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Neidhöfer C, Neuenhoff M, Jozič R, Atangcho B, Unsleber S, Neder U, Grumaz S, Parčina M. Exploring clonality and virulence gene associations in bloodstream infections using whole-genome sequencing and clinical data. Front Cell Infect Microbiol 2023; 13:1274573. [PMID: 38035332 PMCID: PMC10682671 DOI: 10.3389/fcimb.2023.1274573] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Accepted: 09/18/2023] [Indexed: 12/02/2023] Open
Abstract
Background Bloodstream infections (BSIs) remain a significant cause of mortality worldwide. Causative pathogens are routinely identified and susceptibility tested but only very rarely investigated for their resistance genes, virulence factors, and clonality. Our aim was to gain insight into the clonality patterns of different species causing BSI and the clinical relevance of distinct virulence genes. Methods For this study, we whole-genome-sequenced over 400 randomly selected important pathogens isolated from blood cultures in our diagnostic department between 2016 and 2021. Genomic data on virulence factors, resistance genes, and clonality were cross-linked with in-vitro data and demographic and clinical information. Results The investigation yielded extensive and informative data on the distribution of genes implicated in BSI as well as on the clonality of isolates across various species. Conclusion Associations between survival outcomes and the presence of specific genes must be interpreted with caution, and conducting replication studies with larger sample sizes for each species appears mandatory. Likewise, a deeper knowledge of virulence and host factors will aid in the interpretation of results and might lead to more targeted therapeutic and preventive measures. Monitoring transmission dynamics more efficiently holds promise to serve as a valuable tool in preventing in particular BSI caused by nosocomial pathogens.
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Affiliation(s)
- Claudio Neidhöfer
- Institute of Medical Microbiology, Immunology and Parasitology. University Hospital Bonn, Bonn, Germany
- Institute of Experimental Haematology and Transfusion Medicine, University of Bonn, Bonn, Germany
| | - Marcel Neuenhoff
- Bioinformatics and Systems Biology, Justus Liebig University Giessen, Giessen, Germany
| | - Robert Jozič
- Institute of Medical Microbiology, Immunology and Parasitology. University Hospital Bonn, Bonn, Germany
| | - Brenda Atangcho
- Institute of Medical Microbiology, Immunology and Parasitology. University Hospital Bonn, Bonn, Germany
- Institute for Functional Gene Analytics, Bonn-Rhein-Sieg University of Applied Sciences, Sankt Augustin, Germany
| | | | | | | | - Marijo Parčina
- Institute of Medical Microbiology, Immunology and Parasitology. University Hospital Bonn, Bonn, Germany
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2
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Goretzki SC, Schäfer M, Dogan B, Bruns N, Tschiedel E, Rath PM, Voigt S, Grumaz S, Horvatek P, Schönberger S, Stehling F, Brenner T, Dohna-Schwake C. Next Generation Sequencing of Free Microbial DNA for Rapid Identification of Pathogens in Critically Ill Children with Systemic Inflammatory Response Syndrome (SIRS). FRONT BIOSCI-LANDMRK 2022; 27:302. [PMID: 36472101 DOI: 10.31083/j.fbl2711302] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Revised: 09/28/2022] [Accepted: 10/07/2022] [Indexed: 11/13/2022]
Abstract
BACKGROUND Infections, major surgeries, and hyperinflammatory syndromes are known to trigger Systemic Inflammatory Response Syndrome (SIRS). Discrimination between infectious and noninfectious inflammation often poses a challenge in chronically ill patients with multiple comorbidities. These patients are routinely treated with a variety of anti-infective medications before a pathogen is identified. With the goal of improving pathogen detection rates and interventions, we evaluated Next Generation Sequencing (NGS) as a highly sensitive and fast means of detecting free microbial DNA in a small amount of serum samples from children with ongoing SIRS. METHODS We describe seven complex pediatric patients of SIRS or prolonged fever (>38.5 °C) >72 hours in which serum samples analyzed by NGS had a major impact on therapy. One patient was analyzed twice. RESULTS In eight NGS there were six positive results (two bacterial, three viral, one fungal) which were subsequently confirmed by microbiological culture or polymerase chain reaction (PCR) in five of the six NGS. In five of the eight performed NGS, results led to a change of therapy: antibiotic therapy was discontinued in two, escalated in one, an initiated in another; in one an antiviral was administered. CONCLUSIONS NGS may become a valuable addition to infectious disease diagnostics in cases of pediatric SIRS. However, NGS has not yet been validated as a diagnostic method in pediatric as a diagnostic method in pediatric patients and results should therefore be interpreted with caution. Multi-center NGS evaluation studies are currently being planned.
