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Comparison and Validation of IS900-Sequence and Putative Sequences as Specific Target to Detect Mycobacterium avium subsp. paratuberculosis

  Teshome Yehualaeshet1*      Martha Graham2      Temesgen Samuel1      Sarah E Rowe Morton3      Soren Rodning4      Tsegaye Habtemariam5   

1Department of Pathobiology, College of Veterinary Medicine, Tuskegee University, Analysis Tuskegee, Alabama, USA
2Pharmaceutical Sciences, Mercer University Atlanta Campus, Atlanta, Georgia, USA
3Thompson-Bishop-Sparks State Diagnostic Laboratory, Auburn, Alabama, USA
4Department of Animal Sciences, Auburn University, Auburn, Alabama, USA
5Center for Computational Epidemiology, Bioinformatics & Risk, College of Veterinary Medicine, Tuskegee University, Analysis Tuskegee, Alabama, USA

*Corresponding author: Teshome Yehualaeshet, Department of Pathobiology, College of Veterinary Medicine, Tuskegee University, USA, Tel: (334) 727-8107; Fax: (334) 724-4110; E-mail:


Polymerase chain reaction (PCR) has been used to improve the identification of Mycobacterium avium subsp. paratuberculosis (MAP). The objective of this study was to compare and validate real-time PCR results of IS900-insertion sequence and nine putative sequences as diagnostic templates to detect MAP. MAP reference strains, field isolates, and non-MAP species were included in the study to validate the specificity of the target genes by PCR detection. All the IS900 insertion sequences and the putative sequences were specifically amplified from the field isolates and reference MAP strains whereas no amplifications were found from the six non-MAP strains. Uniplex and multiplex-PCR of IS900 and putative sequences showed the presence of two distinct amplicons respectively. Furthermore, in silico PCR simulation showed that the primers used in this study for IS900 sequences and the putative sequences amplified only from known MAP and were negative for 63 non-MAP species. Early, accurate and precise diagnostic protocol will assist to track contaminated herds, food products and would ultimately contribute to the control and prevention of Johne’s disease. Based on our results within the size of our samples, the IS900 insertion sequence and the repetitive sequences were amplified only in MAP. The insertion/repetitive sequences targeted in the PCR are not found in the non-MAP species tested in the experiment. Furthermore, the in silico PCR amplification supported the in vivo PCR results.


M. avium subsp. Paratuberculosis; IS900 insertion sequence; PCR; Putative sequence; Detection


Johne’s disease, caused by Mycobacterium avium subspecies paratuberculosis (MAP), is being increasingly recognized as a significant herd health problem; thus, there is a need for a reliable diagnostic tool for large-scale use to facilitate control and prevention programs and eventually eradicate the disease. MAP is an extremely slow-growing, acidfast and mycobactin-dependent pathogen to grow. Infection with this bacterium leads to a chronic granulomatous enteritis in a broad range of hosts mainly in cattle and other wild and domestic ruminants [1].

Detection of MAP-infected animals poses great difficulties, thus rapid and reliable procedures for the direct detection of MAP in the herd and food samples are still challenging. Efforts have been made in the last few decades to develop protocols for the detection of MAP in feces, milk, tissue, food, and environmental samples using various methods. Fecal culture and serology are the most commonly used tests in the clinical laboratories [1]. The gold standard for Johne’s disease is identification of the etiologic agent, MAP, in tissues that show characteristic histopathologic lesions [2]. Culture will require 8 to 12 weeks and has well known limitations in sensitivity, especially in sub clinically infected cattle, and turnaround time; nonetheless, culture or some other method to detect MAP directly still has a place at certain stages of a Johne’s disease control program [3].

