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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:e0351023. [PMID: 38656204 DOI: 10.1128/spectrum.03510-23] [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: 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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Dyrhovden R, Eagan TM, Kommedal Ø. Pleural infection: Contemporary Microbiology Completing the Picture. Clin Infect Dis 2024:ciae103. [PMID: 38446997 DOI: 10.1093/cid/ciae103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Accepted: 02/22/2024] [Indexed: 03/08/2024] Open
Affiliation(s)
- Ruben Dyrhovden
- Department of Microbiology, Haukeland University Hospital, Bergen, Norway
| | - Tomas Mikal Eagan
- Department of Clinical Science, University of Bergen, Norway
- Department of Thoracic Medicine, Haukeland University Hospital, Bergen, Norway
| | - Øyvind Kommedal
- Department of Microbiology, Haukeland University Hospital, Bergen, Norway
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Dyrhovden R, Eagan TM, Fløtten Ø, Siljan W, Leegaard TM, Bø B, Fardal H, Grøvan F, Kildahl-Andersen A, Larssen KW, Tilseth R, Hjetland R, Løes S, Lindemark F, Tellevik M, Breistein R, Kommedal Ø. Pleural Empyema Caused by Streptococcus intermedius and Fusobacterium nucleatum: A Distinct Entity of Pleural Infections. Clin Infect Dis 2023; 77:1361-1371. [PMID: 37348872 PMCID: PMC10654859 DOI: 10.1093/cid/ciad378] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Accepted: 06/20/2023] [Indexed: 06/24/2023] Open
Abstract
BACKGROUND Many community-acquired pleural infections are caused by facultative and anaerobic bacteria from the human oral microbiota. The epidemiology, clinical characteristics, pathogenesis, and etiology of such infections are little studied. The aim of the present prospective multicenter cohort study was to provide a thorough microbiological and clinical characterization of such oral-type pleural infections and to improve our understanding of the underlying etiology and associated risk factors. METHODS Over a 2-year period, we included 77 patients with community-acquired pleural infection, whereof 63 (82%) represented oral-type pleural infections. Clinical and anamnestic data were systematically collected, and patients were offered a dental assessment by an oral surgeon. Microbial characterizations were done using next-generation sequencing. Obtained bacterial profiles were compared with microbiology data from previous investigations on odontogenic infections, bacteremia after extraction of infected teeth, and community-acquired brain abscesses. RESULTS From the oral-type pleural infections, we made 267 bacterial identifications representing 89 different species. Streptococcus intermedius and/or Fusobacterium nucleatum were identified as a dominant component in all infections. We found a high prevalence of dental infections among patients with oral-type pleural infection and demonstrate substantial similarities between the microbiology of such pleural infections and that of odontogenic infections, odontogenic bacteremia, and community-acquired brain abscesses. CONCLUSIONS Oral-type pleural infection is the most common type of community-acquired pleural infection. Current evidence supports hematogenous seeding of bacteria from a dental focus as the most important underlying etiology. Streptococcus intermedius and Fusobacterium nucleatum most likely represent key pathogens necessary for establishing the infection.
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Affiliation(s)
- Ruben Dyrhovden
- 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
| | - William Siljan
- Department of Pulmonary Medicine, Akershus University Hospital, Lørenskog, Norway
| | - Truls Michael Leegaard
- Division of Medicine and Laboratory Sciences, Faculty of Medicine, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
- Department of Microbiology and Infection Control, Akershus University Hospital, Akershus, Norway
| | - Bjørnar Bø
- Department of Pulmonary Medicine, Stavanger University Hospital, Stavanger, Norway
| | - Hilde Fardal
- Department of Microbiology, Stavanger University Hospital, Stavanger, Norway
| | - Fredrik Grøvan
- Department of Medicine, Haraldsplass Deaconess Hospital, Bergen, Norway
| | - Arne Kildahl-Andersen
- Department of Thoracic Medicine, St Olavs Hospital, Trondheim University Hospital, Trondheim, Norway
| | - Kjersti Wik Larssen
- Department of Medical Microbiology, St Olavs Hospital, Trondheim University Hospital, Trondheim, Norway
| | - Rune Tilseth
- Department of Medicine, Førde Central Hospital, Førde, Norway
| | - Reidar Hjetland
- Department of Microbiology, Førde Central Hospital, Førde, Norway
| | - Sigbjørn Løes
- Department of Maxillofacial Surgery, Haukeland University Hospital, Bergen, Norway
- Faculty of Health Sciences, UiT The Arctic University of Norway, Tromsø, Norway
| | - Frode Lindemark
- Department of Thoracic Medicine, Haukeland University Hospital, Bergen, Norway
| | - Marit Tellevik
- Department of Microbiology, Haukeland University Hospital, Bergen, Norway
| | - Rebecca Breistein
- Department of Microbiology, Haukeland University Hospital, Bergen, Norway
| | - Øyvind Kommedal
- Department of Microbiology, Haukeland University Hospital, Bergen, Norway