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Affiliation(s)
- Sarah C Goretzki
- Department of Pediatrics I, Neonatology, Pediatric Intensive Care, Pediatric Neurology, Pediatric Infectious Diseases, Essen University Hospital, 45147 Essen, Germany.,West German Centre of Infectious Diseases (WZI), University Hospital Essen, 45147 Essen, Germany
| | - Miriam Schäfer
- Department of Pediatrics I, Neonatology, Pediatric Intensive Care, Pediatric Neurology, Pediatric Infectious Diseases, Essen University Hospital, 45147 Essen, Germany.,West German Centre of Infectious Diseases (WZI), University Hospital Essen, 45147 Essen, Germany
| | - Burcin Dogan
- Department of Pediatrics I, Neonatology, Pediatric Intensive Care, Pediatric Neurology, Pediatric Infectious Diseases, Essen University Hospital, 45147 Essen, Germany.,West German Centre of Infectious Diseases (WZI), University Hospital Essen, 45147 Essen, Germany
| | - Nora Bruns
- Department of Pediatrics I, Neonatology, Pediatric Intensive Care, Pediatric Neurology, Pediatric Infectious Diseases, Essen University Hospital, 45147 Essen, Germany
| | - Eva Tschiedel
- Department of Pediatrics I, Neonatology, Pediatric Intensive Care, Pediatric Neurology, Pediatric Infectious Diseases, Essen University Hospital, 45147 Essen, Germany
| | - Peter-Michael Rath
- Institute of Medical Microbiology, University Medicine Essen, University Duisburg-Essen, 45147 Essen, Germany
| | - Sebastian Voigt
- Institute of Virology, University Medicine Essen, University Duisburg-Essen, 45147 Essen, Germany
| | - Silke Grumaz
- Noscendo GmbH, Duisburg, 47198 Duisburg, Germany
| | | | - Stefan Schönberger
- Department of Pediatrics III, Pediatric Hematology and Oncology, Cardiology, Pulmonology, University Hospital Essen, 45147 Essen, Germany
| | - Florian Stehling
- Department of Pediatrics III, Pediatric Hematology and Oncology, Cardiology, Pulmonology, University Hospital Essen, 45147 Essen, Germany
| | - Thorsten Brenner
- Department of Anesthesiology and Intensive Care Medicine, University Hospital Essen, University Duisburg-Essen, 45147 Essen, Germany
| | - Christian Dohna-Schwake
- Department of Pediatrics I, Neonatology, Pediatric Intensive Care, Pediatric Neurology, Pediatric Infectious Diseases, Essen University Hospital, 45147 Essen, Germany.,West German Centre of Infectious Diseases (WZI), University Hospital Essen, 45147 Essen, Germany
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3
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Schulz E, Grumaz S, Hatzl S, Gornicec M, Valentin T, Huber-Kraßnitzer B, Kriegl L, Uhl B, Deutsch A, Greinix H, Krause R, Neumeister P. Pathogen detection by metagenomic next generation sequencing during neutropenic fever in patients with hematological malignancies. Open Forum Infect Dis 2022; 9:ofac393. [PMID: 36004313 PMCID: PMC9394763 DOI: 10.1093/ofid/ofac393] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Accepted: 07/29/2022] [Indexed: 11/12/2022] Open
Abstract
Abstract
Background
Febrile neutropenia (FN) following chemotherapy is a major cause of morbidity during cancer treatment. The performance of metagenomic next-generation sequencing (mNGS) of circulating cell-free DNA from plasma may be superior to blood culture (BC) diagnostics for identification of causative pathogens. The aim of this study was to validate mNGS (DISQVER test) for the detection of pathogens in hematologic patients with FN.
Methods
We collected paired whole blood specimens from central venous catheter and peripheral vein during FN for BC and mNGS testing. We repeated paired sampling at the earliest after 3 days of fever, which was defined as one FN episode. All clinical data were retrospectively reviewed by an infectious disease expert panel. We calculated percent positive agreement (PPA), percent negative agreement (PNA), percent overall agreement (POA), and sensitivity and specificity.
Results
We analyzed a total of 98 unselected FN episodes in 61 patients who developed predominantly FN after conditioning therapy for allogeneic (n = 22) or autologous (n = 21) hematopoietic stem cell transplantation. Success rate of mNGS was 99% (97/98). Positivity rate of mNGS was 43% (42/97) overall and 32% (31/97) excluding viruses compared to 14% (14/98) in BC. PPA, PNA and POA between mNGS and BC were 84.6% (95% CI, 54.6% to 98.1%), 63.1% (51.9% to 73.4%) and 66% (55.7% to 75.3%), respectively. Sensitivity for bacteria or fungi was 40% (28.0% to 52.9%) and 18.5% (9.9% to 30.0%), respectively.
Conclusion
Pathogen detection by mNGS (DISQVER) during unselected FN episodes shows twofold higher sensitivity and a broader pathogen spectrum than BC.