With the development of new molecular techniques, more powerful protocols have become available to improve the detection of MAP. PCR is a powerful method for specific detection of DNA sequences, for which samples can be taken from colostrum, milk, feces, and tissues [4,5]. For molecular detection of MAP, PCR assays targeting various regions specific for MAP were reported from different laboratories. Some of the PCR target genes include MAP-specific genomic sequences such as the insertion sequence IS900, F57 element, IS1311 insertion sequence and hsp X gene [5-7]. Of these, multi-copy IS900 is a target of choice and is the most widely used in the characterization of MAP. The characterization of IS900 insertion sequence, which has 1,451 base pairs and is present as 15 to 20 copies in the MAP genome, has enabled the accurate identification of minimum amounts of bacterial DNA by the polymerase chain reaction (PCR) assay [8]. Furthermore, by suppression subtractive hybridization-based method, nine novel MAP fragments of between 318 and 596 bp have been identified and characterized. A database search revealed little or no similarity with other Mycobacterium species [9].

It is essential to authenticate the existing protocol and targets to have an efficient method for the detection of M. avium subsp. paratuberculosis. The objective of this study was to compare and validate the real-time PCR results of IS900-insertion sequence and nine putative sequences as diagnostic tools to detect MAP.

Materials and Methods
Bacterial strains and growth

Three M. avium subsp. paratuberculosis strains, (baa-968, 19851 and 43015), six non-MAP species (M. fortuitum subsp. fortuitum, M. intracellulare, M. kansasii, M. marinum, M. phlei, and M. scrofulaceum) and 13 MAP clinical isolates were included in this study. The MAP strains and the non-MAP species were purchased from American Type Culture Collection (ATCC, Manassas, VA). The clinical MAP strains, isolated from cattle feces with naturally acquired Johne’s disease, were obtained from Thompson-Bishop-Sparks State Diagnostic Laboratory, Auburn, Alabama. The MAP was grown in Lowenstein-Jensen media (Becton Dickinson and Company, Sparks, MD) and 7H9 broth supplemented with 2 mg of Mycobactin (Difco Laboratories, Detroit, MI).

DNA Extraction

PrepMan kit (Applied Biosystems, Carlsbad, CA) was used to extract DNA from the culture. Briefly, the samples were centrifuged at a medium speed (3 min at 10,000 × g) on a tabletop centrifuge to pellet the cells. After the supernatant has been discarded, the pellet was washed and resuspended in 100 µl of the PrepMan reagent. After brief vortexing, the mixture was boiled at 100°C for 10 min. The preparation was centrifuged, and the supernatant was used as the template for PCR and stored at -20°C for future use. Before PCR assay, the extracted DNA was quantified by ND-1000 spectrophotometer (NanoDrop, Wilmington, DE).

Real-time Polymerase Chain Reaction

The sample preparation, DNA extraction, PCR mixture assembly, and post-PCR analysis were performed in separate laboratory rooms. DNA extracted from the culture was quantified and subjected to real-time PCR. The real-time PCR assay was performed using Brilliant III Ultra-Fast SYBR Green QPCR Master Mix (Agilent Technologies, Santa Clara, CA). The PCR targets were IS900 insertion sequence and other nine putative sequences [AF503872 (Mptb52.1), AF503873 (Mptb52.16), AF503874 (Mptb52.6), AF503875 (Mptb54.16), AF503876 (Mptb54.24), AF503877 (Mptb54.33), AF503878 (Mptb55.15), AF503879 (Mptb61.32), AF503880 (Mptb62.12)] described and deposited in GenBank [9,10].

Primers specific for the targeted genes (Table 1) were selected from previously published literature and optimized. Controls consisted of reaction mixture alone (negative control) and a positive control containing one µl of genomic DNA from reference M. avium subsp. paratuberculosis (ATCC baa 968, 19851 and 43015). Melting curve profile and conventional gel analysis were performed to confirm the positive PCR results. All realtime PCR assays were performed at least in duplicate using Stratagene Mx3000P® real-time PCR instrument (Stratagene, La Jolla, CA).

