Mycobacterium avium subspecies paratuberculosis and its relationship with Crohn’s disease

Pathogens in Crohn's Disease: The Role of Adherent Invasive Escherichia coli

In Crohn's disease (CD), gut dysbiosis is marked by the prevalence of pathogenic bacterial species. Although several microbes have been reported as risk factors or causative agents of CD, it is not yet clear which is the real trigger of the disease. Thirty years ago, a new pathovar of Escherichia coli strain was isolated in the ileal mucosa of CD patients. This strain, called adherent invasive E. coli (AIEC), for its ability to invade the intestinal mucosa, could represent the causative agent of the disease. Several authors studied the mechanisms by which the AIEC penetrate and replicate within macrophages, and release inflammatory cytokines sustaining inflammation. In this review we will discuss about the role of AIEC in the pathogenesis of CD, the virulence factors mediating adhesion and invasion of AIEC in mucosal tissue, the environmental conditions improving AIEC survival and replication within macrophages. Finally, we will also give an overview of the new strategies developed to limit AIEC overgrowth.

A survey of enteric disease agents in UK deer populations

Wild deer products have been linked to outbreaks of Escherichia coli 0157 in humans and bovine tuberculosis (bTB) in domestic cats, raising concerns around foodborne diseases from venison. This study investigated the prevalence of several enteric disease agents in UK deer populations, including foodborne pathogens and other diseases of import to livestock health. Intestinal samples were collected from slaughtered farmed deer (N = 211, eight farms), shot wild deer (N = 136) and ground faecal samples were collected from two farms (N = 90), six parks (N = 228) and five zoos (N = 67). DNA was extracted and multiplex qPCR assays were run to amplify targets of, C. perfringens toxins, Campylobacter spp., E. coli toxins, Mycobacterium avium subsp. Paratuberculosis (MAP), Salmonella spp. and Yersinia spp. The most commonly amplified targets were E. coli astA (61.2%) and Campylobacter spp. (43.3%), but the prevalence of C. coli and C. jejuni were ≤ 3.0% and Salmonella spp., MAP and Yersinia pseudotuberculosis also had low overall prevalences of 1.6%, 3.3% and 2.6%, respectively. However, notable targets included C. perfringens toxins α (20.4%) and β2 (16.9%); E. coli stx1 (14.6% overall, 28.0% in abattoir samples) and stx2 (17.8% overall, 31.6% in wild samples); and Yersinia enterocolitica (10.8% overall, 25% in wild samples). The low prevalence of some foodborne pathogens is reassuring for food safety; further investigations into the commonly found targets are needed to quantify the risk to public health and the possibility of wild deer acting as reservoirs of disease.

Application of Volatilome Analysis to the Diagnosis of Mycobacteria Infection in Livestock

Volatile organic compounds (VOCs) are small molecular mass metabolites which compose the volatilome, whose analysis has been widely employed in different areas. This innovative approach has emerged in research as a diagnostic alternative to different diseases in human and veterinary medicine, which still present constraints regarding analytical and diagnostic sensitivity. Such is the case of the infection by mycobacteria responsible for tuberculosis and paratuberculosis in livestock. Although eradication and control programs have been partly managed with success in many countries worldwide, the often low sensitivity of the current diagnostic techniques against Mycobacterium bovis (as well as other mycobacteria from Mycobacterium tuberculosis complex) and Mycobacterium avium subsp. paratuberculosis together with other hurdles such as low mycobacteria loads in samples, a tedious process of microbiological culture, inhibition by many variables, or intermittent shedding of the mycobacteria highlight the importance of evaluating new techniques that open different options and complement the diagnostic paradigm. In this sense, volatilome analysis stands as a potential option because it fulfills part of the mycobacterial diagnosis requirements. The aim of the present review is to compile the information related to the diagnosis of tuberculosis and paratuberculosis in livestock through the analysis of VOCs by using different biological matrices. The analytical techniques used for the evaluation of VOCs are discussed focusing on the advantages and drawbacks offered compared with the routine diagnostic tools. In addition, the differences described in the literature among in vivo and in vitro assays, natural and experimental infections, and the use of specific VOCs (targeted analysis) and complete VOC pattern (non-targeted analysis) are highlighted. This review emphasizes how this methodology could be useful in the problematic diagnosis of tuberculosis and paratuberculosis in livestock and poses challenges to be addressed in future research.

Genetic Involvement of Mycobacterium avium Complex in the Regulation and Manipulation of Innate Immune Functions of Host Cells

Mycobacterium avium complex (MAC), a collection of mycobacterial species representing nontuberculous mycobacteria, are characterized as ubiquitous and opportunistic pathogens. The incidence and prevalence of infectious diseases caused by MAC have been emerging globally due to complications in the treatment of MAC-pulmonary disease (PD) in humans and the lack of understating individual differences in genetic traits and pathogenesis of MAC species or subspecies. Despite genetically close one to another, mycobacteria species belonging to the MAC cause diseases to different host range along with a distinct spectrum of disease. In addition, unlike Mycobacterium tuberculosis, the underlying mechanisms for the pathogenesis of MAC infection from environmental sources of infection to their survival strategies within host cells have not been fully elucidated. In this review, we highlight unique genetic and genotypic differences in MAC species and the virulence factors conferring the ability to MAC for the tactics evading innate immune attacks of host cells based on the recent advances in genetic analysis by exemplifying M. avium subsp. hominissuis, a major representative pathogen causing MAC-PD in humans. Further understanding of the genetic link between host and MAC may contribute to enhance host anti-MAC immunity, but also provide novel therapeutic approaches targeting the pangenesis-associated genes of MAC.