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Affiliation(s)
- Eduard Schulz
- Division of Hematology, Department of Internal Medicine, Medical University of Graz , Graz , Austria
- Center for Cancer Research, National Cancer Institute, National Institutes of Health , Bethesda, Maryland , USA
| | | | - Stefan Hatzl
- Division of Hematology, Department of Internal Medicine, Medical University of Graz , Graz , Austria
- Intensive Care Unit, Department of Internal Medicine, Medical University of Graz , Graz , Austria
| | - Maximilian Gornicec
- Division of Infectious Diseases, Department of Internal Medicine, Medical University of Graz , Graz , Austria
| | - Thomas Valentin
- Division of Infectious Diseases, Department of Internal Medicine, Medical University of Graz , Graz , Austria
| | - Bianca Huber-Kraßnitzer
- Division of Hematology, Department of Internal Medicine, Medical University of Graz , Graz , Austria
| | - Lisa Kriegl
- Division of Infectious Diseases, Department of Internal Medicine, Medical University of Graz , Graz , Austria
| | - Barbara Uhl
- Division of Hematology, Department of Internal Medicine, Medical University of Graz , Graz , Austria
| | - Alexander Deutsch
- Division of Hematology, Department of Internal Medicine, Medical University of Graz , Graz , Austria
| | - Hildegard Greinix
- Division of Hematology, Department of Internal Medicine, Medical University of Graz , Graz , Austria
| | - Robert Krause
- Division of Infectious Diseases, Department of Internal Medicine, Medical University of Graz , Graz , Austria
| | - Peter Neumeister
- Division of Hematology, Department of Internal Medicine, Medical University of Graz , Graz , Austria
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4
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Ziegler S, Disqué C, Grumaz S, Sakka SG. Potential impact of cell-free DNA blood testing in the diagnosis of sepsis. Int J Infect Dis 2022; 119:77-79. [PMID: 35331935 DOI: 10.1016/j.ijid.2022.03.030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 02/28/2022] [Accepted: 03/16/2022] [Indexed: 11/29/2022] Open
Abstract
BACKGROUND Classical blood culture testing is still the gold standard in correct and timely diagnosis of the responsible microorganisms in sepsis. CASE SUMMARY In this case (a patient with a colon perforation and severe peritonitis with septic shock), an alternative approach (cell-free DNA next-generation sequencing from full blood samples, NGS) showed the responsible microorganisms, whereas the classical blood culture testing remainedstayed sterile. Interestingly, samples from the abdominal fluid showed the same bacteria as NGS. CONCLUSION These findings may be interpreted as that the threshold for positive testing is lower through the molecular approach than through culture techniques; however, more studies are necessary to prove this theory.
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Affiliation(s)
- Steffen Ziegler
- Department of Intensive Care Medicine, Gemeinschaftsklinikum Mittelrhein gGmbH, Ev. Stift St. Martin, Academic teaching hospital of the Johannes Gutenberg University of Mainz, Koblenz, Germany.
| | | | | | - Samir G Sakka
- Department of Intensive Care Medicine, Gemeinschaftsklinikum Mittelrhein gGmbH, Ev. Stift St. Martin, Academic teaching hospital of the Johannes Gutenberg University of Mainz, Koblenz, Germany
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5
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Brenner T, Skarabis A, Stevens P, Axnick J, Haug P, Grumaz S, Bruckner T, Luntz S, Witzke O, Pletz MW, Ruprecht TM, Marschall U, Altin S, Greiner W, Berger MM. Optimization of sepsis therapy based on patient-specific digital precision diagnostics using next generation sequencing (DigiSep-Trial)-study protocol for a randomized, controlled, interventional, open-label, multicenter trial. Trials 2021; 22:714. [PMID: 34663439 PMCID: PMC8522064 DOI: 10.1186/s13063-021-05667-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Accepted: 09/28/2021] [Indexed: 12/19/2022] Open
Abstract
Background Sepsis is triggered by an infection and represents one of the greatest challenges of modern intensive care medicine. With regard to a targeted antimicrobial treatment strategy, the earliest possible pathogen detection is of crucial importance. Until now, culture-based detection methods represent the diagnostic gold standard, although they are characterized by numerous limitations. Culture-independent molecular diagnostic procedures represent a promising alternative. In particular, the plasmatic detection of circulating, cell-free DNA by next-generation sequencing (NGS) has shown to be suitable for identifying disease-causing pathogens in patients with bloodstream infections. Methods The DigiSep-Trial is a randomized, controlled, interventional, open-label, multicenter trial characterizing the effect of the combination of NGS-based digital precision diagnostics with standard-of-care microbiological analyses compared to solely standard-of-care microbiological analyses in the clinical picture of sepsis/septic shock. Additional anti-infective expert consultations are provided for both study groups. In 410 patients (n = 205 per arm) with sepsis/septic shock, the study examines whether the so-called DOOR-RADAR (Desirability of Outcome Ranking/Response Adjusted for Duration of Antibiotic Risk) score (representing a combined endpoint including the criteria (1) intensive/intermediate care unit length of stay, (2) consumption of antibiotics, (3) mortality, and (4) acute kidney injury (AKI)) can be improved by an additional NGS-based diagnostic concept. We also aim to investigate the cost-effectiveness of this new diagnostic procedure. It is postulated that intensive/intermediate care unit length of stay, mortality rate, incidence of AKI, the duration of antimicrobial therapy as well as the costs caused by complications and outpatient aftercare can be reduced. Moreover, a significant improvement in patient’s quality of life is expected. Discussion The authors´ previous work suggests that NGS-based diagnostics have a higher specificity and sensitivity compared to standard-of-care microbiological analyses for detecting bloodstream infections. In combination with the here presented DigiSep-Trial, this work provides the optimal basis to establish a new NGS-driven concept as part of the national standard based on the best possible evidence. Trial registrations DRKS-ID DRKS00022782. Registered on August 25, 2020 ClinicalTrials.govNCT04571801. Registered October 1, 2020 Supplementary Information The online version contains supplementary material available at 10.1186/s13063-021-05667-x.
