Solid-Phase Hybridization Capture of Low-Abundance Target DNA Sequences: Application to the Polymerase Chain Reaction Detection of Mycobacterium paratuberculosis and Mycobacterium avium subsp. silvaticum

Millar, Douglas; Withey, Stephen B.; Tizard, Mark; Ford, Jon; Hermon‐Taylor, John

doi:10.1006/abio.1995.1232

Cited by 97 publications

(51 citation statements)

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“…For example, a 10-fold increase in Mycobacterium avium subspecies paratuberculosis DNA detection sensitivity was achieved by a 2-step MCH-PCR method compared to PCR alone (8 ). Moreover, more positive results were achieved from intestinal tissue extracts from patients with Crohn disease, and only MCH-PCR detected this bacterium in feces of bovines (containing approximately 10 -100 CFU/g) with Johne disease.…”

Section: Discussionmentioning

confidence: 99%

Specific Magnetic Bead–Based Capture of Genomic DNA from Clinical Samples: Application to the Detection of Group B Streptococci in Vaginal/Anal Swabs

Parham

Picard²,

Peytavi³

et al. 2007

Clinical Chemistry

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Background: Group B streptococci (GBS) are a leading cause of sepsis and meningitis in newborns. We previously developed a rapid diagnostic system for GBS detection from vaginal/anal samples obtained from pregnant women during delivery. To facilitate the adaptation of this method for point-of-care testing, we have developed a specific and efficient GBS DNA capture method that is compatible with both PCR and nonamplification detection technologies. Methods: Superparamagnetic beads were functionalized with oligonucleotide capture probes of different lengths and used to capture GBS genomic DNA (gDNA). A rapid extraction procedure was used to provide DNA from GBS cultures or vaginal/anal samples with added GBS. Hybridization reactions consisting of functionalized beads and target DNA in 30 L of hybridization buffer were performed for 1 h at room temperature, followed by washing and resuspension in water. Captured DNA was then detected using quantitative PCR. Results: A 25-mer capture probe allowed detection of 1000 genome copies of purified GBS DNA. The ability to detect GBS was improved by use of a 50-mer (100 copies) and a 70-mer capture probe (10 copies). Detection of approximately 1250 CFU/mL was achieved for diluted GBS broth culture and for vaginal/anal swab samples with added GBS.

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Section: Discussionmentioning

confidence: 99%

Specific Magnetic Bead–Based Capture of Genomic DNA from Clinical Samples: Application to the Detection of Group B Streptococci in Vaginal/Anal Swabs

Parham

Picard²,

Peytavi³

et al. 2007

Clinical Chemistry

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“…The IS900 element is by far the most widely used target for the molecular detection of M. avium subsp. paratuberculosis and has been used in the form of direct PCR (161,235,284), in situ PCR (228), sequence/hybridization capture PCR (109,159,161,177), nested PCR (28,187,224), and real-time PCR (89,214), with the references listed representing only a small portion of what is available in the literature. However, other similar elements found across other mycobacteria, including M. terrae, M. xenopi, M. scrofulaceum and related strains, M. chelonae, and strain 2333 (related to M. cookii), have been shown to crossreact with IS900 primers used for detection of M. avium subsp.…”

Section: Genetic Methods To Detect Is Elementsmentioning

confidence: 99%

Mycobacterium avium in the Postgenomic Era

2007

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SUMMARY The past several years have witnessed an upsurge of genomic data pertaining to the Mycobacterium avium complex (MAC). Despite clear advances, problems with the detection of MAC persist, spanning the tests that can be used, samples required for their validation, and the use of appropriate nomenclature. Additionally, the amount of genomic variability documented to date greatly outstrips the functional understanding of epidemiologically different subsets of the organism. In this review, we discuss how postgenomic insights into the MAC have helped to clarify the relationships between MAC organisms, highlighting the distinction between environmental and pathogenic subsets of M. avium. We discuss the availability of various genetic targets for accurate classification of organisms and how these results provide a framework for future studies of MAC variability. The results of postgenomic M. avium study provide optimism that a functional understanding of these organisms will soon emerge, with genomically defined subsets that are epidemiologically distinct and possess different survival mechanisms for their various niches. Although the status quo has largely been to study different M. avium subsets in isolation, it is expected that attention to the similarities and differences between M. avium organisms will provide greater insight into their fundamental differences, including their propensity to cause disease.

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“…In general, PCR analysis has been unable to match the sensitivity of fecal culture for identifying small numbers of bacteria (319,332), but attempts to increase the sensitivity of this diagnostic test have yielded promising results (72,202). In part, the lack of sensitivity of the PCR technique is due to the extreme difficulty of removing PCR inhibitors when preparing DNA from fecal extracts.…”

Section: Molecular Genetic-based Diagnostic Testsmentioning

confidence: 99%

“…This tool is also valuable for differentiating species of M. avium. The IS900 sequence is the most commonly chosen target gene and is used to distinguish M. paratuberculosis from M. avium (209) and M. silvaticum (202), with the limitations described below.…”

Section: Molecular Genetic-based Diagnostic Testsmentioning

confidence: 99%

Mycobacterium aviumsubsp.paratuberculosisin Veterinary Medicine

2001

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Mycobacterium avium subsp. paratuberculosis (basonym M. paratuberculosis) is the etiologic agent of a severe gastroenteritis in ruminants known as Johne's disease. Economic losses to the cattle industry in the United States are staggering, reaching $1.5 billion annually. A potential pathogenic role in humans in the etiology of Crohn's disease is under investigation. In this article, we review the epidemiology, pathogenesis, diagnostics, and disease control measures of this important veterinary pathogen. We emphasize molecular genetic aspects including the description of markers used for strain identification, diagnostics, and phylogenetic analysis. Recent important advances in the development of animal models and genetic systems to study M. paratuberculosis virulence determinants are also discussed. We conclude with proposals for the applications of these models and recombinant technology to the development of diagnostic, control, and therapeutic measures

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Solid-Phase Hybridization Capture of Low-Abundance Target DNA Sequences: Application to the Polymerase Chain Reaction Detection of Mycobacterium paratuberculosis and Mycobacterium avium subsp. silvaticum

Cited by 97 publications

References 0 publications

Specific Magnetic Bead–Based Capture of Genomic DNA from Clinical Samples: Application to the Detection of Group B Streptococci in Vaginal/Anal Swabs

Specific Magnetic Bead–Based Capture of Genomic DNA from Clinical Samples: Application to the Detection of Group B Streptococci in Vaginal/Anal Swabs

Mycobacterium avium in the Postgenomic Era

Mycobacterium aviumsubsp.paratuberculosisin Veterinary Medicine

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