Skip to main content
Browse Subject Areas

Click through the PLOS taxonomy to find articles in your field.

For more information about PLOS Subject Areas, click here.

  • Loading metrics

The Association of Mycobacterium avium subsp. paratuberculosis with Inflammatory Bowel Disease

  • Verlaine J. Timms,

    Current address: Centre for Infectious Disease and Microbiology–Public Health, Level 3, ICPMR Westmead Hospital, Westmead, Sydney, Australia

    Affiliation School of Biotechnology and Biomolecular Sciences, Level 3, Biosciences Building, University of New South Wales, Sydney, Australia

  • George Daskalopoulos,

    Affiliation Inner West Endoscopy Centre, Endoscopy Services Pty. Ltd., Marrickville, Sydney, Australia

  • Hazel M. Mitchell,

    Affiliation School of Biotechnology and Biomolecular Sciences, Level 3, Biosciences Building, University of New South Wales, Sydney, Australia

  • Brett A. Neilan

    Affiliation School of Biotechnology and Biomolecular Sciences, Level 3, Biosciences Building, University of New South Wales, Sydney, Australia


The association of Mycobacterium avium subspecies paratuberculosis (M. paratuberculosis) with Crohn’s disease is a controversial issue. M. paratuberculosis is detected by amplifying the IS900 gene, as microbial culture is unreliable from humans. We determined the presence of M. paratuberculosis in patients with Crohn’s disease (CD) (n = 22), ulcerative colitis (UC) (n = 20), aphthous ulcers (n = 21) and controls (n = 42) using PCR assays validated on bovine tissue. Culture from human tissue was also performed. M. paratuberculosis prevalence in the CD and UC groups was compared to the prevalence in age and sex matched non-inflammatory bowel disease controls. Patients and controls were determined to be M. paratuberculosis positive if all three PCR assays were positive. A significant association was found between M. paratuberculosis and Crohn’s disease (p = 0.02) that was not related to age, gender, place of birth, smoking or alcohol intake. No significant association was detected between M. paratuberculosis and UC or aphthous ulcers; however, one M. paratuberculosis isolate was successfully cultured from a patient with UC. We report the resistance of this isolate to ethambutol, rifampin, clofazamine and streptomycin. Interestingly this isolate could not only survive but could grow slowly at 5°C. We demonstrate a significant association between M. paratuberculosis and CD using multiple pre-validated PCR assays and that M. paratuberculosis can be isolated from patients with UC.


Inflammatory Bowel Disease (IBD) and its divisions of Crohn’s disease (CD) and ulcerative colitis (UC) often strike in the prime of life and remain a life-long burden [1]. While the aetiology of IBD remains unclear, there is strong evidence to support the role of both microorganisms [2] and host genetic factors [36]. A number of microorganisms, including Mycobacterium avium subsp. paratuberculosis (M. paratuberculosis), have been associated with IBD, but as yet, evidence to support the role of a specific microorganism in IBD is missing.

There has been considerable controversy regarding the potential role of M. paratuberculosis in CD. The prevalence of M. paratuberculosis in patients with CD and UC has been shown to be highly variable (92% and 0–35%, respectively) [79], however, a meta-analysis in 2007 [10] demonstrated a significant association between M. paratuberculosis and CD. A comparison of M. paratuberculosis prevalence in patients with CD, UC and controls was undertaken and in addition, samples from patients with aphthous ulcers of the GI tract (as opposed to oral aphthous ulcers) were included as it is currently believed that these are likely precursors of CD [11].

M. paratuberculosis can infect the gastrointestinal tract of a range of hosts and is the known cause of Johne’s disease in ruminants, a disease typified by diarrhoea, weight loss and eventual death [12]. The controversy regarding the association of M. paratuberculosis with CD relates in part to the fastidious nature of M. paratuberculosis and the consequent inability to reliably culture this organism. M. paratuberculosis is a subspecies of the Mycobacterium avium complex (MAC) and the genetic similarity between the subspecies of the MAC is greater than 97% [13, 14]. Given the high genetic similarity between MAC members, unique markers for the detection of M. paratuberculosis are limited. The majority of studies investigating the association of M. paratuberculosis and CD have used one marker, IS900, a unique insertion sequence of M. paratuberculosis [1517].