Detection of Wood Mice (Apodemus sylvaticus) Carrying Non-Tuberculous Mycobacteria Able to Infect Cattle and Interfere with the Diagnosis of Bovine Tuberculosis

Mycobacterial infections caused by the Mycobacterium tuberculosis complex (MTC) and non-tuberculous mycobacteria (NTM) are of great medical and veterinary relevance. The aim of this research was to study whether small mammals play a role in the epidemiology of mycobacterioses. Four samplings of 100 traps were performed in each of three cattle farms with previous history of tuberculosis or NTM between 2017 and 2018. A total of 108 animals belonging to seven species were trapped, classified, and necropsied, and tissues were submitted to microbiological and molecular methods for mycobacteria identification. The wood mouse (Apodemus sylvaticus) was the most abundant species (87%). No MTC was detected but six different NTM were identified (M. intracellulare, M. avium subsp. paratuberculosis, M. gordonae, M. celatum, M. fortuitum, and a not determined Mycobacterium sp.), showing a prevalence of 6.5%. No significant association was found between mycobacteria prevalence and the analyzed factors. Although a role in the epidemiology of MTC could not be attributed to small mammals, A. sylvaticus carries NTM that could be pathogenic or interfere with the diagnosis of tuberculosis. According to our results, there is a risk of NTM transmission at the wildlife–livestock interface through potential indirect contacts between small mammals and cattle.

Peripheral blood bovine lymphocytes and MAP show distinctly different proteome changes and immune pathways in host-pathogen interaction

Mycobacterium avium subsp. paratuberculosis (MAP) is a pathogen causing paratuberculosis in cattle and small ruminants. During the long asymptomatic subclinical stage, high numbers of MAP are excreted and can be transmitted to food for human consumption, where they survive many of the standard techniques of food decontamination. Whether MAP is a human pathogen is currently under debate. The aim of this study was a better understanding of the host-pathogen response by analyzing the interaction of peripheral blood lymphocytes (PBL) from cattle with MAP in their exoproteomes/secretomes to gain more information about the pathogenic mechanisms of MAP. Because in other mycobacterial infections, the immune phenotype correlates with susceptibility, we additionally tested the interaction of MAP with recently detected cattle with a different immune capacity referred as immune deviant (ID) cows. In PBL, different biological pathways were enhanced in response to MAP dependent on the immune phenotype of the host. PBL of control cows activated members of cell activation and chemotaxis of leukocytes pathway as well as IL-12 mediated signaling. In contrast, in ID cows CNOT1 was detected as highly abundant protein, pointing to a different immune response, which could be favorable for MAP. Additionally, MAP exoproteomes differed in either GroEL1 or DnaK abundance, depending on the interacting host immune response. These finding point to an interdependent, tightly regulated response of the bovine immune system to MAP and vise versa.

Mycobacterium avium paratuberculosis and Mycobacterium avium complex and related subspecies as causative agents of zoonotic and occupational diseases

Mycobacterium avium complex (MAC) and Mycobacterium avium paratuberculosis (MAP) cause zoonotic infections transmitted by birds and livestock herds. These pathogens have remained as serious economic and health threats in most areas of the world. As zoonotic diseases, the risk of development of occupational disease and even death outcome necessitate implementation of control strategies to prevent its spread. Zoonotic MAP infections include Crohn's disease, inflammatory bowel disease, ulcerative colitis, sarcoidosis, diabetes mellitus, and immune-related diseases (such as Hashimoto's thyroiditis). Paratuberculosis has classified as type B epidemic zoonotic disease according to world health organization which is transmitted to human through consumption of dairy and meat products. In addition, MAC causes pulmonary manifestations and lymphadenitis in normal hosts and human immunodeficiency virus (HIV) progression (by serotypes 1, 4, and 8). Furthermore, other subspecies have caused respiratory abscesses, neck lymph nodes, and disseminated osteomyelitis in children and ulcers. However, the data over the occupational relatedness of these subspecies is rare. These agents can cause occupational infections in susceptible herd breeders. Several molecular methods have been recognized as proper strategies for tracking the infection. In this study, some zoonotic aspects, worldwide prevalence and control strategies regarding infections due to MAP and MAC and related subspecies has been reviewed.

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.

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

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

Immunopathogenesis of granulomas in chronic autoinflammatory diseases

Granulomas are clusters of immune cells. These structures can be formed in reaction to infection and display signs of necrosis, such as in tuberculosis. Alternatively, in several immune disorders, such as sarcoidosis, Crohn's disease and common variable immunodeficiency, non-caseating granulomas are formed without an obvious infectious trigger. Despite advances in our understanding of the human immune system, the pathogenesis underlying these non-caseating granulomas in chronic inflammatory diseases is still poorly understood. Here, we review the current knowledge about the immunopathogenesis of granulomas, and we discuss how the involved immune cells can be targeted with novel therapeutics.

