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Kommedal Ø, Eagan TM, Fløtten Ø, Leegaard TM, Siljan W, Fardal H, Bø B, Grøvan F, Larssen KW, Kildahl-Andersen A, Hjetland R, Tilseth R, Hareide SKØ, Tellevik M, Dyrhovden R. Microbiological diagnosis of pleural infections: a comparative evaluation of a novel syndromic real-time PCR panel. Microbiol Spectr 2024; 12:e0351023. [PMID: 38656204 DOI: 10.1128/spectrum.03510-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Accepted: 02/19/2024] [Indexed: 04/26/2024] Open
Abstract
Current microbial diagnostics for pleural infections are insufficient. Studies using 16S targeted next-generation sequencing report that only 10%-16% of bacteria present are cultured and that 50%-78% of pleural fluids containing relevant microbial DNA remain culture negative. As a rapid diagnostic alternative suitable for clinical laboratories, we wanted to explore a PCR-based approach. Based on the identification of key pathogens, we developed a syndromic PCR panel for community-acquired pleural infections (CAPIs). This was a pragmatic PCR panel, meaning that it was not designed for detecting all possibly involved bacterial species but for confirming the diagnosis of CAPI, and for detecting bacteria that might influence choice of antimicrobial treatment. We evaluated the PCR panel on 109 confirmed CAPIs previously characterized using culture and 16S targeted next-generation sequencing. The PCR secured the diagnosis of CAPI in 107/109 (98.2%) and detected all present pathogens in 69/109 (63.3%). Culture secured the diagnosis in 54/109 (49.5%) and detected all pathogens in 31/109 (28.4%). Corresponding results for 16S targeted next-generation sequencing were 109/109 (100%) and 98/109 (89.9%). For bacterial species included in the PCR panel, PCR had a sensitivity of 99.5% (184/185), culture of 21.6% (40/185), and 16S targeted next-generation sequencing of 92.4% (171/185). None of the bacterial species present not covered by the PCR panel were judged to impact antimicrobial therapy. A syndromic PCR panel represents a rapid and sensitive alternative to current diagnostic approaches for the microbiological diagnosis of CAPI.IMPORTANCEPleural empyema is a severe infection with high mortality and increasing incidence. Long hospital admissions and long courses of antimicrobial treatment drive healthcare and ecological costs. Current methods for microbiological diagnostics of pleural infections are inadequate. Recent studies using 16S targeted next-generation sequencing as a reference standard find culture to recover only 10%-16% of bacteria present and that 50%-78% of samples containing relevant bacterial DNA remain culture negative. To confirm the diagnosis of pleural infection and define optimal antimicrobial therapy while limiting unnecessary use of broad-spectrum antibiotics, there is a need for rapid and sensitive diagnostic approaches. PCR is a rapid method well suited for clinical laboratories. In this paper we show that a novel syndromic PCR panel can secure the diagnosis of pleural infection and detect all bacteria relevant for choice of antimicrobial treatment with a high sensitivity.
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Affiliation(s)
- Øyvind Kommedal
- Department of Microbiology, Haukeland University Hospital, Bergen, Norway
| | - Tomas Mikal Eagan
- Department of Clinical Science, University of Bergen, Bergen, Norway
- Department of Thoracic Medicine, Haukeland University Hospital, Bergen, Norway
| | - Øystein Fløtten
- Department of Clinical Science, University of Bergen, Bergen, Norway
- Department of Thoracic Medicine, Haukeland University Hospital, Bergen, Norway
| | - Truls Michael Leegaard
- Division of Medicine and Laboratory Sciences, Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
- Department of Microbiology and Infection Control, Akershus University Hospital, Lørenskog, Akershus, Norway
| | - William Siljan
- Department of Pulmonary Medicine, Akershus University Hospital, Lorenskog, Akershus, Norway
| | - Hilde Fardal
- Department of Microbiology, Stavanger University Hospital, Stavanger, Norway
| | - Bjørnar Bø
- Department of Pulmonary Medicine, Stavanger University Hospital, Stavanger, Norway
| | - Fredrik Grøvan
- Department of Medicine, Haraldsplass Deaconess Hospital, Bergen, Norway
| | - Kjersti Wik Larssen
- Department of Medical Microbiology, St. Olavs Hospital, Trondheim University Hospital, Trondheim, Norway
| | - Arne Kildahl-Andersen
- Department of Thoracic Medicine, St. Olavs Hospital, Trondheim University Hospital, Trondheim, Norway
| | - Reidar Hjetland
- Department of Microbiology, Førde Central Hospital, Førde, Norway
| | - Rune Tilseth
- Department of Medicine, Førde Central Hospital, Førde, Norway
| | | | - Marit Tellevik
- Department of Microbiology, Haukeland University Hospital, Bergen, Norway
| | - Ruben Dyrhovden
- Department of Microbiology, Haukeland University Hospital, Bergen, Norway
