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Kubiak J, Morgan A, Kirmaier A, Arnaout R, Riedel S. Universal PCR for bacteria, mycobacteria, and fungi: a 10-year retrospective review of clinical indications and patient outcomes. J Clin Microbiol 2023; 61:e0095223. [PMID: 38014970 PMCID: PMC10729690 DOI: 10.1128/jcm.00952-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Accepted: 10/12/2023] [Indexed: 11/29/2023] Open
Abstract
IMPORTANCE Our work provides a retrospective analysis of universal PCR orders for bacteria, mycobacteria, and fungi across our institution across a 10-year period. We assessed the positivity rates for this diagnostic tool by test type and specimen type and, critically, studied whether and how the results influenced the outcomes from treatment change, to readmission, to death.
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Affiliation(s)
- Jeffrey Kubiak
- Department of Pathology, Beth Israel Deaconess Medical Center, Boston, Massachusetts, USA
| | - Alexandra Morgan
- Department of Pathology, Beth Israel Deaconess Medical Center, Boston, Massachusetts, USA
| | - Andrea Kirmaier
- Department of Pathology, Beth Israel Deaconess Medical Center, Boston, Massachusetts, USA
| | - Ramy Arnaout
- Department of Pathology, Beth Israel Deaconess Medical Center, Boston, Massachusetts, USA
- Division of Clinical Informatics, Department of Medicine, Beth Israel Deaconess Medical Center, Boston, Massachusetts, USA
| | - Stefan Riedel
- Department of Pathology, Beth Israel Deaconess Medical Center, Boston, Massachusetts, USA
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2
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Elsheikh A, Bhatnagar M, Rahman NM. Diagnosis and management of pleural infection. Breathe (Sheff) 2023; 19:230146. [PMID: 38229682 PMCID: PMC10790177 DOI: 10.1183/20734735.0146-2023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Accepted: 11/07/2023] [Indexed: 01/18/2024] Open
Abstract
Pleural infection remains a medical challenge. Although closed tube drainage revolutionised treatment in the 19th century, pleural infection still poses a significant health burden with increasing incidence. Diagnosis presents challenges due to non-specific clinical presenting features. Imaging techniques such as chest radiographs, thoracic ultrasound and computed tomography scans aid diagnosis. Pleural fluid analysis, the gold standard, involves assessing gross appearance, biochemical markers and microbiology. Novel biomarkers such as suPAR (soluble urokinase plasminogen activator receptor) and PAI-1 (plasminogen activator inhibitor-1) show promise in diagnosis and prognosis, and microbiology demonstrates complex microbial diversity and is associated with outcomes. The management of pleural infection involves antibiotic therapy, chest drain insertion, intrapleural fibrinolytic therapy and surgery. Antibiotic therapy relies on empirical broad-spectrum antibiotics based on local policies, infection setting and resistance patterns. Chest drain insertion is the mainstay of management, and use of intrapleural fibrinolytics facilitates effective drainage. Surgical interventions such as video-assisted thoracoscopic surgery and decortication are considered in cases not responding to medical therapy. Risk stratification tools such as the RAPID (renal, age, purulence, infection source and dietary factors) score may help guide tailored management. The roles of other modalities such as local anaesthetic medical thoracoscopy and intrapleural antibiotics are debated. Ongoing research aims to improve outcomes by matching interventions with risk profile and to better understand the development of disease.
