Characterization of Genetic Differences between
            <i>Mycobacterium avium</i>
            subsp.
            <i>paratuberculosis</i>
            Type I and Type II Isolates

Dohmann, Karen; Strommenger, Birgit; Stevenson, Karen; Juan, Lucía de; Stratmann, Janin; Kapur, Vivek; Bull, Tim J.; Gerlach, Gerald-F.

doi:10.1128/jcm.41.11.5215-5223.2003

Cited by 45 publications

(40 citation statements)

References 30 publications

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“…1) ing from C strains of M. avium subsp. paratuberculosis are in agreement with and expand upon findings from a representational difference analysis-based study that identified three loci missing from type II (C type) strains (9). The 233-bp locus they identified as pig-RDA10 (AY266300) forms part of the 16-kb region we called LSP A 18.…”

Section: Discussionsupporting

confidence: 73%

Differentiating Host-Associated Variants of Mycobacterium avium by PCR for Detection of Large Sequence Polymorphisms

et al. 2006

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The Mycobacterium avium species consists of a group of organisms that are genetically related but phenotypically diverse, with certain variants presenting clear differences in terms of their host association and disease manifestations. The ability to distinguish between these subtypes is of relevance for accurate diagnosis and for control programs. Using a comparative genomics approach, we have uncovered large sequence polymorphisms that are, respectively, absent from bird-type M. avium isolates and from cattle types and sheep types of M. avium subsp. paratuberculosis. By evaluating the distribution of these genomic polymorphisms across a panel of strains, we were able to assign unique genomic signatures to these host-associated variants. We propose a simple PCR-based strategy based on these polymorphisms that can rapidly type M. avium isolates into these subgroups.Mycobacterium avium organisms responsible for Johne's disease, avian tuberculosis, and opportunistic infections in humans have been classified as belonging to one species based on numerical taxonomy (27), DNA-DNA hybridization (20), and 16S rRNA sequencing (29). This shared designation has placed emphasis on the genetic relatedness of these organisms. Yet, there is ample evidence that members of this group exhibit phenotypic differences in laboratory characteristics and have widely varying propensities to cause disease in different hosts. In agreement with this diversity, M. avium organisms differ according to the presence of genetic elements, such as insertion elements (11,12,14), and also vary extensively at certain genomic regions (18,22,23).Of the M. avium organisms, M. avium subsp. paratuberculosis presents a clear diagnostic concern, as it is a serious pathogen of cattle and other ruminants and a potential zoonotic agent (1,2,4,5,13,21). Traditionally identified through phenotypic assays, and more recently by the presence of the insertion element IS900, M. avium subsp. paratuberculosis can now be specifically characterized by the deletion of a large sequence called LSP A 8 that is present in other M. avium organisms (22). Whole-genome comparisons of a small number of M. avium subsp. paratuberculosis isolates have shown relatively few genomic differences among strains (18, 23), suggesting genomic features specific to tested strains should lend themselves to robust diagnostic algorithms. One source of variability described within M. avium subsp. paratuberculosis is the existence of two host-associated types: the more prevalent cattle (C) strains, also known as type II strains, and the rarer sheep (S) strains, also called type I strains. These types have been distinguished through molecular fingerprints and PCR assays exploiting the variable presence of the mobile insertion elements IS900 and IS1311 (7,8,25). The ability to both detect and differentiate between these types of strains is of obvious importance for both accurate diagnosis and to guide control programs.Among M. avium members other than M. avium subsp. paratuberculosis, phenotypic and g...

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Section: Discussionsupporting

confidence: 73%

Differentiating Host-Associated Variants of Mycobacterium avium by PCR for Detection of Large Sequence Polymorphisms

et al. 2006

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“…paratuberculosis. The presence of LSP P 12, a previously described 19-kb island (8,23), was also highly predictive of the identification of M. avium subsp. paratuberculosis.…”

Section: Discussionmentioning

confidence: 85%

“…avium strains were then tested across the extended panel of 383 M. avium complex isolates. Since LSP P 14, which includes but is not restricted to a known 38-kb island (24), and LSP P 12, a 19-kb sequence (8,23), were previously postulated to be of potential diagnostic utility, we tested each of these LSPs with two and three different sets of primers targeting distinct loci, respectively. Primer sequences for each of the LSP P s tested are listed in (23).…”

Section: Methodsmentioning

confidence: 99%

“…paratuberculosis strain K10; we call these LSP P s. Such sequences can be expected to lend themselves to nucleic acid-based diagnostic tests and, if they encode immunogenic proteins, to immunological assays as well. One of these, a 19-kb sequence that we call LSP P 12, has been previously documented (8,23). Another, a 98-kb segment of the genome that encompasses elements we call LSP P 14 and LSP P 15, also includes within it a 38-kb element that was recently described as an M. avium subsp.…”

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confidence: 99%

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Genomic Polymorphisms for Mycobacterium avium subsp. paratuberculosis Diagnostics

