identification. We have provided here evidence pertaining to the usefulness of MALDI-TOF MS approach for a rapid identification of this mycobacterium among other members of M. avium complex.

Application of IS1311 locus 2 PCR-REA assay for the specific detection of 'Bison type' Mycobacterium avium subspecies paratuberculosis isolates of Indian origin

BACKGROUND & OBJECTIVES

Of the three major genotypes of Mycobacterium avium subspecies paratuberculosis (MAP), 'Bison type' is most prevalent genotype in the domestic livestock species of the country, and has also been recovered from patients suffering from Crohn's disease. Recently, a new assay based on IS1311 locus 2 PCR- restriction endonuclease analysis (REA) was designed to distinguish between 'Indian Bison type' and non-Indian genotypes. The present study investigated discriminatory potential of this new assay while screening of a panel of MAP isolates of diverse genotypes and from different geographical regions.

METHODS

A total of 53 mycobacterial isolates (41 MAP and 12 mycobacterium other than MAP), three MAP genomic DNA and 36 MAP positive faecal DNA samples from different livestock species (cattle, buffaloes, goat, sheep and bison) and geographical regions (India, Canada, USA, Spain and Portugal) were included in the study. The extracted DNA samples (n=92) were analyzed for the presence of MAP specific sequences (IS900, ISMav 2 and HspX) using PCR. DNA samples were further subjected to genotype differentiation using IS1311 PCR-REA and IS1311 L2 PCR-REA methods.

RESULTS

All the DNA samples (except DNA from non-MAP mycobacterial isolates) were positive for all the three MAP specific sequences based PCRs. IS1311 PCR-REA showed that MAP DNA samples of Indian origin belonged to 'Bison type'. Whereas, of the total 19 non-Indian MAP DNA samples, 2, 15 and 2 were genotyped as 'Bison type', 'Cattle type' and 'Sheep type', respectively. IS1311 L2 PCR-REA method showed different restriction profiles of 'Bison type' genotype as compared to non-Indian DNA samples.

INTERPRETATION & CONCLUSIONS

IS1311 L2 PCR-REA method successfully discriminated 'Indian Bison type' from other non-Indian genotypes and showed potential to be future epidemiological tool and for genotyping of MAP isolates.

Molecular typing of Argentinian Mycobacterium avium subsp. paratuberculosis isolates by multiple-locus variable number-tandem repeat analysis

Multiple-locus variable number-tandem repeat analysis (MLVA) of Mycobacterium avium subspecies paratuberculosis (MAP) isolates may contribute to the knowledge of strain diversity in Argentina. Although the diversity of MAP has been previously investigated in Argentina using IS900-RFLP, a small number of isolates were employed, and a low discriminative power was reached. The aim of the present study was to test the genetic diversity among MAP isolates using an MLVA approach based on 8 repetitive loci. We studied 97 isolates from cattle, goat and sheep and could describe 7 different patterns: INMV1, INMV2, INMV11, INMV13, INMV16, INMV33 and one incomplete pattern. INMV1 and INMV2 were the most frequent patterns, grouping 76.3% of the isolates. We were also able to demonstrate the coexistence of genotypes in herds and co-infection at the organism level. This study shows that all the patterns described are common to those described in Europe, suggesting an epidemiological link between the continents.

Experimental colitis is exacerbated by concomitant infection with Mycobacterium avium ssp. paratuberculosis

BACKGROUND

Crohn's disease (CD) is a chronic inflammatory disorder of the human gastrointestinal tract. Although genetic, immunological, environmental, and bacterial factors have been implicated, the pathogenesis is incompletely understood. The histopathological appearance of CD strikingly resembles Johne's disease, a ruminant inflammatory bowel disease, caused by Mycobacterium avium ssp. paratuberculosis (MAP), but a causative role of MAP in CD has not been established. In this work, we hypothesized that MAP might exacerbate an already existing intestinal disease.

METHODS

We combined dextran sulfate sodium (DSS)-induced colitis with MAP infection in mice and monitored the immune response and bacterial count in different organs.

RESULTS

An increased size of liver and spleen was observed in DSS-treated and MAP-infected animals (DSS + MAP) as compared with DSS-treated uninfected (DSS + PBS) mice. Similarly, DSS treatment increased the number and size of MAP-induced liver granulomas and enhanced the MAP counts in enteric tissue. MAP infection in turn delayed the mucosal healing of DSS-induced tissue damage. Finally, high numbers of MAP were found in mesenteric fat tissue causing large granuloma and necrotic regions.

