**1. Introduction**

Since 2020, the coronavirus disease-2019 (COVID-19) has posed a serious burden on the global healthcare system and especially on intensive care units (ICUs). The progressive availability of vaccines, the emergence of less virulent strains, the growth of clinical experience, and the development of new treatments effectively decreased the number of ICU admissions and overall mortality rates over the course of the pandemic [1–4]. However, in critically ill patients requiring invasive mechanical ventilation, mortality rates remained high throughout the later waves of the pandemic [5,6]. In particular, secondary infections, such as bloodstream infections (BSIs) are strongly associated with poorer outcomes [7–9].

Delayed or inadequate antimicrobial treatment is associated with increased morbidity and mortality rates in sepsis [10–12]. Consequently, the rapid initiation of empiric antimicrobial therapy and the identification of the causative pathogen is crucial.

However, conventional, culture-based methods—which form the current gold-standard for pathogen identification—suffer from limitations, such as delayed results and low test sensitivity, especially with previous exposure to antibiotics [13–15]. Polymerase chain reaction (PCR)-based techniques have been developed as rapid alternatives to culture-based

**Citation:** Leitl, C.J.; Stoll, S.E.; Wetsch, W.A.; Kammerer, T.; Mathes, A.; Böttiger, B.W.; Seifert, H.; Dusse, F. Next-Generation Sequencing in Critically Ill COVID-19 Patients with Suspected Bloodstream Infections: A Retrospective Cohort Study. *J. Clin. Med.* **2023**, *12*, 1466. https://doi.org/ 10.3390/jcm12041466

Academic Editors: Timothy E. Albertson and Peter Markus Spieth

Received: 13 January 2023 Revised: 28 January 2023 Accepted: 9 February 2023 Published: 12 February 2023

**Copyright:** © 2023 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https:// creativecommons.org/licenses/by/ 4.0/).

methods, but these approaches often rely on targeted pathogen detection with limited coverages [16].

Recently, next-generation sequencing (NGS)-based methods have emerged as powerful diagnostic platforms for the detection of pathogens in critically ill patients [13,17,18]. The concept of unbiased sequence analysis of circulating cell-free deoxyribonucleic acid (cfDNA) from plasma allows for the identification of bacterial, fungal, and viral microorganisms in one single test, including non-culturable pathogens (e.g., *Tropheryma whipplei* or *Coxiella burnetii*) and irrespective of antimicrobial treatment. In particular, the DISQVER® pathogen test (Noscendo GmbH, Duisburg, Germany) provides comprehensive data analysis and allows differentiation between relevant pathogens and potential microbial contaminants, such as coagulase-negative staphylococci (CNS), by calculating a sepsis-indicating quantifier score [19]. Previous studies have shown a higher sensitivity of NGS-based methods compared to blood cultures (BCs) in patients with suspected sepsis or BSIs, which is potentially beneficial for the optimization of antimicrobial treatments [13,17,18]. However, to date, only a few studies have addressed the clinical impact of complementary NGS diagnostics in patients with either suspected sepsis or BSIs [13,20].

Given the high rate of secondary infections and associated increased mortality in patients with severe COVID-19, we hypothesized that this group in particular would benefit from improved pathogen diagnostics. The aim of this descriptive study was to evaluate the diagnostic performance of NGS-based methods and their potential impact on antimicrobial therapy in a cohort of critically ill COVID-19 patients. To the best of our knowledge, this is the first study investigating the implementation of this new approach in the diagnosis of BSIs in patients with severe COVID-19.
