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Burban A, Słupik D, Reda A, Szczerba E, Grabowski M, Kołodzińska A. Novel Diagnostic Methods for Infective Endocarditis. Int J Mol Sci 2024; 25:1245. [PMID: 38279244 PMCID: PMC10816594 DOI: 10.3390/ijms25021245] [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: 12/15/2023] [Revised: 01/14/2024] [Accepted: 01/15/2024] [Indexed: 01/28/2024] Open
Abstract
Infective endocarditis (IE) remains a dangerous disease and continues to have a high mortality rate. Unfortunately, despite continuous improvements in diagnostic methods, in many cases, blood cultures remain negative, and the pathogen causing endocarditis is unknown. This makes targeted therapy and the selection of appropriate antibiotics impossible. Therefore, we present what methods can be used to identify the pathogen in infective endocarditis. These are mainly molecular methods, including PCR and MGS, as well as imaging methods using radiotracers, which offer more possibilities for diagnosing IE. However, they are still not widely used in the diagnosis of IE. The article summarizes in which cases we should choose them and what we are most hopeful about in further research into the diagnosis of IE. In addition, registered clinical trials that are currently underway for the diagnosis of IE are also presented.
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Affiliation(s)
- Anna Burban
- 1st Chair and Department of Cardiology, Medical University of Warsaw, 02-097 Warsaw, Poland
- Doctoral School, Medical University of Warsaw, 02-091 Warsaw, Poland
| | - Dorota Słupik
- 1st Chair and Department of Cardiology, Medical University of Warsaw, 02-097 Warsaw, Poland
| | - Aleksandra Reda
- 1st Chair and Department of Cardiology, Medical University of Warsaw, 02-097 Warsaw, Poland
| | - Ewa Szczerba
- 1st Chair and Department of Cardiology, Medical University of Warsaw, 02-097 Warsaw, Poland
| | - Marcin Grabowski
- 1st Chair and Department of Cardiology, Medical University of Warsaw, 02-097 Warsaw, Poland
| | - Agnieszka Kołodzińska
- 1st Chair and Department of Cardiology, Medical University of Warsaw, 02-097 Warsaw, Poland
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Johansson G, Sunnerhagen T, Ragnarsson S, Rasmussen M. Clinical Significance of a 16S-rDNA Analysis of Heart Valves in Patients with Infective Endocarditis: a Retrospective Study. Microbiol Spectr 2023; 11:e0113623. [PMID: 37195215 PMCID: PMC10269717 DOI: 10.1128/spectrum.01136-23] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Accepted: 04/28/2023] [Indexed: 05/18/2023] Open
Abstract
A substantial proportion of patients with infective endocarditis (IE) are subjected to heart valve surgery. Microbiological findings on valves are important both for diagnostics and for tailored antibiotic therapy, post-operatively. The aims of this study were to describe microbiological findings on surgically removed valves and to examine the diagnostic benefits of 16S-rDNA PCR and sequencing (16S-analysis). Adult patients who were subjected to heart valve surgery for IE between 2012 and 2021 at Skåne University Hospital, Lund, where a 16S-analysis had been performed on the valve, constituted the study population. Data were gathered from medical records, and the results from blood cultures, valve cultures, and 16S-analyses of valves were compared. A diagnostic benefit was defined as providing an agent in blood culture negative endocarditis, providing a new agent in episodes with positive blood cultures, or confirming one of the findings in episodes with a discrepancy between blood and valve cultures. 279 episodes in 272 patients were included in the final analysis. Blood cultures were positive in 259 episodes (94%), valve cultures in 60 episodes (22%), and 16S-analyses in 227 episodes (81%). Concordance between the blood cultures and the 16S-analysis was found in 214 episodes (77%). The 16S-analyses provided a diagnostic benefit in 25 (9.0%) of the episodes. In blood culture negative endocarditis, the 16S-analyses had a diagnostic benefit in 15 (75%) of the episodes. A 16S-analysis should be routinely performed on surgically removed valves in blood culture negative endocarditis. In patients with positive blood cultures, 16S-analysis may also be considered, as a diagnostic benefit was provided in some patients. IMPORTANCE This work demonstrates that it can be of importance to perform both cultures and analysis using 16S-rDNA PCR and sequencing of valves excised from patients undergoing surgery for infective endocarditis. 16S-analysis may help both to establish a microbiological etiology in cases of blood culture negative endocarditis and to provide help in situations where there are discrepancies between valve and blood cultures. In addition, our results show a high degree of concordance between blood cultures and 16S-analyses, indicating that the latter has a high sensitivity and specificity for the etiological diagnosis of endocarditis in patients who were subjected to heart valve surgery.
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Affiliation(s)
- Gustav Johansson
- Division of Infection Medicine, Department of Clinical Sciences Lund, Lund University, Lund, Sweden
| | - Torgny Sunnerhagen
- Division of Infection Medicine, Department of Clinical Sciences Lund, Lund University, Lund, Sweden
- Department of Clinical Microbiology, Infection Control and Prevention, Office for Medial Services, Region Skåne, Lund, Sweden
- Department of Clinical Microbiology, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
| | - Sigurdur Ragnarsson
- Division of Cardiothoracic Surgery, Department of Clinical Sciences Lund, Lund University, Lund, Sweden
- Department of Cardiothoracic and Vascular Surgery, Skåne University Hospital, Lund, Sweden
| | - Magnus Rasmussen
- Division of Infection Medicine, Department of Clinical Sciences Lund, Lund University, Lund, Sweden
- Department of Infectious Diseases, Skåne University Hospital, Lund, Sweden
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3
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Berge A, Carlsén C, Petropoulos A, Gadler F, Rasmussen M. Staphylococcus aureus bacteraemia, cardiac implantable electronic device, and the risk of endocarditis: a retrospective population-based cohort study. Eur J Clin Microbiol Infect Dis 2023; 42:583-591. [PMID: 36920628 PMCID: PMC10105663 DOI: 10.1007/s10096-023-04585-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Accepted: 03/02/2023] [Indexed: 03/16/2023]
Abstract
Patients with cardiac implantable electronic device (CIED) and Staphylococcus aureus bacteraemia (SAB) are at risk of having infective endocarditis (IE). The objectives were to describe a Swedish population-based cohort of patients with CIED and SAB, to identify risk factors, and to construct a predictive score for IE. Patients over 18 years old in the Stockholm Region identified to have SAB in the Karolinska Laboratory database from January 2015 through December 2019 were matched to the Swedish Pacemaker and Implantable Cardioverter-Defibrillator ICD Registry to identify the study cohort. Data were collected from study of medical records. A cohort of 274 patients with CIED and SAB was identified and in 38 episodes (14%) IE were diagnosed, 19 with changes on the CIED, and 35 with changes on the left side of the heart. The risk factors predisposition for IE, community acquisition, embolization, time to positivity of blood cultures, and growth in blood culture after start of therapy in blood cultures were independently associated to IE. A score to identify patients with IE was constructed, the CTEPP score, and the chosen cut-off generated a sensitivity of 97%, specificity of 25%, and a negative predictive value of 98%. The score was externally validated in a population-based cohort of patients with CIED and SAB from another Swedish region. We found that 14% of patients with CIED and SAB had definite IE diagnosed. The CTEPP-score can be used to predict the risk of IE and, when negative, the risk is negligible.