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Affiliation(s)
- Thorsten Brenner
- Department of Anesthesiology and Intensive Care Medicine, Essen University Hospital, University Duisburg-Essen, Hufelandstr. 55, 45147, Essen, Germany.
| | - Annabell Skarabis
- Department of Anesthesiology and Intensive Care Medicine, Essen University Hospital, University Duisburg-Essen, Hufelandstr. 55, 45147, Essen, Germany
| | | | | | - Peter Haug
- Noscendo GmbH, Königstraße 34, 47198, Duisburg, Germany
| | - Silke Grumaz
- Noscendo GmbH, Königstraße 34, 47198, Duisburg, Germany
| | - Thomas Bruckner
- Institute of Medical Biometry, University of Heidelberg, Im Neuenheimer Feld 130.3, 69120, Heidelberg, Germany
| | - Steffen Luntz
- Coordination Centre for Clinical Trials (KKS), Ruprecht-Karls-University, Im Neuenheimer Feld 130.3, 69120, Heidelberg, Germany
| | - Oliver Witzke
- Department of Infectious Diseases, University Hospital Essen, University Duisburg-Essen, Hufelandstr. 55, 45147, Essen, Germany
| | - Mathias W Pletz
- Center for Infectious Diseases and Infection Control, Jena University Hospital, Erlanger Allee 101, 07740, Jena, Germany
| | - Thomas M Ruprecht
- Techniker Krankenkasse, Bramfelder Str. 140, 22305, Hamburg, Germany
| | | | - Sibel Altin
- AOK Rheinland/Hamburg, Kasernenstr. 61, 40213, Düsseldorf, Germany
| | - Wolfgang Greiner
- Health Economics and Health Care Management, Bielefeld University, P.O. Box 10 01 31, 33501, Bielefeld, Germany
| | - Marc Moritz Berger
- Department of Anesthesiology and Intensive Care Medicine, Essen University Hospital, University Duisburg-Essen, Hufelandstr. 55, 45147, Essen, Germany
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6
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Obrová K, Grumaz S, Remely M, Czurda S, Krickl I, Herndlhofer S, Gleixner KV, Sperr WR, Größlinger L, Frank T, Andrade N, Egger‐Matiqi T, Peters C, Engstler G, Dworzak M, Attarbaschi A, Grotel M, Heuvel‐Eibrink MM, Moiseev IS, Rogacheva Y, Zubarovskaya L, Zubarovskaya N, Pichler H, Lawitschka A, Koller E, Keil F, Valent P, Sohn K, Lion T. Presence of viremia during febrile neutropenic episodes in patients undergoing chemotherapy for malignant neoplasms. Am J Hematol 2021; 96:719-726. [PMID: 33784434 DOI: 10.1002/ajh.26177] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Revised: 03/25/2021] [Accepted: 03/25/2021] [Indexed: 12/17/2022]
Abstract
The importance of viral infections as a leading cause of morbidity and mortality is well documented in severely immunosuppressed patients undergoing allogeneic stem cell transplantation. By contrast, viral infections generally receive less attention in patients with malignant disorders undergoing chemotherapy, where the onset of neutropenic fever is mostly associated with bacterial or fungal infections, and screening for viral infections is not routinely performed. To address the occurrence of invasive viral infections in a clinical setting commonly associated with less pronounced immunosuppression, we have prospectively screened 237 febrile neutropenic episodes in pediatric (n = 77) and adult (n = 69) patients undergoing intensive chemotherapy, primarily for treatment of acute leukemia. Serial peripheral blood specimens were tested by RQ-PCR assays for the presence and quantity of the clinically relevant viruses CMV, EBV, HHV6 and HAdV, commonly reactivated in highly immunocompromised patients. Viremia was documented in 36 (15%) episodes investigated, including the detection of HHV6 (n = 14), EBV (n = 15), CMV (n = 6), or HAdV (n = 1). While low or intermediate levels of viremia (<104 virus copies/mL) were commonly associated with bacterial or fungal co-infection, viremia at higher levels (>104 copies/mL) was documented in patients without evidence for other infections, raising the possibility that at least in some instances the onset of fever may have been attributable to the virus detected. The observations suggest that viral infections, potentially resulting from reactivation, might also play a clinically relevant role in patients receiving chemotherapy for treatment of malignant neoplasms, and routine screening for viremia in this clinical setting might be warranted.