Five PCR assays were applied to our patient set, all of which were previously validated on bovine tissue [18]. In addition, IBD patients were age and sex matched to non-IBD controls. Data on place of birth, smoking and other clinical data was collected on both patients and controls and collated with M. paratuberculosis status. A pure isolate of M. paratuberculosis was obtained from a patient with UC and a comprehensive biochemical and molecular characterisation of the second subculture of this isolate is also reported.


Ethics Statement

The study was approved by the Research Ethics Committee of the University of New South Wales (HREC 06233)/ (SESAHS (ES) 06/164). Written informed consent was obtained from study participants on forms approved by the above committee.

Patients and samples

Biopsies were obtained from a total of 105 patients (including 42 controls), undergoing colonoscopy at the Inner West Endoscopy Centre, Marrickville, Sydney between January 2007 to December 2009. Controls, termed nIBD controls, were selected from patients undergoing colonoscopy for conditions unrelated to inflammatory bowel disease. Patients were included as controls if IBD was excluded on clinical and histopathological examination. One control was age (±5 years) and sex matched to each CD and UC patient for which PCR results were obtained. At the time of routine colonoscopy, mucosal biopsy specimens (approximately 20 mg wet weight) were collected from the terminal ileum or colon of each patient and control and placed in a sterile reaction tube. Samples were frozen at -20°C until they were transported to the laboratory (between 1–2 days) then stored at -80°C until required.

Culture conditions and biochemical tests

Each biopsy was decontaminated in 60 μL of 0.75% (w/v) hexadecylpyridinium chloride (HPC) (Sigma) for 24 hours at room temperature. The HPC was then removed with a pipette and the biopsy washed in sterile H20, then crushed between two sterile glass slides. To encourage growth from potential, as yet unknown growth factors that may be present in viable cultures of M. paratuberculosis, a sterile supernatant of a growing culture of M. paratuberculosis ATCC19698 was obtained using methodology outlined previously [19]. One hundred microlitres of this sterile supernatant was added to the crushed biopsies and inoculated onto Middlebrook 7H10 agar with 10% v/v oleic acid, albumin, dextrose and catalase supplement (Sigma) and 2 μg mycobactin J mL-1 (Allied Monitor). Two slopes, to which sterile supernatant only was added, were set up as controls with each batch. The sterile supernatant was prepared freshly each time and was never stored. The slopes were then incubated at 37°C, aerated weekly and checked for growth monthly for 18 months.

Standard Ziehl-Neelsen (Z-N) staining was performed on any apparent growth [20]. Growth on Lowenstein–Jensen (L-J) (Difco) with 2 μg mycobactin J mL-1, MacConkey (Oxoid) and mycobactin free L-J and Middlebrook 7H10 agar was assessed by adding a 10 μL inoculum of a McFarland no. 1 standard to the respective media and checking for growth over 3 months. Thermostable and semiquantitative standard catalase assays were performed [20]. Bacterial size was determined using the AxioVision LE software.

To confirm the identity of the new isolate, strain 43525, DNA extraction for PCR assays and biochemical tests were conducted on the second subculture as there was insufficient growth on the first subculture. A previously published PCR assay was used to determine whether strain 43525 was a Cow (C) or a Sheep (S) strain [21]. Automated sequencing to identify PCR products was carried out using the PRISM BigDyeTM cycle sequencing system v3.1 and ABI 3730 capillary Applied Biosystem.

DNA extraction and PCR assays

DNA was extracted from biopsies using a method from previously published studies [15, 16, 18]. The primers used for the nested IS900 assay and the single round IS900, f57, myco16S and universal 16S assays were validated in previous publications [15, 2225]. The conditions for each PCR assay were validated on bovine tissue in a previous study [18] and the sensitivity of the IS900, nested IS900 and myco16S PCR assays was calculated to be 80% while the sensitivity of the f57 assay was 60%. The single round IS900 PCR assay was performed using 5 mM MgCl2, 100 μM dNTPs, 1 x reaction buffer, 1 U Taq, 2.5 μM of each primer and 5 μL (corresponding to 20–100 ng) of DNA sample per tube. Cycle conditions were as follows: 96°C for 1 min, then 96°C for 15 s, 50°C for 15 s, 72°C for 1 min for 35 cycles then 72°C for 5 min and 20°C hold.