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Affiliation(s)
- Andreas Berge
- Unit of Infectious Diseases, Department of Medicine, SolnaKarolinska Institutet, 17176, Stockholm, Sweden. .,Department of Infectious Diseases, Karolinska University Hospital, Stockholm, Sweden.
| | - Casper Carlsén
- Unit of Infectious Diseases, Department of Medicine, SolnaKarolinska Institutet, 17176, Stockholm, Sweden
| | - Alexandros Petropoulos
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden.,Department of Clinical Microbiology, Karolinska University Hospital, Stockholm, Sweden
| | - Fredrik Gadler
- Unit of Cardiology, Department of Medicine, SolnaKarolinska Institutet, Stockholm, Sweden.,Department of Cardiology, Karolinska University Hospital, Stockholm, Sweden
| | - Magnus Rasmussen
- Department of Clinical Sciences Lund, Division of Infection Medicine, Lund University, Lund, Sweden.,Division for Infectious Diseases, Skåne University Hospital, Lund, Sweden
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El-Ashry AH, Saad K, Obiedallah AA, Elhoufey A, Dailah HG, Hussein MSA. Molecular and Serological Diagnostic Approach to Define the Microbiological Origin of Blood Culture-Negative Infective Endocarditis. Pathogens 2022; 11:pathogens11111220. [PMID: 36364971 PMCID: PMC9696817 DOI: 10.3390/pathogens11111220] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Revised: 10/13/2022] [Accepted: 10/20/2022] [Indexed: 11/22/2022] Open
Abstract
Blood culture-negative infective endocarditis (BCNIE) poses a significant challenge in determining the best antibiotic regimen for this life-threatening infection, which should be treated with as specific and effective a regimen as feasible. The goal of this study was to determine the prevalence of BCNIE among definite infective endocarditis (IE) cases and to study the impact of a molecular and serological diagnostic approach in defining the microbiological origin of BCNIE. This study included 94 definite IE cases. Serum and blood samples from BCNIE patients were tested using serological, broad-range PCR, and sequencing assays. Valve tissue sections obtained from 42 operated patients were subjected to culture and molecular studies. BCNIE accounted for 63 (67%) of the cases. Of these cases, blood PCR followed by sequencing could diagnose 11 cases. Zoonotic infective endocarditis was detected in 7 (11%) patients by serology and PCR (four Brucella, two Bartonella, and one Coxiella). Sequencing of valve PCR bands revealed 30 positive cases. Therefore, the percentage of BCNIE with unidentified etiology was reduced from 67% to 27.7% through a combination of all diagnostic procedures utilized in our study. Blood and valve PCR and sequencing assays are valuable techniques for the etiological diagnosis of BCNIE, especially in cases with previous antibiotic therapy. However, these tests should be used as part of a larger diagnostic strategy that includes serology, microscopy, and valve culture. The use of an automated blood culture system, and proper blood culture collection before ordering antibiotics, will guide IE etiological diagnosis.
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Affiliation(s)
- Amira H. El-Ashry
- Medical Microbiology & Immunology Department, Faculty of Medicine, Mansoura University, Mansoura 35516, Egypt
| | - Khaled Saad
- Department of Pediatrics, Faculty of Medicine, Assiut University, Assiut 71111, Egypt
- Correspondence: ; Tel.: +20-882368373
| | - Ahmed A. Obiedallah
- Department of Internal Medicine, Faculty of Medicine, Assiut University, Assiut 71111, Egypt
| | - Amira Elhoufey
- Department of Community Health Nursing, Faculty of Nursing, Assiut University, Assiut 71111, Egypt
- Department of Community Health Nursing, Alddrab University College, Jazan University, Jazan 45142, Saudi Arabia
| | - Hamad Ghaleb Dailah
- Research and Scientific Studies Unit, College of Nursing, Jazan University, Jazan 45142, Saudi Arabia
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Mularoni A, Mikulska M, Barbera F, Graziano E, Medaglia AA, Di Carlo D, Monaco F, Bellavia D, Cascio A, Raffa G, Sciacca S, Luca A, Pilato M, Conaldi PG. Molecular Analysis With 16S rRNA PCR/Sanger Sequencing and Molecular Antibiogram Performed on DNA Extracted From Valve Improve Diagnosis and Targeted Therapy of Infective Endocarditis: A Prospective Study. Clin Infect Dis 2022; 76:e1484-e1491. [PMID: 35686318 PMCID: PMC9907470 DOI: 10.1093/cid/ciac452] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Revised: 05/25/2022] [Accepted: 06/01/2022] [Indexed: 11/12/2022] Open
Abstract
BACKGROUND Molecular analysis (MA) on heart valve (HV) improves the microbiologic diagnosis of infectious endocarditis (IE). The main drawback of MA is the lack of antimicrobial susceptibility information. METHODS We conducted a prospective cohort observational study of consecutive adult patients from April 2012 to May 2021 who underwent valve surgery at our hospital. The performance of MA, blood cultures (BC) and valve cultures (VC), and the diagnostic and therapeutic impact of MA were evaluated. Molecular antibiogram results were compared to culture-based antimicrobial susceptibility testing (AST). RESULTS A total of 137 patients with definite IE and 52 patients with no IE were enrolled in the study. Among IE cases BC, VC, and MA were positive in 75 (55%), 30 (22%), and 120 (88%) of IE cases, respectively. Among 62 cases of BC-negative IE (BCNE), 57 achieved diagnosis with MA. MA led to a change of antimicrobial therapy in 92% of BCNE. MA was negative in 100% of patients with no IE. Molecular antibiogram performed on 17 valve specimens that resulted positive for pathogens potential carrier of genes encoding for multidrug resistant mechanisms showed 100% concordance with AST. CONCLUSIONS MA showed a high specificity and sensitivity in etiological diagnosis of IE. Molecular antibiogram could overcome the major limitation of MA that is the lack of susceptibility testing. We advocate for the inclusion of MA among diagnostic criteria for IE and for a more extensive use of molecular antibiogram when the culture result is negative, and MA is the only positive test.