CONCLUSIONS

Taken together, we present an in vivo model to study the role of MAP infection in CD. Our results confirm the hypothesis that MAP is able to exacerbate existing intestinal inflammation.

Molecular epidemiology of Mycobacterium avium subsp. paratuberculosis isolated from sheep, cattle and deer on New Zealand pastoral farms

The present study aimed to describe the molecular diversity of Mycobacterium avium subsp. paratuberculosis (MAP) isolates obtained from sheep, cattle (beef and dairy) and deer farms in New Zealand. A total of 206 independent MAP isolates (15 beef cattle, 89 dairy cattle, 35 deer, 67 sheep) were sourced from 172 species-mobs (15 beef cattle, 66 dairy cattle, 31 deer, 60 sheep). Seventeen subtypes were identified, using a combination of variable number of tandem repeats (VNTR) and short sequence repeat (SSR) methods. Rarefaction analysis, analysis of molecular variance (AMOVA), Fst pairwise comparisons and proportional similarity index (PSI) were used to describe subtype population richness, genetic structure and potential associations between livestock sectors and New Zealand two main islands (North and South). The rarefaction analysis suggests a significantly higher subtype richness in dairy cattle herds when compared to the other livestock sectors. AMOVA results indicate that the main source of subtype variation is attributable to the livestock sector from which samples were sourced suggesting that subtypes are generally sector-specific. The pairwise Fst results were similar, with low Fst values for island differences within a livestock sector when compared to between sector analyses, representing a low subtype differentiation between islands. However, for a given island, potential associations were seen between dominant subtypes and specific livestock sectors. Three subtypes accounted for 76% of the isolates. The most common of these was isolated from sheep and beef cattle in the North Island, the second most frequent subtype was mainly isolated from dairy cattle (either island), while the third most common subtype was associated with deer farmed in the South Island. The PSI analysis suggests similarities in subtypes sourced from sheep and beef cattle. This contrasted with the isolates sourced from other livestock sectors, which tended to present sector-specific subtypes. Sheep and beef cattle were mainly infected with MAP Type I, while dairy cattle and deer were almost exclusively infected with MAP Type II. However, when beef cattle and deer were both present at farm level, they harboured similar subtypes. This study indicates that cross-species transmission of MAP occurs on New Zealand farms although close contact between species appears to be required, as in the case of sheep and beef cattle which are commonly grazed together in New Zealand.

Genetic structure of Mycobacterium avium subsp. paratuberculosis population in cattle herds in Quebec as revealed by using a combination of multilocus genomic analyses

Mycobacterium avium subsp. paratuberculosis is the etiological agent of paratuberculosis, a granulomatous enteritis affecting a wide range of domestic and wild ruminants worldwide. A variety of molecular typing tools are used to distinguish M. avium subsp. paratuberculosis strains, contributing to a better understanding of M. avium subsp. paratuberculosis epidemiology. In the present study, PCR-based typing methods, including mycobacterial interspersed repetitive units/variable-number tandem repeats (MIRU-VNTR) and small sequence repeats (SSR) in addition to IS1311 PCR-restriction enzyme analysis (PCR-REA), were used to investigate the genetic heterogeneity of 200 M. avium subsp. paratuberculosis strains from dairy herds located in the province of Quebec, Canada. The majority of strains were of the "cattle type," or type II, although 3 strains were of the "bison type." A total of 38 genotypes, including a novel one, were identified using a combination of 17 genetic markers, which generated a Simpson's index of genetic diversity of 0.876. Additional analyses revealed no differences in genetic diversity between environmental and individual strains. Of note, a spatial and spatiotemporal cluster was evidenced regarding the distribution of one of the most common genotypes. The population had an overall homogeneous genetic structure, although a few strains stemmed out of the consensus cluster, including the bison-type strains. The genetic structure of M. avium subsp. paratuberculosis populations within most herds suggested intraherd dissemination and microevolution, although evidence of interherd contamination was also revealed. The level of genetic diversity obtained by combining MIRU-VNTR and SSR markers shows a promising avenue for molecular epidemiology investigations of M. avium subsp. paratuberculosis transmission patterns.

Molecular analysis of sarcoidosis lymph nodes for microorganisms: a case-control study with clinical correlates

INTRODUCTION

Sarcoidosis is an incurable, chronic granulomatous disease primarily involving the lungs and lymph nodes of unknown aetiology, treated with non-specific anti-inflammatory/immunosuppressive drugs. Persistently symptomatic patients worsen with a disabling, potentially fatal clinical course. To determine a possible infectious cause, we correlated in a case-control study the clinical information with the presence of bacterial DNA in sarcoidosis mediastinal lymph nodes compared with control lymph nodes resected during cancer surgery.