Responses of Bovine Innate Immunity to Mycobacterium avium subsp. paratuberculosis Infection Revealed by Changes in Gene Expression and Levels of MicroRNA

Paratuberculosis in cattle is a chronic granulomatous gastroenteritis caused by Mycobacterium avium subsp. paratubercolosis (MAP) which is endemic worldwide. In dairy herds, it is responsible for huge economic losses. However, current diagnostic methods do not detect subclinical infection making control of the disease difficult. The identification of MAP infected animals during the sub-clinical phase of infection would play a key role in preventing the dissemination of the pathogen and in reducing transmission. Gene expression and circulating microRNA (miRNA) signatures have been proposed as biomarkers of disease both in the human and veterinary medicine. In this paper, gene expression and related miRNA levels were investigated in cows positive for MAP, by ELISA and culture, in order to identify potential biomarkers to improve diagnosis of MAP infection. Three groups, each of 5 animals, were used to compare the results of gene expression from positive, exposed and negative cows. Overall 258 differentially expressed genes were identified between unexposed, exposed, but ELISA negative and positive groups which were involved in biological functions related to inflammatory response, lipid metabolism and small molecule biochemistry. Differentially expressed miRNA was also found among the three groups: 7 miRNAs were at a lower level and 2 at a higher level in positive animals vs unexposed animals, while 5 and 3 miRNAs were respectively reduced and increased in the exposed group compared to the unexposed group. Among the differentially expressed miRNAs 6 have been previously described as immune-response related and two were novel miRNAs. Analysis of the miRNA levels showed correlation with expression of their target genes, known to be involved in the immune process. This study suggests that miRNA expression is affected by MAP infection and play a key role in tuning the host response to infection. The miRNA and gene expression profiles may be biomarkers of infection and potential diagnostic of MAP infection earlier than the current ELISA based diagnostic tests.

Avian Mycobacteriosis: Still Existing Threat to Humans

The nontuberculous mycobacteria are typically environmental organisms residing in soil and water. These microorganisms can cause a wide range of clinical diseases; pulmonary disease is most frequent, followed by lymphadenitis in children, skin and soft tissue disease, and rare extra pulmonary or disseminated infections. Mycobacterium avium complex is the second most common cause of pulmonary mycobacterioses after M. tuberculosis. This review covers the clinical and laboratory diagnosis of infection caused by the members of this complex and particularities for the treatment of different disease types and patient populations.

Persistence of bacterial indicators and zoonotic pathogens in contaminated cattle wastes

BACKGROUND

Manure can provide a favourable environment for pathogens' survival. De-contamination may be conducted by extended storage, until field conditions are suitable for application to land as source of agricultural nutrients.

RESULTS

The hygienic evaluation of manure and slurry coming from a plant that collects cattle livestock wastes from a big slaughterhouse was carried out. Samples were even collected from spillages in the area around the plant. Microbial analyses highlighted the massive presence of faecal indicators in all samples: mean counts of Escherichia coli and enterococci were always above EU limits for marketable processed manure products. Cultures referable to the genus Brucella spp. were recorded in two samples of fresh manure but not in the aged ones. Conventional isolation techniques failed to detect members of the Mycobacterium genus, while by means of IS900 and F57 PCR real-time system on DNA directly extracted from environmental samples, the pathogen was detected in all cases.

CONCLUSIONS

Thoughtful design of manure storage infrastructure is critical to prevent spills and over-topping of an open structure. The documented overload situation seems to lay the basis for an ongoing environmental contamination by enteric organisms and opportunistic pathogens circuit faecal-oral route. Moreover, the type of wastes analysed during this study, namely a mixture of fresh cattle manure, bedding and rumen content, needs a longer storage period or, alternatively, of specific chemical, biological or thermal treatments for stabilization.

Koch's postulates, microbial dysbiosis and inflammatory bowel disease

Over the past 20 years, a growing amount of evidence supports the role of microbes and an imbalanced microbiota in inflammatory bowel disease (IBD). While many reviews have been written on the microbiota in IBD, few have considered how they fulfil the Koch's postulates. In this review, we consider how the Koch's postulates might be modified so that they can be fulfilled for polymicrobial diseases, and we discuss the progress made to date in fulfilling them.

Isolation and identification of nontuberculous mycobacteria from hospitalized patients and drinking water samples--examination of their correlation by chemometrics

Nontuberculous mycobacteria (NTM) have been found to be widely dispersed in the environment and are being considered potentially pathogenic for humans and animals, while reports of their human to human transmission are absent. Water and aerosols are potential transmission modes of NTM to humans. Hospitalized patients with NTM infections were studied together with drinking water samples from their respective residence areas during 2003-2013. Cluster analysis and factor analysis were used to analyze the data matrix. A total of 367 hospitalized patients living in 30 localities in the Prefecture of Larissa were tested positive for NTM. The most frequently isolated NTM species of the 383 NTM isolates from the clinical specimens were Mycobacterium fortuitum (n = 118, 30.8 %), M. gordonae (n = 87, 22.7 %), M. peregrinum (n = 46, 12.0 %), M. chelonae (n = 11, 2.9 %), M. avium (n = 8, 2.1 %), and M. intracellulare (n = 7, 1.8 %), while 88 (23.0 %) of these isolates were not identified. It is noted that in 8 patients, M. tuberculosis was isolated simultaneously with one NTM, in 15 patients, together with two types of NTM, while in 1 patient, it was found at the same time as three different NTM. In addition, 3360 drinking water samples were collected from 30 localities and analyzed during 2010 to 2013; they were found 11.2 % NTM positive. Cluster analysis and factor analysis results confirm that NTM strains are correlated to each other in both isolated samples from patients and drinking water, while the strength of their correlation varied from weak to moderate (e.g., factor loadings ranged from 0.69 to 0.74 when all data are considered). These results provide indications that drinking water could be linked with NTM cases in humans.