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Affiliation(s)
- Alessandra Mularoni
- Correspondence: A. Mularoni, IRCCS-ISMETT (Mediterranean Institute for Transplantation and Advanced Specialized Therapies), Via Ernesto Tricomi 5, 90100, Palermo, Italy ()
| | - Malgorzata Mikulska
- Division of Infectious Diseases, University of Genoa (DISSAL), Genova, Italy,IRCCS Ospedale Policlinico San Martino, Genova, Italy
| | - Floriana Barbera
- Pathology Unit, IRCCS-ISMETT (Mediterranean Institute for Transplantation and Advanced Specialized Therapies), Palermo, Italy
| | - Elena Graziano
- Infectious Diseases Unit, IRCCS-ISMETT (Mediterranean Institute for Transplantation and Advanced Specialized Therapies), Palermo, Italy,Infectious and Tropical Diseases Unit, Department of Medicine and Surgery, University of Insubria, ASST-Sette Laghi, Varese, Italy
| | | | - Daniele Di Carlo
- Pathology Unit, IRCCS-ISMETT (Mediterranean Institute for Transplantation and Advanced Specialized Therapies), Palermo, Italy
| | - Francesco Monaco
- Pathology Unit, IRCCS-ISMETT (Mediterranean Institute for Transplantation and Advanced Specialized Therapies), Palermo, Italy
| | - Diego Bellavia
- Department for the Treatment and Study of Cardiothoracic Diseases and Cardiothoracic Transplantation, IRCCS-ISMETT (Mediterranean Institute for Transplantation and Advanced Specialized Therapies), Palermo, Italy
| | - Antonio Cascio
- Department of Health Promotion, Mother and Child Care, Internal Medicine and Medical Specialties, Infectious Diseases Unit, University of Palermo, Palermo, Italy
| | - Giuseppe Raffa
- Department for the Treatment and Study of Cardiothoracic Diseases and Cardiothoracic Transplantation, IRCCS-ISMETT (Mediterranean Institute for Transplantation and Advanced Specialized Therapies), Palermo, Italy
| | - Sergio Sciacca
- Department for the Treatment and Study of Cardiothoracic Diseases and Cardiothoracic Transplantation, IRCCS-ISMETT (Mediterranean Institute for Transplantation and Advanced Specialized Therapies), Palermo, Italy
| | - Angelo Luca
- Department of Diagnostic and Therapeutic Services, IRCCS-ISMETT (Mediterranean Institute for Transplantation and Advanced Specialized Therapies), Palermo, Italy
| | - Michele Pilato
- Department for the Treatment and Study of Cardiothoracic Diseases and Cardiothoracic Transplantation, IRCCS-ISMETT (Mediterranean Institute for Transplantation and Advanced Specialized Therapies), Palermo, Italy
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Impact of Valve Culture Positivity on Prognosis in Patients with Infective Endocarditis Who Underwent Valve Surgery. Infect Dis Ther 2022; 11:1253-1265. [PMID: 35489001 PMCID: PMC9124244 DOI: 10.1007/s40121-022-00642-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Accepted: 04/11/2022] [Indexed: 12/13/2022] Open
Abstract
Introduction Infective endocarditis (IE) is a severe and fatal infection with high in-hospital and overall mortality rates of approximately up to 30%. Valve culture positivity was associated with in-hospital mortality and postoperative complications; however, few studies have analyzed the relationship between valve cultures and overall mortality over a long observation period. This study aimed to compare the association of valve culture positivity with overall mortality in patients with IE who underwent valve surgery. Methods A total of 416 IE patients admitted to a tertiary hospital in South Korea from November 2005 to August 2017 were retrospectively reviewed. A total of 202 IE patients who underwent valve surgery and valve culture were enrolled. The primary endpoint was long-term overall mortality. Kaplan–Meier curve and Cox proportional hazards model were used for survival analysis. Results The median follow-up duration was 63 (interquartile range, 38–104) months. Valve cultures were positive in 22 (10.9%) patients. The overall mortality rate was 15.8% (32/202) and was significantly higher in valve culture-positive patients (36.4%, p = 0.011). Positive valve culture [hazard ratio (HR) 3.921, p = 0.002], Charlson Comorbidity Index (HR 1.181, p = 0.004), Coagulase-negative staphylococci (HR 4.233, p = 0.001), new-onset central nervous system complications (HR 3.689, p < 0.001), and new-onset heart failure (HR 4.331, p = 0.001) were significant risk factors for overall mortality. Conclusions Valve culture positivity is a significant risk factor for long-term overall mortality in IE patients who underwent valve surgery. The importance of valve culture positivity needs to be re-evaluated, as the valve culture positivity rate increases with increasing early surgical intervention.
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Ren Z, Li W, Liu Q, Dong Y, Huang Y. Profiling of the Conjunctival Bacterial Microbiota Reveals the Feasibility of Utilizing a Microbiome-Based Machine Learning Model to Differentially Diagnose Microbial Keratitis and the Core Components of the Conjunctival Bacterial Interaction Network. Front Cell Infect Microbiol 2022; 12:860370. [PMID: 35558101 PMCID: PMC9086711 DOI: 10.3389/fcimb.2022.860370] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2022] [Accepted: 03/28/2022] [Indexed: 12/29/2022] Open
Abstract
Both healthy and diseased human ocular surfaces possess their own microbiota. If allowed, opportunistic pathogens within the ocular microbiota may cause microbial keratitis (MK). However, the nonpathogenic component of the ocular microbiota has been proven to undermine the performance of culture, the gold standard of the etiological diagnosis for MK. As the conjunctival bacterial microbiota generates unique alterations with various oculopathies, this study aimed to evaluate the feasibility of distinguishing MK using machine learning based on the characteristics of the conjunctival bacterial microbiome associated with various types of MK. This study also aimed to reveal which bacterial genera constitute the core of the interaction network of the conjunctival bacterial microbiome. Conjunctival swabs collected from the diseased eyes of MK patients and the randomly chosen normal eyes of healthy volunteers were subjected for high-throughput 16S rDNA sequencing. The relative content of each bacterial genus and the composition of bacterial gene functions in every sample were used to establish identification models with the random forest algorithm. Tenfold cross validation was adopted. Accuracy was 96.25% using the bacterial microbiota structure and 93.75% using the bacterial gene functional composition. Therefore, machine learning with the conjunctival bacterial microbiome characteristics might be used for differentiation of MKs as a noninvasive supplementary approach. In addition, this study found that Actinobacteria, Lactobacillus, Clostridium, Helicobacter, and Sphingomonas constitute the core of the interaction network of the conjunctival bacterial microbiome.
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Affiliation(s)
- Zhichao Ren
- Qingdao University Medical College, Qingdao, China
- Qingdao Eye Hospital of Shandong First Medical University, Qingdao, China
- State Key Laboratory Cultivation Base, Shandong Provincial Key Laboratory of Ophthalmology, Eye Institute of Shandong First Medical University, Qingdao, China
| | - Wenfeng Li
- Department of Medical Oncology, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Qing Liu
- Qingdao Eye Hospital of Shandong First Medical University, Qingdao, China
- State Key Laboratory Cultivation Base, Shandong Provincial Key Laboratory of Ophthalmology, Eye Institute of Shandong First Medical University, Qingdao, China
| | - Yanling Dong
- Qingdao Eye Hospital of Shandong First Medical University, Qingdao, China
- State Key Laboratory Cultivation Base, Shandong Provincial Key Laboratory of Ophthalmology, Eye Institute of Shandong First Medical University, Qingdao, China
| | - Yusen Huang
- Qingdao Eye Hospital of Shandong First Medical University, Qingdao, China
- State Key Laboratory Cultivation Base, Shandong Provincial Key Laboratory of Ophthalmology, Eye Institute of Shandong First Medical University, Qingdao, China
- *Correspondence: Yusen Huang,
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Yu YY, Liang L, Xiao HB. Comparative study on fecal flora and blood biochemical indexes in normal and diarrhea British Shorthair cats. Arch Microbiol 2022; 204:257. [PMID: 35416536 DOI: 10.1007/s00203-022-02805-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2021] [Revised: 02/10/2022] [Accepted: 02/13/2022] [Indexed: 11/28/2022]
Abstract
In recent years, 16S ribosomal DNA (16S rDNA) sequencing has been widely developed. In the present study, we investigated the changes of fecal flora analyzed by sequencing of 16S rDNA and the alteration of blood biochemical indexes in cats during diarrhea. Seven normal fecal samples and seven fecal samples of British Shorthair cats with bacterial diarrhea about 6 months old were collected. The 16S rDNA V3 region of the bacteria was amplified for high-throughput sequencing. Finally, species analysis at various levels was performed. At the same time, samples of blood were taken to examine the changes of biochemical indexes in cats with diarrhea. The abundance and diversity of microflora in the healthy group were greater than those in the diarrhea group. The normal floras in the feces of healthy cats were Firmicutes, Actinobacteria, Bacteroidetes and Proteobacteria. The content of Proteobacteria and Firmicutes varied greatly in diarrheal cats. In addition, the number of white blood cells, lymphocytes, neutrophils, and globulin were increased in cats with diarrhea, whereas albumin level was decreased in diarrheal cats. In conclusion, the present study suggests 16SrDNA technology showed that the intestinal Proteus was abundant, and the content of Firmicutes was scarce in cats with diarrhea. Escherichia-Shigella was the main pathogens in this sample. Rapid blood biochemical tests may help clinicians to assess the severity and prognosis of cats with diarrhea.