For the nested IS900 PCR, the conditions were for the first stage; 1.25 mM MgCl2, 50 μM of dNTPs, 1 x reaction buffer, 1 U of Taq, 2 μM each primer and 2 μL (corresponding to 20–100 ng) of DNA sample added together and made up to 20 μL per tube. Cycling conditions were: 94°C for 1 min, 94°C for 10 s, 50°C annealing for 20 s, 72°C extension for 30 s for 35 cycles, then 72°C for 7 min. For the second stage 1.25 mM MgCl2, 100 μM of dNTPs, 1 x reaction buffer, 0.4 U Taq, 5 μM of primers and 5 μL of PCR product from the first stage was added together and made up to 20 μL per tube. The reaction conditions were as follows: 94°C for 1 min, then 94°C for 10 s, 58°C for 20 s, 72°C for 30 s for 30 cycles followed by 72°C for 7 min.

For the f57 PCR assay 0.75 mM MgCl2, 50 μM dNTPs, 1 x reaction buffer, 0.5 U Taq, 10 μM primer and 5 μL (corresponding to 20–100 ng) DNA were added together and made up to 20 μL. The cycling conditions were: 95°C for 4 mins, 94°C for 45 s, 62°C for 45 s, 72°C for 45 s for 40 cycles then 72°C 10 min and hold at 20°C.

The myco16S PCR was performed using 1.25 mM MgCl2, 100 μM dNTPs, 1 x reaction buffer, 0.4 U Taq, 5 μM of each primer and 2 μL (corresponding to 20–100 ng) DNA added together and made up to 20 μL. The cycling conditions were: 95°C for 3 mins, then 94°C for 30 s, 56°C for 1 min, 72°C for 1 min for 30 cycles and then 72°C 2 min.

The 16S rRNA gene PCR assay was performed using the following conditions: 2.5 mM MgCl2, 200 μM dNTPs, 1 x reaction buffer, 1 U of Taq polymerase, 0.4 μM of 16S rRNA gene primers [25] and 2 μL of DNA added together, and made up to 20 μL with sterilised distilled water. The PCR conditions were the following: 95°C for 3 min, then 94°C 30 s, 56°C 1 min, 72°C 1 min for 30 cycles then 7 min at 72°C. Patients were classified as M. paratuberculosis positive if all three PCR assays (IS900, f57 and nested IS900) were positive.

Growth at 5°C

Isolate 43525 appeared to be growing on a slope placed in a refrigerator, therefore we determined how fast isolate 43525 could grow at 5°C. A 20 μL bacterial suspension at a concentration equal to a McFarland No. 1 standard was added to Middlebrook 7H9 broth containing 10% albumin, dextrose and catalase (ADC) (Difco) and 2 μg mycobactin J mL-1. Flasks were incubated at 5°C with shaking and each week, for 6 weeks a 2 μL aliquot was plated onto slopes of Middlebrook 7H10 agar with 2 μg mycobactin J mL-1 to determine Colony Forming Units (CFU).

Antibiotic susceptibility

Antibiotic susceptibility and resistance of isolate 43525 was determined in triplicate by the agar proportion method as previously described [26]. Clarithromycin, rifampin and clofazimine were tested at 1–4 μg mL-1 while ciprofloxacin, ethambutol and streptomycin were tested in the range of 2–8 μg mL-1, all using Middlebrook 7H10 agar with 2 μg mycobactin J mL-1. An inoculum equivalent to a McFarland No.1 standard was added to slopes and incubated for 3 weeks. Any negative slopes were left for a total of 12 weeks.

Statistical analysis

The χ2 test and Kruskal-Wallis test was used to analyse the effect of factors such as age, gender, smoking, alcohol and place of birth. The Fisher’s exact test (two tailed) was used to compare the prevalence of M. paratuberculosis in patients and controls (Graphpad Prism software).


Of the 105 patients in the study, 22 patients had CD (13 male, 59%), 20 had UC (8 male, 40%), 21 had aphthous ulcers of the terminal ileum (13 male, 62%) and 42 were non-IBD (nIBD) controls. Patient characteristics including place of birth and smoking are presented in Table 1. Of the CD patients that were M. paratuberculosis positive (n = 6), four had CD of the terminal ileum (L1) and two had CD of the ileum and colon (L3). Of the UC patients that were M. paratuberculosis positive (n = 3), two had left-sided disease (E2) and one had extensive disease (E3), according to the Montreal classification [27]. The results of the PCR assays are presented in Table 2. The three PCR assays used to detect M. paratuberculosis across patients and controls gave variable results (Table 3). As observed in Table 3, in the CD control group not one patient was positive for M. paratuberculosis across the three assays and only one patient was positive in two assays (IS900 and f57). Conversely, in the CD group, six patients were M. paratuberculosis positive across all three assays.