Phenotype definition is a main point in genome-wide association studies for bovine Mycobacterium avium ssp. paratuberculosis infection status

Paratuberculosis caused by Mycobacterium avium ssp. paratuberculosis (MAP) causes economic losses and is present in dairy herds worldwide. Different studies used different diagnostic tests to detect infection status and are the basis of genome-wide association (GWA) studies with inconsistent results. Therefore, the aim of this study was to identify and compare genomic regions associated with MAP susceptibility in the same cohort of cattle using different diagnostic tests. The GWA study was performed in German Holsteins within a case-control assay using 305 cows tested for MAP by fecal culture and additional with four different commercial ELISA-tests. Genotyping was performed with the Illumina Bovine SNP50 BeadChip. The results using fecal culture or ELISA test led to the identification of different genetic loci. Two single-nucleotide polymorphisms showed significant association with the ELISA-status. However, no significant association for MAP infection could be confirmed. Our results show that the definition of the MAP-phenotype has an important impact on the outcome of GWA studies for paratuberculosis.

Species-specific engagement of human nucleotide oligomerization domain 2 (NOD)2 and Toll-like receptor (TLR) signalling upon intracellular bacterial infection: role of Crohn's associated NOD2 gene variants

Recognition of bacterial peptidoglycan-derived muramyl-dipeptide (MDP) by nucleotide oligomerization domain 2 (NOD2) induces crucial innate immune responses. Most bacteria carry the N-acetylated form of MDP (A-MDP) in their cell membranes, whereas N-glycolyl MDP (G-MDP) is typical for mycobacteria. Experimental murine studies have reported G-MDP to have a greater NOD2-stimulating capacity than A-MDP. As NOD2 polymorphisms are associated with Crohn's disease (CD), a link has been suggested between mycobacterial infections and CD. Thus, the aim was to investigate if NOD2 responses are dependent upon type of MDP and further to determine the role of NOD2 gene variants for the bacterial recognition in CD. The response pattern to A-MDP, G-MDP, Mycobacterium segmatis (expressing mainly G-MDP) and M. segmatisΔnamH (expressing A-MDP), Listeria monocytogenes (LM) (an A-MDP-containing bacteria) and M. avium paratuberculosis (MAP) (a G-MDP-containing bacteria associated with CD) was investigated in human peripheral blood mononuclear cells (PBMCs). A-MDP and M. segmatisΔnamH induced significantly higher tumour necrosis factor (TNF)-α protein levels in healthy wild-type NOD2 PBMCs compared with G-MDP and M. segmatis. NOD2 mutations resulted in a low tumour necrosis factor (TNF)-α protein secretion following stimulation with LM. Contrary to this, TNF-α levels were unchanged upon MAP stimulation regardless of NOD2 genotype and MAP solely activated NOD2- and Toll-like receptor (TLRs)-pathway with an enhanced production of interleukin (IL)-1β and IL-10. In conclusion, the results indicate that CD-associated NOD2 deficiencies might affect the response towards a broader array of commensal and pathogenic bacteria expressing A-MDP, whereas they attenuate the role of mycobacteria in the pathogenesis of CD.

In Vivo Volatile Organic Compound Signatures of Mycobacterium avium subsp. paratuberculosis

Mycobacterium avium ssp. paratuberculosis (MAP) is the causative agent of a chronic enteric disease of ruminants. Available diagnostic tests are complex and slow. In vitro, volatile organic compound (VOC) patterns emitted from MAP cultures mirrored bacterial growth and enabled distinction of different strains. This study was intended to determine VOCs in vivo in the controlled setting of an animal model. VOCs were pre-concentrated from breath and feces of 42 goats (16 controls and 26 MAP-inoculated animals) by means of needle trap microextraction (breath) and solid phase microextraction (feces) and analyzed by gas chromatography/ mass spectrometry. Analyses were performed 18, 29, 33, 41 and 48 weeks after inoculation. MAP-specific antibodies and MAP-specific interferon-γ-response were determined from blood. Identities of all marker-VOCs were confirmed through analysis of pure reference substances. Based on detection limits in the high pptV and linear ranges of two orders of magnitude more than 100 VOCs could be detected in breath and in headspace over feces. Twenty eight substances differed between inoculated and non-inoculated animals. Although patterns of most prominent substances such as furans, oxygenated substances and hydrocarbons changed in the course of infection, differences between inoculated and non-inoculated animals remained detectable at any time for 16 substances in feces and 3 VOCs in breath. Differences of VOC concentrations over feces reflected presence of MAP bacteria. Differences in VOC profiles from breath were linked to the host response in terms of interferon-γ-response. In a perspective in vivo analysis of VOCs may help to overcome limitations of established tests.

Matrix metalloproteinases in inflammatory bowel disease: an update

Matrix metalloproteinases (MMPs) are known to be upregulated in inflammatory bowel disease (IBD) and other inflammatory conditions, but while their involvement is clear, their role in many settings has yet to be determined. Studies of the involvement of MMPs in IBD since 2006 have revealed an array of immune and stromal cells which release the proteases in response to inflammatory cytokines and growth factors. Through digestion of the extracellular matrix and cleavage of bioactive proteins, a huge diversity of roles have been revealed for the MMPs in IBD, where they have been shown to regulate epithelial barrier function, immune response, angiogenesis, fibrosis, and wound healing. For this reason, MMPs have been recognised as potential biomarkers for disease activity in IBD and inhibition remains a huge area of interest. This review describes new roles of MMPs in the pathophysiology of IBD and suggests future directions for the development of treatment strategies in this condition.