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Affiliation(s)
- Yuan-Yuan Yu
- College of Veterinary Medicine, Hunan Agricultural University, Furong District, Changsha, 410128, China
| | - Lin Liang
- College of Veterinary Medicine, Hunan Agricultural University, Furong District, Changsha, 410128, China
| | - Hong-Bo Xiao
- College of Veterinary Medicine, Hunan Agricultural University, Furong District, Changsha, 410128, China.
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Rodríguez-García R, Rodríguez-Esteban MÁ, Fernández-Suárez J, Morilla A, García-Carús E, Telenti M, Morales C, Albaiceta GM, Fernández J. Evaluation of 16S rDNA Heart Tissue PCR as a Complement to Blood Cultures for the Routine Etiological Diagnosis of Infective Endocarditis. Diagnostics (Basel) 2021; 11:1372. [PMID: 34441306 PMCID: PMC8394467 DOI: 10.3390/diagnostics11081372] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 07/18/2021] [Accepted: 07/27/2021] [Indexed: 12/12/2022] Open
Abstract
Identification of the causative pathogen is required to optimize the effective therapy in infective endocarditis (IE). The aim of this study was to assess a 16S rDNA PCR to identify bacteria from heart valve tissues and to evaluate its usefulness as a complement to blood and removed valves cultures. A total of 266 patients diagnosed with IE from January 2015 to December 2019 were evaluated. Results between 16S rDNA PCR from heart valve tissues were compared with microbiological cultures. Blood cultures were positive in 83.5% of patients diagnosed with IE, while 39.6% and 71.8% of the evaluated heart valve samples were positive by culture and 16S rDNA PCR, respectively. For 32 (12%) patients, 16S rDNA tissue PCR provided valuable information supporting the results of blood cultures in the case of bacteria characteristic from the skin microbiota. Additionally, a microorganism was identified by using 16S rDNA PCR in 36% of blood culture-negative cases. The present study reveals that molecular diagnosis using 16S rDNA tissue PCR provides complementary information for the diagnosis of IE, and it should be recommended in surgical endocarditis, especially when blood cultures are negative.
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Affiliation(s)
- Raquel Rodríguez-García
- Unidad de Cuidados Intensivos Cardiológicos, Hospital Universitario Central de Asturias, 33011 Oviedo, Spain; (R.R.-G.); (M.Á.R.-E.); (G.M.A.)
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), 33011 Oviedo, Spain
- CIBER-Enfermedades Respiratorias, Instituto de Salud Carlos III, 28220 Madrid, Spain
| | - María Ángeles Rodríguez-Esteban
- Unidad de Cuidados Intensivos Cardiológicos, Hospital Universitario Central de Asturias, 33011 Oviedo, Spain; (R.R.-G.); (M.Á.R.-E.); (G.M.A.)
| | - Jonathan Fernández-Suárez
- Servicio de Microbiología Clínica, Hospital Universitario Central de Asturias, 33011 Oviedo, Spain; (J.F.-S.); (A.M.); (M.T.)
| | - Ana Morilla
- Servicio de Microbiología Clínica, Hospital Universitario Central de Asturias, 33011 Oviedo, Spain; (J.F.-S.); (A.M.); (M.T.)
| | - Enrique García-Carús
- Servicio de Medicina Interna, Hospital Universitario Central de Asturias, 33011 Oviedo, Spain;
| | - Mauricio Telenti
- Servicio de Microbiología Clínica, Hospital Universitario Central de Asturias, 33011 Oviedo, Spain; (J.F.-S.); (A.M.); (M.T.)
| | - Carlos Morales
- Servicio de Cirugía Cardiaca, Hospital Universitario Central de Asturias, 33011 Oviedo, Spain;
| | - Guillermo Muñiz Albaiceta
- Unidad de Cuidados Intensivos Cardiológicos, Hospital Universitario Central de Asturias, 33011 Oviedo, Spain; (R.R.-G.); (M.Á.R.-E.); (G.M.A.)
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), 33011 Oviedo, Spain
- CIBER-Enfermedades Respiratorias, Instituto de Salud Carlos III, 28220 Madrid, Spain
- Departamento de Biología Funcional, Instituto Universitario de Oncología del Principado de Asturias, Universidad de Oviedo, 33003 Oviedo, Spain
| | - Javier Fernández
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), 33011 Oviedo, Spain
- Servicio de Microbiología Clínica, Hospital Universitario Central de Asturias, 33011 Oviedo, Spain; (J.F.-S.); (A.M.); (M.T.)
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10
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Benedetto U, Spadaccio C, Gentile F, Moon MR, Nappi F. A narrative review of early surgery versus conventional treatment for infective endocarditis: do we have an answer? ANNALS OF TRANSLATIONAL MEDICINE 2020; 8:1626. [PMID: 33437825 PMCID: PMC7791236 DOI: 10.21037/atm-20-3880] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The most appropriate strategy and timing for surgery in infective endocarditis (IE) remains an argument of debate. Despite some authors promote the adoption of an early surgical approach (within 48 hours) to limit mortality and complications, no robust randomized trials are available on this argument and the evidence on this subject remain at the "expert opinion" level. Additionally, the different messages promulgated by the American and European guidelines contributed to fuel confusion regarding the relative priority of the surgical over medical therapy in IE. The European Society of Cardiology (ESC) guidelines individuates three level of urgency: emergency surgery, to be performed within 24 hours; urgent surgery, recommended within a few days; elective surgery to be performed after 1-2 weeks of antibiotic therapy. Urgent surgery is recommended for most cases of IE. In the American Heart Association (AHA)'s guidelines define early surgery as "during the initial hospitalization and before completion of a full course of antibiotics." Some of the available evidences showed that are no proven benefits in delaying surgery if a definite diagnosis of IE has been established. However, this argument is controversial across the literature and several factors including the center specific experience can play a role in decision-making. In this review the latest evidences on IE clinical and surgical characteristics along with the current studies on the adoption of an early surgical approach are analyzed to clarify whether enough evidence is available to inform an update of the guidelines.