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Affiliation(s)
- Alguili Elsheikh
- Oxford Centre for Respiratory Medicine, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
- Oxford Respiratory Trials Unit, University of Oxford, Oxford, UK
- Both authors contributed equally
| | - Malvika Bhatnagar
- Cardiothoracic Unit, Freeman Hospital, Newcastle upon Tyne, UK
- Both authors contributed equally
| | - Najib M. Rahman
- Oxford Centre for Respiratory Medicine, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
- Oxford Respiratory Trials Unit, University of Oxford, Oxford, UK
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3
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Cao XS, Zheng WQ, Hu ZD. Diagnostic value of soluble biomarkers for parapneumonic pleural effusion. Crit Rev Clin Lab Sci 2023; 60:233-247. [PMID: 36593742 DOI: 10.1080/10408363.2022.2158779] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Parapneumonic pleural effusion (PPE) is a common complication in patients with pneumonia. Timely and accurate diagnosis of PPE is of great value for its management. Measurement of biomarkers in circulating and pleural fluid have the advantages of easy accessibility, short turn-around time, objectiveness and low cost and thus have utility for PPE diagnosis and stratification. To date, many biomarkers have been reported to be of value for the management of PPE. Here, we review the values of pleural fluid and circulating biomarkers for the diagnosis and stratification PPE. The biomarkers discussed are C-reactive protein, procalcitonin, presepsin, soluble triggering receptor expressed on myeloid cells 1, lipopolysaccharide-binding protein, inflammatory markers, serum amyloid A, soluble urokinase plasminogen activator receptor, matrix metalloproteinases, pentraxin-3 and cell-free DNA. We found that none of the available biomarkers has adequate performance for diagnosing and stratifying PPE. Therefore, further work is needed to identify and validate novel biomarkers, and their combinations, for the management of PPE.
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Affiliation(s)
- Xi-Shan Cao
- Department of Laboratory Medicine, The Affiliated Hospital of Inner Mongolia Medical University, Hohhot, China
| | - Wen-Qi Zheng
- Department of Laboratory Medicine, The Affiliated Hospital of Inner Mongolia Medical University, Hohhot, China
| | - Zhi-De Hu
- Department of Laboratory Medicine, The Affiliated Hospital of Inner Mongolia Medical University, Hohhot, China
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Bapat A, Lucey O, Eckersley M, Ciesielczuk H, Ranasinghe S, Lambourne J. Invasive Aggregatibacter infection: shedding light on a rare pathogen in a retrospective cohort analysis. J Med Microbiol 2022; 71. [PMID: 36748613 DOI: 10.1099/jmm.0.001612] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Introduction. Aggregatibacter are Gram-negative, facultatively anaerobic rods or coccobacilli that are infrequently encountered as pathogens causing infection.Hypothesis/Gap Statement. The range of invasive infection that Aggregatibacter cause is poorly described. The pathogenicity of species such as Aggregatibacter segnis is debated.Aim. To identify invasive infection due to Aggregatibacter species in a large healthcare organization and to characterize clinical syndromes, co-morbidities and risk factors.Methodology. All microbiological samples positive for Aggregatibacter species were identified by conventional culture or 16S rRNA PCR between October 2017 and March 2021. Electronic records for all patients with positive samples were reviewed and the infection syndrome classified for patients with invasive disease.Results. Twenty-seven patients with invasive infection were identified, with a statistically significant difference in species-specific patterns of invasive infection (P=0.02) and a statistically significant association with residence in the 30 % most deprived households in the UK by postcode (P<0.01). The three most common co-morbidities were periodontitis or recent dental work (29.6%), cardiovascular disease (25.9%) and diabetes (18.5 %).Conclusion. We describe a novel association of Aggregatibacter segnis with skin and soft tissue infection. The propensity of the Aggregatibacter species to cause invasive infection at different body sites and be associated with deprivation is reported. Aggregatibacter actinomycetemcomitans bacteraemia was associated with infective endocarditis, and Aggregatibacter aphrophilus was implicated in severe appendicitis and noted to cause brain abscess. Areas warranting future research include exploring the risk-factors required for invasive infection and those that may determine the species-specific differences in patterns of invasive disease.
