Characterization of Novel Coding Sequences Specific to
            <i>Mycobacterium avium</i>
            subsp.
            <i>paratuberculosis</i>
            : Implications for Diagnosis of Johne's Disease

Paustian, Michael L.; Amonsin, Alongkorn; Kapur, Vivek; Bannantine, John P.

doi:10.1128/jcm.42.6.2675-2681.2004

Cited by 58 publications

(40 citation statements)

References 23 publications

(18 reference statements)

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“…Other studies have shown that unique sequences have considerable potential for use in the development of more specific and sensitive diagnostic assays for the detection of M. avium subsp. paratuberculosis infection by both molecular assay-and immunoassaybased approaches (2)(3)(4)40). It is also possible that these different amino acid sequences have significant impacts on the protein functions.…”

Section: Discussionmentioning

confidence: 99%

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Genomic Comparison of PE and PPE Genes in the Mycobacterium avium Complex

et al. 2009

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The Mycobacterium avium complex (MAC) comprises genomically similar but phenotypically divergent bacteria that inhabit diverse environments and that cause disease in different hosts. In this study, a wholegenome approach was used to examine the polymorphic PE (Pro-Glu) and PPE (Pro-Pro-Glu) gene families, implicated in immunostimulation and virulence. The four major groups of MAC organisms were examined, including the newly sequenced type strains of M. intracellulare and M. avium subsp. avium, plus M. avium subsp. paratuberculosis and M. avium subsp. hominissuis, for the purpose of finding genetic differences that could be exploited to design diagnostic tests specific to these groups and that could help explain their divergence in pathogenesis and host specificity. Unique and missing PPE genes were found in all MAC members except M. avium subsp. avium. Only M. intracellulare had a unique PE gene. Apart from this, most PE and PPE sequences were conserved, with average nucleotide sequence identities of 99.1 and 98.1%, respectively, among the M. avium subspecies, but only 82.9 and 79.7% identities with the PE and PPE sequences of M. intracellulare, respectively. A detailed analysis of the amino acid sequences was performed between M. avium subsp. paratuberculosis and M. avium subsp. hominissuis. Most differences were detected in the PPE proteins, with amino acid substitutions and frame shifts leading to unique amino acid sequences. In conclusion, several unique PPE proteins were identified in MAC organisms next to numerous polymorphisms in both the PE and PPE gene families. These substantial differences could help explain the divergence in phenotypes within the MAC and could lead to diagnostic tests with better discriminatory abilities.Mycobacterium avium and Mycobacterium intracellulare are collectively known as the Mycobacterium avium complex (MAC). For genotypic, phenotypic, and historical reasons, multiple subspecies of M. avium are recognized; these include Mycobacterium avium subsp. paratuberculosis, M. avium subsp. hominissuis, Mycobacterium avium subsp. avium, and M. avium subsp. silvaticum (50). All four M. avium subspecies and M. intracellulare possess a high degree of genetic similarity but are capable of infecting a diverse range of host species.M. avium subsp. paratuberculosis is the causative organism of Johne's disease (paratuberculosis), a debilitating chronic enteritis in ruminants (49), and has been implicated in Crohn's disease in humans (18). M. avium subsp. avium and M. avium subsp. silvaticum are limited almost exclusively to avian species (53), in which they cause tuberculosis. M. avium subsp. hominissuis is a recent designation and was added to reflect the distinction of human and porcine isolates from bird-type strains when genotypic methods showed that M. avium isolates from humans in particular but also pigs rarely shared the genetic profiles of organisms found in birds (38,53). M. avium subsp. hominissuis and M. intracellulare are ubiquitous, saprophytic mycobacteria commonly found in so...

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Section: Discussionmentioning

confidence: 99%

“…paratuberculosis coding sequences are absent from M. avium subsp. hominissuis (3,40). The unique PPE proteins mentioned above are not included in these lists since they were all recognized as members of the polymorphic PPE protein family, and the various other differences between M. avium subsp.…”

Section: Discussionmentioning

confidence: 99%

Genomic Comparison of PE and PPE Genes in the Mycobacterium avium Complex

et al. 2009

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“…1). More importantly, our preliminary studies show that these unique sequences have considerable potential for the development of more specific and sensitive diagnostic assays for detection of Map infection with both molecular and immunoassay based approaches (58)(59)(60)(61). Our more recent studies, enabled by the identification of the unique regions in the Map genome, have resulted in the development of highly sensitive real-time PCR-based approaches for the sensitive and specific detection of Map directly from bovine feces (N.B., L.L., A.A., J.P.B., V.K., and S.K., unpublished data).…”

Section: Immunological and Virulence-related Insights From The Map Gementioning

confidence: 99%

The complete genome sequence ofMycobacterium aviumsubspeciesparatuberculosis

Bannantine

Zhang

et al. 2005

Proc. Natl. Acad. Sci. U.S.A.

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407

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We describe here the complete genome sequence of a common clone of Mycobacterium avium subspecies paratuberculosis (Map) strain K-10, the causative agent of Johne's disease in cattle and other ruminants. The K-10 genome is a single circular chromosome of 4,829,781 base pairs and encodes 4,350 predicted ORFs, 45 tRNAs, and one rRNA operon. In silico analysis identified >3,000 genes with homologs to the human pathogen, M. tuberculosis (Mtb), and 161 unique genomic regions that encode 39 previously unknown Map genes. Analysis of nucleotide substitution rates with Mtb homologs suggest overall strong selection for a vast majority of these shared mycobacterial genes, with only 68 ORFs with a synonymous to nonsynonymous substitution ratio of >2. Comparative sequence analysis reveals several noteworthy features of the K-10 genome including: a relative paucity of the PE͞PPE family of sequences that are implicated as virulence factors and known to be immunostimulatory during Mtb infection; truncation in the EntE domain of a salicyl-AMP ligase (MbtA), the first gene in the mycobactin biosynthesis gene cluster, providing a possible explanation for mycobactin dependence of Map; and Map-specific sequences that are likely to serve as potential targets for sensitive and specific molecular and immunologic diagnostic tests. Taken together, the availability of the complete genome sequence offers a foundation for the study of the genetic basis for virulence and physiology in Map and enables the development of new generations of diagnostic tests for bovine Johne's disease.

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“…However, recent reports have challenged the specificity of IS900-based assays due to the discovery of IS900-like sequences in non-Map mycobacteria (Englund et al, 2002;Cousins et al, 1999;Godfroid et al, 2005;Motiwala et al, 2004;Tasara et al, 2005). In order to improve PCR identification of Map, a triplex realtime PCR (TRT-PCR) co-amplifying in the same tube the multi-copy IS900, the single-copy Map-restricted f57 target (Coetsier et al, 2000;Godfroid et al, 2005;Poupart et al, 1993) and the new multi-copy Map-restricted ISMAP02 genetic target (Paustian et al, 2004) was designed. TRT-PCR results were compared on the same faecal samples with methods routinely used for Map identification (i.e.…”

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confidence: 99%