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Affiliation(s)
- Umberto Benedetto
- Department of Cardiothoracic Surgery, Bristol Heart Institute, University of Bristol, Bristol, UK
| | - Cristiano Spadaccio
- Department of Cardiac Surgery, Golden Jubilee National Hospital, Glasgow, UK.,Institute of Cardiovascular and Medical Sciences, University of Glasgow, UK
| | | | - Marc R Moon
- Department of Cardiac Thoracic Surgery, Washington University School of Medicine, Saint Louis, MO, USA
| | - Francesco Nappi
- Department of Cardiac Surgery, Centre Cardiologique du Nord de Saint-Denis, Paris, France
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11
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Di Filippo S. Clinical outcomes for congenital heart disease patients presenting with infective endocarditis. Expert Rev Cardiovasc Ther 2020; 18:331-342. [PMID: 32476525 DOI: 10.1080/14779072.2020.1768847] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
INTRODUCTION Infective endocarditis (IE) is a life-threatening adverse event for patients with congenital heart disease (CHD). Its incidence has changed little over time despite progress in techniques for diagnosis and treatment, and guidelines for prophylaxis. AREAS COVERED The review sought for key-words: 'congenital heart disease,' 'infective endocarditis,' 'microbial diagnosis,' 'imaging diagnosis,' 'surgical techniques,' 'prognosis,' 'prophylaxis.' Objectives were to investigate epidemiology, novel techniques for imaging and microbial diagnosis, therapeutic management and prognosis, and guidelines for prophylaxis in patients with CHD. The incidence of IE is increasing in adults with CHD. Morbidity caused by a broad clinical spectrum of cardiac and extracardiac episode-related complications is high. Surgical management is increasingly required in the early phase of the disease. Despite new techniques for diagnosis and microbiological therapy, mortality rate is still up to 10-20%. EXPERT OPINION IE has increased in the growing cohort of adults with complex heart disease, living with residual cardiac lesions and prosthetic materials. Diagnosis is challenging for complex heart defects. Pet-scan technique can provide beneficial information to locate intracardiac lesions and embolic foci. Identification of the microbiological agents is improving. Innovative surgical techniques aim to avoid prosthetic material. Guidelines for prophylaxis currently emphasize oral and skin daily hygiene.
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Affiliation(s)
- Sylvie Di Filippo
- Department of Pediatric Cardiology and Congenital Heart Disease, Claude Bernard Lyon 1 Medical University, Cardiovascular Hospital Louis Pradel , Lyon, France
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12
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Damlin A, Westling K, Maret E, Stålsby Lundborg C, Caidahl K, Eriksson MJ. Associations between echocardiographic manifestations and bacterial species in patients with infective endocarditis: a cohort study. BMC Infect Dis 2019; 19:1052. [PMID: 31842764 PMCID: PMC6916238 DOI: 10.1186/s12879-019-4682-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Accepted: 11/29/2019] [Indexed: 11/10/2022] Open
Abstract
Background The diagnosis of infective endocarditis (IE) is based on microbiological analyses and diagnostic imaging of cardiac manifestations. Echocardiography (ECHO) is preferred for visualization of IE-induced cardiac manifestations. We investigated associations between bacterial infections and IE manifestations diagnosed by ECHO. Methods In this cohort study, data from patients aged 18 years or above, with definite IE admitted at the Karolinska University Hospital between 2008 and 2017 were obtained from Swedish National Registry of Endocarditis. Bacteria registered as pathogen were primarily selected from positive blood culture and for patients with negative blood culture, bacteria found in culture or PCR from postoperative material was registered as pathogen. Patients with negative results from culture or PCR, and patients who did not undergo ECHO during hospital stay, were excluded. IE manifestations diagnosed by ECHO were obtained from the registry. Chi-squared test and two-sided Fisher’s exact test was used for comparisons between categorical variables, and student’s t test was used for continuous numerical variables. Multivariable analyses were performed using logistic regression. Secular trend analyses were performed using linear regression. Associations and the strength between the variables were estimated using odds ratios (ORs) with 95% confidence intervals (CIs). P < 0.05 was considered significant. Results The most common bacteria were Staphylococcus aureus (n = 239, 49%) and viridans group streptococci (n = 102, 21%). The most common manifestations were vegetation in the mitral (n = 195, 40%), aortic (n = 190, 39%), and tricuspid valves (n = 108, 22%). Associations were seen between aortic valve vegetations and Enterococcus faecalis among patients with native aortic valves, between mitral valve vegetations and streptococci of group B or viridans group, between tricuspid valve vegetations and S. aureus among patients with intravenous drug abuse, and between perivalvular abscesses as well as cardiovascular implantable electronic device (CIED)-associated IE and coagulase negative staphylococci (all P < 0.05). Conclusions Associations were found between certain bacterial species and specific ECHO manifestations. Our study contributes to a better understanding of IE manifestations and their underlying bacterial etiology, which pathogens can cause severe infections and might require close follow-up and surgical treatment.
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Affiliation(s)
- A Damlin
- Department of Molecular Medicine and Surgery, Division of Clinical Physiology, Karolinska Institutet, (L1:00), SE-171 76, Stockholm, Sweden. .,Department of Clinical Physiology, Karolinska University Hospital, A8:01, Eugeniavägen 3, SE-171 76, Stockholm, Sweden. .,Global Health - Health Systems and Policy: Medicines, focusing antibiotics. Department of Global Public Health, Karolinska Institutet, SE-171 77, Stockholm, Sweden.
| | - K Westling
- Department of Medicine Huddinge, Division of Infectious Diseases and Dermatology, Karolinska Institutet, SE-141 86, Stockholm, Sweden.,Department of Infectious Diseases, Karolinska University Hospital Huddinge, SE-141 86, Stockholm, Sweden
| | - E Maret
- Department of Molecular Medicine and Surgery, Division of Clinical Physiology, Karolinska Institutet, (L1:00), SE-171 76, Stockholm, Sweden.,Department of Clinical Physiology, Karolinska University Hospital, A8:01, Eugeniavägen 3, SE-171 76, Stockholm, Sweden
| | - C Stålsby Lundborg
- Global Health - Health Systems and Policy: Medicines, focusing antibiotics. Department of Global Public Health, Karolinska Institutet, SE-171 77, Stockholm, Sweden
| | - K Caidahl
- Department of Molecular Medicine and Surgery, Division of Clinical Physiology, Karolinska Institutet, (L1:00), SE-171 76, Stockholm, Sweden.,Department of Clinical Physiology, Karolinska University Hospital, A8:01, Eugeniavägen 3, SE-171 76, Stockholm, Sweden.,Institute of Medicine, Sahlgrenska Academy, University of Gothenburg, SE-413 45, Gothenburg, Sweden.,Region Västra Götaland, Department of Clinical Physiology, Sahlgrenska University Hospital, SE-413 45, Gothenburg, Sweden
| | - M J Eriksson
- Department of Molecular Medicine and Surgery, Division of Clinical Physiology, Karolinska Institutet, (L1:00), SE-171 76, Stockholm, Sweden.,Department of Clinical Physiology, Karolinska University Hospital, A8:01, Eugeniavägen 3, SE-171 76, Stockholm, Sweden
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13
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Abstract
RATIONALE The clinical utility of culture-independent testing of pediatric BAL specimens is unknown. In addition, the variability of the pediatric pulmonary microbiome with patient characteristics is not well understood. OBJECTIVES To compare testing with 16S rRNA gene-based sequencing to conventional cultures of BAL specimens in children Methods: Study subjects were not more than 22 years old and underwent BAL from May 2013 to August 2015 as part of clinical care. DNA extracted from BAL specimens was used for 16S rRNA gene-based analysis, and results were compared with routine cultures from the same samples. Indices of microbial diversity and relative taxon abundances were compared on the basis of subject characteristics (diagnosis and antibiotic use). RESULTS From 81 participants (male, 51%; median age, 9 yr), 89 samples were collected. The 16S rRNA genes of 77 samples (86.5%) from 70 subjects were successfully analyzed. These 70 subjects included 23 with cystic fibrosis, 19 who were immunocompromised, and 28 who were nonimmunocompromised. Of 68 organisms identified in culture, 16S rRNA gene-based analyses detected corresponding taxa in 66 (97.1%) and also identified potentially clinically significant organisms missed by cultures (e.g., Staphylococcus, Legionella, and Pseudomonas). Taxa that varied significantly with diagnosis and antibiotic use included Veillonella, Corynebacterium, Haemophilus, and Streptococcus. The microbiota of cystic fibrosis samples was less diverse. A "core" group of 15 taxa present in all three diagnosis groups was identified. CONCLUSIONS Culture-independent analysis was concordant with routine cultures and showed the potential to detect noncultured pathogens. Although culture-independent testing identified relative changes in organism abundance associated with clinical characteristics, distinct microbiome profiles associated with disease states were not identified.