METHODS

We retrospectively studied formalin-fixed, paraffin-embedded, mediastinal lymph nodes from 30 patients with sarcoidosis and 30 control patients with lung cancer. Nucleic acids were extracted from nodes, evaluated by ribosomal RNA PCR for bacterial 16S ribosomal DNA and the results were sequenced and compared with a bacterial sequence library. Clinical information was correlated.

RESULTS

11/30 (36.7%) of lymph nodes from patients with sarcoidosis had detectable bacterial DNA, significantly more than control patient lymph nodes (2/30, 6.7%), p=0.00516. At presentation, 19/30 (63.3%) patients with sarcoidosis were symptomatic including all patients with detectable bacterial DNA. Radiographically, there were 18 stage I and 12 stage II patients. All stage II patients were symptomatic and 75% had PCR-detectable bacteria. After a mean follow-up of 52.8±32.8 months, all patients with PCR-detectable bacteria in this series were persistently symptomatic requiring treatment.

DISCUSSION

36.6% of patients with sarcoidosis had detectable bacterial DNA on presentation, all of these patients were quite symptomatic and most were radiographically advanced stage II. These findings suggest that bacterial DNA-positive, symptomatic patients have more aggressive sarcoidosis that persists long term and might benefit from antimicrobial treatment directed against this presumed chronic granulomatous infection.

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.

Mycobacterium avium subspecies paratuberculosis: an insidious problem for the ruminant industry

Mycobacterium avium subspecies paratuberculosis is considered as one of the most serious problems affecting the world's ruminant industry due to its significant impact on the global economy and the controversial issue that it may be pathogenic for humans. M. avium subspecies paratuberculosis is the causative agent of Johne's disease in animals and might be implicated in cases of human Crohn's disease. We provide an insight into M. avium subspecies paratuberculosis from some bacteriological, clinical, and molecular epidemiological perspectives.

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.

Diagnosis and Molecular Characterization of Mycobacterium avium subsp. paratuberculosis from Dairy Cows in Colombia

The objective of this study was the serological, bacteriological and molecular diagnosis, as well as the molecular characterization of Mycobacterium avium subsp. paratuberculosis (Map) in adult cows of five Colombian dairy herds. Serum samples were tested by an indirect absorbed enzyme–linked immunosorbent assay (ELISA-C). All fecal samples were tested by pooled culture. After that, fecal samples of Map positive pools were tested individually by culture and polymerase chain reaction (PCR). In one herd, slurry and tissue samples from one animal were also taken and tested by PCR and culture. Map isolates were analyzed by the Multilocus Short Sequence Repeat (MLSSR) and the Mycobacterial Interspersed Repetitive Units-Variable Number of Tandem Repeats (MIRU-VNTR) methods. ELISA produced positive results in 1.8% (6/329) of the animals and 40% (2/5) of the herds. Four fecal, two tissue, and two slurry samples from a herd were Map positive by culture and PCR. MLSSR and MIRU-VNTR revealed two different strain profiles among eight Map isolates recovered. This study reports the first molecular characterization of Map in one dairy herd in Colombia, the limitations for individual diagnosis of subclinical Map infections in cattle, and the usefulness of pooled fecal samples and environmental sampling for Map diagnosis.

Molecular epidemiology of Mycobacterium avium subsp. paratuberculosis in a longitudinal study of three dairy herds

The objective of this study was to evaluate whether cows that were low shedders of Mycobacterium avium subsp. paratuberculosis were passively shedding or truly infected with M. avium subsp. paratuberculosis. We also investigated whether it is possible that these M. avium subsp. paratuberculosis-infected animals could have been infected as adults by contemporary high-shedding animals (supershedders). The M. avium subsp. paratuberculosis isolates were obtained from a longitudinal study of three dairy herds in the northeastern United States. Isolates were selected from fecal samples and tissues at slaughter from all animals that were culture positive at the same time that supershedders were present in the herds. Shedding levels (CFU of M. avium subsp. paratuberculosis/g of feces) for the animals at each culture-positive occasion were determined. Using a multilocus short-sequence-repeat technique, we found 15 different strains of M. avium subsp. paratuberculosis from a total of 142 isolates analyzed. Results indicated herd-specific infection patterns; there was a clonal infection in herd C, with 89% of isolates from animals sharing the same strain, whereas herds A and B showed several different strains infecting the animals at the same time. Tissues from 80% of cows with at least one positive fecal culture (other than supershedders) were culture positive, indicating a true M. avium subsp. paratuberculosis infection. The results of M. avium subsp. paratuberculosis strain typing and observed shedding levels showed that at least 50% of low shedders have the same strain as that of a contemporary supershedder. Results of this study suggest that in a dairy herd, more of the low-shedding cows are truly infected with M. avium subsp. paratuberculosis than are passively shedding M. avium subsp. paratuberculosis. The sharing of strains between low shedders and the contemporary supershedders suggests that low shedders may have been infected by environmental exposure of M. avium subsp. paratuberculosis.