et al. 2005

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Mycobacterium avium subsp. paratuberculosis is an emerging pathogen of mammals and is being actively investigated as a possible zoonotic agent. The lack of reliable diagnostic assays has hampered rational assessment of the prevalence of this organism in humans and animals. We have used a comparative genomic approach to reveal genomic differences between M. avium subsp. paratuberculosis and its close relative M. avium subsp. avium, a highly prevalent environmental organism. From computational and DNA microarray-based study of two prototype strains, M. avium subsp. avium strain 104 and M. avium subsp. paratuberculosis strain K10, we have uncovered two types of large sequence polymorphisms (LSPs): those present in the former but missing in the latter (LSP A s) and those only present in the latter (LSP P s). We examined the distribution of 3 LSP A s and 17 LSP P s across a panel of 383 M. avium complex isolates in order to determine their potential utility for the development of accurate diagnostic tests. Our results show that the absence of LSP A 8 is 100% specific for the identification of M. avium subsp. paratuberculosis. Of the 17 LSP P s, 10 regions were not specific for M. avium subsp. paratuberculosis while 7 were shown to be highly specific (>98%) and, in some cases, highly sensitive as well (up to 95%). These data highlight the need to evaluate these regions across a diverse panel of clinical and environmental isolates and indicate the LSPs best suited for M. avium subsp. paratuberculosis diagnostics.Mycobacterium avium subsp. paratuberculosis is a serious pathogen of domestic ruminants, in which it causes paratuberculosis (Johne's disease), a chronic and eventually fatal inflammatory bowel disease. Its rising incidence in many regions of the world has resulted in significant economic losses to the livestock industry (13). This organism also infects free-ranging wildlife species (16). The impact of M. avium subsp. paratuberculosis in nonruminant wildlife species is largely unknown; however, the potential for interspecies transmission has important implications for paratuberculosis control programs. M. avium subsp. paratuberculosis is also being actively investigated as the possible cause of a debilitating human inflammatory bowel disease, Crohn's disease (4, 5, 18).Effective control of Johne's disease and investigation of the potential link to Crohn's disease have been hampered by the lack of effective assays to easily and accurately diagnose M. avium subsp. paratuberculosis infections. Commercially available serological assays for bovine disease are convenient but offer poor sensitivity, especially during subclinical disease. Moreover, owing to the high degree of genetic similarity between M. avium subsp. paratuberculosis and the other members of the M. avium complex, many of the proteins that are recognized during the early stages of infection are not specific for M. avium subsp. paratuberculosis (14). Since M. avium subsp. avium is highly prevalent in the environment but not associated with a similar cli...

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“…Immediately, a correlation was noticed between strain type and ease of isolation, as the S strains were notoriously difficult to grow. Greater genetic diversity was later identified, particularly between S and C strains, as small and large genomic deletions and insertions and single nucleotide polymorphisms were found (13,(24)(25)(26). The so-called S and C strains probably represent the extremes of a taxon; a continuum may exist, and this will be determined when representative genomes have been sequenced and annotated.…”

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confidence: 99%

Culture Phenotypes of Genomically and Geographically Diverse Mycobacterium avium subsp. paratuberculosis Isolates from Different Hosts

et al. 2011

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Mycobacterium avium subsp. paratuberculosis causes paratuberculosis (Johne's disease) in ruminants in most countries. Historical data suggest substantial differences in culturability of M. avium subsp. paratuberculosis isolates from small ruminants and cattle; however, a systematic comparison of culture media and isolates from different countries and hosts has not been undertaken. Here, 35 field isolates from the United States, Spain, Northern Ireland, and Australia were propagated in Bactec 12B medium and Middlebrook 7H10 agar, genomically characterized, and subcultured to Lowenstein-Jensen (LJ), Herrold's egg yolk (HEY), modified Middlebrook 7H10, Middlebrook 7H11, and Watson-Reid (WR) agars, all with and without mycobactin J and some with sodium pyruvate. Fourteen genotypes of M. avium subsp. paratuberculosis were represented as determined by BstEII IS900 and IS1311 restriction fragment length polymorphism analysis. There was no correlation between genotype and overall culturability, although most S strains tended to grow poorly on HEY agar. Pyruvate was inhibitory to some isolates. All strains grew on modified Middlebrook 7H10 agar but more slowly and less prolifically on LJ agar. Mycobactin J was required for growth on all media except 7H11 agar, but growth was improved by the addition of mycobactin J to 7H11 agar. WR agar supported the growth of few isolates. The differences in growth of M. avium subsp. paratuberculosis that have historically been reported in diverse settings have been strongly influenced by the type of culture medium used. When an optimal culture medium, such as modified Middlebrook 7H10 agar, is used, very little difference between the growth phenotypes of diverse strains of M. avium subsp. paratuberculosis was observed. This optimal medium is recommended to remove bias in the isolation and cultivation of M. avium subsp. paratuberculosis.Mycobacterium avium subsp. paratuberculosis is the causative agent of Johne's disease of ruminants, which occurs in most countries. Usually it is an enteric infection with a long incubation period and progressively worsening granulomatous infiltration of the small and large intestines leading to weight loss and death. It is economically significant in farmed cattle, goats, sheep, and deer and is known to be capable of infecting a wide range of domesticated and free-living herbivores and occasionally also the carnivores that prey upon them (2, 4, 6, 15). Like many pathogenic mycobacteria, M. avium subsp. paratuberculosis is not host specific, and cross-species transmission is common where there are high contact rates. Although tissue colonization and histological lesions may occur, clinical disease in response to infection is rarely reported for nonruminant species, except for rabbits (2, 4). There is a long-standing debate about the role of M. avium subsp. paratuberculosis in chronic inflammatory bowel disease of humans, specifically Crohn's disease. Consequently, the isolation and cultivation of M. avium subsp. paratuberculosis are attempted in both vet...

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Characterization of Genetic Differences between Mycobacterium avium subsp. paratuberculosis Type I and Type II Isolates

Cited by 45 publications

References 30 publications

Differentiating Host-Associated Variants of Mycobacterium avium by PCR for Detection of Large Sequence Polymorphisms

Differentiating Host-Associated Variants of Mycobacterium avium by PCR for Detection of Large Sequence Polymorphisms

Genomic Polymorphisms for Mycobacterium avium subsp. paratuberculosis Diagnostics

Culture Phenotypes of Genomically and Geographically Diverse Mycobacterium avium subsp. paratuberculosis Isolates from Different Hosts

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