Identification of
 Mycobacterium avium
 Genotypes with Distinctive Traits by Combination of IS
 1245
 -Based Restriction Fragment Length Polymorphism and Restriction Analysis of
 hsp65

Oliveira, Rosângela Siqueira de; Sircili, Marcelo Palma; Oliveira, Eugênia Márcia de Deus; Balian, S. C.; Neto, José Soares Ferreira; Leão, Sylvia Cardoso

doi:10.1128/jcm.41.1.44-49.2003

Cited by 29 publications

(27 citation statements)

References 25 publications

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“…Human immunodeficiency virus coinfection information was available for some, but not all, of the isolates. The isolates are summarized in Table 1 and were originally isolated and archived from other studies (2,5,6,13,17,18,23).…”

Section: Methodsmentioning

confidence: 99%

Isolation of the Genome Sequence Strain Mycobacterium avium 104 from Multiple Patients over a 17-Year Period

et al. 2006

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The genome sequence strain 104 of the opportunistic pathogen Mycobacterium avium was isolated from an adult AIDS patient in Southern California in 1983. Isolates of non-paratuberculosis M. avium from 207 other patients in Southern California and elsewhere were examined for genotypic identity to strain 104. This process was facilitated by the use of a novel two-step approach. In the first step, all 208 strains in the sample were subjected to a high-throughput, large sequence polymorphism (LSP)-based genotyping test, in which DNA from each strain was tested by PCR for the presence or absence of 4 hypervariable genomic regions. Nineteen isolates exhibited an LSP type that resembled that of strain 104. This subset of 19 isolates was then subjected to high-resolution repetitive sequence-based PCR typing, which identified 10 isolates within the subset that were genotypically identical to strain 104. These isolates came from 10 different patients at 5 clinical sites in the western United States, and they were isolated over a 17-year time span. Therefore, the sequenced genome of M. avium strain 104 has been associated with disease in multiple patients in the western United States. Although M. avium is known for its genetic plasticity, these observations also show that strains of the pathogen can be genotypically stable over extended time periods.The Mycobacterium avium complex (MAC) includes the most clinically significant of the environmental mycobacteria that opportunistically infect susceptible humans. Sequencing of the genome of M. avium strain 104 is nearing completion by The Institute for Genomic Research (TIGR). Strain 104 was isolated in the mid-1980s from an adult patient with AIDS in Southern California. Like many genome sequence strains, its laboratory characteristics are amenable to genetic analysis, but there is little clinical or epidemiologic information regarding its incidence in human MAC disease. The draft sequence of strain 104 has 4,480 predicted open reading frames (ORFs). Annotation of the strain 104 genome identified genes that are shared with other virulent mycobacteria as well as genes that are unique to MAC (23). Whole-genome DNA microarray and PCR evaluation of 43 clinical isolates of M. avium relative to strain 104 revealed a 13.5% polymorphism rate between isolates (23). In comparison to M. tuberculosis, this represents an eightfold-greater strain-to-strain variability on the genomic level. In view of this genomic heterogeneity, the extent to which strain 104 is representative of virulent MAC isolates is an open question.To assess the clinical incidence of infections involving strain 104, we examined a sample of clinical isolates of M. avium from Southern California and elsewhere for genotypic identity with the genome sequence strain. Although these isolates were initially classified as M. avium subsp. avium, new data suggest that true M. avium subsp. avium strains infect a narrow spectrum of avian hosts and are described genotypically by a characteristic restriction fragment length polymorp...

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Section: Methodsmentioning

confidence: 99%

Isolation of the Genome Sequence Strain Mycobacterium avium 104 from Multiple Patients over a 17-Year Period

et al. 2006

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“…The bird strains belong to the serovar 1, 2, or 3 and contain IS901 (2, 16). They also have an identical three-banded pattern with the standardized IS1245 RFLP, often referred to as the "birdtype" profile (1,11,13,16). The bird strains in the present study showed the same three-banded pattern with the standardized long IS1245 probe (Fig.…”

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Distribution of IS1311and IS1245inMycobacterium aviumSubspecies Revisited