Multiplexed typing of Mycobacterium avium subsp. paratuberculosis types I, II, and III by Luminex xMAP suspension array

Differentiation among types I, II, and III is the primary step in typing Mycobacterium avium subsp. paratuberculosis. We propose an innovative approach based on detection of gyrase B (gyrB) gene polymorphisms by suspension array technology, with high discriminatory power and high-throughput potential.

Iron-sparing response of Mycobacterium avium subsp. paratuberculosis is strain dependent

Background

Two genotypically and microbiologically distinct strains of Mycobacterium avium subsp. paratuberculosis (MAP) exist - S and C MAP strains that primarily infect sheep and cattle, respectively. Concentration of iron in the cultivation medium has been suggested as one contributing factor for the observed microbiologic differences. We recently demonstrated that S strains have defective iron storage systems, leading us to propose that these strains might experience iron toxicity when excess iron is provided in the medium. To test this hypothesis, we carried out transcriptional and proteomic profiling of these MAP strains under iron-replete or -deplete conditions.

Results

We first complemented M. smegmatisΔideR with IdeR of C MAP or that derived from S MAP and compared their transcription profiles using M. smegmatis mc²155 microarrays. In the presence of iron, sIdeR repressed expression of bfrA and MAP2073c, a ferritin domain containing protein suggesting that transcriptional control of iron storage may be defective in S strain. We next performed transcriptional and proteomic profiling of the two strain types of MAP under iron-deplete and -replete conditions. Under iron-replete conditions, C strain upregulated iron storage (BfrA), virulence associated (Esx-5 and antigen85 complex), and ribosomal proteins. In striking contrast, S strain downregulated these proteins under iron-replete conditions. iTRAQ (isobaric tag for relative and absolute quantitation) based protein quantitation resulted in the identification of four unannotated proteins. Two of these were upregulated by a C MAP strain in response to iron supplementation. The iron-sparing response to iron limitation was unique to the C strain as evidenced by repression of non-essential iron utilization enzymes (aconitase and succinate dehydrogenase) and upregulation of proteins of essential function (iron transport, [Fe-S] cluster biogenesis and cell division).

Conclusions

Taken together, our study revealed that C and S strains of MAP utilize divergent metabolic pathways to accommodate in vitro iron stress. The knowledge of the metabolic pathways these divergent responses play a role in are important to 1) advance our ability to culture the two different strains of MAP efficiently, 2) aid in diagnosis and control of Johne's disease, and 3) advance our understanding of MAP virulence.

Occurrence of Mycobacterium avium subspecies paratuberculosis across host species and European countries with evidence for transmission between wildlife and domestic ruminants

Background

Mycobacterium avium subspecies paratuberculosis (Map) causes an infectious chronic enteritis (paratuberculosis or Johne's disease) principally of ruminants. The epidemiology of Map is poorly understood, particularly with respect to the role of wildlife reservoirs and the controversial issue of zoonotic potential (Crohn's disease). Genotypic discrimination of Map isolates is pivotal to descriptive epidemiology and resolving these issues. This study was undertaken to determine the genetic diversity of Map, enhance our understanding of the host range and distribution and assess the potential for interspecies transmission.

Results

164 Map isolates from seven European countries representing 19 different host species were genotyped by standardized IS900 - restriction fragment length polymorphism (IS900-RFLP), pulsed-field gel electrophoresis (PFGE), amplified fragment length polymorphisms (AFLP) and mycobacterial interspersed repeat unit-variable number tandem repeat (MIRU-VNTR) analyses. Six PstI and 17 BstEII IS900-RFLP, 31 multiplex [SnaBI-SpeI] PFGE profiles and 23 MIRU-VNTR profiles were detected. AFLP gave insufficient discrimination of isolates for meaningful genetic analysis. Point estimates for Simpson's index of diversity calculated for the individual typing techniques were in the range of 0.636 to 0.664 but a combination of all three methods increased the discriminating power to 0.879, sufficient for investigating transmission dynamics. Two predominant strain types were detected across Europe with all three typing techniques. Evidence for interspecies transmission between wildlife and domestic ruminants on the same property was demonstrated in four cases, between wildlife species on the same property in two cases and between different species of domestic livestock on one property.