Resolution of Crohn's disease and complex regional pain syndrome following treatment of paratuberculosis

A cohort of family members with various chronic diseases including Crohn's disease, asthma, complex regional pain syndrome, hypothyroidism, type 1 diabetes mellitus, and lymphangiomatosis and/or evidence of infection by Mycobacterium avium subsp. paratuberculosis (MAP) are described in this series of case reports. MAP was cultured from the blood of three members affected by the first five diseases and there was accompanying elevated anti-MAP IgG in two members. The patient affected by the sixth disease has a markedly elevated anti-MAP titer. The two patients affected by the first four diseases have been treated with a combination of anti-MAP antibiotics and ultraviolet blood irradiation therapy with resolution of the disease symptomatology and inability to culture MAP in post treatment blood samples. These case reports of patients with MAP infections provide supportive evidence of a pathogenic role of MAP in humans.

Environment and the inflammatory bowel diseases

Inflammatory bowel diseases (IBD), which consists of Crohn disease and ulcerative colitis, are chronic inflammatory conditions of the gastrointestinal tract. In genetically susceptible individuals, the interaction between environmental factors and normal intestinal commensal flora is believed to lead to an inappropriate immune response that results in chronic inflammation. The incidence of IBD have increased in the past century in developed and developing countries. The purpose of the present review is to summarize the current knowledge of the association between environmental risk factors and IBD. A number of environmental risk factors were investigated including smoking, hygiene, microorganisms, oral contraceptives, antibiotics, diet, breastfeeding, geographical factors, pollution and stress. Inconsistent findings among the studies highlight the complex pathogenesis of IBD. Additional studies are necessary to identify and elucidate the role of environmental factors in IBD etiology.

The Mycobacterium avium ssp. paratuberculosis specific mptD gene is required for maintenance of the metabolic homeostasis necessary for full virulence in mouse infections

Mycobacterium avium subspecies paratuberculosis (MAP) causes Johne's disease, a chronic granulomatous enteritis in ruminants. Furthermore, infections of humans with MAP have been reported and a possible association with Crohn's disease and diabetes type I is currently discussed. MAP owns large sequence polymorphisms (LSPs) that were exclusively found in this mycobacteria species. The relevance of these LSPs in the pathobiology of MAP is still unclear. The mptD gene (MAP3733c) of MAP belongs to a small group of functionally uncharacterized genes, which are not present in any other sequenced mycobacteria species. mptD is part of a predicted operon (mptABCDEF), encoding a putative ATP binding cassette-transporter, located on the MAP-specific LSP14. In the present study, we generated an mptD knockout strain (MAPΔmptD) by specialized transduction. In order to investigate the potential role of mptD in the host, we performed infection experiments with macrophages. By this, we observed a significantly reduced cell number of MAPΔmptD early after infection, indicating that the mutant was hampered with respect to adaptation to the early macrophage environment. This important role of mptD was supported in mouse infection experiments where MAPΔmptD was significantly attenuated after peritoneal challenge. Metabolic profiling was performed to determine the cause for the reduced virulence and identified profound metabolic disorders especially in the lipid metabolism of MAPΔmptD. Overall our data revealed the mptD gene to be an important factor for the metabolic adaptation of MAP required for persistence in the host.

Facts, myths and hypotheses on the zoonotic nature of Mycobacterium avium subspecies paratuberculosis

Mycobacterium avium subspecies paratuberculosis (MAP) is the causative agent of paratuberculosis (Johne's disease [JD]), a chronic granulomatous enteritis in ruminants. JD is one of the most widespread bacterial diseases of domestic animals with significant economic impact. The histopathological picture of JD resembles that of Crohn's disease (CD), a human chronic inflammatory bowel disease of still unresolved aetiology. An aetiological relevance of MAP for CD has been proposed. This and the ambiguity of other published epidemiological findings raise the question whether MAP represents a zoonotic agent. In this review, we will discuss evidence that MAP has zoonotic capacity.

Mycobacterium avium paratuberculosis infection augments innate immune responses following intestinal epithelial injury

We wanted to determine if augmented innate immune activation is associated with lesion development in a mycobacterial enhanced intestinal injury model. We evaluated the local immune response in a Mycobacterium avium paratuberculosis + dextran sulfate sodium (Map + DSS) model using BALB/c and severe combined immunodeficient (SCID) mice. Map + DSS BALB/c and SCID mice displayed a similar disease phenotype. Moreover, Map + DSS SCID mice had increased expression of interleukin 1β (IL-1β), tumor necrosis factor α (TNF-α), inducible nitric oxide synthase (iNOS) and increased numbers of F4/80 positive cells. Additionally, Map antigen is co-localized with iNOS and IL-1β positive cells. This suggests that subclinical Map infection promotes innate immune activation following injury to the intestinal epithelium.

Reasonable selection and application of antibiotics in the treatment of Crohn's disease

Crohn's disease (CD) is one of the two major forms of inflammatory bowel disease (IBD). Although the etiology of CD is unclear, many experimental and clinical observations support the potential role for intestinal microflora in the pathogenesis of CD. Manipulation of the luminal content using antibiotics may therefore represent a potentially effective therapeutic option. Some randomized controlled trials have demonstrated the efficacy of these drugs in treating the perianal disease, inducing and maintaining of CD remission and decreasing CD recurrence rates in operated patients. But, the use of antibacterial therapy for CD is also controversial, even this approach is frequently and successfully adopted in clinical practice. Fairly narrow indications for antibiotics are suggested by current management guidelines. Large studies are required to better define the role of antibacterial agents and combination regimens in CD. Broad-spectrum antibiotics, such as metronidazole, fluoroquinolones and rifaximin, are widely used to treat CD, and their effects have been recognized. Because of the lack of adequate theoretical support and adverse drug reactions, the reasonable application of antibiotics to treat CD is still a clinical problem.