et al. 2005

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We demonstrated that IS1245 is not present in Mycobacterium avium subsp. paratuberculosis by restriction fragment length polymorphism and that the designated three-banded bird pattern of IS1245 in M. avium subsp. avium consists of one copy of IS1245 and two copies of IS1311. Cross hybridization between the two elements can be avoided by using more specific probes.The Mycobacterium avium complex (MAC) comprises a heterogeneous group of slow-growing, acid-fast bacilli that are divided into the two species Mycobacterium avium and Mycobacterium intracellulare (20). MAC organisms are ubiquitous in nature and can cause various diseases in animals and humans (8). M. avium subsp. avium can cause disease in different animal species such as poultry and swine and has been an increasingly important pathogen for humans because of the AIDS epidemic (6,8). The bacteria can also cause pulmonary infections in patients without AIDS and cervical lymphadenitis in children (6). M. avium subsp. paratuberculosis causes paratuberculosis in ruminants and has been suggested as the etiologic agent of Crohn's disease (3, 10).Different insertion sequences present in the MAC have been used for identification and strain differentiation. IS1245 has been used for restriction fragment length polymorphism (RFLP) of M. avium subsp. avium by the proposed standardized method of van Soolingen et al. (18). The 1,414-bp-long element was initially found to be present in M. avium subsp. avium, M. avium subsp. paratuberculosis, and M. avium subsp. silvaticum by PCR amplification of a 427-bp target sequence (7) and has also been found in some other mycobacteria (9). A closely related IS element is IS1311, which shows 85% sequence identity with IS1245 at the DNA level (9,16,17). The element is present in M. avium subsp. avium and M. avium subsp. paratuberculosis (21) and has been detected in strains of M. intracellulare, Mycobacterium malmoense, and Mycobacterium scrofulaceum (9). There is, however, considerably discrepancy in the literature about the presence and the copy number of IS1245 and IS1311 in the M. avium subspecies (4, 7, 16). The close relationship between the two elements makes cross hybridization a possible explanation for this dissention.The objective of this study was to clarify some of the discrepancy in the literature by examining strains of M. avium subsp. avium and M. avium subsp. paratuberculosis for the presence of IS1245 and IS1311. A method for standardization of IS1245 RFLP has been proposed (18). However, the suggested 427-bp IS1245 probe (long IS1245 probe) has an identity of 82% (National Center for Biotechnology Information BLAST; http://www.ncbi.nlm.nih.gov/BLAST/BLAST.cgi) with IS1311 on the DNA level. We therefore designed probes from the 5Ј end of each insertion element, where there is a lower homology of 75% between the two elements in order to reduce the possibility for cross hybridization. The primers with the location of the probes are described in Table 1.The short IS1245 probe (175 bp) and the IS1311 probe (198 bp) we...

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“…La variante I de M. avium se ha encontrado con mayor frecuencia asociada con infección diseminada en pacientes con sida mientras que las variantes II y III han sido descritas con mayor frecuencia en muestras ambientales (11). Estos hallazgos sugieren que las variantes PRA de M. avium pueden diferir en cuanto a su virulencia y transmisibilidad (12).…”

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Distribución de patrones PRA en aislamientos clínicos del complejo Mycobacterium avium procedentes de España y Suramérica.

et al. 2004

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La infección por el complejo Mycobacterium avium (MAC) es la infección sistémica más frecuente en la fase terminal del SIDA. Las sondas de ADN disponibles en el mercado para la identificación de micobacterias son muy precisas pero extremadamente costosas. Por eso, la mayoría de los laboratorios clínicos de Latinoamérica aún tipifican micobacterias mediante pruebas fenotípicas que son lentas, laboriosas y poco precisas. En este trabajo se aplicó el análisis del polimorfismo de los fragmentos de restricción del gen hsp65 (PRA) a la identificación de MAC en 163 aislamientos clínicos procedentes de España y Suramérica. El genotipo PRA predominante en cada país fue: M. avium tipo I en Argentina (23/42, 55%) y Brasil (48/72, 67%), M. avium tipo II en España (18/26, 69%) y M. avium tipo III en Colombia (10/23, 43%). Este último genotipo, que aún no fue descrito fuera del continente americano, resultó muy infrecuente en los otros tres países del estudio. Se discuten ventajas e inconvenientes de la aplicación del PRA al diagnóstico micobacteriológico.Palabras clave: complejo Mycobacterium avium, gen hsp65, patrones PRA, Suramérica, España, M. avium tipo III Distribution of PRA patterns of clinical isolates of the Mycobacterium avium complex from Spain and South AmericaMycobacterium avium complex (MAC) infections are the most frequent systemic infections associated with advanced AIDS. DNA probes for accurate identification of mycobacteria are available but are very expensive in many Latin American settings. Consequently, most Latin American diagnostic laboratories employ inaccurate and outdated tests for mycobacteria identification. Therefore, PCR restriction analysis (PRA) of the hsp65 gene was evaluated for the identification of 163 MAC human isolates originated from Spain and South America. The predominant PRA type in each country was: M. avium type I in Argentina (23/42, 55%) and Brazil (48/72, 67%), M. avium type II in Spain (18/26, 69%) and M. avium type III in Colombia (10/ 23, 43%). The Colombia frequency is noteworthy, since the PRA type III was quite infrequent in the other three countries. Furthermore, its presence has not been reported outside the Americas. The advantages and disadvantages of PRA in diagnostic mycobacteriology are discussed.

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Identification of Mycobacterium avium Genotypes with Distinctive Traits by Combination of IS 1245 -Based Restriction Fragment Length Polymorphism and Restriction Analysis of hsp65

Cited by 29 publications

References 25 publications

Isolation of the Genome Sequence Strain Mycobacterium avium 104 from Multiple Patients over a 17-Year Period

Isolation of the Genome Sequence Strain Mycobacterium avium 104 from Multiple Patients over a 17-Year Period

Distribution of IS1311and IS1245inMycobacterium aviumSubspecies Revisited

Distribución de patrones PRA en aislamientos clínicos del complejo Mycobacterium avium procedentes de España y Suramérica.

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