Conclusion

The results of this study showed that it is necessary to use multiple genotyping techniques targeting different sources of genetic variation to obtain the level of discrimination necessary to investigate transmission dynamics and trace the source of Map infections. Furthermore, the combination of genotyping techniques may depend on the geographical location of the population to be tested. Identical genotypes were obtained from Map isolated from different host species co-habiting on the same property strongly suggesting that interspecies transmission occurs. Interspecies transmission of Map between wildlife species and domestic livestock on the same property provides further evidence to support a role for wildlife reservoirs of infection.

Identification and functional characterization of the iron-dependent regulator (IdeR) of Mycobacterium avium subsp. paratuberculosis

Mycobacterium avium subspecies paratuberculosis (MAP), the causative agent of Johne's disease in cattle and sheep, has unique iron requirements in that it is mycobactin-dependent for cultivation in vitro. The iron-dependent regulator (IdeR) is a well-characterized global regulator responsible for maintaining iron homeostasis in Mycobacterium tuberculosis (MTB). We identified an orthologous segment in the MAP genome, MAP2827, with >93 % amino acid identity to MTB IdeR. Electrophoretic mobility shift assays and DNase protection assays confirmed that MAP2827 binds the 19 bp consensus motif (iron box) on the MAP genome. Sequencing of MAP2827 from multiple isolates revealed a non-synonymous change (R91G) exclusive to sheep strains. Reporter gene assays and quantitative real-time RT-PCR assays in two diverse MAP strains and in an ideR deletion mutant of M. smegmatis (mc(2)155) suggested that both sheep MAP IdeR (sIdeR) and cattle MAP IdeR (cIdeR) repress mbtB transcription at high iron concentrations and relieve repression at low iron concentrations. On the other hand, bfrA (an iron storage gene) was upregulated by cIdeR when presented with MTB or the cattle MAP bfrA promoter, and was downregulated by sIdeR in the presence of MTB, or sheep or cattle MAP bfrA promoters, at high iron concentrations. The differential iron regulatory mechanisms between IdeR-regulated genes across strains may contribute to the differential growth or pathogenic characteristics of sheep and cattle MAP strains. Taken together, our study provides a possible reason for mycobactin dependency and suggests strong implications in the differential iron acquisition and storage mechanisms in MAP.

A novel insertion sequence, IS1642, of Mycobacterium avium, which forms long direct repeats of variable length

A new insertion sequence (IS), IS1642, was identified in a Mycobacterium avium strain isolated from a human patient. IS1642 had a size of 1642 bp and contained a single ORF encoding a probable transposase of 503 amino acid residues homologous (79% identity) to that of IS1549 found in Mycobacterium smegmatis. The IS1642 included imperfect inverted repeats (5'-cctgacttttatca-3', 5'-tgataaaagtcggg-3') on its ends, and was flanked by direct repeats of variable length ranging from 5 to 161 bp. It was suggested that the IS1642 was widely distributed in many M. avium strains of human patients, and the Southern blot profile of IS1642 was very diverse among the strains examined. The transposition event of IS1642 was observed by in vitro repeated passages, showing that the IS1642 is actually a transposable element. In light of these characteristics, IS1642 could be a new useful marker when genotyping with high discrimination is required.

Defining mycobacteria: Shared and specific genome features for different lifestyles