Accession (definition) Primer sequence (5’-3’) Amplicon size (bp) Start -End position: References
371 3332937-3333307 [9]
396 3907417-3907812 [9]
266 3327332-3327597 [9]
403 3324756-3325158 [9]
410 1823028-1823437 [9]
415 1823550-1823964 [9]
546 1825825-1826370 [9]
523 29424-29946 [9]
474 4262495-4262968 [9]
229 4747310-4747538 [10]
F- forward primer and R- reverse primer.

Table 1: Specific primers used in the real-time PCR to amplify IS900 and the putative sequences with the corresponding amplicon size.

Gel electrophoresis

After PCR was completed, 10 µl of the real-time PCR amplification reaction was mixed with GelRed (Biotium, Hayward, CA) mixture and electrophoresed in Tris- acetate-EDTA buffer through a 2% agarose gel. Bands of the appropriate size were identified by comparison with a DNA ladder (Roche Molecular Biochemicals, Indianapolis, IN).

In silico PCR

In silico PCR (virtual PCR) was performed from a sequence database with selected pairs of PCR primers, using an indexing strategy for fast performance. The virtual PCR is considered to have high stringency [11].

The specificity of the primers was confirmed by in silico PCR Amplification against 65 Mycobacterium species. In silico PCR searches a sequence database with a pair of PCR primers, using an indexing strategy for fast performance. This PCR simulation was performed against the most current sequenced Mycobacterium genomes which allow a maximum of 2 mismatches between primers and templates, so the stringency of in silico PCR must be considered high. All the currently available Mycobacterium species sequence data (Table 2) were checked against the selected primers.

S.No Mycobacterium Species Strains
1. Mycobacterium abscessus ATCC 19977
2. Mycobacterium abscessus subsp. bolletii 50594
3. Mycobacterium africanum GM041182
4. Mycobacterium avium 104
5. Mycobacteriumaviumsubsp.paratuberculosis MAP4
6. Mycobacterium avium subsp. paratuberculosis str. k10
7. Mycobacterium bovis BCG str. Korea 1168P
8. Mycobacterium bovis BCG str. Mexico
9. Mycobacterium bovis BCG str. Pasteur 1173P2
10. Mycobacterium bovis BCG str. Tokyo 172
11. Mycobacterium bovis subsp. bovis AF2122/97
12. Mycobacterium canettii CIPT 140010059
13. Mycobacterium canettii CIPT 140060008
14. Mycobacterium canettii CIPT 140070008
15. Mycobacterium canettii CIPT 140070010
16. Mycobacterium canettii CIPT 140070017
17. Mycobacterium chubuense NBB4
18. Mycobacterium gilvum PYR-GCK
19. Mycobacterium indicus pranii MTCC 9506
20. Mycobacterium intracellulare ATCC 13950
21. Mycobacterium intracellulare MOTT-02
22. Mycobacterium intracellulare MOTT-64
23. Mycobacterium kansasii ATCC 12478
24. Mycobacterium leprae Br4923
25. Mycobacterium leprae strain TN
26. Mycobacterium liflandii 128FXT
27. Mycobacterium marinum M
28. Mycobacterium massiliense str. GO 06
29. Mycobacterium neoaurum VKM Ac-1815D
30. Mycobacterium rhodesiae NBB3
31. Mycobacterium smegmatis JS623
32. Mycobacterium smegmatis str. MC2 155
33. Mycobacterium smegmatis str. MC2 155
34. Mycobacterium sp. JDM601
35. Mycobacterium sp. JLS
36. Mycobacterium sp. KMS
37. Mycobacterium sp. MCS
38. Mycobacterium sp. MOTT36Y
39. Mycobacterium sp. Spyr1
40. Mycobacterium tuberculosis 7199-99
41. Mycobacterium tuberculosis CAS NITR204
42. Mycobacterium tuberculosis CCDC5079
43. Mycobacterium tuberculosis CCDC5079
44. Mycobacterium tuberculosis CCDC5180
45. Mycobacterium tuberculosis CDC1551
46. Mycobacterium tuberculosis CTRI-2
47. Mycobacterium tuberculosis EAI5
48. Mycobacterium tuberculosis EAI5 NITR206
49. Mycobacterium tuberculosis F11
50. Mycobacterium tuberculosis H37Ra
51. Mycobacterium tuberculosis H37Rv
52. Mycobacterium tuberculosis H37Rv
53. Mycobacterium tuberculosis KZN 1435
54. Mycobacterium tuberculosis KZN 4207
55. Mycobacterium tuberculosis KZN 605
56. Mycobacterium tuberculosis RGTB327
57. Mycobacterium tuberculosis RGTB423
58. Mycobacterium tuberculosis UT205
59. Mycobacterium tuberculosis str. Beijing NITR203
60. Mycobacterium tuberculosis str. Erdman = ATCC 35801 DNA
61. Mycobacterium tuberculosis str. Haarlem  
62. Mycobacterium tuberculosis str. Haarlem NITR202
63. Mycobacterium ulcerans Agy99
64. Mycobacterium vanbaalenii PYR-1
65. Mycobacterium yongonense 05-1390