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14
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Solomon IH, Lin C, Horback KL, Kanjilal S, Rojas-Rudilla V, Brigl M, Laga AC, Lindeman NI, Padera RF. Utility of Histologic and Histochemical Screening for 16S Ribosomal RNA Gene Sequencing of Formalin-Fixed, Paraffin-Embedded Tissue for Bacterial Endocarditis. Am J Clin Pathol 2019; 152:431-437. [PMID: 31172185 DOI: 10.1093/ajcp/aqz055] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
OBJECTIVES 16S ribosomal RNA (rRNA) sequencing is a powerful but expensive tool for the identification of bacteria in culture-negative endocarditis. Histologic criteria to screen formalin-fixed, paraffin-embedded (FFPE) specimens for testing are evaluated. METHODS Sixty-eight cases of infective endocarditis and controls were histologically reviewed and analyzed by 16S rRNA gene sequencing. RESULTS Sequencing identified a specific pathogenic organism in 33 (49%) of 68 cases with acute inflammation and in 0 of 10 controls (P = .004). Visualization of organisms by Gram or Grocott methenamine silver stains had the strongest association with positive sequencing, while antibiotic treatment effect and acid decalcification decreased sensitivity. Molecular identifications were concordant with blood culture results in 90% of the cases, and a positive sequencing result was obtained in approximately half of the cases with negative valve cultures. CONCLUSIONS Histologic screening criteria are extremely helpful for identifying cases likely to be positive by molecular testing and can provide significant cost savings in filtering out low-yield specimens.
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Affiliation(s)
- Isaac H Solomon
- Department of Pathology, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA
| | - Chieyu Lin
- Department of Pathology, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA
| | - Katharine L Horback
- Department of Pathology, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA
| | - Sanjat Kanjilal
- Department of Pathology, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA
| | - Vanesa Rojas-Rudilla
- Department of Pathology, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA
| | - Manfred Brigl
- Department of Pathology, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA
| | - Alvaro C Laga
- Department of Pathology, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA
| | - Neal I Lindeman
- Department of Pathology, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA
| | - Robert F Padera
- Department of Pathology, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA
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15
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Cheng J, Hu H, Fang W, Shi D, Liang C, Sun Y, Gao G, Wang H, Zhang Q, Wang L, Wu H, Hu L, Chen L, Zhang J, Lee S, Wang F, Zhou Z. Detection of pathogens from resected heart valves of patients with infective endocarditis by next-generation sequencing. Int J Infect Dis 2019; 83:148-153. [DOI: 10.1016/j.ijid.2019.03.007] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2019] [Revised: 03/05/2019] [Accepted: 03/05/2019] [Indexed: 12/12/2022] Open
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16
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Halavaara M, Martelius T, Järvinen A, Antikainen J, Kuusela P, Salminen US, Anttila VJ. Impact of pre-operative antimicrobial treatment on microbiological findings from endocardial specimens in infective endocarditis. Eur J Clin Microbiol Infect Dis 2019; 38:497-503. [PMID: 30680557 PMCID: PMC6394703 DOI: 10.1007/s10096-018-03451-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Accepted: 12/05/2018] [Indexed: 01/13/2023]
Abstract
Treatment of infective endocarditis (IE) should be initiated promptly. This might hamper the chances to identify the causative organism in blood cultures. Microbiological sampling of infected valve in patients undergoing surgery might identify the causative organism. The impact of pre-operative antimicrobial treatment on the yield of valve samples is not known. This study evaluated the impact of the duration of the pre-operative antibiotic treatment on valve culture and 16S rRNA PCR findings from resected endocardial samples. Patients meeting the modified Duke criteria of definite or possible IE and undergoing valve surgery due to IE during 2011–2016 were included from Southern Finland. Eighty-seven patients were included. In patients with shorter than 2 weeks of pre-operative antimicrobial treatment, PCR was positive in 91% (n = 42/46) and valve culture in 41% (n = 19/46) of cases. However, in patients who had 2 weeks or longer therapy before operation, PCR was positive in 53% (n = 18/34) and all valve cultures were negative. In 14% of patients, PCR had a diagnostic impact. In blood-culture negative cases (n = 13), PCR could detect the causative organism in ten patients (77%). These included five cases of Bartonella quintana, one Tropheryma whipplei, and one Coxiella burnetii. Long pre-operative antimicrobial treatment was shown to have a negative impact on microbiological tests done on resected endocardial material. After 2 weeks of therapy, all valve cultures were negative, but PCR was positive in half of the cases. PCR aided in diagnostic work-up, especially in blood culture negative cases.
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Affiliation(s)
- Mika Halavaara
- Department of Infectious Diseases, Inflammation Center, Helsinki University Hospital (HUH) and University of Helsinki, Meilahti Triangle Hospital, open-plan office, 1st floor, P.O. BOX 372, 00029, Helsinki, Finland.
| | - Timi Martelius
- Department of Infectious Diseases, Inflammation Center, Helsinki University Hospital (HUH) and University of Helsinki, Meilahti Triangle Hospital, open-plan office, 1st floor, P.O. BOX 372, 00029, Helsinki, Finland
| | - Asko Järvinen
- Department of Infectious Diseases, Inflammation Center, Helsinki University Hospital (HUH) and University of Helsinki, Meilahti Triangle Hospital, open-plan office, 1st floor, P.O. BOX 372, 00029, Helsinki, Finland
| | - Jenni Antikainen
- Division of Clinical Microbiology, HUSLAB, Helsinki University Hospital and University of Helsinki, Helsinki, Finland
| | - Pentti Kuusela
- Division of Clinical Microbiology, HUSLAB, Helsinki University Hospital and University of Helsinki, Helsinki, Finland
| | - Ulla-Stina Salminen
- Department of Cardiac Surgery, Heart and Lung Center, Helsinki University Hospital and University of Helsinki, Helsinki, Finland
| | - Veli-Jukka Anttila
- Department of Infectious Diseases, Inflammation Center, Helsinki University Hospital (HUH) and University of Helsinki, Meilahti Triangle Hospital, open-plan office, 1st floor, P.O. BOX 372, 00029, Helsinki, Finland
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17
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Johansson N, Vondracek M, Backman-Johansson C, Sköld MC, Andersson-Ydsten K, Hedlund J. The bacteriology in adult patients with pneumonia and parapneumonic effusions: increased yield with DNA sequencing method. Eur J Clin Microbiol Infect Dis 2018; 38:297-304. [PMID: 30547334 DOI: 10.1007/s10096-018-3426-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2018] [Accepted: 11/06/2018] [Indexed: 12/25/2022]
Abstract
The aim of this study was to use a 16S rDNA sequencing method in combination with conventional culture in patients with parapneumonic effusions (PPE) to evaluate the methods, study the microbiological spectrum, and examine the presence of bacteria within the different stages of PPE. Adults with community-acquired pneumonia (CAP) and PPE (n = 197) admitted to the Departments of Infectious Diseases at four hospitals in Stockholm County during 2011-2014 were prospectively studied. All patients underwent thoracentesis. Twenty-seven non-infectious pleural effusions were used as controls. The pleural samples were analyzed with culture, 16S rDNA sequencing, pH, glucose, and lactate dehydrogenase. Microbiological etiology was found in 99/197 (50%) of the patients with mixed infections in 20 cases. The most common pathogens were viridans streptococci (n = 37) and anaerobic bacteria (n = 40). Among the 152 patients with both methods performed, 26/152 (17%) and 94/152 (62%) had bacteria identified with culture and 16S rDNA sequencing respectively (p < 0.001). In 24/26 (92%) culture-positive cases, the same organism was identified by 16S rDNA. All controls were negative in both methods. Among the patients with complicated PPE and complete sampling, bacteria were found in 69/74 patients (93%), all detected with 16S rDNA sequencing, compared to 23/74 (31%) culture-positive samples (p < 0.001). Compared with culture, 16S rDNA sequencing substantially improved the microbiological yield, a microbiological diagnosis was achieved in almost all patients with complicated PPE, and the specificity seemed to be high. 16S rDNA sequencing should be used together with culture in patients with PPE to guide antibiotic therapy.