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Affiliation(s)
- Klára Obrová
- St.Anna Children's Cancer Research Institute (CCRI) Vienna Austria
| | | | - Marlene Remely
- St.Anna Children's Cancer Research Institute (CCRI) Vienna Austria
| | - Stefan Czurda
- St.Anna Children's Cancer Research Institute (CCRI) Vienna Austria
| | - Isabella Krickl
- St.Anna Children's Cancer Research Institute (CCRI) Vienna Austria
| | - Susanne Herndlhofer
- Department of Internal Medicine I, Division of Hematology & Hemostaseology Medical University of Vienna Vienna Austria
| | - Karoline V. Gleixner
- Department of Internal Medicine I, Division of Hematology & Hemostaseology Medical University of Vienna Vienna Austria
- Ludwig Boltzmann Institute for Hematology & Oncology Medical University of Vienna Vienna Austria
| | - Wolfgang R. Sperr
- Department of Internal Medicine I, Division of Hematology & Hemostaseology Medical University of Vienna Vienna Austria
- Ludwig Boltzmann Institute for Hematology & Oncology Medical University of Vienna Vienna Austria
| | | | - Tijana Frank
- St.Anna Children's Cancer Research Institute (CCRI) Vienna Austria
| | - Nuno Andrade
- St.Anna Children's Cancer Research Institute (CCRI) Vienna Austria
| | - Teresa Egger‐Matiqi
- St. Anna Children's Hospital, Department of Pediatrics Medical University of Vienna Vienna Austria
| | - Christina Peters
- St. Anna Children's Hospital, Department of Pediatrics Medical University of Vienna Vienna Austria
| | - Gernot Engstler
- St. Anna Children's Hospital, Department of Pediatrics Medical University of Vienna Vienna Austria
| | - Michael Dworzak
- St. Anna Children's Hospital, Department of Pediatrics Medical University of Vienna Vienna Austria
| | - Andishe Attarbaschi
- St. Anna Children's Hospital, Department of Pediatrics Medical University of Vienna Vienna Austria
| | - Martine Grotel
- Princess Máxima Center for Pediatric Oncology Utrecht The Netherlands
| | | | - Ivan S. Moiseev
- I. P. Pavlov First Saint Petersburg State Medical University Saint Petersburg Russia
| | - Yuliya Rogacheva
- I. P. Pavlov First Saint Petersburg State Medical University Saint Petersburg Russia
| | - Ludmilla Zubarovskaya
- I. P. Pavlov First Saint Petersburg State Medical University Saint Petersburg Russia
| | - Natalia Zubarovskaya
- St. Anna Children's Hospital, Department of Pediatrics Medical University of Vienna Vienna Austria
| | - Herbert Pichler
- St. Anna Children's Hospital, Department of Pediatrics Medical University of Vienna Vienna Austria
| | - Anita Lawitschka
- St. Anna Children's Hospital, Department of Pediatrics Medical University of Vienna Vienna Austria
| | | | - Felix Keil
- Ludwig Boltzmann Institute for Hematology & Oncology Medical University of Vienna Vienna Austria
- 3rd Medical Department Hanuschhospital Vienna Austria
| | - Peter Valent
- Department of Internal Medicine I, Division of Hematology & Hemostaseology Medical University of Vienna Vienna Austria
- Ludwig Boltzmann Institute for Hematology & Oncology Medical University of Vienna Vienna Austria
| | - Kai Sohn
- Fraunhofer IGB Stuttgart Germany
| | - Thomas Lion
- St.Anna Children's Cancer Research Institute (CCRI) Vienna Austria
- Ludwig Boltzmann Institute for Hematology & Oncology Medical University of Vienna Vienna Austria
- Labdia Labordiagnostik GmbH Vienna Austria
- Department of Pediatrics Medical University of Vienna Vienna Austria
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7
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Grumaz C, Hoffmann A, Vainshtein Y, Kopp M, Grumaz S, Stevens P, Decker SO, Weigand MA, Hofer S, Brenner T, Sohn K. Rapid Next-Generation Sequencing-Based Diagnostics of Bacteremia in Septic Patients. J Mol Diagn 2021; 22:405-418. [PMID: 32146977 DOI: 10.1016/j.jmoldx.2019.12.006] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Revised: 11/18/2019] [Accepted: 12/11/2019] [Indexed: 01/23/2023] Open
Abstract
The increasing incidence of bloodstream infections including sepsis is a major challenge in intensive care units worldwide. However, current diagnostics for pathogen identification mainly depend on culture- and molecular-based approaches, which are not satisfactory regarding specificity, sensitivity, and time to diagnosis. Herein, we established a complete diagnostic workflow for real-time high-throughput sequencing of cell-free DNA from plasma based on nanopore sequencing for the detection of the causative agents, which was applied to the analyses of eight samples from four septic patients and three healthy controls, and subsequently validated against standard next-generation sequencing results. By optimization of library preparation protocols for short fragments with low input amounts, a 3.5-fold increase in sequencing throughput could be achieved. With tailored bioinformatics workflows, all eight septic patient samples were found to be positive for relevant pathogens. When considering time to diagnosis, pathogens were identified within minutes after start of sequencing. Moreover, an extrapolation of real-time sequencing performance on a cohort of 239 septic patient samples revealed that more than 90% of pathogen hits would have also been detected using the optimized MinION workflow. Reliable identification of pathogens based on circulating cell-free DNA sequencing using optimized workflows and real-time nanopore-based sequencing can be accomplished within 5 to 6 hours following blood draw. Therefore, this approach might provide therapy-relevant results in a clinically critical timeframe.