During the last decade, the combination of rapid whole genome sequencing capabilities, application of genetic and computational tools, and establishment of model systems for the study of a range of species for a spectrum of biological questions has enhanced our cumulative knowledge of mycobacteria in terms of their growth properties and requirements. The adaption of the corynebacterial surrogate system has simplified the study of cell wall biosynthetic machinery common to actinobacteria. Comparative genomics supported by experimentation reveals that superimposed on a common core of 'mycobacterial' gene set, pathogenic mycobacteria are endowed with multiple copies of several protein families that encode novel secretion and transport systems such as mce and esx; immunomodulators named PE/PPE proteins, and polyketide synthases for synthesis of complex lipids. The precise timing of expression, engagement and interactions involving one or more of these redundant proteins in their host environments likely play a role in the definition and differentiation of species and their disease phenotypes. Besides these, only a few species specific 'virulence' factors i.e., macromolecules have been discovered. Other subtleties may also arise from modifications of shared macromolecules. In contrast, to cope with the broad and changing growth conditions, their saprophytic relatives have larger genomes, in which the excess coding capacity is dedicated to transcriptional regulators, transporters for nutrients and toxic metabolites, biosynthesis of secondary metabolites and catabolic pathways. In this review, we present a sampling of the tools and techniques that are being implemented to tease apart aspects of physiology, phylogeny, ecology and pathology and illustrate the dominant genomic characteristics of representative species. The investigation of clinical isolates, natural disease states and discovery of new diagnostics, vaccines and drugs for existing and emerging mycobacterial diseases, particularly for multidrug resistant strains are the challenges in the coming decades.

Comparative analysis of Mycobacterium avium subsp. paratuberculosis isolates from cattle, sheep and goats by short sequence repeat and pulsed-field gel electrophoresis typing

Background

Mycobacterium avium subsp. paratuberculosis (Map) causes the chronic enteritis called paratuberculosis mainly in cattle, sheep and goats. Evidences that point out an association between Map and Crohn's Disease in humans are increasing. Strain differentiation among Map isolates has proved to be difficult and has limited the study of the molecular epidemiology of paratuberculosis. In order to asses the usefulness of the PCR based short sequence repeat (SSR) analysis of locus 1 and locus 8 in the epidemiological tracing of paratuberculosis strains we here compare for the first time the results of SSR and SnaBI-SpeI pulsed-field gel electrophoresis (PFGE) typing methods in a set of 268 Map isolates from different hosts (cattle, sheep, goats, bison, deer and wild boar).

Results

A total of nineteen different multi-locus SSR (SSR1_SSR8) types were identified amongst the 268 isolates compared to the 37 multiplex profiles differentiated by the SnaBI-SpeI PFGE. SSR type 7_4 was the predominant genotype (51.2% of all isolates and 54.3% of cattle isolates), but combined with PFGE results the abundance of the most prevalent genotype (7_4&{2-1}) dropped down to 37.7%. SSR types 7_3 and 14_3 were significantly spread amongst isolates recovered from small ruminants. The comparison of SSR1_SSR8 and SnaBI-SpeI PFGE typing of these isolates has shown that both methods perform at similar discriminatory level. These were 0.691 and 0.693, respectively for SSR and PFGE as indicated Simpson's Index of Diversity, and 0.82 when calculated for combined SSR and PFGE genotypes. Overall, SSR1_SSR8 analysis seemed to detect higher levels of within-farm strain diversity and seemed to give higher year-related information. Combination of both typing methods revealed 20 multi-type farms out of the 33 bovine farms studied with more than one isolate.

Conclusion

The particular SSR and PFGE typing approaches described here are in general agreement but they showed some discrepancies that might reflect differing evolutionary processes of Map strains. Both methods are able to reciprocally complement their results and neither should be replaced with the other if sufficient material and time is available. Overall, the results of our comparative analyses suggest that, based on current methodologies available, a combined approach that includes SSR and PFGE seems to provide the highest level of discrimination for Map strain typing with meaningful epidemiological information.

Combined multilocus short-sequence-repeat and mycobacterial interspersed repetitive unit-variable-number tandem-repeat typing of Mycobacterium avium subsp. paratuberculosis isolates

Short-sequence-repeat (SSR) sequencing was applied to 127 Mycobacterium avium subsp. paratuberculosis isolates typed by mycobacterial interspersed repetitive unit-variable-number tandem repeats (MIRU-VNTR) and IS900 restriction fragment length polymorphism (RFLP). Combined MIRU-VNTR and SSR typing followed by secondary IS900 RFLP typing is an improved approach to high-resolution genotyping of this pathogen.

The zoonotic potential of Mycobacterium avium spp. paratuberculosis: a systematic review

BACKGROUND

The zoonotic potential of Mycobacterium avium ssp. paratuberculosis (MAP) has been debated for almost a century because of similarities between Johne's Disease (JD) in cattle and Crohn's disease (CD) in humans. Our objective was to evaluate scientific literature investigating the potential association between these two diseases (MAP and CD) and the presence of MAP in retail milk or dairy products using a qualitative systematic review.

METHOD

The search strategy included 19 bibliographic databases, 8 conference proceedings, reference lists of 15 articles and contacting 28 topic-related scientists. Two independent reviewers performed relevance screening, quality assessment and data extraction stages of the review.