Table 1. Characteristics of patients included in the study.

Table 2. The M. paratuberculosis (MAP) prevalence in patients with either Crohn’s or UC as compared to age and sex-matched controls.

Table 3. A comparison of each individual PCR assay and the patient/ control samples (by identity number) that were M. paratuberculosis positive.

In 12 patients, the DNA sample produced no PCR product with any of the assays. These samples were obtained from, one patient with CD, three with UC, eight with aphthous ulcers. For the aphthous ulcers group, 2/21 patients were positive with the single round IS900 only and no other PCR assay, therefore this group was not compared to a control group.

Four patients that were not M. paratuberculosis positive were found to be positive by the myco16S PCR. In two samples, the product quality was too poor to be sequenced. In the other two patients (one with UC and one control) sequencing found that the 16S rRNA gene product matched M. abscessus subsp. bolleti or M. massiliense. These two mycobacterial species have identical 16S rRNA genes and therefore cannot be distinguished by the sequence of this gene.

No significant difference was observed between the CD, UC or aphthous ulcer group and controls in regard to age, place of birth, smoking or alcohol intake (Table 1). A significant association was found between M. paratuberculosis PCR positivity and CD (p = 0.02) (Table 2).

For culture, isolate 43525, was obtained from the colon of a 66 year old female with UC. The patient was Australian born, did not smoke or drink alcohol and was suffering diarrhoea. Histological examination of the colonic mucosa revealed diffuse inflammation of both an acute and chronic nature consistent with UC. Although this was her first presentation, she underwent a total colectomy six months after the biopsy sample was taken, in which histological examination of the resected colon remained consistent with the diagnosis of active chronic UC.

Isolate 43525 initially took 40 weeks to grow at 37°C (S1A Fig), however, following the first subculture it grew vigorously on solid media. Attempts were made to amplify the IS900 and f57 genes directly on another colonic biopsy from the same patient without success. In addition, a universal 16S rRNA gene PCR assay also failed to produce a band. Unfortunately, this was all the material we had from that patient. The major characteristics of this isolate are outlined in Table 4 and are compared to the type strain ATCC19698 and the biochemical properties of human strains characterised in a previous publication [28].

Table 4. Comparison of the biochemical test results for isolate 43525 compared to other M. paratuberculosis isolates reported in the literature.

Growth at 5°C

Isolate 43525 grew at 5°C, as determined by the viable count method. The highest cell count was retrieved three weeks after inoculation (Fig 1). This experiment was repeated twice, with duplicate cultures and a negative control included each time, with the same results obtained. The temperature fluctuations of the cold incubator were recorded between 5.02–4.52°C, with a mean temperature of 4.62°C.

Fig 1. Natural log of Colony Forming Units (CFU) of isolate 43525 growing at 5°C.

Error bars indicate standard deviation. The increase in CFUs on day 21 was greater than 2 standard deviations.

Mycobactin independence

Isolate 43525 was C type and when grown on Middlebrook 7H10 agar without mycobactin, a perceptible reduction in the number of colonies, as compared with media containing mycobactin, was observed (S1B and S1C Fig). To confirm this, colonies were picked from media with and without mycobactin and streaked on to mycobactin-free Middlebrook 7H10. All colonies retained the ability to grow on mycobactin-free Middlebrook 7H10. In contrast, no growth was ever obtained on mycobactin-free L-J media, however growth was apparent when mycobactin was added. The mycobactin dependency was only apparent on L-J media. The sequences for IS900 and f57 of strain 43525 were 100% identical to those of M. paratuberculosis strains ATCC19698 and K10 (Table 4).

Antibiotic susceptibility

The MICs for ciprofloxacin, streptomycin, clofazimine and rifampin were higher for 43525 as compared with ATCC19698 (Table 5), while the MIC of clarithromycin was lower.

Table 5. Comparison of MIC values between ATCC19698 and isolate 43525.


The current study is the first to employ and to compare the detection rates of M. paratuberculosis in human tissue using two IS900 assays and the f57 assay. As M. paratuberculosis culture from humans is unreliable and there are a limited number of unique markers, a sample was deemed positive for M. paratuberculosis only if all three assays were positive. Using these criteria, we found the prevalence of M. paratuberculosis to be significantly higher (p = 0.02) in CD patients (29%) as compared with controls (0%). In contrast, no significant difference was found with the prevalence of M. paratuberculosis in patients with UC or aphthous ulcers.

