Cargando…

Detection of bacterial DNA from central venous catheter removed from patients by next generation sequencing: a preliminary clinical study

BACKGROUND: Catheter-related infection (CRI) is one of the serious challenges in clinical practice. This preliminary clinical study aimed to examine whether next-generation sequencing (NGS) targeting 16S rDNA, which was PCR-amplified directly from the tip of a central venous catheter (CVC), can be u...

Descripción completa

Detalles Bibliográficos
Autores principales: Okuda, Ken-ichi, Yoshii, Yutaka, Yamada, Satomi, Chiba, Akio, Hironaka, Ippei, Hori, Seiji, Yanaga, Katsuhiko, Mizunoe, Yoshimitsu
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2018
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6303997/
https://www.ncbi.nlm.nih.gov/pubmed/30577829
http://dx.doi.org/10.1186/s12941-018-0297-2
_version_ 1783382275777363968
author Okuda, Ken-ichi
Yoshii, Yutaka
Yamada, Satomi
Chiba, Akio
Hironaka, Ippei
Hori, Seiji
Yanaga, Katsuhiko
Mizunoe, Yoshimitsu
author_facet Okuda, Ken-ichi
Yoshii, Yutaka
Yamada, Satomi
Chiba, Akio
Hironaka, Ippei
Hori, Seiji
Yanaga, Katsuhiko
Mizunoe, Yoshimitsu
author_sort Okuda, Ken-ichi
collection PubMed
description BACKGROUND: Catheter-related infection (CRI) is one of the serious challenges in clinical practice. This preliminary clinical study aimed to examine whether next-generation sequencing (NGS) targeting 16S rDNA, which was PCR-amplified directly from the tip of a central venous catheter (CVC), can be used to identify causative pathogens in CRI, compared to the culture method. METHODS: Hospitalized patients, from whom a CVC had just been removed, were prospectively enrolled and divided into the CRI-suspected and routine removal groups. DNA was extracted from the sonication fluid of CVC specimens derived from patients. For analysis of bacterial composition by NGS, the V3–V4 fragments of bacterial 16S rDNA were PCR-amplified, followed by index PCR and paired-end sequencing on an Illumina MiSeq device. Conventional culture methods were also performed in the CRI-suspected group. RESULTS: Of CVCs collected from the 156 enrolled patients (114 men; mean age 65.6 years), a total of 14 specimens [nine out of 31 patients suspected with CRI and five out of 125 patients without infection symptoms (routine removal group)] were PCR-positive. In five patients with definite CRI, Staphylococcus was the most frequently detected genus by NGS (4/5 specimens), although no pathogens were detected by NGS in the one remaining specimen. The genera identified by NGS were consistent with those from conventional culture tests. There was high agreement between NGS and the culture method in the CRI-suspected group, with sensitivity and specificity values of 80.0% and 76.9%, respectively; meanwhile, the false-positive rate of NGS was as low as 4.0% in the routine removal group. Moreover, several genera, besides the genus identified by culture test, were detected in each patient with definite CRI and surgical site infection (SSI). Additionally, in one patient with SSI, Enterococcaceae were detected not only by NGS but also by abdominal abscess drainage culture. CONCLUSIONS: NGS targeting 16S rDNA was able to analyze the bacterial composition of CVC specimens and detect causative pathogens in patients with CRI and was therefore suggested as a promising diagnostic tool for CRI.
format Online
Article
Text
id pubmed-6303997
institution National Center for Biotechnology Information
language English
publishDate 2018
publisher BioMed Central
record_format MEDLINE/PubMed
spelling pubmed-63039972019-01-03 Detection of bacterial DNA from central venous catheter removed from patients by next generation sequencing: a preliminary clinical study Okuda, Ken-ichi Yoshii, Yutaka Yamada, Satomi Chiba, Akio Hironaka, Ippei Hori, Seiji Yanaga, Katsuhiko Mizunoe, Yoshimitsu Ann Clin Microbiol Antimicrob Research BACKGROUND: Catheter-related infection (CRI) is one of the serious challenges in clinical practice. This preliminary clinical study aimed to examine whether next-generation sequencing (NGS) targeting 16S rDNA, which was PCR-amplified directly from the tip of a central venous catheter (CVC), can be used to identify causative pathogens in CRI, compared to the culture method. METHODS: Hospitalized patients, from whom a CVC had just been removed, were