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Affiliation(s)
- Christian Grumaz
- Department of in-Vitro Diagnostics, Fraunhofer Institute for Interfacial Engineering and Biotechnology IGB, Stuttgart, Germany
| | - Anne Hoffmann
- Department of in-Vitro Diagnostics, Fraunhofer Institute for Interfacial Engineering and Biotechnology IGB, Stuttgart, Germany
| | - Yevhen Vainshtein
- Department of in-Vitro Diagnostics, Fraunhofer Institute for Interfacial Engineering and Biotechnology IGB, Stuttgart, Germany
| | - Maria Kopp
- Department of in-Vitro Diagnostics, Fraunhofer Institute for Interfacial Engineering and Biotechnology IGB, Stuttgart, Germany
| | - Silke Grumaz
- Department of in-Vitro Diagnostics, Fraunhofer Institute for Interfacial Engineering and Biotechnology IGB, Stuttgart, Germany
| | | | - Sebastian O Decker
- Department of Anesthesiology, Heidelberg University Hospital, Heidelberg, Germany
| | - Markus A Weigand
- Department of Anesthesiology, Heidelberg University Hospital, Heidelberg, Germany
| | - Stefan Hofer
- Westpfalz-Klinikum GmbH, Kaiserslautern, Germany
| | - Thorsten Brenner
- Department of Anesthesiology, Heidelberg University Hospital, Heidelberg, Germany
| | - Kai Sohn
- Department of in-Vitro Diagnostics, Fraunhofer Institute for Interfacial Engineering and Biotechnology IGB, Stuttgart, Germany.
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8
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Kattner S, Herbstreit F, Schmidt K, Stevens P, Grumaz S, Dubler S, Rath PM, Brenner T. Next-Generation Sequencing-Based Decision Support for Intensivists in Difficult-to-Diagnose Disease States: A Case Report of Invasive Cerebral Aspergillosis. A A Pract 2021; 15:e01447. [PMID: 33955856 DOI: 10.1213/xaa.0000000000001447] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Aspergillus spp. are widespread environmental pathogens that can induce invasive aspergillosis, especially in immunocompromised patients. An 86-year-old female patient presented with a rare case of invasive cerebral aspergillosis. The aspergilloma invaded the intracranial region originating from the ethmoidal sinus and the orbital apex. In contrast to routine diagnostic procedures, next-generation sequencing (NGS) was able to identify the fungal pathogen in the cerebrospinal fluid as well as in plasma samples, supporting the biopsy-based diagnosis of invasive cerebral aspergillosis. Therefore, NGS-based diagnostics may be of particular importance for difficult-to-diagnose disease states, when conventional diagnostic procedures fail.
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Affiliation(s)
- Simone Kattner
- From the Department of Anesthesiology and Intensive Care Medicine, University Hospital Essen, University Duisburg-Essen, Essen, Germany
| | - Frank Herbstreit
- From the Department of Anesthesiology and Intensive Care Medicine, University Hospital Essen, University Duisburg-Essen, Essen, Germany
| | - Karsten Schmidt
- From the Department of Anesthesiology and Intensive Care Medicine, University Hospital Essen, University Duisburg-Essen, Essen, Germany
| | | | | | - Simon Dubler
- From the Department of Anesthesiology and Intensive Care Medicine, University Hospital Essen, University Duisburg-Essen, Essen, Germany
| | - Peter-Michael Rath
- Institute of Medical Microbiology, Essen Center of Excellence in Clinical and Laboratory Mycology and Clinical Studies, University Hospital Essen, University Duisburg-Essen, Essen, Germany
| | - Thorsten Brenner
- From the Department of Anesthesiology and Intensive Care Medicine, University Hospital Essen, University Duisburg-Essen, Essen, Germany
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9
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Decker SO, Krüger A, Wilk H, Grumaz S, Vainshtein Y, Schmitt FCF, Uhle F, Bruckner T, Zimmermann S, Mehrabi A, Mieth M, Weiss KH, Weigand MA, Hofer S, Sohn K, Brenner T. New approaches for the detection of invasive fungal diseases in patients following liver transplantation-results of an observational clinical pilot study. Langenbecks Arch Surg 2019; 404:309-325. [PMID: 30834971 DOI: 10.1007/s00423-019-01769-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Accepted: 02/21/2019] [Indexed: 12/13/2022]
Abstract
PURPOSE Despite antifungal prophylaxis following liver transplantation (LTX), patients are at risk for the development of subsequent opportunistic infections, such as an invasive fungal disease (IFD). However, culture-based diagnostic procedures are associated with relevant weaknesses. METHODS Culture and next-generation sequencing (NGS)-based fungal findings as well as corresponding plasma levels of ß-D-glucan (BDG), galactomannan (GM), interferon gamma (IFN-γ), tumor necrosis factor alpha (TNF-α), interleukin (IL)-2, -4, -6, -10, -17A and mid-regional proadrenomedullin (MR-proADM) were evaluated in 93 patients at 6 consecutive time points within 28 days following LTX. RESULTS A NGS-based diagnostic approach was shown to be suitable for the early identification of fungal pathogens in patients following LTX. Moreover, MR-proADM and IL-17A in plasma proved suitable for the identification of patients with an IFD. CONCLUSION Plasma measurements of MR-proADM and IL-17A as well as a NGS-based diagnostic approach were shown to be attractive methodologies to attenuate the weaknesses of routinely used culture-based diagnostic procedures for the determination of an IFD in patients following LTX. However, an additional confirmation within a larger multicenter trial needs to be recommended. TRIAL REGISTRATION German Clinical Trials Register: DRKS00005480 .
