Advantages and Limitations of Ribosomal RNA PCR and DNA Sequencing for Identification of Bacteria in Cardiac Valves of Danish Patients

Michael Kemp; Jette Bangsborg; Anne Kjerulf; Thomas Andersen Schmidt; John Christensen; Akhmadjon 6 Irmukhamedov; Niels Eske Bruun; Rimtas Dargis; Keld Andresen; Jens Jørgen Christensen

doi:10.2174/1874285801307010146

Advantages and Limitations of Ribosomal RNA PCR and DNA Sequencing for Identification of Bacteria in Cardiac Valves of Danish Patients

Michael Kemp, Jette Bangsborg, Anne Kjerulf, Thomas Andersen Schmidt, John Christensen, Akhmadjon 6 Irmukhamedov, Niels Eske Bruun, Rimtas Dargis, Keld Andresen, Jens Jørgen Christensen

11 Citations (Scopus)

Abstract

Studies on the value of culture-independent molecular identification of bacteria in cardiac valves are mostly restricted to comparing agreement of identification to what is obtained by culture to the number of identified bacteria in culture-negative cases. However, evaluation of the usefulness of direct molecular identification should also address weaknesses, their relevance in the given setting, and possible improvements. In this study cardiac valves from 56 Danish patients referred for surgery for infective endocarditis were analysed by microscopy and culture as well as by PCR targeting part of the bacterial 16S rRNA gene followed by DNA sequencing of the PCR product. PCR and DNA sequencing identified significant bacteria in 49 samples from 43 patients, including five out of 13 culture-negative cases. No rare, exotic, or intracellular bacteria were identified. There was a general agreement between bacterial identity obtained by ribosomal PCR and DNA sequencing from the valves and bacterial isolates from blood culture. However, DNA sequencing of the 16S rRNA gene did not discriminate well among non-haemolytic streptococci, especially within the Streptococcus mitis group. Ribosomal PCR with subsequent DNA sequencing is an efficient and reliable method of identifying the cause of IE, but exact species identification of some of the most common causes, i.e. non-haemolytic streptococci, may be improved with other molecular methods.

Original language	English
Journal	The Open Microbiology Journal
Volume	7
Pages (from-to)	146-151
Number of pages	6
ISSN	1874-2858
DOIs	https://doi.org/10.2174/1874285801307010146
Publication status	Published - 2013

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Kemp, M., Bangsborg, J., Kjerulf, A., Schmidt, T. A., Christensen, J., Irmukhamedov, A. ., Bruun, N. E., Dargis, R., Andresen, K., & Christensen, J. J. (2013). Advantages and Limitations of Ribosomal RNA PCR and DNA Sequencing for Identification of Bacteria in Cardiac Valves of Danish Patients. The Open Microbiology Journal, 7, 146-151. https://doi.org/10.2174/1874285801307010146

Kemp, M, Bangsborg, J, Kjerulf, A, Schmidt, TA, Christensen, J, Irmukhamedov, A, Bruun, NE, Dargis, R, Andresen, K & Christensen, JJ 2013, 'Advantages and Limitations of Ribosomal RNA PCR and DNA Sequencing for Identification of Bacteria in Cardiac Valves of Danish Patients', The Open Microbiology Journal, vol. 7, pp. 146-151. https://doi.org/10.2174/1874285801307010146

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title = "Advantages and Limitations of Ribosomal RNA PCR and DNA Sequencing for Identification of Bacteria in Cardiac Valves of Danish Patients",

abstract = "Studies on the value of culture-independent molecular identification of bacteria in cardiac valves are mostly restricted to comparing agreement of identification to what is obtained by culture to the number of identified bacteria in culture-negative cases. However, evaluation of the usefulness of direct molecular identification should also address weaknesses, their relevance in the given setting, and possible improvements. In this study cardiac valves from 56 Danish patients referred for surgery for infective endocarditis were analysed by microscopy and culture as well as by PCR targeting part of the bacterial 16S rRNA gene followed by DNA sequencing of the PCR product. PCR and DNA sequencing identified significant bacteria in 49 samples from 43 patients, including five out of 13 culture-negative cases. No rare, exotic, or intracellular bacteria were identified. There was a general agreement between bacterial identity obtained by ribosomal PCR and DNA sequencing from the valves and bacterial isolates from blood culture. However, DNA sequencing of the 16S rRNA gene did not discriminate well among non-haemolytic streptococci, especially within the Streptococcus mitis group. Ribosomal PCR with subsequent DNA sequencing is an efficient and reliable method of identifying the cause of IE, but exact species identification of some of the most common causes, i.e. non-haemolytic streptococci, may be improved with other molecular methods.",