We showed that the nested IS900 assay and f57 assay produced comparable results, while the single round IS900 assay resulted in a higher percentage of positive samples across all groups. These results are in agreement with the reported heterogeneity of IS900 detection, that is, the lack of specificity of the IS900 assay, in human tissue and the recommendation that the diagnosis of M. paratuberculosis should not rely upon a single IS900 result [7, 29].

Although the lack of concordance in the M. paratuberculosis positivity across assays can be explained in some part by the lack of specificity of the IS900 it cannot totally explain this phenomenon. It is possible that these results could reflect the presence of f57 and IS900-like sequences in the human gut microbiome in this group of subjects, particularly since only 20% of the genetic composition of the gut microbiome is known [30]. A follow-up of patients such as these may shed light on whether these PCR results are wholly due to the lack of specificity of the PCR assay or are an indication of transient bacteria passing through the human gastrointestinal tract. In addition, an internal positive control (IPC) was used to identify samples containing PCR inhibitors. The 16S rRNA PCR assay does not impair detection sensitivity by competing with the target DNA for reaction components. However, in light of the lack of concordance across in the M. paratuberculosis positivity across assays, the inclusion of a defined exogenous IPC such as that used in previous studies [15] could provide additional insight and may lead to more reliable detection.

Although it has been suggested that aphthous ulcers of the GI tract are precursors of CD, we found no evidence of M. paratuberculosis infection in any of our patients with aphthous ulcers. If aphthous ulcers are indeed a precursor of CD our results raise the question as to when M. paratuberculosis infection may occur. One possible scenario is that M. paratuberculosis may colonise only once inflammation has been initiated.

To our knowledge, this is also the only study to have matched controls by age and sex when investigating the association of M. paratuberculosis with CD. Although not reflected in our patient set, the majority of CD cases are usually women, in contrast to UC where both sexes are equally affected [31]. Significant differences in age and sex between CD, UC and controls have been demonstrated previously in studies exploring M. paratuberculosis associated CD, hence we endeavoured to remove these possibly confounding factors [15, 16].

Having established that M. paratuberculosis can be isolated from the human GI tract in this study [28, 32, 33] and the repeated demonstration of the association of M. paratuberculosis with some CD cases [10], future studies could investigate whether treating patients with M. paratuberculosis infection would benefit their disease course. In 2007, the Australian IBD study endeavoured to treat M. paratuberculosis associated CD, using a combination antibiotic therapy (clarithromycin, rifabutin and clofazamine) for up to 2 years [34]. A sustained benefit was not reported in the Australian study, however, the treatment administered in that study and a clinical trial currently recruiting [35], is based on limited knowledge as to what constitutes a successful M. paratuberculosis antibiotic treatment regimen in humans. The antibiotic profile of human isolate 43525 demonstrated differences in the susceptibility pattern as compared with bovine and other human M. paratuberculosis isolates [28]. In line with a previous study, isolate 43525 was resistant to ethambutol, clofazimine and rifampin [36]. Whether this resistance is widespread among M. paratuberculosis remains to be investigated. Based on the antibiotic resistance pattern reported here, use of the currently recommended antibiotic regimens would be ineffective, thus improvement in the symptomatology associated with CD would be unlikely.

Mycobactin dependency is still used to differentiate M. paratuberculosis from other subspecies of the M. avium complex. The mycobactin dependency of isolate 43525 was media based, hence, in a clinical laboratory this isolate may be misidentified as M. avium subsp. avium, an organism with different consequences in human infection. Interestingly, ovine isolates of M. paratuberculosis have also been found to grow on Middlebrook agar without the addition of mycobactin [37] and may be explained by the finding that the mycobactin operon promoter is active in M. paratuberculosis [38]. The genome of M. paratuberculosis 43525 has since been sequenced and the mycobactin cluster was found to differ to the mycobactin clusters of other M. paratuberculosis isolates [39]. In addition, isolate 43525 grew across a range of temperatures from 5°C to 44°C. M. smegmatis has been shown to grow at 10°C but was not tested below this [40]. The significance of this requires further investigation, particularly whether growth can also occur in milk, given reports that M. paratuberculosis survives pasteurisation [41].