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Affiliation(s)
- Sebastian O Decker
- Department of Anesthesiology, Heidelberg University Hospital, Im Neuenheimer Feld 110, 69120, Heidelberg, Germany
| | - Albert Krüger
- Department of Anesthesiology, Heidelberg University Hospital, Im Neuenheimer Feld 110, 69120, Heidelberg, Germany
| | - Henryk Wilk
- Department of Anesthesiology, Heidelberg University Hospital, Im Neuenheimer Feld 110, 69120, Heidelberg, Germany
| | - Silke Grumaz
- Fraunhofer IGB, Nobelstraße 12, 70569, Stuttgart, Germany
| | | | - Felix C F Schmitt
- Department of Anesthesiology, Heidelberg University Hospital, Im Neuenheimer Feld 110, 69120, Heidelberg, Germany
| | - Florian Uhle
- Department of Anesthesiology, Heidelberg University Hospital, Im Neuenheimer Feld 110, 69120, Heidelberg, Germany
| | - Thomas Bruckner
- Institute of Medical Biometry and Informatics, University of Heidelberg, Im Neuenheimer Feld 130, 69120, Heidelberg, Germany
| | - Stefan Zimmermann
- Department of Infectious Diseases, Medical Microbiology and Hygiene, Heidelberg University Hospital, Im Neuenheimer Feld 324, 69120, Heidelberg, Germany
| | - Arianeb Mehrabi
- Department of General, Visceral and Transplant Surgery, Heidelberg University Hospital, Im Neuenheimer Feld 110, 69120, Heidelberg, Germany
| | - Markus Mieth
- Department of General, Visceral and Transplant Surgery, Heidelberg University Hospital, Im Neuenheimer Feld 110, 69120, Heidelberg, Germany
| | - Karl Heinz Weiss
- Department of Internal Medicine IV, Heidelberg University Hospital, Im Neunheimer Feld 410, 69120, Heidelberg, Germany
| | - Markus A Weigand
- Department of Anesthesiology, Heidelberg University Hospital, Im Neuenheimer Feld 110, 69120, Heidelberg, Germany
| | - Stefan Hofer
- Department of Anesthesiology, Westpfalzklinikum, Hellmut-Hartert-Straße 1, 67655, Kaiserslautern, Germany
| | - Kai Sohn
- Fraunhofer IGB, Nobelstraße 12, 70569, Stuttgart, Germany
| | - Thorsten Brenner
- Department of Anesthesiology, Heidelberg University Hospital, Im Neuenheimer Feld 110, 69120, Heidelberg, Germany.
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Brenner T, Decker SO, Grumaz S, Stevens P, Bruckner T, Schmoch T, Pletz MW, Bracht H, Hofer S, Marx G, Weigand MA, Sohn K. Next-generation sequencing diagnostics of bacteremia in sepsis (Next GeneSiS-Trial): Study protocol of a prospective, observational, noninterventional, multicenter, clinical trial. Medicine (Baltimore) 2018; 97:e9868. [PMID: 29419698 PMCID: PMC5944698 DOI: 10.1097/md.0000000000009868] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Sepsis remains a major challenge, even in modern intensive care medicine. The identification of the causative pathogen is crucial for an early optimization of the antimicrobial treatment regime. In this context, culture-based diagnostic procedures (e.g., blood cultures) represent the standard of care, although they are associated with relevant limitations. Accordingly, culture-independent molecular diagnostic procedures might be of help for the identification of the causative pathogen in infected patients. The concept of an unbiased sequence analysis of circulating cell-free DNA (cfDNA) from plasma samples of septic patients by next-generation sequencing (NGS) has recently been identified to be a promising diagnostic platform for critically ill patients suffering from bloodstream infections. Although this new approach might be more sensitive and specific than culture-based state-of-the-art technologies, additional clinical trials are needed to exactly define the performance as well as clinical value of a NGS-based approach. METHODS Next GeneSiS is a prospective, observational, noninterventional, multicenter study to assess the diagnostic performance of a NGS-based approach for the detection of relevant infecting organisms in patients with suspected or proven sepsis [according to recent sepsis definitions (sepsis-3)] by the use of the quantitative sepsis indicating quantifier (SIQ) score in comparison to standard (culture-based) microbiological diagnostics. The clinical value of this NGS-based approach will be estimated by a panel of independent clinical specialists, retrospectively identifying potential changes in patients' management based on NGS results. Further subgroup analyses will focus on the clinical value especially for patients suffering from a failure of empiric treatment within the first 3 days after onset [as assessed by death of the patient or lack of improvement of the patient's clinical condition (in terms of an inadequate decrease of SOFA-score) or persistent high procalcitonin levels]. DISCUSSION This prospective, observational, noninterventional, multicenter study for the first time investigates the performance as well as the clinical value of a NGS-based approach for the detection of bacteremia in patients with sepsis and may therefore be a pivotal step toward the clinical use of NGS in this indication. TRIAL REGISTRATION DRKS-ID: DRKS00011911 (registered October 9, 2017) https://www.drks.de/drks_web/navigate.do?navigationId=trial.HTML&TRIAL_ID=DRKS00011911; ClinicalTrials.gov Identifier: NCT03356249 (registered November 29, 2017) https://clinicaltrials.gov/ct2/show/NCT03356249.