Genetic association between NOD2 polymorphism and infection status by Mycobacterium avium ssp. paratuberculosis in German Holstein cattle

The aim of the study was the analysis of the nucleotide-binding oligomerization domain containing 2 (NOD2, formerly CARD15) as a candidate gene for Mycobacterium avium ssp. paratuberculosis infection in cattle. Eleven SNPs in the NOD2 gene were identified, and finally, four SNPs were included in a case-control study using 324 German Holstein cows tested for paratuberculosis using fecal culture and ELISA. The SNP (GenBank) AY518738S04:g.521G>A in exon 4 showed a significant association between the fecal culture status of the animals and NOD2 allele variants. The other three SNPs showed no associations in German Holstein cows.

Comparison of prevalence estimation of Mycobacterium avium subsp. paratuberculosis infection by sampling slaughtered cattle with macroscopic lesions vs. systematic sampling

The objective of this study was to identify the most reliable approach for prevalence estimation of Mycobacterium avium ssp. paratuberculosis (MAP) infection in clinically healthy slaughtered cattle. Sampling of macroscopically suspect tissue was compared to systematic sampling. Specimens of ileum, jejunum, mesenteric and caecal lymph nodes were examined for MAP infection using bacterial microscopy, culture, histopathology and immunohistochemistry. MAP was found most frequently in caecal lymph nodes, but sampling more tissues optimized the detection rate. Examination by culture was most efficient while combination with histopathology increased the detection rate slightly. MAP was detected in 49/50 animals with macroscopic lesions representing 1.35% of the slaughtered cattle examined. Of 150 systematically sampled macroscopically non-suspect cows, 28.7% were infected with MAP. This indicates that the majority of MAP-positive cattle are slaughtered without evidence of macroscopic lesions and before clinical signs occur. For reliable prevalence estimation of MAP infection in slaughtered cattle, systematic random sampling is essential.

Lactase persistence, NOD2 status and Mycobacterium avium subsp. paratuberculosis infection associations to Inflammatory Bowel Disease

Background

Inflammatory Bowel Disease (IBD), which includes both Crohn’s disease (CD) and ulcerative colitis (UC), is caused by a complex interplay involving genetic predisposition, environmental factors and an infectious agent. Mycobacterium avium subsp. paratuberculosis (MAP) is a promising pathogen candidate since it produces a chronic intestinal inflammatory disease in ruminants that resembles CD in humans. MAP is a ubiquitous microorganism, although its presence in the food chain, especially in milk from infected animals, is what made us think that there could be an association between lactase persistence (LP) and IBD. The LCT mutation has brought adaptation to dairy farming which in turn would have increased exposure of the population to infection by MAP. NOD2 gene mutations are highly associated to CD.

Methods

In our study, CD and UC patients and controls from the North of Spain were genotyped for the lactase gene (LCT) and for three NOD-2 variants, R702W, G908R and Cins1007fs. MAP PCR was carried out in order to assess MAP infection status and these results were correlated with LCT and NOD2 genotypes.

Results

As for LP, no association was found with IBD, although UC patients were less likely to present the T/T₋₁₃₉₁₀ variant compared to controls, showing a higher C-allele frequency and a tendency to lactase non-persistence (LNP). NOD2 mutations were associated to CD being the per-allele risk higher for the Cins1007fs variant. MAP infection was more extended among the healthy controls (45.2%) compared to CD patients (21.38%) and UC patients (19.04%) and this was attributed to therapy. The Asturian CD cohort presented higher levels of MAP prevalence (38.6%) compared to the Basque CD cohort (15.5%), differences also attributed to therapy. No interaction was found between MAP infection and LCT or NOD2 status.

Conclusions

We conclude that LP is not significantly associated with IBD, but that MAP infection and NOD2 do show not mutually interacting associations with IBD.

Recent research on bovine paratuberculosis in South Korea

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

Macrophage-related diseases of the gut: a pathologist's perspective

The resident macrophages of the gastrointestinal tract represent the largest population of macrophages in the human body and are usually located in the subepithelial lamina propria. This strategic location guarantees a first-line defense to the huge numbers of potentially harmful bacteria and antigenic stimuli that are present in the intestinal lumen. In non-inflamed mucosa, macrophages phagocytose and kill microbes in the absence of an inflammatory response. However, in the event of an epithelial breach and/or microbial invasion, new circulating monocytes and lymphocytes will be recruited to the damaged area of the gut, which will result in the secretion of proinflammatory mediators and engage a protective inflammatory response. Although macrophages are usually not conspicuous in normal mucosal samples of the gut, they can easily be detected when they accumulate exogenous particulate material or endogenous substances or when they become very numerous. These events will mostly occur in pathologic conditions, and this review presents an overview of the diseases which are either mediated by or affecting the resident macrophages of the gut.

Molecular pathogenesis of bovine paratuberculosis and human inflammatory bowel diseases

Paratuberculosis (Ptb), caused by Mycobacterium avium subsp. paratuberculosis (Map), is a chronic enteritis that affects many ruminants and other wild animals worldwide. Ptb is a great concern in animal health and in etiology of human Crohn's disease (CD). In the present study, we detected Map-specific insertion sequence IS900 of DNA in tissue sections surgically removed from lesions of patients with CD (29 samples), ulcerative colitis (UC) (17 samples), and non-inflammatory bowel disease (IBD) (20 samples). We then compared the histopathological findings of 29 CD and 17 UC cases with those of 35 cases of bovine Ptb, since few comparative pathological studies of human IBD and Ptb have been conducted. The QPCR examination indicated positive results in 13.37% of CD cases, 3.57% of UC cases, and 10% of non-IBD cases. Human CD tissues typically exhibited destructive full thickness enteritis with severe lympho-plasma infiltration and scattered additional granulomas; UC lesions exhibited much less inflammation than CD lesions. Non-IBD control samples did not exhibit pathological changes. Human CD and UC lesions were very different from Ptb lesions that are characterized by predominant granuloma formation. Immunohistochemistry for Map antigen and acid-fast staining were negative in all human IBD cases but were always positive in Ptb cases. Our present comparative study strongly suggests that we reconsider the previous hypothesis that "Map infection" causes CD, even though human intestines were considered to have been exposed to the Map antigen containing the DNA.