The mycobacteria contain species that are ubiquitous in the environment and are some of the most persistent pathogens known to man. M. paratuberculosis, the little known subspecies of the MAC complex is a pathogen of animals and shares 97% of its genetic makeup with known human pathogens of that complex [42]. This is the first study to apply PCR assays to human tissue that have been pre-validated on a panel of M. paratuberculosis infected and non-infected bovine tissue [18]. In the absence of more reliable microbial culture data, combining three pre-validated PCR assays is an important step forward for confirming the detection of M. paratuberculosis in human mucosal biopsies. Like the study by Naser et. al. in 2004 [32], we report the characterisation of M. paratuberculosis from a patient with UC with a view that further work should strive to improve our technical ability to detect and monitor the presence of this species in humans.

Supporting Information

S1 Fig. Growth of 43525.

A) The appearance of original slope of isolate 43525, 8 weeks after growth first appeared, B) Isolate 43525 growing on Middlebrook 7H10 without mycobactin, C) Isolate 43525 growing on Middlebrook 7H10 with mycobactin added.



We would like to thank Michelle Gehringer for helpful discussions about this study.

Author Contributions

Conceived and designed the experiments: VJT GD BAN. Performed the experiments: VJT. Analyzed the data: VJT GD HMM BAN. Contributed reagents/materials/analysis tools: HMM BAN. Wrote the paper: VJT GD HMM BAN.


