Molecular diagnosis of bacterial endocarditis by broad-range PCR amplification and direct sequencing

Goldenberger, Daniel; Künzli, Andreas; Vogt, Peter R.; Zbinden, Reinhard; Altwegg, Martin

doi:10.1128/jcm.35.11.2733-2739.1997

Cited by 352 publications

(102 citation statements)

References 36 publications

Supporting

Mentioning

Contrasting

Unclassified

Order By: Relevance

“…Up to one-third of all cases of infective endocarditis are culture-negative [108], and diagnosis has relied mainly upon clinical and ultrasonographic findings. Goldenberger et al reported one of the earliest situations in which 16S rDNA PCR amplification and sequencing were performed on DNA extracted from infected valves [109]. Many subsequent studies confirmed the usefulness of the method [110][111][112][113][114][115][116][117][118][119].…”

Section: Detection Of Uncultivable Bacteria and Diagnosis Of Culture-mentioning

confidence: 99%

Then and now: use of 16S rDNA gene sequencing for bacterial identification and discovery of novel bacteria in clinical microbiology laboratories

Woo

Lau

Teng

et al. 2008

Clinical Microbiology and Infection

694

424

View full text Add to dashboard Cite

In the last decade, as a result of the widespread use of PCR and DNA sequencing, 16S rDNA sequencing has played a pivotal role in the accurate identification of bacterial isolates and the discovery of novel bacteria in clinical microbiology laboratories. For bacterial identification, 16S rDNA sequencing is particularly important in the case of bacteria with unusual phenotypic profiles, rare bacteria, slow-growing bacteria, uncultivable bacteria and culture-negative infections. Not only has it provided insights into aetiologies of infectious disease, but it also helps clinicians in choosing antibiotics and in determining the duration of treatment and infection control procedures. With the use of 16S rDNA sequencing, 215 novel bacterial species, 29 of which belong to novel genera, have been discovered from human specimens in the past 7 years of the 21st century (2001-2007). One hundred of the 215 novel species, 15 belonging to novel genera, have been found in four or more subjects. The largest number of novel species discovered were of the genera Mycobacterium (n = 12) and Nocardia (n = 6). The oral cavity/dental-related specimens (n = 19) and the gastrointestinal tract (n = 26) were the most important sites for discovery and/or reservoirs of novel species. Among the 100 novel species, Streptococcus sinensis, Laribacter hongkongensis, Clostridium hathewayi and Borrelia spielmanii have been most thoroughly characterized, with the reservoirs and routes of transmission documented, and S. sinensis, L. hongkongensis and C. hathewayi have been found globally. One of the greatest hurdles in putting 16S rDNA sequencing into routine use in clinical microbiology laboratories is automation of the technology. The only step that can be automated at the moment is input of the 16S rDNA sequence of the bacterial isolate for identification into one of the software packages that will generate the result of the identity of the isolate on the basis of its sequence database. However, studies on the accuracy of the software packages have given highly varied results, and interpretation of results remains difficult for most technicians, and even for clinical microbiologists. To fully utilize 16S rDNA sequencing in clinical microbiology, better guidelines are needed for interpretation of the identification results, and additional/supplementary methods are necessary for bacterial species that cannot be identified confidently by 16S rDNA sequencing alone.

show abstract

Section: Detection Of Uncultivable Bacteria and Diagnosis Of Culture-mentioning

confidence: 99%

Then and now: use of 16S rDNA gene sequencing for bacterial identification and discovery of novel bacteria in clinical microbiology laboratories

Woo

Lau

Teng

et al. 2008

Clinical Microbiology and Infection

694

424

View full text Add to dashboard Cite

show abstract

“…While PCR product detection and analysis have typically been achieved using gel-electrophoresis and sequencing techniques, these approaches are laborious and timeconsuming, which detracts from clinical applicability. 139 The introduction of real-time PCR technology with the potential use of differentially labelled fluorescent probes for simultaneous identification of multiple amplified products in a single assay holds promise. 140 Unfortunately, current ability to spectrally differentiate multiple fluorescent signals is quite limited.…”

Section: Pcr-based Diagnosticsmentioning

confidence: 99%

PCR-based diagnostics for infectious diseases: uses, limitations, and future applications in acute-care settings

Yang

Rothman

2004

The Lancet Infectious Diseases

819

545

View full text Add to dashboard Cite

Molecular diagnostics are revolutionising the clinical practice of infectious disease. Their effects will be significant in acute-care settings where timely and accurate diagnostic tools are critical for patient treatment decisions and outcomes. PCR is the most well-developed molecular technique up to now, and has a wide range of already fulfilled, and potential, clinical applications, including specific or broad-spectrum pathogen detection, evaluation of emerging novel infections, surveillance, early detection of biothreat agents, and antimicrobial resistance profiling. PCR-based methods may also be cost effective relative to traditional testing procedures. Further advancement of technology is needed to improve automation, optimise detection sensitivity and specificity, and expand the capacity to detect multiple targets simultaneously (multiplexing). This review provides an up-to-date look at the general principles, diagnostic value, and limitations of the most current PCR-based platforms as they evolve from bench to bedside.

show abstract

“…ebi.ac.uk/Tools/sequence.html). Sequence homology identity was determined in accordance with criteria as described previously (25).…”

Section: Snp Detectionmentioning

confidence: 99%

Polymorphism of thePEMTgene and susceptibility to nonalcoholic fatty liver disease (NAFLD)

et al. 2005

View full text Add to dashboard Cite

Phosphatidylethanolamine N-methyltransferase (PEMT) catalyzes phosphatidylcholine synthesis. PEMT knockout mice have fatty livers, and it is possible that, in humans, nonalcoholic fatty liver disease (NAFLD) might be associated with PEMT gene polymorphisms. DNA samples from 59 humans without fatty liver and from 28 humans with NAFLD were genotyped for a single nucleotide polymorphism in exon 8 of PEMT which leads to a V175M substitution. V175M is a loss of function mutation, as determined by transiently transfecting McArdle-RH7777 cells with constructs of wildtype PEMT open reading frame or the V175M mutant. Met/Met at residue 175 (loss of function SNP) occurred in 67.9% of the NAFLD subjects and in only 40.7% of control subjects (p< 0.03). For the first time we report that a polymorphism of the human PEMT gene (V175M) is associated with diminished activity and may confer susceptibility to NAFLD.

show abstract

Molecular diagnosis of bacterial endocarditis by broad-range PCR amplification and direct sequencing

Cited by 352 publications

References 36 publications

Then and now: use of 16S rDNA gene sequencing for bacterial identification and discovery of novel bacteria in clinical microbiology laboratories

Then and now: use of 16S rDNA gene sequencing for bacterial identification and discovery of novel bacteria in clinical microbiology laboratories

PCR-based diagnostics for infectious diseases: uses, limitations, and future applications in acute-care settings

Polymorphism of thePEMTgene and susceptibility to nonalcoholic fatty liver disease (NAFLD)

Contact Info

Product

Resources

About