Genetic evaluation of IS900 partial sequence of Mycobacterium avium subsp. paratuberculosis Brazilian isolates from bovine milk

Mycobacterium avium subsp. paratuberculosis (MAP) is the causative agent of paratuberculosis. Insertion sequence IS900 is used for the identification of MAP. The objective of this study was to verify the genetic conservation of IS900 sequences in raw milk samples. To evaluate genetic conservation, 206 quarter milk samples and 16 bulk-tank milk samples were collected. DNA extraction and IS900 PCR were performed in all samples. Six samples amplified the expected fragment. To confirm the identity of the amplified fragments, PCR products were cloned and sequenced. The resulting sequences were compared with other MAP sequences from GenBank, and it was possible to identify eight polymorphic regions and to form five distinct haplotypes. The number of mutations in each haplotype was verified. IS900 sequence is a very well-conserved sequence that could be used as tool for the molecular detection of this agent and epidemiological purposes. The results showed the first genetic analysis on Brazilian isolates of MAP.

Induction of matrix metalloproteinases and TLR2 and 6 in murine colon after oral exposure to Mycobacterium avium subsp. paratuberculosis

Mycobacterium avium subspecies paratuberculosis (MAP) is suspected to be a causative agent in Crohn's disease. Recent evidence suggests that MAP can induce the expression of Matrix Metalloproteinases (MMPs), which are the main proteases in the pathogenesis of mucosal ulcerations in inflammatory bowel disease (IBD). Within the present study, we analysed whether oral MAP exposure can induce colonic MMP expression in vivo. In MAP exposed mice MAP and spheroplasts were visualized in intramucosal leukocyte aggregates. MAP exposed mice exhibited a higher colonic expression of Mmp-2, -9, -13, -14, Timp-1, Tlr2, Tlr6, Il-1β, and Tnf-α. Cell clusters of MMP-9 positive cells adjacent to intramucosal leukocyte aggregates and CD45(+) leukocytes were identified as the major cellular sources of MMP-9. Enhanced TLR2 expression was visualized on the luminal side of colonic enterocytes. Although MAP exposure did not lead to macroscopic intestinal inflammation, the observed MAP spheroplasts in intramucosal leukocyte aggregates together with increased colonic expression of toll-like receptors, pro-inflammatory cytokines, and MMPs upon MAP exposure represents a part of the host immune response towards MAP.

Serum antibodies to Mycobacterium avium subspecies paratuberculosis combined with anti-Saccharomyces cerevisiae antibodies in Crohn's disease patients: prevalence and diagnostic role

BACKGROUND

Because Mycobacterium avium subspecies paratuberculosis (MAP), the etiologic agent of Johne's disease in ruminant, has been identified in the mucosal layer and deeper bowel wall in CD patients, the seroactivity against MAP may define a distinct subset of patients requiring individual treatment. The aim of this study was to assess the performance of anti-MAP antibodies in the diagnostic strategy for CD.

METHODS

Two hundred seventy-two individuals were included: 81 with CD, 36 with ulcerative colitis, 35 with coeliac diseases and 120 healthy blood donors. Anti-MAP were detected by ELISA using a purified protein derivative from MAP. Anti-Saccharomyces cerevisiae antibodies (ASCA) were detected by indirect immunofluorescence.

RESULTS

The sensitivity and specificity of anti-MAP and ASCA for CD diagnosis were similar (sensitivity: 0.33 ± 0.10 and 0.31 ± 0.10; specificity: 0.96 ± 0.03 and 0.98 ± 0.02, respectively). A combination of these two tests enabled an increase in sensitivity (0.53 ± 0.10), although specificity remained unchanged (0.95 ± 0.04). No correlation was found between anti-MAP positivity and clinical features such as age at onset and the duration of CD, disease location, or intestinal complications. Conversely, extra-intestinal manifestations of CD were statistically associated with a positivity of anti-MAP (48% vs. 24%, P = 0.028), mostly with respect to arthritis (44.5% vs. 13%, P < 0.002). Interestingly, anti-MAP and ASCA were also found in an active form of coeliac disease.

CONCLUSION

Our results suggest a complementary role of ASCA and anti-MAP for CD diagnosis and a possible common role of bacteria in small intestinal mucosal damage in CD and coeliac disease.

Presence of intestinal Mycobacterium avium subspecies paratuberculosis (MAP) DNA is not associated with altered MMP expression in ulcerative colitis

BACKGROUND

Mycobacterium avium subspecies paratuberculosis (MAP) is suspected to be a causative agent in human Crohn's disease (CD). Recent evidence suggests that pathogenic mycobacteria and MAP can induce the expression of Matrix Metalloproteinases (MMP), which are the main proteases in the pathogenesis of mucosal ulcerations in inflammatory bowel disease (IBD). Within this study we assessed the prevalence of intestinal MAP specific DNA in patients with Crohn's disease, ulcerative colitis (UC), and healthy controls. We further analysed regulation patterns of MMPs in mucosal tissues of UC patients with and without intestinal MAP DNA detection.