  1. 1. Sartor RB. Mechanisms of disease: pathogenesis of Crohn's disease and ulcerative colitis. Nat Clin Pract Gastroenterol Hepatol. 2006 Jul;3(7):390–407. pmid:16819502
  2. 2. Phavichitr N, Cameron DJ, Catto-Smith AG. Increasing incidence of Crohn's disease in Victorian children. J Gastroenterol Hepatol. 2003 Mar;18(3):329–32. pmid:12603535
  3. 3. Ahmad T, Armuzzi A, Bunce M, Mulcahy-Hawes K, Marshall SE, Orchard TR, et al. The molecular classification of the clinical manifestations of Crohn's disease. Gastroenterology. 2002 Apr;122(4):854–66. pmid:11910336
  4. 4. Bonen DK, Cho JH. The genetics of inflammatory bowel disease. Gastroenterology. 2003 Feb;124(2):521–36. pmid:12557156
  5. 5. Orholm M, Binder V, Sorensen TI, Rasmussen LP, Kyvik KO. Concordance of inflammatory bowel disease among Danish twins. Results of a nationwide study. Scand J Gastroenterol. 2000 Oct;35(10):1075–81. pmid:11099061
  6. 6. Barrett JC, Hansoul S, Nicolae DL, Cho JH, Duerr RH, Rioux JD, et al. Genome-wide association defines more than 30 distinct susceptibility loci for Crohn's disease. Nat Genet. 2008 Aug;40(8):955–62. pmid:18587394
  7. 7. Behr MA, Kapur V. The evidence for Mycobacterium paratuberculosis in Crohn's disease. Curr Opin Gastroenterol. 2008 Jan;24(1):17–21. pmid:18043227
  8. 8. Bernstein CN, Blanchard JF, Rawsthorne P, Collins MT. Population-based case control study of seroprevalence of Mycobacterium paratuberculosis in patients with Crohn's disease and ulcerative colitis. J Clin Microbiol. 2004 Mar;42(3):1129–35. pmid:15004064
  9. 9. Ellingson JL, Cheville JC, Brees D, Miller JM, Cheville NF. Absence of Mycobacterium avium subspecies paratuberculosis components from Crohn's disease intestinal biopsy tissues. Clin Med Res. 2003 Jul;1(3):217–26. pmid:15931311
  10. 10. Feller M, Huwiler K, Stephan R, Altpeter E, Shang A, Furrer H, et al. Mycobacterium avium subspecies paratuberculosis and Crohn's disease: a systematic review and meta-analysis. Lancet Infect Dis. 2007 Sep;7(9):607–13. pmid:17714674
  11. 11. Ambrosini R, Barchiesi A, Di Mizio V, Di Terlizzi M, Leo L, Filippone A, et al. Inflammatory chronic disease of the colon: how to image. Eur J Radiol. 2007 Mar;61(3):442–8. pmid:17197146
  12. 12. OIE. Paratuberculosis (Johne's Disease). OIE Terrestrial Manual: World Organisation for Animal Health; 2008. p. 276.
  13. 13. Mackenzie N, Alexander DC, Turenne CY, Behr MA, De Buck JM. Genomic comparison of PE and PPE genes in the Mycobacterium avium complex. J Clin Microbiol. 2009 Apr;47(4):1002–11. pmid:19144814
  14. 14. Uchiya K, Takahashi H, Yagi T, Moriyama M, Inagaki T, Ichikawa K, et al. Comparative Genome Analysis of Mycobacterium avium Revealed Genetic Diversity in Strains that Cause Pulmonary and Disseminated Disease. PLoS One. 2013;8(8):e71831. pmid:23990995
  15. 15. Bull TJ, McMinn EJ, Sidi-Boumedine K, Skull A, Durkin D, Neild P, et al. Detection and verification of Mycobacterium avium subsp. paratuberculosis in fresh ileocolonic mucosal biopsy specimens from individuals with and without Crohn's disease. J Clin Microbiol. 2003 Jul;41(7):2915–23. pmid:12843021
  16. 16. Autschbach F, Eisold S, Hinz U, Zinser S, Linnebacher M, Giese T, et al. High prevalence of Mycobacterium avium subspecies paratuberculosis IS900 DNA in gut tissues from individuals with Crohn's disease. Gut. 2005 Jul;54(7):944–9. pmid:15951539
  17. 17. Tuci A, Tonon F, Castellani L, Sartini A, Roda G, Marocchi M, et al. Fecal detection of Mycobacterium avium paratuberculosis using the IS900 DNA sequence in Crohn's disease and ulcerative colitis patients and healthy subjects. Dig Dis Sci. 2011 Oct;56(10):2957–62. pmid:21484317
  18. 18. Timms VJ, Mitchell HM, Neilan BA. Optimisation of DNA extraction and validation of PCR assays to detect Mycobacterium avium subsp. paratuberculosis. Journal of Microbiological Methods. 2015;112:99–103. pmid:25797305
  19. 19. Shleeva M, Mukamolova GV, Young M, Williams HD, Kaprelyants AS. Formation of 'non-culturable' cells of Mycobacterium smegmatis in stationary phase in response to growth under suboptimal conditions and their Rpf-mediated resuscitation. Microbiology. 2004 Jun;150(Pt 6):1687–97. pmid:15184555
  20. 20. Parish T, Stoker NG. Mycobacteria Protocols. Totowa: Humana Press; 1998.
  21. 21. Collins DM, De Zoete M, Cavaignac SM. Mycobacterium avium subsp. paratuberculosis strains from cattle and sheep can be distinguished by a PCR test based on a novel DNA sequence difference. Journal of clinical microbiology. [Evaluation Studies Research Support, Non-U.S. Gov't]. 2002 Dec;40(12):4760–2. pmid:12454189
