Automated Broad-Range Molecular Detection of Bacteria in Clinical Samples

Research output: Contribution to journalArticleAcademicpeer-review

Abstract

Molecular detection methods, such as quantitative PCR (qPCR), have found their way into clinical microbiology laboratories for the detection of an array of pathogens. Most routinely used methods, however, are directed at specific species. Thus, anything that is not explicitly searched for will be missed. This greatly limits the flexibility and universal application of these techniques. We investigated the application of a rapid universal bacterial molecular identification method, IS-pro, to routine patient samples received in a clinical microbiology laboratory. IS-pro is a eubacterial technique based on the detection and categorization of 16S-23S rRNA gene interspace regions with lengths that are specific for each microbial species. As this is an open technique, clinicians do not need to decide in advance what to look for. We compared routine culture to IS-pro using 66 samples sent in for routine bacterial diagnostic testing. The samples were obtained from patients with infections in normally sterile sites (without a resident microbiota). The results were identical in 20 (30%) samples, IS-pro detected more bacterial species than culture in 31 (47%) samples, and five of the 10 culture-negative samples were positive with IS-pro. The case histories of the five patients from whom these culture-negative/IS-pro-positive samples were obtained suggest that the IS-pro findings are highly clinically relevant. Our findings indicate that an open molecular approach, such as IS-pro, may have a high added value for clinical practice.

Original languageEnglish
Pages (from-to)934-43
Number of pages10
JournalJournal of Clinical Microbiology
Volume54
Issue number4
DOIs
Publication statusPublished - Apr 2016

Cite this

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title = "Automated Broad-Range Molecular Detection of Bacteria in Clinical Samples",
abstract = "Molecular detection methods, such as quantitative PCR (qPCR), have found their way into clinical microbiology laboratories for the detection of an array of pathogens. Most routinely used methods, however, are directed at specific species. Thus, anything that is not explicitly searched for will be missed. This greatly limits the flexibility and universal application of these techniques. We investigated the application of a rapid universal bacterial molecular identification method, IS-pro, to routine patient samples received in a clinical microbiology laboratory. IS-pro is a eubacterial technique based on the detection and categorization of 16S-23S rRNA gene interspace regions with lengths that are specific for each microbial species. As this is an open technique, clinicians do not need to decide in advance what to look for. We compared routine culture to IS-pro using 66 samples sent in for routine bacterial diagnostic testing. The samples were obtained from patients with infections in normally sterile sites (without a resident microbiota). The results were identical in 20 (30{\%}) samples, IS-pro detected more bacterial species than culture in 31 (47{\%}) samples, and five of the 10 culture-negative samples were positive with IS-pro. The case histories of the five patients from whom these culture-negative/IS-pro-positive samples were obtained suggest that the IS-pro findings are highly clinically relevant. Our findings indicate that an open molecular approach, such as IS-pro, may have a high added value for clinical practice.",
keywords = "Automation, Laboratory, Bacteria, Bacterial Infections, Bacteriological Techniques, Child, Preschool, DNA, Intergenic, Female, Humans, Middle Aged, Molecular Diagnostic Techniques, RNA, Ribosomal, 16S, RNA, Ribosomal, 23S, Sensitivity and Specificity, Time Factors, Comparative Study, Evaluation Studies, Journal Article",
author = "Budding, {Andries E} and Martine Hoogewerf and Vandenbroucke-Grauls, {Christina M J E} and Savelkoul, {Paul H M}",
note = "Copyright {\circledC} 2016, American Society for Microbiology. All Rights Reserved.",
year = "2016",
month = "4",
doi = "10.1128/JCM.02886-15",
language = "English",
volume = "54",
pages = "934--43",
journal = "Journal of Clinical Microbiology",
issn = "0095-1137",
publisher = "American Society for Microbiology",
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}

Automated Broad-Range Molecular Detection of Bacteria in Clinical Samples. / Budding, Andries E; Hoogewerf, Martine; Vandenbroucke-Grauls, Christina M J E; Savelkoul, Paul H M.

