Next- and Third-Generation Sequencing Outperforms Culture-Based Methods in the Diagnosis of Ascitic Fluid Bacterial Infections of ICU Patients

Objectives: Infections of the ascitic fluid are serious conditions that require rapid diagnosis and treatment. Ascites is often accompanied by other critical pathologies such as gastrointestinal bleeding and bowel perforation, and infection increases the risk of mortality in intensive care patients....

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Autores principales:	Hanna Goelz, Simon Wetzel, Negin Mehrbarzin, Stefan Utzolino, Georg Häcker, Mohamed Tarek Badr
Formato:	article
Lenguaje:	EN
Publicado:	MDPI AG 2021
Materias:	ascitic fluid infections intensive care unit next-generation sequencing nanopore anaerobic bacteria full length 16S rRNA sequencing Biology (General) QH301-705.5
Acceso en línea:	https://doaj.org/article/70f807f6083040c2b75344f6b1683196
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spelling	oai:doaj.org-article:70f807f6083040c2b75344f6b16831962021-11-25T17:13:04ZNext- and Third-Generation Sequencing Outperforms Culture-Based Methods in the Diagnosis of Ascitic Fluid Bacterial Infections of ICU Patients10.3390/cells101132262073-4409https://doaj.org/article/70f807f6083040c2b75344f6b16831962021-11-01T00:00:00Zhttps://www.mdpi.com/2073-4409/10/11/3226https://doaj.org/toc/2073-4409Objectives: Infections of the ascitic fluid are serious conditions that require rapid diagnosis and treatment. Ascites is often accompanied by other critical pathologies such as gastrointestinal bleeding and bowel perforation, and infection increases the risk of mortality in intensive care patients. Owing to a relatively low success rate of conventional culture methods in identifying the responsible pathogens, new methods may be helpful to guide antimicrobial therapy and to refine empirical regimens. Here, we aim to assess outcomes and to identify responsible pathogens in ascitic fluid infections, in order to improve patients’ care and to guide empirical therapy. Methods: Between October 2019 and March 2021, we prospectively collected 50 ascitic fluid samples from ICU patients with suspected infection. Beside standard culture-based microbiology methods, excess fluid underwent DNA isolation and was analyzed by next- and third-generation sequencing (NGS) methods. Results: NGS-based methods had higher sensitivity in detecting additional pathogenic bacteria such as <i>E. faecalis</i> and <i>Klebsiella</i> in 33 out of 50 (66%) ascitic fluid samples compared with culture-based methods (26%). Anaerobic bacteria were especially identified by sequencing-based methods in 28 samples (56%), in comparison with only three samples in culture. Analysis of clinical data showed a correlation between sequencing results and various clinical parameters such as peritonitis and hospitalization outcomes. Conclusions: Our results show that, in ascitic fluid infections, NGS-based methods have a higher sensitivity for the identification of clinically relevant pathogens than standard microbiological culture diagnostics, especially in detecting hard-to-culture anaerobic bacteria. Patients with such infections may benefit from the use of NGS methods by the possibility of earlier and better targeted antimicrobial therapy, which has the potential to lower the high morbidity and mortality in critically ill patients with ascitic bacterial infection.Hanna GoelzSimon WetzelNegin MehrbarzinStefan UtzolinoGeorg HäckerMohamed Tarek BadrMDPI AGarticleascitic fluid infectionsintensive care unitnext-generation sequencingnanoporeanaerobic bacteriafull length 16S rRNA sequencingBiology (General)QH301-705.5ENCells, Vol 10, Iss 3226, p 3226 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	ascitic fluid infections intensive care unit next-generation sequencing nanopore anaerobic bacteria full length 16S rRNA sequencing Biology (General) QH301-705.5
spellingShingle	ascitic fluid infections intensive care unit next-generation sequencing nanopore anaerobic bacteria full length 16S rRNA sequencing Biology (General) QH301-705.5 Hanna Goelz Simon Wetzel Negin Mehrbarzin Stefan Utzolino Georg Häcker Mohamed Tarek Badr Next- and Third-Generation Sequencing Outperforms Culture-Based Methods in the Diagnosis of Ascitic Fluid Bacterial Infections of ICU Patients
description	Objectives: Infections of the ascitic fluid are serious conditions that require rapid diagnosis and treatment. Ascites is often accompanied by other critical pathologies such as gastrointestinal bleeding and bowel perforation, and infection increases the risk of mortality in intensive care patients. Owing to a relatively low success rate of conventional culture methods in identifying the responsible pathogens, new methods may be helpful to guide antimicrobial therapy and to refine empirical regimens. Here, we aim to assess outcomes and to identify responsible pathogens in ascitic fluid infections, in order to improve patients’ care and to guide empirical therapy. Methods: Between October 2019 and March 2021, we prospectively collected 50 ascitic fluid samples from ICU patients with suspected infection. Beside standard culture-based microbiology methods, excess fluid underwent DNA isolation and was analyzed by next- and third-generation sequencing (NGS) methods. Results: NGS-based methods had higher sensitivity in detecting additional pathogenic bacteria such as <i>E. faecalis</i> and <i>Klebsiella</i> in 33 out of 50 (66%) ascitic fluid samples compared with culture-based methods (26%). Anaerobic bacteria were especially identified by sequencing-based methods in 28 samples (56%), in comparison with only three samples in culture. Analysis of clinical data showed a correlation between sequencing results and various clinical parameters such as peritonitis and hospitalization outcomes. Conclusions: Our results show that, in ascitic fluid infections, NGS-based methods have a higher sensitivity for the identification of clinically relevant pathogens than standard microbiological culture diagnostics, especially in detecting hard-to-culture anaerobic bacteria. Patients with such infections may benefit from the use of NGS methods by the possibility of earlier and better targeted antimicrobial therapy, which has the potential to lower the high morbidity and mortality in critically ill patients with ascitic bacterial infection.
format	article
author	Hanna Goelz Simon Wetzel Negin Mehrbarzin Stefan Utzolino Georg Häcker Mohamed Tarek Badr
author_facet	Hanna Goelz Simon Wetzel Negin Mehrbarzin Stefan Utzolino Georg Häcker Mohamed Tarek Badr
author_sort	Hanna Goelz
title	Next- and Third-Generation Sequencing Outperforms Culture-Based Methods in the Diagnosis of Ascitic Fluid Bacterial Infections of ICU Patients
title_short	Next- and Third-Generation Sequencing Outperforms Culture-Based Methods in the Diagnosis of Ascitic Fluid Bacterial Infections of ICU Patients
title_full	Next- and Third-Generation Sequencing Outperforms Culture-Based Methods in the Diagnosis of Ascitic Fluid Bacterial Infections of ICU Patients
title_fullStr	Next- and Third-Generation Sequencing Outperforms Culture-Based Methods in the Diagnosis of Ascitic Fluid Bacterial Infections of ICU Patients
title_full_unstemmed	Next- and Third-Generation Sequencing Outperforms Culture-Based Methods in the Diagnosis of Ascitic Fluid Bacterial Infections of ICU Patients
title_sort	next- and third-generation sequencing outperforms culture-based methods in the diagnosis of ascitic fluid bacterial infections of icu patients
publisher	MDPI AG
publishDate	2021
url	https://doaj.org/article/70f807f6083040c2b75344f6b1683196
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_version_	1718412596080541696

Next- and Third-Generation Sequencing Outperforms Culture-Based Methods in the Diagnosis of Ascitic Fluid Bacterial Infections of ICU Patients

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