  22. 22. Mobius P, Hotzel H, Rassbach A, Kohler H. Comparison of 13 single-round and nested PCR assays targeting IS900, ISMav2, f57 and locus 255 for detection of Mycobacterium avium subsp. paratuberculosis. Vet Microbiol. 2008 Jan 25;126(4):324–33. pmid:17889455
  23. 23. Vansnick E, De Rijk P, Vercammen F, Geysen D, Rigouts L, Portaels F. Newly developed primers for the detection of Mycobacterium avium subspecies paratuberculosis. Vet Microbiol. 2004 Jun 3;100(3–4):197–204. pmid:15145498
  24. 24. Tasara T, Hoelzle LE, Stephan R. Development and evaluation of a Mycobacterium avium subspecies paratuberculosis (MAP) specific multiplex PCR assay. Int J Food Microbiol. 2005 Oct 25;104(3):279–87. pmid:15982769
  25. 25. Weisburg WG, Barns SM, Pelletier DA, Lane DJ. 16S ribosomal DNA amplification for phylogenetic study. J Bacteriol. 1991 Jan;173(2):697–703. pmid:1987160
  26. 26. Parrish NM, Ko CG, Dick JD, Jones PB, Ellingson JL. Growth, Congo Red agar colony morphotypes and antibiotic susceptibility testing of Mycobacterium avium subspecies paratuberculosis. Clin Med Res. 2004 May;2(2):107–14. pmid:15931343
  27. 27. Silverberg MS, Satsangi J, Ahmad T, Arnott ID, Bernstein CN, Brant SR, et al. Toward an integrated clinical, molecular and serological classification of inflammatory bowel disease: report of a Working Party of the 2005 Montreal World Congress of Gastroenterology. Can J Gastroenterol. 2005 Sep;19 Suppl A:5A–36A. pmid:16151544
  28. 28. Chiodini RJ, Van Kruiningen HJ, Merkal RS, Thayer WR Jr, Coutu JA. Characteristics of an unclassified Mycobacterium species isolated from patients with Crohn's disease. J Clin Microbiol. 1984 Nov;20(5):966–71. pmid:6511878
  29. 29. Chiodini RJ, Chamberlin WM, Pfaller S. What is Mycobacterium avium subsp. paratuberculosis? Appl Environ Microbiol. 2011 Mar;77(5):1923–4; author reply -4. pmid:21350052
  30. 30. Qin J, Li R, Raes J, Arumugam M, Burgdorf KS, Manichanh C, et al. A human gut microbial gene catalogue established by metagenomic sequencing. Nature. 2010 Mar 4;464(7285):59–65. pmid:20203603
  31. 31. Tran QT, Han XY. Subspecies Identification and Significance of 257 Clinical Strains of Mycobacterium avium. J Clin Microbiol. 2014 Feb 5.
  32. 32. Naser SA, Ghobrial G, Romero C, Valentine JF. Culture of Mycobacterium avium subspecies paratuberculosis from the blood of patients with Crohn's disease. Lancet. 2004 Sep 18–24;364(9439):1039–44. pmid:15380962
  33. 33. Kirkwood CD, Wagner J, Boniface K, Vaughan J, Michalski WP, Catto-Smith AG, et al. Mycobacterium avium subspecies paratuberculosis in children with early-onset Crohn's disease. Inflamm Bowel Dis. 2009 Nov;15(11):1643–55. pmid:19462429
  34. 34. Selby W, Pavli P, Crotty B, Florin T, Radford-Smith G, Gibson P, et al. Two-year combination antibiotic therapy with clarithromycin, rifabutin, and clofazimine for Crohn's disease. Gastroenterology. 2007 Jun;132(7):2313–9. pmid:17570206
  35. 35. Kalfus I. A Randomized, Double Blind, Placebo-controlled, Multicenter, Parallel Group Study to Assess the Efficacy and Saefty of Fixed-dose Combination RHB-104 in Subjects With Moderately to Severely Active Crohn's Disease.: U.S. National Institutes of Health; 2013.
  36. 36. Krishnan MY, Manning EJ, Collins MT. Comparison of three methods for susceptibility testing of Mycobacterium avium subsp. paratuberculosis to 11 antimicrobial drugs. The Journal of antimicrobial chemotherapy. [Comparative Study Evaluation Studies Research Support, Non-U.S. Gov't]. 2009 Aug;64(2):310–6. pmid:19457932
  37. 37. Aduriz JJ, Juste RA, Cortabarria N. Lack of mycobactin dependence of mycobacteria isolated on Middlebrook 7H11 from clinical cases of ovine paratuberculosis. Vet Microbiol. 1995 Jul;45(2–3):211–7. pmid:7571372
  38. 38. Janagama HK, Senthilkumar TM, Bannantine JP, Rodriguez GM, Smith I, Paustian ML, et al. Identification and functional characterization of the iron-dependent regulator (IdeR) of Mycobacterium avium subsp. paratuberculosis. Microbiology. 2009 Nov;155(Pt 11):3683–90. pmid:19684064
  39. 39. Timms VJ, Hassan KA, Mitchell HM, Neilan BA. Comparative genomics between human and animal associated subspecies of the Mycobacterium avium complex: a basis for pathogenicity. BMC Genomics. 2015;16:695. pmid:26370227
  40. 40. Shires K, Steyn L. The cold-shock stress response in Mycobacterium smegmatis induces the expression of a histone-like protein. Mol Microbiol. 2001 Feb;39(4):994–1009. pmid:11251819
  41. 41. Grant IR. Mycobacterium paratuberculosis and milk. Acta Vet Scand. 2003;44(3–4):261–6. pmid:15074643
  42. 42. Bannantine JP, Zhang Q, Li LL, Kapur V. Genomic homogeneity between Mycobacterium avium subsp. avium and Mycobacterium avium subsp. paratuberculosis belies their divergent growth rates. BMC Microbiol. 2003 May 9;3:10. pmid:12740027