Table 2: Mycobacterium strains validated using virtual in silico PCR amplification. The corresponding primers are listed in Table 1.

Results and Discussion

Availability of the completed sequences of MAP genome supported the identification of more specific diagnostic sequences [12,13]. The availability of the sequence database brings clarity to unresolved questions surrounding the pathogenesis of MAP in animals and humans and also facilitates the development of detection kits. The introduction of PCR targeting repetitive sequences like IS900 insertion element, which is present in multiple copies in MAP genome, has been reported to reduce the time and labor required for the MAP detection [10]. The primary focus of this study was to evaluate and optimize the specificity of PCR-based molecular detection for the MAP targeting insertion sequence IS900 and other repetitive sequences as uniplex and/or multiplex PCR to detect MAP. To validate the IS900 insertion sequence and the repetitive/putative sequences, appropriate primers were selected/adopted and validated by both real-time PCR and in silico PCR.

Real-time PCR

In this study, the specificity of the real-time PCR assays was optimized by the analysis of genomic DNA from a panel of different Mycobacterium species which includes three MAP reference strains, 13 MAP clinical isolates from cattle and six non-MAP isolates. The genomic DNA samples were subjected to PCR assays targeting IS900 insertion sequence and additional nine putative sequences against MAP and non-MAP cultures as uniplex and also multiplex platforms. The results showed that IS900 and the putative sequence-specific primer pairs were amplified only from genomic DNA extract of the MAP reference strains and clinical MAP isolates. As shown in Figure 1, there is no amplification from the nonMAP strains (M. fortuitum subsp. fortuitum, M. intracellulare, M. kansasii, M. marinum, M. phlei, and M. scrofulaceum). As demonstrated on the gel, the amplicons from MAP were at the expected molecular weight and no signals were detected for the non-MAP species (Figure 2). Uniplex and/ or multiplex-PCR of IS900 insertion sequence and the putative sequences showed the presence of single or two distinct amplicons, respectively (Figure 2). The lower band represented the IS900 sequence amplicon (229 bp), and the top band represents amplicon from Mptb52.1 (371 bp).

Figure 1: Real time PCR of a unique IS900 target sequence amplified from two M. avium subsp. paratuberculosis reference strains (A: ATCC baa-968; B : 43015 B), clinical MAP isolates (C and D) and E: non-MAP species (M. fortuitum subsp. fortuitum, M.intracellulare, M. kansasii, M. marinum, M. phlei, and M. scrofulaceum).

Figure 2: PCR amplification of IS900 and Mptb52.6, putative sequence, from M. avium subsp. paratuberculosis.. PCR products were subjected to 1.5% agarose gel electrophoresis and amplification products were verified by gel electrophoresis. (A) Lane 1, Low DNA Mass Ladder; lanes 2, 3 and 8 PCR product of IS900 Insertion sequence; lanes 4 & 5, PCR product of Mptb52.6; lanes 6 & 7, amplifications of double-PCR product of targeting IS900 & Mptb52.16 sequences.