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Affiliation(s)
- Thorsten Brenner
- Department of Anesthesiology, Heidelberg University Hospital, Heidelberg
| | | | | | | | - Thomas Bruckner
- Institute of Medical Biometry and Informatics, University of Heidelberg, Heidelberg
| | - Thomas Schmoch
- Department of Anesthesiology, Heidelberg University Hospital, Heidelberg
| | - Mathias W. Pletz
- Institute of Infectious Diseases and Infection Control, Jena University Hospital, Jena
| | - Hendrik Bracht
- Department of Anaesthesiology, Division of Intensive Care, University Clinic Ulm, Ulm
| | - Stefan Hofer
- Department of Anesthesiology, Westpfalzklinikum, Kaiserslautern
| | - Gernot Marx
- Department of Intensive Care and Intermediate Care, RWTH University Hospital Aachen, Aachen, Germany
| | - Markus A. Weigand
- Department of Anesthesiology, Heidelberg University Hospital, Heidelberg
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11
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Grumaz S, Stevens P, Grumaz C, Decker SO, Weigand MA, Hofer S, Brenner T, von Haeseler A, Sohn K. Next-generation sequencing diagnostics of bacteremia in septic patients. Genome Med 2016; 8:73. [PMID: 27368373 PMCID: PMC4930583 DOI: 10.1186/s13073-016-0326-8] [Citation(s) in RCA: 213] [Impact Index Per Article: 26.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2016] [Accepted: 06/10/2016] [Indexed: 02/08/2023] Open
Abstract
Background Bloodstream infections remain one of the major challenges in intensive care units, leading to sepsis or even septic shock in many cases. Due to the lack of timely diagnostic approaches with sufficient sensitivity, mortality rates of sepsis are still unacceptably high. However a prompt diagnosis of the causative microorganism is critical to significantly improve outcome of bloodstream infections. Although various targeted molecular tests for blood samples are available, time-consuming blood culture-based approaches still represent the standard of care for the identification of bacteria. Methods Here we describe the establishment of a complete diagnostic workflow for the identification of infectious microorganisms from seven septic patients based on unbiased sequence analyses of free circulating DNA from plasma by next-generation sequencing. Results We found significant levels of DNA fragments derived from pathogenic bacteria in samples from septic patients. Quantitative evaluation of normalized read counts and introduction of a sepsis indicating quantifier (SIQ) score allowed for an unambiguous identification of Gram-positive as well as Gram-negative bacteria that exactly matched with blood cultures from corresponding patient samples. In addition, we also identified species from samples where blood cultures were negative. Reads of non-human origin also comprised fragments derived from antimicrobial resistance genes, showing that, in principle, prediction of specific types of resistance might be possible. Conclusions The complete workflow from sample preparation to species identification report could be accomplished in roughly 30 h, thus making this approach a promising diagnostic platform for critically ill patients suffering from bloodstream infections. Electronic supplementary material The online version of this article (doi:10.1186/s13073-016-0326-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Silke Grumaz
- Fraunhofer IGB, Nobelstr. 12, 70569, Stuttgart, Germany
| | - Philip Stevens
- IGVP, University of Stuttgart, Nobelstr. 12, 70569, Stuttgart, Germany.,Center for Integrative Bioinformatics Vienna, Max F. Perutz Laboratories, University of Vienna, Medical University of Vienna, Vienna, Austria
| | | | - Sebastian O Decker
- Department of Anesthesiology, Heidelberg University Hospital, Im Neuenheimer Feld 110, 69120, Heidelberg, Germany
| | - Markus A Weigand
- Department of Anesthesiology, Heidelberg University Hospital, Im Neuenheimer Feld 110, 69120, Heidelberg, Germany
| | - Stefan Hofer
- Department of Anesthesiology, Heidelberg University Hospital, Im Neuenheimer Feld 110, 69120, Heidelberg, Germany
| | - Thorsten Brenner
- Department of Anesthesiology, Heidelberg University Hospital, Im Neuenheimer Feld 110, 69120, Heidelberg, Germany
| | - Arndt von Haeseler
- Center for Integrative Bioinformatics Vienna, Max F. Perutz Laboratories, University of Vienna, Medical University of Vienna, Vienna, Austria.,Bioinformatics and Computational Biology, Faculty of Computer Science, University of Vienna, Vienna, Austria
| | - Kai Sohn
- Fraunhofer IGB, Nobelstr. 12, 70569, Stuttgart, Germany. .,IGVP, University of Stuttgart, Nobelstr. 12, 70569, Stuttgart, Germany.
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