RESULTS

Seventy-five articles were included. Among 60 case-control studies that investigated the association between MAP and CD, 37 were of acceptable quality. Twenty-three studies reported significant positive associations, 23 reported non-significant associations, and 14 did not detect MAP in any sample. Different laboratory tests, test protocols, types of samples and source populations were used in these studies resulting in large variability among studies. Seven studies investigated the association between CD and JD, two challenge trials reported contradictory results, one cross-sectional study did not support the association, and four descriptive studies suggested that isolated MAP is often closely related to cattle isolates. MAP detection in raw and pasteurized milk was reported in several studies.

CONCLUSIONS

Evidence for the zoonotic potential of MAP is not strong, but should not be ignored. Interdisciplinary collaboration among medical, veterinary and other public health officials may contribute to a better understanding of the potential routes of human exposure to MAP.

Sequence polymorphisms in a surface PPE protein distinguish types I, II, and III of Mycobacterium avium subsp. paratuberculosis

In the last 2 decades, a variety of different molecular typing methods have been developed to differentiate strains of Mycobacterium avium subsp. paratuberculosis. The most successful techniques are based on insertion sequences, repetitive loci, comparative genomics, or single nucleotide polymorphisms. In the present study, we chose to examine whether a single M. avium subsp. paratuberculosis gene could serve as a means of differentiation of a variety of isolates. The MAP1506 gene locus encodes a member of the polymorphic PPE protein family that has putative roles relevant to M. avium subsp. paratuberculosis pathogenicity. The MAP1506 locus was sequenced from a collection of 58 M. avium subsp. paratuberculosis isolates from different sources, hosts, and typing profiles. Following sequence alignment and analysis, it was found that bovine (type II) strains of M. avium subsp. paratuberculosis consistently differed from ovine (type I) and intermediate (type III) strains in seven and eight nucleotides, respectively. Polymorphic regions of the MAP1506 locus were selected for analysis by denaturing gradient gel electrophoresis, allowing visual discrimination of the three subtypes of M. avium subsp. paratuberculosis isolates. This is the first report describing the use of PCR and denaturing gradient gel electrophoresis on a single gene as a method to distinguish types I, II, and III of M. avium subsp. paratuberculosis.

High genetic diversity among Mycobacterium avium subsp. paratuberculosis strains from German cattle herds shown by combination of IS900 restriction fragment length polymorphism analysis and mycobacterial interspersed repetitive unit-variable-number tandem-repeat typing

Mycobacterium avium subsp. paratuberculosis is the etiologic agent of Johne's disease and is endemic to the national cattle herds of many countries. Because of the very low level of genetic heterogeneity of this organism, it is difficult to select a workable procedure for strain differentiation at a resolution sufficient to investigate epidemiological links between herds or different ruminant species and the suggested zoonotic potential of M. avium subsp. paratuberculosis for Crohn's disease. Analysis of restriction fragment length polymorphisms (RFLPs) based on the insertion element IS900 (IS900 RFLP) with four restriction enzymes and 10 markers of specific mycobacterial interspersed repetitive units (MIRUs) and variable-number tandem repeats (VNTRs) was applied to 71 bovine M. avium subsp. paratuberculosis isolates originating from 14 herds from different regions in Germany. Among these isolates, all of which belonged to the M. avium subsp. paratuberculosis type II group, 17 genotypes were detected by IS900 RFLP and consisted of a combination of seven BstEII, eight PstI, nine PvuII, and four BamHI restriction patterns. Novel RFLP types were found. The diversity of the M. avium subsp. paratuberculosis isolates inside the herds was different depending on the frequency of animal purchase. The results of typing by IS900 RFLP and MIRU-VNTR analyses were not associated. Fifteen MIRU-VNTR patterns were identified with a discriminatory index of 0.905. The most common BstEII-based IS900 RFLP type, type C1 (72%), was subdivided into 14 types by MIRU-VNTR analysis. A combination of fingerprinting and PCR-based techniques resulted in 24 M. avium subsp. paratuberculosis genotypes and achieved a discriminatory index of 0.997. By using only BstEII and PstI digestion together with typing by MIRU-VNTR analysis, a discriminatory index of 0.993 was achieved. This is high enough to support epidemiological studies on a national as well as a global scale.