prospectively enrolled and divided into the CRI-suspected and routine removal groups. DNA was extracted from the sonication fluid of CVC specimens derived from patients. For analysis of bacterial composition by NGS, the V3–V4 fragments of bacterial 16S rDNA were PCR-amplified, followed by index PCR and paired-end sequencing on an Illumina MiSeq device. Conventional culture methods were also performed in the CRI-suspected group. RESULTS: Of CVCs collected from the 156 enrolled patients (114 men; mean age 65.6 years), a total of 14 specimens [nine out of 31 patients suspected with CRI and five out of 125 patients without infection symptoms (routine removal group)] were PCR-positive. In five patients with definite CRI, Staphylococcus was the most frequently detected genus by NGS (4/5 specimens), although no pathogens were detected by NGS in the one remaining specimen. The genera identified by NGS were consistent with those from conventional culture tests. There was high agreement between NGS and the culture method in the CRI-suspected group, with sensitivity and specificity values of 80.0% and 76.9%, respectively; meanwhile, the false-positive rate of NGS was as low as 4.0% in the routine removal group. Moreover, several genera, besides the genus identified by culture test, were detected in each patient with definite CRI and surgical site infection (SSI). Additionally, in one patient with SSI, Enterococcaceae were detected not only by NGS but also by abdominal abscess drainage culture. CONCLUSIONS: NGS targeting 16S rDNA was able to analyze the bacterial composition of CVC specimens and detect causative pathogens in patients with CRI and was therefore suggested as a promising diagnostic tool for CRI. BioMed Central 2018-12-22 /pmc/articles/PMC6303997/ /pubmed/30577829 http://dx.doi.org/10.1186/s12941-018-0297-2 Text en © The Author(s) 2018 Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
spellingShingle Research
Okuda, Ken-ichi
Yoshii, Yutaka
Yamada, Satomi
Chiba, Akio
Hironaka, Ippei
Hori, Seiji
Yanaga, Katsuhiko
Mizunoe, Yoshimitsu
Detection of bacterial DNA from central venous catheter removed from patients by next generation sequencing: a preliminary clinical study
title Detection of bacterial DNA from central venous catheter removed from patients by next generation sequencing: a preliminary clinical study
title_full Detection of bacterial DNA from central venous catheter removed from patients by next generation sequencing: a preliminary clinical study
title_fullStr Detection of bacterial DNA from central venous catheter removed from patients by next generation sequencing: a preliminary clinical study
title_full_unstemmed Detection of bacterial DNA from central venous catheter removed from patients by next generation sequencing: a preliminary clinical study
title_short Detection of bacterial DNA from central venous catheter removed from patients by next generation sequencing: a preliminary clinical study
title_sort detection of bacterial dna from central venous catheter removed from patients by next generation sequencing: a preliminary clinical study
topic Research
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6303997/
https://www.ncbi.nlm.nih.gov/pubmed/30577829
http://dx.doi.org/10.1186/s12941-018-0297-2
work_keys_str_mv AT okudakenichi detectionofbacterialdnafromcentralvenouscatheterremovedfrompatientsbynextgenerationsequencingapreliminaryclinicalstudy
AT yoshiiyutaka detectionofbacterialdnafromcentralvenouscatheterremovedfrompatientsbynextgenerationsequencingapreliminaryclinicalstudy
AT yamadasatomi detectionofbacterialdnafromcentralvenouscatheterremovedfrompatientsbynextgenerationsequencingapreliminaryclinicalstudy
AT chibaakio detectionofbacterialdnafromcentralvenouscatheterremovedfrompatientsbynextgenerationsequencingapreliminaryclinicalstudy
AT hironakaippei detectionofbacterialdnafromcentralvenouscatheterremovedfrompatientsbynextgenerationsequencingapreliminaryclinicalstudy
AT horiseiji detectionofbacterialdnafromcentralvenouscatheterremovedfrompatientsbynextgenerationsequencingapreliminaryclinicalstudy
AT yanagakatsuhiko detectionofbacterialdnafromcentralvenouscatheterremovedfrompatientsbynextgenerationsequencingapreliminaryclinicalstudy
AT mizunoeyoshimitsu detectionofbacterialdnafromcentralvenouscatheterremovedfrompatientsbynextgenerationsequencingapreliminaryclinicalstudy