author = "Michael Kemp and Jette Bangsborg and Anne Kjerulf and Schmidt, {Thomas Andersen} and John Christensen and Irmukhamedov, {Akhmadjon 6} and Bruun, {Niels Eske} and Rimtas Dargis and Keld Andresen and Christensen, {Jens J{\o}rgen}",

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T1 - Advantages and Limitations of Ribosomal RNA PCR and DNA Sequencing for Identification of Bacteria in Cardiac Valves of Danish Patients

AU - Kemp, Michael

AU - Bangsborg, Jette

AU - Kjerulf, Anne

AU - Schmidt, Thomas Andersen

AU - Christensen, John

AU - Irmukhamedov, Akhmadjon 6

AU - Bruun, Niels Eske

AU - Dargis, Rimtas

AU - Andresen, Keld

AU - Christensen, Jens Jørgen

PY - 2013

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N2 - Studies on the value of culture-independent molecular identification of bacteria in cardiac valves are mostly restricted to comparing agreement of identification to what is obtained by culture to the number of identified bacteria in culture-negative cases. However, evaluation of the usefulness of direct molecular identification should also address weaknesses, their relevance in the given setting, and possible improvements. In this study cardiac valves from 56 Danish patients referred for surgery for infective endocarditis were analysed by microscopy and culture as well as by PCR targeting part of the bacterial 16S rRNA gene followed by DNA sequencing of the PCR product. PCR and DNA sequencing identified significant bacteria in 49 samples from 43 patients, including five out of 13 culture-negative cases. No rare, exotic, or intracellular bacteria were identified. There was a general agreement between bacterial identity obtained by ribosomal PCR and DNA sequencing from the valves and bacterial isolates from blood culture. However, DNA sequencing of the 16S rRNA gene did not discriminate well among non-haemolytic streptococci, especially within the Streptococcus mitis group. Ribosomal PCR with subsequent DNA sequencing is an efficient and reliable method of identifying the cause of IE, but exact species identification of some of the most common causes, i.e. non-haemolytic streptococci, may be improved with other molecular methods.

AB - Studies on the value of culture-independent molecular identification of bacteria in cardiac valves are mostly restricted to comparing agreement of identification to what is obtained by culture to the number of identified bacteria in culture-negative cases. However, evaluation of the usefulness of direct molecular identification should also address weaknesses, their relevance in the given setting, and possible improvements. In this study cardiac valves from 56 Danish patients referred for surgery for infective endocarditis were analysed by microscopy and culture as well as by PCR targeting part of the bacterial 16S rRNA gene followed by DNA sequencing of the PCR product. PCR and DNA sequencing identified significant bacteria in 49 samples from 43 patients, including five out of 13 culture-negative cases. No rare, exotic, or intracellular bacteria were identified. There was a general agreement between bacterial identity obtained by ribosomal PCR and DNA sequencing from the valves and bacterial isolates from blood culture. However, DNA sequencing of the 16S rRNA gene did not discriminate well among non-haemolytic streptococci, especially within the Streptococcus mitis group. Ribosomal PCR with subsequent DNA sequencing is an efficient and reliable method of identifying the cause of IE, but exact species identification of some of the most common causes, i.e. non-haemolytic streptococci, may be improved with other molecular methods.

U2 - 10.2174/1874285801307010146

DO - 10.2174/1874285801307010146

M3 - Journal article

C2 - 24403979

SN - 1874-2858

VL - 7

SP - 146

EP - 151

JO - The Open Microbiology Journal

JF - The Open Microbiology Journal

ER -

Advantages and Limitations of Ribosomal RNA PCR and DNA Sequencing for Identification of Bacteria in Cardiac Valves of Danish Patients

Abstract

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