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Affiliation(s)
- Niclas Johansson
- Department of Medicine, Solna, Infectious Diseases Unit, Karolinska University Hospital, Karolinska Institutet, Stockholm, Sweden. .,Department of Infectious Diseases, Karolinska University Hospital Solna, SE-171 76, Stockholm, Sweden.
| | - Martin Vondracek
- Department of Clinical Microbiology, Department of Microbiology, Tumor and Cell Biology, Karolinska University Hospital, Karolinska Institutet, Stockholm, Sweden
| | | | - Magnus C Sköld
- Respiratory Medicine Unit, Department of Medicine Solna and Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden.,Lung-Allergy Clinic, Karolinska University Hospital Solna, Stockholm, Sweden
| | - Karin Andersson-Ydsten
- Department of Medicine, Solna, Infectious Diseases Unit, Karolinska University Hospital, Karolinska Institutet, Stockholm, Sweden.,Department of Infectious Diseases, Karolinska University Hospital Solna, SE-171 76, Stockholm, Sweden
| | - Jonas Hedlund
- Department of Medicine, Solna, Infectious Diseases Unit, Karolinska University Hospital, Karolinska Institutet, Stockholm, Sweden. .,Department of Infectious Diseases, Karolinska University Hospital Solna, SE-171 76, Stockholm, Sweden.
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18
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Rutanga JP, Van Puyvelde S, Heroes AS, Muvunyi CM, Jacobs J, Deborggraeve S. 16S metagenomics for diagnosis of bloodstream infections: opportunities and pitfalls. Expert Rev Mol Diagn 2018; 18:749-759. [PMID: 29985081 DOI: 10.1080/14737159.2018.1498786] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
INTRODUCTION Bacterial bloodstream infections (BSI) form a large public health threat worldwide. Current routine diagnosis is based on blood culture (BC) but this technique suffers from limited sensitivity. Molecular diagnostic tools have been developed for identification of bacteria in the blood of BSI patients. 16S metagenomics is an open-ended technique that can detect simultaneously all bacteria in a given sample based on PCR amplification of the 16S ribosomal RNA gene (rDNA) followed by sequencing of the PCR amplicons and taxonomic labeling of the sequence reads at genus or species level. Areas covered: Here we review the studies that have used 16S metagenomics for the identification of bacteria in human blood samples. We also discuss the potential added value of 16S metagenomics in the diagnosis of BSI, challenges as well as future directions for implementation in clinical settings. Expert commentary: 16S metagenomics has the potential to complement conventional BC; however, the technique currently suffers from several technical limitations jeopardizing implementation in routine clinical microbiology laboratories. Further studies are required to assess the cost-efficiency and clinical impact of 16S metagenomics in comparison to BC which remains the gold standard diagnostic method for BSI.
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Affiliation(s)
- Jean Pierre Rutanga
- a College of Science and Technology , University of Rwanda , Kigali , Rwanda.,b Department of Biomedical Sciences , Institute of Tropical Medicine , Antwerp , Belgium.,d Department of Microbiology and Immunology , KU Leuven , Leuven , Belgium
| | - Sandra Van Puyvelde
- b Department of Biomedical Sciences , Institute of Tropical Medicine , Antwerp , Belgium.,c Wellcome Trust Sanger Institute , Hinxton , United Kingdom
| | - Anne-Sophie Heroes
- d Department of Microbiology and Immunology , KU Leuven , Leuven , Belgium.,e Department of Clinical Sciences , Institute of Tropical Medicine , Antwerp , Belgium
| | - Claude Mambo Muvunyi
- f College of Medicine and Health Sciences , University of Rwanda , Kigali , Rwanda
| | - Jan Jacobs
- d Department of Microbiology and Immunology , KU Leuven , Leuven , Belgium.,e Department of Clinical Sciences , Institute of Tropical Medicine , Antwerp , Belgium
| | - Stijn Deborggraeve
- b Department of Biomedical Sciences , Institute of Tropical Medicine , Antwerp , Belgium
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19
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Kim SL, Gordon SM, Shrestha NK. Distribution of streptococcal groups causing infective endocarditis: a descriptive study. Diagn Microbiol Infect Dis 2018; 91:269-272. [PMID: 29567126 DOI: 10.1016/j.diagmicrobio.2018.02.015] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2017] [Revised: 02/12/2018] [Accepted: 02/21/2018] [Indexed: 11/17/2022]
Abstract
The purpose of this study was to describe the distribution of streptococci causing infective endocarditis (IE). A total of 296 patients with definite IE admitted from July 2007 to December 2014 were identified, with microbial identification done by a combination of blood culture, valve culture, and valve polymerase chain reaction (PCR). The overall distribution of streptococci was 76% viridans (n = 224), 17% pyogenic (50), 6% nutritionally variant (17), and 2% anaerobic (5). Sixty-three (21%) viridans group streptococci were not identified further. The distribution of the remaining 161 viridans group streptococci was Streptococcus mitis group 61%, S. bovis group 15%, S. mutans group 13%, S. anginosus group 9%, and S. salivarius group 1%. Of the 50 pyogenic streptococci, 78% were S. agalactiae and 16% were S. dysgalactiae. PCR was significantly more sensitive than culture in identifying streptococci in excised heart valves.
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Affiliation(s)
- So Lim Kim
- Case Western Reserve University School of Medicine, 2109 Adelbert Rd, Cleveland, OH 44106, USA.
| | - Steven M Gordon
- Department of Infectious Diseases, Cleveland Clinic, 9500 Euclid Avenue, G21, Cleveland, OH 44195, USA.
| | - Nabin K Shrestha
- Department of Infectious Diseases, Cleveland Clinic, 9500 Euclid Avenue, G21, Cleveland, OH 44195, USA.