In: Journal of Clinical Microbiology, Vol. 54, No. 4, 04.2016, p. 934-43.

Research output: Contribution to journalArticleAcademicpeer-review

TY - JOUR

T1 - Automated Broad-Range Molecular Detection of Bacteria in Clinical Samples

AU - Budding, Andries E

AU - Hoogewerf, Martine

AU - Vandenbroucke-Grauls, Christina M J E

AU - Savelkoul, Paul H M

N1 - Copyright © 2016, American Society for Microbiology. All Rights Reserved.

PY - 2016/4

Y1 - 2016/4

N2 - Molecular detection methods, such as quantitative PCR (qPCR), have found their way into clinical microbiology laboratories for the detection of an array of pathogens. Most routinely used methods, however, are directed at specific species. Thus, anything that is not explicitly searched for will be missed. This greatly limits the flexibility and universal application of these techniques. We investigated the application of a rapid universal bacterial molecular identification method, IS-pro, to routine patient samples received in a clinical microbiology laboratory. IS-pro is a eubacterial technique based on the detection and categorization of 16S-23S rRNA gene interspace regions with lengths that are specific for each microbial species. As this is an open technique, clinicians do not need to decide in advance what to look for. We compared routine culture to IS-pro using 66 samples sent in for routine bacterial diagnostic testing. The samples were obtained from patients with infections in normally sterile sites (without a resident microbiota). The results were identical in 20 (30%) samples, IS-pro detected more bacterial species than culture in 31 (47%) samples, and five of the 10 culture-negative samples were positive with IS-pro. The case histories of the five patients from whom these culture-negative/IS-pro-positive samples were obtained suggest that the IS-pro findings are highly clinically relevant. Our findings indicate that an open molecular approach, such as IS-pro, may have a high added value for clinical practice.

AB - Molecular detection methods, such as quantitative PCR (qPCR), have found their way into clinical microbiology laboratories for the detection of an array of pathogens. Most routinely used methods, however, are directed at specific species. Thus, anything that is not explicitly searched for will be missed. This greatly limits the flexibility and universal application of these techniques. We investigated the application of a rapid universal bacterial molecular identification method, IS-pro, to routine patient samples received in a clinical microbiology laboratory. IS-pro is a eubacterial technique based on the detection and categorization of 16S-23S rRNA gene interspace regions with lengths that are specific for each microbial species. As this is an open technique, clinicians do not need to decide in advance what to look for. We compared routine culture to IS-pro using 66 samples sent in for routine bacterial diagnostic testing. The samples were obtained from patients with infections in normally sterile sites (without a resident microbiota). The results were identical in 20 (30%) samples, IS-pro detected more bacterial species than culture in 31 (47%) samples, and five of the 10 culture-negative samples were positive with IS-pro. The case histories of the five patients from whom these culture-negative/IS-pro-positive samples were obtained suggest that the IS-pro findings are highly clinically relevant. Our findings indicate that an open molecular approach, such as IS-pro, may have a high added value for clinical practice.

KW - Automation, Laboratory

KW - Bacteria

KW - Bacterial Infections

KW - Bacteriological Techniques

KW - Child, Preschool

KW - DNA, Intergenic

KW - Female

KW - Humans

KW - Middle Aged

KW - Molecular Diagnostic Techniques

KW - RNA, Ribosomal, 16S

KW - RNA, Ribosomal, 23S

KW - Sensitivity and Specificity

KW - Time Factors

KW - Comparative Study

KW - Evaluation Studies

KW - Journal Article

U2 - 10.1128/JCM.02886-15

DO - 10.1128/JCM.02886-15

M3 - Article

VL - 54

SP - 934

EP - 943

JO - Journal of Clinical Microbiology

JF - Journal of Clinical Microbiology

SN - 0095-1137

IS - 4

ER -