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Affiliation(s)
- Anjaneya Bapat
- Centre for Immunobiology, Blizard Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK.,Division of Infection, Barts Health NHS Trust, London, UK
| | - Olivia Lucey
- Division of Infection, Barts Health NHS Trust, London, UK
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Alnimr A. Pneumococcal empyema: Resistance patterns, fitness cost and serotype distribution. Am J Med Sci 2022; 364:766-771. [PMID: 35902025 DOI: 10.1016/j.amjms.2022.07.011] [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: 11/20/2021] [Revised: 04/20/2022] [Accepted: 07/22/2022] [Indexed: 01/25/2023]
Abstract
BACKGROUND Streptococcus pneumoniae is a recognized etiology of invasive infections including parapneumonic empyema, and its resistance to antibiotics is evolving worldwide, raising concerns of encountering untreatable strains. This study measured the serotype distribution, antimicrobial susceptibility and biological cost incurred by resistance of pneumococci from pleural samples. METHODS The serotype profiles, susceptibility results and growth rates were phenotypically determined for a panel of clinical strains of S. pneumoniae from cases of empyema between 2011 and 2019. RESULTS Of 24 empyema cases, the isolated strains belonged to seven serotypes in the following descending order; 19A, 11A/D, 19F, 3, 7F, 1/6B while two strains remained non-typable. Penicillin susceptibility was shown in <80% of the isolates, while parenteral cephalosporins (cefuroxime and ceftriaxone) demonstrated activity in 83.3 and 95.8% respectively. High resistance frequency was noted for macrolides and sulfonamides, but the strains were uniformly sensitive to respiratory fluroquinolones, vancomycin and linezolid. The macrolide-resistant strain exhibited a high growth rate, suggesting a possible beneficial effect. Phenotypes with mono-resistance to sulfonamides and clindamycin were equally fit as the susceptible counterpart strains. Resistance to multiple antimicrobial agents resulted in a high degree of fitness deficit, while other resistant phenotypes were less fit. CONCLUSIONS The pneumococcal conjugate vaccine PCV13 serotypes still circulate in the community. The data indicate that resistance to certain antimicrobials incurs an apparent fitness cost in pneumococci which may limit the dissemination of such strains while low fitness cost, seen in case of resistance to macrolides, may contribute to the spread of resistant clones.
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Affiliation(s)
- Amani Alnimr
- Department of Microbiology, College of Medicine, King Fahad University Hospital, Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia.
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Harris KA, Brown JR. Diagnostic yield of broad-range 16s rRNA gene PCR varies by sample type and is improved by the addition of qPCR panels targeting the most common causative organisms. J Med Microbiol 2022; 71. [PMID: 36748452 DOI: 10.1099/jmm.0.001633] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Introduction. Molecular techniques are used in the clinical microbiology laboratory to support culture-based diagnosis of infection and are particularly useful for detecting difficult to culture bacteria or following empirical antimicrobial treatment.Hypothesis/Gap Statement. Broad-range 16S rRNA PCR is a valuable tool that detects a wide range of bacterial species. Diagnostic yield is low for some sample types but can be improved with the addition of qPCR panels targeting common bacterial pathogens.Aim. To evaluate the performance of a broad-range 16S rRNA gene PCR and the additional diagnostic yield of targeted qPCR applied to specimens according to a local testing algorithm.Methodology. In total, 6130 primary clinical samples were collected as part of standard clinical practice from patients with suspected infection during a 17 month period. Overall, 5497 samples were tested by broad-range 16S rRNA gene PCR and a panel of targeted real-time qPCR assays were performed on selected samples according to a local testing algorithm. An additional 633 samples were tested by real-time qPCR only. The 16S rRNA gene PCR was performed using two assays targeting different regions of the 16S rRNA gene. Laboratory developed qPCR assays for seven common bacterial pathogens were also performed. Data was extracted retrospectively from Epic Beaker Laboratory Information Management System (LIMS).Results. Broad-range 16S rRNA gene PCR improves diagnostic yield in culture-negative samples and detects a large range of bacterial species. Streptococcus spp., Staphylococcus spp. and the Enterobacteriaceae family are detected the most frequently in samples with a single causative organism, but mixed samples frequently contained anaerobic species. The highest diagnostic yield was obtained from abscess, pus and empyema samples; 44.9 % were positive by 16S and 61 % were positive by the combined 16S and targeted qPCR testing algorithm. Samples with a particularly low diagnostic yield were blood, with 3.3 % of samples positive by 16S and CSF with 4.8 % of samples positive by 16S. The increased diagnostic yield of adding targeted qPCR is largest (~threefold) in these two sample types.Conclusion. Broad-range PCR is a powerful technique that can detect a very large range of bacterial pathogens but has limited diagnostic sensitivity. The data in this report supports a testing strategy that combines broad-range and targeted bacterial PCR assays for maximizing diagnosis of infection in culture-negative specimens. This is particularly justified for blood and CSF samples. Alternative approaches, such as metagenomic sequencing, are needed to provide the breadth of broad-range PCR and the sensitivity of targeted qPCR panels.