In silico PCR analysis

This virtual PCR was simulated against up-to-date sequences of Mycobacterium genomes in the database. A total of 23 Mycobacterium spp and 65 strains were verified against IS900 insertion sequence and the other nine repetitive sequences (Table 2). The virtual PCR results showed that IS900 and the putative sequence–specific primer pairs amplified specific targets only from MAP. Furthermore, the in silico simulation results showed that all the primers selected for each of IS900 segment and the putative sequences were amplified only from MAP samples and not from any of the non-MAP species. The amplicon sizes were at the expected range as in published literature and no secondary bands were detected (Figure 3).

Figure 3: In silico PCR amplification results (10 target primers against a total of 65 MAP and non-MAP mycobacterial strains. Mycobacterium strains listed as number 5 (Mycobacterium avium subsp. paratuberculosis MAP4) and number 6 (Mycobacterium avium subsp. paratuberculosis str. k10) were amplified (Refer Table 2 for the Mycobacterium spp. list).

In general Several PCR assays have been developed for the detection of M. avium subsp. paratuberculosis [14,15]. The most prominent target used in several studies to detect DNA of M. avium subsp. paratuberculosis by PCR is the insertion element IS900 [15-17]. The multicopy (17 copies) nature of the IS900 sequence on the M. avium subsp. paratuberculosis chromosome makes it ideal as a target sequence for the detection of MAP, since it exhibits a higher level of sensitivity compared to the use of singlecopy genes as targets [18,19].

The specificity of IS900 diagnostic PCR, however, has been also questioned and some reports indicated the presence of IS900-like sequences in Mycobacterium species other than MAP which may increase the risk of false MAP positive results [20,21]. Rajeev et al. (2005) reported the isolation of one non-MAP Mycobacterium strain positive for IS900 PCR, which has not yet been typed [22].

Some reports described that the problem of false negative PCR results might arise from difficulties in the disruption of the robust cell wall of MAP and insist that the mechanical disruption step may be needed to ensure the maximal release of DNA from MAP cells present in the tissue sample. The efficient procedure to release the DNA could hence maximize the PCR detection sensitivity [10].

In general, the diagnostic performance of IS900 insertion sequencetargeted detection techniques could be limited or misinterpreted due to various factors. These include isolation of organism-specific DNA; origin of the sample; lack of selection of proper primers; PCR amplification in the presence of inhibitory substances in preferred clinical specimens; and also the presence of concurrent Mycobacterium species [1,15]. Furthermore, the possible explanations for this heterogeneity might be host-pathogen interactions, host preference of MAP strains and pathogen adaptation to the environmental factors [10]. Based on the samples tested and the methodology outlined in our study, IS900 and the additional nine putative sequences are specific to use in PCR as uniplex and/or multiplex applications.


This work was supported by U.S. Department of Agriculture Grant (USDA/CRIS, Accession 0203750) and USDA/NIFA (GRANT#2011-51110-31082). We would like to thank Dr. Sircy Moore and the bacteriology staff of the Thompson-Bishop-Sparks State Diagnostic Laboratory, Auburn, AL. We acknowledge Dr. David Nganwa for the editing support and Tuskegee University’s College of Veterinary Medicine (CVM) Center of Excellence (Grant #245 5D34HP00001-20-00) for Tuskegee University Shared Instrumentation Core Facility is supported by NIH/NIMHD grant G12MD007585. The summer research support.


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Article Information

Article Type: Research Article

Citation: Yehualaeshet T, Graham M, Samuel T, Morton SER, Rodning S, et al. (2017) Comparison and Validation of IS900-Sequence and Putative Sequences as Specific Target to Detect Mycobacterium avium subsp. paratuberculosis. J Anim Sci Res 1(1): doi

Copyright: © 2017 Yehualaeshet T, et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

Publication history: 

  • Received date: 25 May 2017

  • Accepted date: 17 Jul 2017

  • Published date: 24 Jul 2017