METHODS

Colonic biopsy samples were obtained from 63 Norwegian and German IBD patients and 21 healthy controls. RNA was quantified by quantitative real-time polymerase chain reaction (PCR) to study MMP gene expression in both pathological and healthy mucosal specimens. The presence of MAP DNA in colonic mucosa was examined using MAP specific PCR.

RESULTS

MAP DNA was detected in 20% of UC patients and 33% of healthy controls but only in 7% of patients with CD. UC patients treated with corticosteroids exhibited a significantly increased frequency of intestinal MAP DNA compared to those not receiving corticosteroids. Expression of MMP-1, -2, -7, -9, -13, -19, -28 and TNF-α did not differ between UC patients with presence of intestinal MAP DNA compared to those without. MMP-2, MMP-9 and MMP-13 were significantly decreased in UC patients receiving corticosteroids.

CONCLUSIONS

The presence of intestinal MAP specific DNA is not associated with altered MMP expression in UC in vivo. Corticosteroids are associated with increased detection of intestinal MAP DNA and decreased expression of certain MMPs. Frequent detection of MAP DNA in healthy controls might be attributable to the wide environmental distribution of MAP and its presence in the food-chain.

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

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

Crohn's disease: evidence for involvement of unregulated transcytosis in disease etio-pathogenesis

Crohn's disease (CD) is a chronic inflammatory bowel disease. Research has identified genetic predisposition and environmental factors as key elements in the development of the disease. However, the precise mechanism that initiates immune activation remains undefined. One pathway for luminal antigenic molecules to enter the sterile lamina propria and activate an immune response is via transcytosis. Transcytosis, although tightly regulated by the cell, has the potential for transepithelial transport of bacteria and highly antigenic luminal molecules whose uncontrolled translocation into the lamina propria can be the source of immune activation. Viewed as a whole, the evidence suggests that unregulated intestinal epithelial transcytosis is involved in the inappropriate presentation of immunogenic luminal macromolecules to the intestinal lamina propria. Thus fulfilling the role of an early pre-morbid mechanism that can result in antigenic overload of the lamina propria and initiate an immune response culminating in chronic inflammation characteristic of this disease. It is the aim of this paper to present evidence implicating enterocyte transcytosis in the early etio-pathogenesis of CD.

Differential proteome analysis of Mycobacterium avium subsp. paratuberculosis grown in vitro and isolated from cases of clinical Johne's disease

Bovine Johne's disease (paratuberculosis), caused by Mycobacterium avium subspecies paratuberculosis, poses a significant economic problem to the beef and dairy industry worldwide. Despite its relevance, however, pathogenesis of Johne's disease is still only partially resolved. Since mycobacterial membrane proteins expressed during infection are likely to play an important role in pathogenesis, membrane-enriched fractions, namely mucosa-derived membranes (MDM) and culture-derived membranes (CDM), of M. avium subsp. paratuberculosis from three cows with clinical paratuberculosis were investigated. An initial analysis by 2D difference gel electrophoresis (2D DIGE) and MALDI-TOF-MS analysis revealed four differentially expressed proteins with only one predicted membrane protein. Due to this limited outcome, membrane preparations were subjected to a tube–gel trypsin digestion and investigated by using nanoflow-liquid-chromatography-coupled tandem MS. Based on this approach a total of 212 proteins were detected in MDM including 32 proteins of bovine origin; 275 proteins were detected in CDM; 59 % of MDM and CDM proteins were predicted to be membrane-associated. A total of 130 of the proteins were detected in both MDM and CDM and 48 predicted membrane proteins were detected in MDM from at least two cows. Four of these proteins were not detected in CDM, implying differential expression in the host. All membrane-associated proteins, especially the four identified as being differentially expressed, might be relevant targets for further analyses into the pathogenesis of bovine paratuberculosis.

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.

Mycobacterium avium paratuberculosis and the etiology of Crohn's disease: a review of the controversy from the clinician's perspective

Mycobacterium avium paratuberculosis (MAP) is an obligate intracellular organism that has frequently been associated with Crohn's disease (CD). Because CD is a chronic inflammatory condition, many researchers have speculated that an infectious agent must be the cause of CD. MAP has often been proposed to be one such agent; however, despite considerable research, the evidence remains inconclusive. Higher levels of MAP have been found in the tissues and blood of CD patients than in controls, forming the foundation for much of the research into the role of MAP in CD and the primary argument in support of a causative role for MAP in CD. MAP is a slow-growing and fastidious organism that is difficult to grow in culture and, therefore, challenging to detect in patients. As a result, there has been variability in the results of studies attempting to detect the presence of MAP in CD patients, and considerable controversy over whether this organism has a causative role in the etiology of CD. Two main hypotheses exist with respect to the role of MAP in CD. The first is that MAP is a principal cause of CD, while the second is that MAP is more prevalent because of the immune dysfunction seen in CD but does not play a causative role. Clinicians are often faced with questions regarding the role of this organism and the need to treat it. The present article attempts to provide an overview of the controversy including the nature of the mycobacterium, the difficulty in detecting it, the use of antimycobacterial agents to treat it and the effect of immunosuppressive agents - all from a clinician's perspective. Although the role of MAP in CD remains controversial and an area of considerable research, it is currently only of academic interest because there is no clinically useful test to identify the presence of the organism, and no evidence to support the use of antibiotics to eradicate it for the treatment of CD.