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Affiliation(s)
- Kathryn A Harris
- Microbiology, Virology and Infection Prevention & Control, Great Ormond Street Hospital NHS Foundation Trust, Great Ormond Street, London, WC1N 3JH, UK.,Queen Mary University of London, Mile End Road, London, E1 4NS, UK
| | - Julianne R Brown
- Microbiology, Virology and Infection Prevention & Control, Great Ormond Street Hospital NHS Foundation Trust, Great Ormond Street, London, WC1N 3JH, UK
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Cheng YF, Cheng CY, Huang CL, Hung WH, Wang BY. Pleural Peels Tissue Culture plus Pleural Fluid Culture Help to Improve Culture Rate for Empyema. J Clin Med 2022; 11:jcm11071882. [PMID: 35407489 PMCID: PMC8999404 DOI: 10.3390/jcm11071882] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2022] [Revised: 03/22/2022] [Accepted: 03/25/2022] [Indexed: 11/25/2022] Open
Abstract
Background: Empyema is known as a serious infection, and outcomes of empyema cases remain poor. Pleural fluid culture and blood culture have been reported to give unsatisfactory results. We introduce a novel pleural peels tissue culture during surgery and aim to improve the culture results of empyema. Methods: This was a retrospective study and was obtained from our institute. Patients with stage II or III empyema undergoing video-assisted thoracic surgery decortication from January 2019 to June 2021 were included in the study. Results: There were 239 patients that received a pleural peels tissue culture, a pleural fluid culture, and a blood culture concurrently during the perioperative period. Of these, 153 patients had at least one positive culture and 86 patients showed triple negative culture results. The positive culture rates were 46.9% for pleural peels tissue cultures, 46.0% for pleural fluid cultures, and 10% for blood cultures. The combination of pleural peels tissue culture and pleural fluid culture increased the positive rate to 62.7%. Streptococcus species and Staphylococcus species were the most common pathogens. Conclusion: The combination of pleural peels tissue culture and pleural fluid culture is an effective method to improve the positive culture rate in empyema.
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Affiliation(s)
- Ya-Fu Cheng
- Division of Thoracic Surgery, Department of Surgery, Changhua Christian Hospital, Changhua 500, Taiwan; (Y.-F.C.); (C.-Y.C.); (C.-L.H.); (W.-H.H.)
| | - Ching-Yuan Cheng
- Division of Thoracic Surgery, Department of Surgery, Changhua Christian Hospital, Changhua 500, Taiwan; (Y.-F.C.); (C.-Y.C.); (C.-L.H.); (W.-H.H.)
| | - Chang-Lun Huang
- Division of Thoracic Surgery, Department of Surgery, Changhua Christian Hospital, Changhua 500, Taiwan; (Y.-F.C.); (C.-Y.C.); (C.-L.H.); (W.-H.H.)
| | - Wei-Heng Hung
- Division of Thoracic Surgery, Department of Surgery, Changhua Christian Hospital, Changhua 500, Taiwan; (Y.-F.C.); (C.-Y.C.); (C.-L.H.); (W.-H.H.)
| | - Bing-Yen Wang
- Division of Thoracic Surgery, Department of Surgery, Changhua Christian Hospital, Changhua 500, Taiwan; (Y.-F.C.); (C.-Y.C.); (C.-L.H.); (W.-H.H.)
- School of Medicine, Chung Shan Medical University, Taichung 201, Taiwan
- School of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan
- Institute of Genomics and Bioinformatics, National Chung Hsing University, Taichung 402, Taiwan
- Department of Post-Baccalaureate Medicine, College of Medicine, National Chung Hsing University, Taichung 402, Taiwan
- Center for General Education, Ming Dao University, Changhua 523, Taiwan
- Correspondence: ; Tel.: +886-(2)-7238595; Fax: +886-(2)-7228289
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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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