Influence of type of culture medium on characterization of Mycobacterium avium subsp. paratuberculosis subtypes

We evaluated the effects of culture and/or enrichment methods on the selection of Mycobacterium avium subsp. paratuberculosis subtypes. M. avium subsp. paratuberculosis isolates from bovine fecal samples processed using a centrifugation protocol were investigated in both liquid (MGIT ParaTb tubes) and solid (Herrold's egg yolk medium) culture media. For this evaluation, M. avium subsp. paratuberculosis subtyping was based on the sequence variation in two of the most discriminatory short sequence repeat loci, i.e., mononucleotide G and trinucleotide GGT, in isolates from liquid and solid cultures. This study identified the existence of one major predominating fingerprint (>13G-5GGT) in bovine fecal samples, regardless of the type of medium used for isolation. Matched-pair analysis of subtypes showed that 69% of samples presented unique subtypes in the two culture media used, while 31% shared the same G-GGT allele. Furthermore, the liquid culture method appeared to select for a more genotypically diverse subtype population than the solid culture method. The variety of subtypes observed between liquid and solid cultures obtained from the same fecal samples suggests that the culture method could provide a "microbiological" bias and lead to a discrepancy in the growth of M. avium subsp. paratuberculosis strains. In conclusion, this study identified that these two types of culture media determined differential growth of M. avium subsp. paratuberculosis strains and that this should be considered in evaluating detection capabilities of diagnostic tests or interpreting data from molecular epidemiological studies performed using conventional solid fecal culture or automated liquid medium culture methods.

Survival of Mycobacterium avium subsp. paratuberculosis in bovine monocyte-derived macrophages is not affected by host infection status but depends on the infecting bacterial genotype

In this study we investigated the ability of different Mycobacterium avium subsp. paratuberculosis (M. paratuberculosis) strains to survive in bovine monocyte-derived macrophages (MDMs) of cows naturally infected with M. paratuberculosis and control cows. We tested the hypotheses that infection status of cows affects macrophage killing ability and that survival of M. paratuberculosis in macrophages is dependent on the strain. Peripheral blood mononuclear cells (PBMC) were obtained from Johne's disease-positive (n=3) and age and stage of lactation matched Johne's disease-negative (n=3) multiparious cows. Following differentiation, MDMs were challenged in vitro with four M. paratuberculosis strains of different host specificity (cattle and sheep). Two hours and 2, 4, and 7 days after infection, ingestion, and intracellular survival of M. paratuberculosis strains were determined by fluorescence microscopy. There was no effect of the origin of MDMs (Johne's disease-positive or control animals) on phagocytosis, survival of bacteria, or macrophage survival. In contrast, important strain differences were observed. These findings suggest that some M. paratuberculosis strains interfere more successfully than others with the ability of macrophages to kill intracellular pathogens which may make it important to include strain typing when designing control programs.

New variable-number tandem-repeat markers for typing Mycobacterium avium subsp. paratuberculosis and M. avium strains: comparison with IS900 and IS1245 restriction fragment length polymorphism typing

Mycobacterium avium subsp. paratuberculosis, the etiological agent of paratuberculosis, affects a wide range of domestic ruminants and has been suggested to be involved in Crohn's disease in humans. Most available methods for identifying and differentiating strains of this difficult species are technically demanding and have limited discriminatory power. Here, we report the identification of novel PCR-based typing markers consisting of variable-number tandem repeats (VNTRs) of genetic elements called mycobacterial interspersed repetitive units (MIRUs). Eight markers were applied to 183 M. avium subsp. paratuberculosis isolates from bovine, caprine, ovine, cervine, leporine, and human origins from 10 different countries and to 82 human isolates of the closely related species M. avium from France. Among the M. avium subsp. paratuberculosis isolates, 21 patterns were found by MIRU-VNTR typing, with a discriminatory index of 0.751. The predominant R01 IS900 restriction fragment length polymorphism type, comprising 131 isolates, was divided into 15 MIRU-VNTR types. Among the 82 M. avium isolates, the eight MIRU-VNTR loci distinguished 30 types, none of which was shared by M. avium subsp. paratuberculosis isolates, resulting in a discriminatory index of 0.889. Our results suggest that MIRU-VNTR typing is a fast typing method that, in combination with other methods, might prove to be optimal for PCR-based molecular epidemiological studies of M. avium/M. avium subsp. paratuberculosis pathogens. In addition, presumably identical M. avium subsp. paratuberculosis 316F vaccine strains originating from the Weybridge laboratory and from different commercial batches from Mérial actually differed by one or both typing methods. These results indicate a substantial degree of genetic drift among different vaccine preparations, which has important implications for prophylactic approaches.