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Poulsen SH, Søgaard KK, Fuursted K, Nielsen HL. Evaluating the diagnostic accuracy and clinical utility of 16S and 18S rRNA gene targeted next-generation sequencing based on five years of clinical experience. Infect Dis (Lond) 2023; 55:767-775. [PMID: 37535652 DOI: 10.1080/23744235.2023.2241550] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Accepted: 07/21/2023] [Indexed: 08/05/2023] Open
Abstract
BACKGROUND The use of 16S/18S rRNA targeted next-generation sequencing (tNGS) has improved microbial diagnostics, however, the use of tNGS in a routine clinical setting requires further elucidation. We retrospectively evaluated the diagnostic accuracy and clinical utility of 16S/18S tNGS, routinely used in the North Denmark Region between 2017 and 2021. METHODS We retrieved 544 tNGS results from 491 patients hospitalised with suspected infection (e.g. meningitis, pneumonia, intraabdominal abscess, osteomyelitis and joint infection). The tNGS assays was performed using the Illumina MiSeq desktop sequencer, and BION software for annotation. The patients' diagnosis and clinical management was evaluated by medical chart review. We calculated sensitivity and specificity, and determined the diagnostic accuracy of tNGS by defining results as true positive, true negative, false positive, and false negative. RESULTS Overall, tNGS had a sensitivity of 56% and a specificity of 97%. tNGS was more frequently true positive compared to culture (32% vs 18%), and tNGS detected a greater variety of bacteria and fungi, and was more frequently polymicrobial. However, the total diagnostic turnaround time was 16 days, and although 73% of tNGS results were true positive or true negative, only 4.4% of results led to changes in clinical management. CONCLUSIONS As a supplement to culture, tNGS improves identification of pathogenic microorganisms in a broad range of clinical specimens. However, the long turnaround time of tNGS in our setting may have contributed to a limited clinical utility. An improved turnaround time can be the key to improved clinical utility in a future setting.
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Affiliation(s)
| | - Kirstine Kobberøe Søgaard
- Department of Clinical Medicine, Aalborg University, Aalborg, Denmark
- Department of Clinical Microbiology, Aalborg University Hospital, Aalborg, Denmark
| | | | - Hans Linde Nielsen
- Department of Clinical Medicine, Aalborg University, Aalborg, Denmark
- Department of Clinical Microbiology, Aalborg University Hospital, Aalborg, Denmark
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Zhang Z, Wang H, Guo Y, Liu Z, Chang Z. Metagenome Analysis of the Bacterial Characteristics in Invasive Klebsiella Pneumoniae Liver Abscesses. Front Cell Infect Microbiol 2022; 12:812542. [PMID: 35909970 PMCID: PMC9334793 DOI: 10.3389/fcimb.2022.812542] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Accepted: 06/01/2022] [Indexed: 11/17/2022] Open
Abstract
Background Klebsiella pneumoniae liver abscess (KPLA) combined with extrahepatic migratory infection (EMI) is defined as invasive KPLA (IKPLA) and is associated with a poor prognosis. The mechanism of IKPLA formation is yet to be elucidated. In this study, metagenomic sequencing was used to compare the bacterial characteristics between IKPLA and KPLA to explore the underlying mechanism of invasiveness. Methods Clinical details, imaging, and microbial features were retrospectively evaluated by medical record review. Metagenomic sequencing was performed on the pus samples of liver abscesses whose culture results were indicative of monomicrobial Klebsiella pneumoniae (K. pneumoniae). Bacterial diversity and composition in IKPLA and KPLA were comparatively analyzed, and the key pathways and genes that may affect invasiveness were further explored. Results Sixteen patients were included in this study. Five patients with EMI were included in the IKPLA group, and the other eleven patients without EMI were assigned to the KPLA group. There was no statistical difference in the hypermucoviscous phenotype and serotype of K. pneumoniae between the two groups. The bacterial diversity of IKPLA was lower than that of KPLA. The abundant taxa in the IKPLA group were primarily species of unclassified Enterobacteriaceae and K. pneumoniae. The KPLA group had a high abundance of the genera Tetrasphaera and Leuconostoc. Metabolic pathway genes represented most of the enriched genes in IKPLA. Fourteen pathogenic genes with significant differences in abundance were identified between the two groups, including ybtS, fepC, phoQ, acrB, fimK, magA, entC, arnT, iucA, fepG, oqxB, entA, tonB, and entF (p < 0.001). Conclusion The diversity and bacterial composition of IKPLA were significantly different from those of KPLA. Microbiological changes in the abscess, activation of the related metabolic pathways, and the pathogenic gene expression may constitute a novel mechanism that regulates the invasiveness of KPLA.