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Ertesvåg NU, Sakkestad ST, Zhou F, Hoff I, Kristiansen T, Jonassen TM, Follesø E, Brokstad KA, Dyrhovden R, Mohn KGI. Persistent Fever and Positive PCR 90 Days Post-SARS-CoV-2 Infection in a Rituximab-Treated Patient: A Case of Late Antiviral Treatment. Viruses 2022; 14:v14081757. [PMID: 36016378 PMCID: PMC9414720 DOI: 10.3390/v14081757] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Revised: 08/10/2022] [Accepted: 08/11/2022] [Indexed: 11/16/2022] Open
Abstract
Background: Persistent fever after SARS-CoV-2 infection in rituximab-treated patients has been reported. Due to reduced sensitivity in conventional sampling methods and unspecific symptoms in these patients, distinguishing between low-grade viral replication or hyperinflammation is challenging. Antiviral treatment is recommended as prophylactic or early treatment in the at-risk population; however, no defined treatment approaches for protracted SARS-CoV-2 infection exist. Results: We present a case of 96 days of persistent fever and SARS-CoV-2 infection in a patient receiving B cell depletion therapy for multiple sclerosis. Migratory lung infiltrates and positive PCR tests from serum (day-58 post infection) and lower airways (day-90 post infection) confirmed continuous viral replication. The dominant symptoms were continuous high fever, dyspnea and mild to moderate hypoxemia, which never developed into severe respiratory failure. The patient was hospitalized three times, with transient improvement after late antiviral treatment and full recovery 6 months post-rituximab infusion. Conclusions: A strategy for securing samples from lower airways and serum should be a prioritization to strengthen diagnostic certainty in immunocompromised patients. B-cell-deprived patients could benefit from late treatment with SARS-CoV-2-specific monoclonal antibodies and antivirals. Importantly, increased intervals between immunosuppressive therapy should be considered where feasible.
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Affiliation(s)
- Nina Urke Ertesvåg
- Influenza Centre, Department of Clinical Science, University of Bergen, 5021 Bergen, Norway
- Department of Medicine, Haukeland University Hospital, 5021 Bergen, Norway
- Correspondence:
| | - Sunniva Todnem Sakkestad
- Department of Medicine, Haukeland University Hospital, 5021 Bergen, Norway
- Department of Medical Biochemistry and Pharmacology, Haukeland University Hospital, 5021 Bergen, Norway
| | - Fan Zhou
- Influenza Centre, Department of Clinical Science, University of Bergen, 5021 Bergen, Norway
| | - Ingrid Hoff
- Department of Medicine, Haukeland University Hospital, 5021 Bergen, Norway
| | - Trygve Kristiansen
- Department of Medicine, Haukeland University Hospital, 5021 Bergen, Norway
| | | | - Elisabeth Follesø
- Radiology Department, Haukeland University Hospital, 5021 Bergen, Norway
| | - Karl Albert Brokstad
- Influenza Centre, Department of Clinical Science, University of Bergen, 5021 Bergen, Norway
- Department of Safety, Chemistry and Biomedical Laboratory Sciences, Western Norway University of Applied Sciences, 5063 Bergen, Norway
| | - Ruben Dyrhovden
- Department of Medicine, Haukeland University Hospital, 5021 Bergen, Norway
- Department of Microbiology, Haukeland University Hospital, 5021 Bergen, Norway
| | - Kristin G.-I. Mohn
- Influenza Centre, Department of Clinical Science, University of Bergen, 5021 Bergen, Norway
- Department of Medicine, Haukeland University Hospital, 5021 Bergen, Norway
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Dyrhovden R, Øvrebø KK, Nordahl MV, Nygaard RM, Ulvestad E, Kommedal Ø. Bacteria and fungi in acute cholecystitis. A prospective study comparing next generation sequencing to culture. J Infect 2019; 80:16-23. [PMID: 31586461 DOI: 10.1016/j.jinf.2019.09.015] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [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: 07/31/2019] [Revised: 09/25/2019] [Accepted: 09/27/2019] [Indexed: 12/24/2022]
Abstract
OBJECTIVES Guidelines for antibiotic treatment of acute cholecystitis are based on studies using culture techniques for microbial identification. Microbial culture has well described limitations and more comprehensive data on the microbial spectrum may support adjustments of these recommendations. We used next generation sequencing to conduct a thorough microbiological characterization of bile-samples from patients with moderate and severe acute cholecystitis. METHODS We prospectively included patients with moderate and severe acute cholecystitis, undergoing percutaneous or perioperative drainage of the gall bladder. Bile samples were analyzed using both culture and deep sequencing of bacterial 16S rRNA and rpoB genes and the fungal ITS2-segment. Clinical details were evaluated by medical record review. RESULTS Thirty-six patients with moderate and severe acute cholecystitis were included. Bile from 31 (86%) of these contained bacteria (29) and/or fungi (5) as determined by sequencing. Culture identified only 40 (38%) of the 106 microbes identified by sequencing. In none of the 15 polymicrobial samples did culture detect all present microbes. Frequently identified bacteria often missed by culture included oral streptococci, anaerobic bacteria, enterococci and Enterobacteriaceae other than Klebsiella spp. and Escherichia coli. CONCLUSIONS Culture techniques display decreased sensitivity for the microbial diagnostics of acute cholecystitis leaving possible pathogens undetected.
