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

Hanna Goelz,Negin Mehrbarzin,Stefan Utzolino,Simon Wetzel,Georg Häcker,Mohamed Tarek Badr

doi:10.3390/cells10113226

Abstract

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 E. faecalis and Klebsiella 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.

Highlights

Ascites is the abnormal accumulation of fluid in the abdomen
To examine possible clinical correlations between patient characteristics and the identified organisms, patients were sub-grouped into three main categories: patients in whose sample both culture and sequencing yielded positive results, patients for whom only sequencing analysis detected bacteria, and patients whose samples were negative in both tests
After grouping the patients based on their clinical characteristics using principle component analysis (PCA), all samples positive in sequencing clustered together, regardless of their culture status, but separate from sequencing negative samples (Figure 1d), suggesting a clinical correlation between the microbes found in sequencing and patients’ characteristics and outcome

Summary

Introduction

Ascites is the abnormal accumulation of fluid in the abdomen. It is a common condition in cirrhotic liver disease [1] that may affect up to 50% of compensated liver disease patients [2]. Infection of the ascitic fluid is a serious complication associated with high morbidity and mortality [3]. Abdominal infections are among the most common infections in the intensive care unit (ICU) [4], and they carry a substantial increase in the risk of mortality [5,6]. Successful identification of pathogenic organisms in ascitic fluid infections is essential to guide antimicrobial therapy and to refine antibiotic treatment [7,8,9]. Targeted treatment will have a positive impact on therapy outcome and reduce the emergence of resistant bacteria as well as the side effects of antibiotic therapy [10,11]

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