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Affiliation(s)
- Zhijie Zhang
- Department of Laboratory Medicine, Shengjing Hospital of China Medical University, Shenyang, China
| | - Hairui Wang
- Department of Radiology, Shengjing Hospital of China Medical University, Shenyang, China
| | - Yawen Guo
- Department of Radiology, Shengjing Hospital of China Medical University, Shenyang, China
| | - Zhaoyu Liu
- Department of Radiology, Shengjing Hospital of China Medical University, Shenyang, China
| | - Zhihui Chang
- Department of Radiology, Shengjing Hospital of China Medical University, Shenyang, China
- *Correspondence: Zhihui Chang,
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Skusa C, Skusa R, Wohlfarth M, Warnke P, Podbielski A, Bath K, Groß J, Schafmayer C, Frickmann H, Weber MA, Hahn A, Meinel FG. Imaging and Clinical Parameters for Distinction between Infected and Non-Infected Fluid Collections in CT: Prospective Study Using Extended Microbiological Approach. Diagnostics (Basel) 2022; 12:diagnostics12020493. [PMID: 35204585 PMCID: PMC8870876 DOI: 10.3390/diagnostics12020493] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Revised: 02/05/2022] [Accepted: 02/08/2022] [Indexed: 12/14/2022] Open
Abstract
The aim of this investigation was to evaluate predictive CT imaging features and clinical parameters to distinguish infected from sterile fluid collections. Detection of infectious agents by advanced microbiological analysis was used as the reference standard. From April 2018 to October 2019, all patients undergoing CT-guided drainages were prospectively enrolled, if drainage material volume was at least 5 mL. Univariate analysis revealed attenuation (p = 0.001), entrapped gas (p < 0.001), fat stranding (p < 0.001), wall thickness (p < 0.001) and enhancement (p < 0.001) as imaging biomarkers and procalcitonin (p = 0.003) as clinical predictive parameters for infected fluid collections. On multivariate analysis, attenuation > 10 HU (p = 0.038), presence of entrapped gas (p = 0.027) and wall enhancement (p = 0.028) were independent parameters for distinguishing between infected and non-infected fluids. Gas entrapment had high specificity (93%) but low sensitivity (48%), while wall enhancement had high sensitivity (91%) but low specificity (50%). CT attenuation > 10 HU showed intermediate sensitivity (74%) and specificity (70%). Evaluation of the published proposed scoring systems did not improve diagnostic accuracy over independent predictors in our study. In conclusion, this prospective study confirmed that CT attenuation > 10 HU, entrapped gas and wall enhancement are the key imaging features to distinguish infected from sterile fluid collections on CT.
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Affiliation(s)
- Christopher Skusa
- Institute of Diagnostic and Interventional Radiology, Pediatric Radiology and Neuroradiology, Rostock University Medical Center, 18057 Rostock, Germany; (M.W.); (K.B.); (M.-A.W.); (F.G.M.)
- Correspondence: ; Tel.: +49-381-4949201
| | - Romy Skusa
- Institute of Medical Microbiology, Virology and Hygiene, Rostock University Medical Center, 18057 Rostock, Germany; (R.S.); (P.W.); (A.P.); (H.F.); (A.H.)
| | - Moritz Wohlfarth
- Institute of Diagnostic and Interventional Radiology, Pediatric Radiology and Neuroradiology, Rostock University Medical Center, 18057 Rostock, Germany; (M.W.); (K.B.); (M.-A.W.); (F.G.M.)
| | - Philipp Warnke
- Institute of Medical Microbiology, Virology and Hygiene, Rostock University Medical Center, 18057 Rostock, Germany; (R.S.); (P.W.); (A.P.); (H.F.); (A.H.)
| | - Andreas Podbielski
- Institute of Medical Microbiology, Virology and Hygiene, Rostock University Medical Center, 18057 Rostock, Germany; (R.S.); (P.W.); (A.P.); (H.F.); (A.H.)
| | - Kristina Bath
- Institute of Diagnostic and Interventional Radiology, Pediatric Radiology and Neuroradiology, Rostock University Medical Center, 18057 Rostock, Germany; (M.W.); (K.B.); (M.-A.W.); (F.G.M.)
| | - Justus Groß
- Department of General, Visceral, Vascular, Thoracic and Transplantation Surgery, Rostock University Medical Center, 18057 Rostock, Germany; (J.G.); (C.S.)
| | - Clemens Schafmayer
- Department of General, Visceral, Vascular, Thoracic and Transplantation Surgery, Rostock University Medical Center, 18057 Rostock, Germany; (J.G.); (C.S.)
| | - Hagen Frickmann
- Institute of Medical Microbiology, Virology and Hygiene, Rostock University Medical Center, 18057 Rostock, Germany; (R.S.); (P.W.); (A.P.); (H.F.); (A.H.)
- Department of Microbiology and Hospital Hygiene, Bundeswehr Hospital Hamburg, 20359 Hamburg, Germany
| | - Marc-André Weber
- Institute of Diagnostic and Interventional Radiology, Pediatric Radiology and Neuroradiology, Rostock University Medical Center, 18057 Rostock, Germany; (M.W.); (K.B.); (M.-A.W.); (F.G.M.)
| | - Andreas Hahn
- Institute of Medical Microbiology, Virology and Hygiene, Rostock University Medical Center, 18057 Rostock, Germany; (R.S.); (P.W.); (A.P.); (H.F.); (A.H.)
| | - Felix G. Meinel
- Institute of Diagnostic and Interventional Radiology, Pediatric Radiology and Neuroradiology, Rostock University Medical Center, 18057 Rostock, Germany; (M.W.); (K.B.); (M.-A.W.); (F.G.M.)
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