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Affiliation(s)
- Ruben Dyrhovden
- Department of Microbiology, Haukeland University Hospital, Jonas Lies vei 65, 5021 Bergen, Norway.
| | - Kjell Kåre Øvrebø
- Department of Surgery, Haukeland University Hospital, Bergen, Norway
| | | | - Randi M Nygaard
- Department of Microbiology, Haukeland University Hospital, Jonas Lies vei 65, 5021 Bergen, Norway
| | - Elling Ulvestad
- Department of Microbiology, Haukeland University Hospital, Jonas Lies vei 65, 5021 Bergen, Norway; Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Øyvind Kommedal
- Department of Microbiology, Haukeland University Hospital, Jonas Lies vei 65, 5021 Bergen, Norway
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Dyrhovden R, Nygaard RM, Patel R, Ulvestad E, Kommedal Ø. The bacterial aetiology of pleural empyema. A descriptive and comparative metagenomic study. Clin Microbiol Infect 2018; 25:981-986. [PMID: 30580031 DOI: 10.1016/j.cmi.2018.11.030] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Revised: 11/15/2018] [Accepted: 11/30/2018] [Indexed: 11/19/2022]
Abstract
OBJECTIVES The view of pleural empyema as a complication of bacterial pneumonia is changing because many patients lack evidence of underlying pneumonia. To further our understanding of pathophysiological mechanisms, we conducted in-depth microbiological characterization of empyemas in clinically well-characterized patients and investigated observed microbial parallels between pleural empyemas and brain abscesses. METHODS Culture-positive and/or 16S rRNA gene PCR-positive pleural fluids were analysed using massive parallel sequencing of the 16S rRNA and rpoB genes. Clinical details were evaluated by medical record review. Comparative analysis with brain abscesses was performed using metagenomic data from a national Norwegian study. RESULTS Sixty-four individuals with empyema were included. Thirty-seven had a well-defined microbial aetiology, while 27, all of whom had community-acquired infections, did not. In the latter subset, Fusobacterium nucleatum and/or Streptococcus intermedius was detected in 26 patients, of which 18 had additional facultative and/or anaerobic species in various combinations. For this group, there was 65.5% species overlap with brain abscesses; predisposing factors included dental infection, minor chest trauma, chronic obstructive pulmonary disease, drug abuse, alcoholism and diabetes mellitus. Altogether, massive parallel sequencing yielded 385 bacterial detections, whereas culture detected 38 (10%) and 16S rRNA gene PCR/Sanger-based sequencing detected 87 (23%). CONCLUSIONS A subgroup of pleural empyema appears to be caused by a set of bacteria not normally considered to be involved in pneumonia. Such empyemas appear to have a similar microbial profile to oral/sinus-derived brain abscesses, supporting spread from the oral cavity, potentially haematogenously. We suggest reserving the term 'primary empyema' for these infections.
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Affiliation(s)
- R Dyrhovden
- Department of Microbiology, Haukeland University Hospital, Bergen, Norway.
| | - R M Nygaard
- Department of Microbiology, Haukeland University Hospital, Bergen, Norway
| | - R Patel
- Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester MN, USA; Division of Infectious Diseases, Department of Medicine, Mayo Clinic, Rochester MN, USA
| | - E Ulvestad
- Department of Microbiology, Haukeland University Hospital, Bergen, Norway; Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Ø Kommedal
- Department of Microbiology, Haukeland University Hospital, Bergen, Norway
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