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20
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Introduction of a hydrolysis probe PCR assay for high-throughput screening of methicillin-resistant Staphylococcus aureus with the ability to include or exclude detection of Staphylococcus argenteus. PLoS One 2018; 13:e0192782. [PMID: 29425233 PMCID: PMC5806904 DOI: 10.1371/journal.pone.0192782] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2017] [Accepted: 01/30/2018] [Indexed: 01/29/2023] Open
Abstract
Many countries using sensitive screening methods for detection of carriage of methicillin-resistant Staphylococcus aureus (MRSA) have a sustained low incidence of MRSA infections. For diagnostic laboratories with high sample volumes, MRSA screening requires stability, low maintenance and high performance at a low cost. Herein we designed oligonucleotides for a new nuc targeted hydrolysis probe PCR to replace the standard in-house nuc SybrGreen PCR assay. This new, more time-efficient, PCR assay resulted in a 40% increase in daily sample capacity, with maintained high specificity and sensitivity. The assay was also able to detect Staphylococcus aureus clonal cluster 75 (CC75) lineage strains, recently re-classified as Staphylococcus argenteus, with a sensitivity considerably increased compared to our previous assay. While awaiting consensus if the CC75 lineage of S. aureus should be considered as S. argenteus, and whether methicillin-resistant S. argenteus should be included in the MRSA definition, many diagnostic laboratories need to update their MRSA assay sensitivity/specificity towards this lineage/species. The MRSA screening assay presented in this manuscript is comprised of nuc oligonucleotides separately targeting S. aureus and CC75 lineage strains/S. argenteus, thus providing high user flexibility for the detection of CC75 lineage strains/S. argenteus.
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21
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Boujelben I, Gdoura R, Hammami A. A broad-range PCR technique for the diagnosis of infective endocarditis. Braz J Microbiol 2018; 49:534-543. [PMID: 29429763 PMCID: PMC6111453 DOI: 10.1016/j.bjm.2017.03.019] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2016] [Revised: 02/18/2017] [Accepted: 03/23/2017] [Indexed: 11/21/2022] Open
Abstract
Infective endocarditis (IE) remains a severe and potentially fatal disease demanding sophisticated diagnostic strategies for detection of the causative microorganisms. The aim of the present study was to develop a broad-range 16S ribosomal RNA gene polymerase chain reaction in the routine diagnostic of IE for the early diagnosis of fatal disease. A broad-range PCR technique was selected and evaluated in terms of its efficiency in the diagnosis of endocarditis using 19 heart valves from patients undergoing cardiovascular surgeries at the Habib Bourguiba Hospital of Sfax, Tunisia, on the grounds of suspected IE. The results demonstrated the efficiency of this technique particularly in cases involving a limited number of bacteria since it helped to increase detection sensitivity. The technique proved to be efficient, particularly, in the bacteriological diagnosis of IE in contexts involving negative results from conventional culture methods and other contexts involving bacterial species that were not amenable to identification by phenotypic investigations. Indeed, the sequencing of the partial 16S ribosomal RNA gene revealed the presence of Bartonella henselae, Enterobacter sp., and Streptococcus pyogenes in three heart valves with the negative culture. It should be noted that the results obtained from the polymerase chain reaction-sequencing identification applied to the heart valve and the strain isolated from the same tissue were not consistent with the ones found by the conventional microbiological methods in the case of IE caused by Gemella morbillorum. In fact, the results from the molecular identification revealed the presence of Lactobacillus jensenii. Overall, the results have revealed that the proposed method is sensitive, reliable and might open promising opportunities for the early diagnosis of IE.
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Affiliation(s)
- Ines Boujelben
- Hospital Sfax, Department of Microbiology and Research Laboratory "Microorganismes et Pathologie Humaine" Habib Bourguiba, Sfax, Tunisia
| | - Radhouane Gdoura
- Université de Sfax, Faculté des Sciences de Sfax, Laboratoire de recherche Toxicologie Microbiologie Environnementale et Santé LR11ES06, Sfax, Tunisia.
| | - Adnane Hammami
- Hospital Sfax, Department of Microbiology and Research Laboratory "Microorganismes et Pathologie Humaine" Habib Bourguiba, Sfax, Tunisia
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22
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Kokosar Ulcar B, Lakic N, Jeverica S, Pecavar B, Logar M, Cerar TK, Lejko-Zupanc T. Contribution of sonicate-fluid cultures and broad-range PCR to microbiological diagnosis in vascular graft infections. Infect Dis (Lond) 2017; 50:429-435. [PMID: 29260928 DOI: 10.1080/23744235.2017.1418529] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
Abstract
BACKGROUND Vascular graft infections (VGI) are associated with considerable morbidity and mortality, and antimicrobial treatment is an important adjunct to surgical treatment. While microbial aetiology of VGI is often difficult to determine, other techniques such as sonication of implanted material may be used to enhance the recovery of biofilm-associated organisms. METHODS We performed a retrospective analysis of 22 consecutive patients treated for VGI at University Medical Centre Ljubljana from May 2011 through January 2015. Explanted vascular grafts were flooded with sterile Ringer solution, sonicated for 1 min at a frequency of 40 kHz and inoculated on solid and liquid culture media. Aerobic and anaerobic cultures were performed, incubated for 14 days and any significant bacterial growth was quantitatively evaluated. Additionally, broad-range PCR from sonicate fluid was performed. Microbiological results were compared with the results of preoperatively taken blood cultures and the results of intraoperative tissue cultures (material from peri-graft collection). RESULTS Identification of the causative organism (irrespective of the method) was achieved in 95.8%. Preoperative blood cultures were positive in 35.3%, intraoperative tissue cultures in 31.8%, sonicate fluid culture in 79.2%, while broad-range PCR from sonicate fluid was positive in 66.7%. In 37.5% the pathogen detected in sonicate fluid culture or broad-range PCR was the only positive microbiological result. CONCLUSIONS Sonicate fluid culture and broad-range PCR from explanted vascular grafts may contribute to optimization of antimicrobial treatment. Optimal timing of antibiotic therapy before explantation should be further assessed to improve diagnostic yield.
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Affiliation(s)
- Barbara Kokosar Ulcar
- a Department of Infectious Diseases and Febrile Illnesses , University Medical Centre Ljubljana , Ljubljana , Slovenia
| | - Nikola Lakic
- b Department of Cardiovascular Surgery , University Medical Centre Ljubljana , Ljubljana , Slovenia
| | - Samo Jeverica
- c Faculty of Medicine, Institute of Microbiology and Immunology , University of Ljubljana , Ljubljana , Slovenia
| | - Blaz Pecavar
- a Department of Infectious Diseases and Febrile Illnesses , University Medical Centre Ljubljana , Ljubljana , Slovenia
| | - Mateja Logar
- a Department of Infectious Diseases and Febrile Illnesses , University Medical Centre Ljubljana , Ljubljana , Slovenia
| | - Tjasa Kisek Cerar
- c Faculty of Medicine, Institute of Microbiology and Immunology , University of Ljubljana , Ljubljana , Slovenia
| | - Tatjana Lejko-Zupanc
- a Department of Infectious Diseases and Febrile Illnesses , University Medical Centre Ljubljana , Ljubljana , Slovenia
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Faraji R, Behjati-Ardakani M, Moshtaghioun SM, Kalantar SM, Namayandeh SM, Soltani M, Emami M, Zandi H, Firoozabadi AD, Kazeminasab M, Ahmadi N, Sarebanhassanabadi M. The diagnosis of microorganism involved in infective endocarditis (IE) by polymerase chain reaction (PCR) and real-time PCR: A systematic review. Kaohsiung J Med Sci 2017; 34:71-78. [PMID: 29413230 DOI: 10.1016/j.kjms.2017.09.011] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2017] [Revised: 09/19/2017] [Accepted: 09/28/2017] [Indexed: 12/18/2022] Open
Abstract
Broad-range bacterial rDNA polymerase chain reaction (PCR) followed by sequencing may be identified as the etiology of infective endocarditis (IE) from surgically removed valve tissue; therefore, we reviewed the value of molecular testing in identifying organisms' DNA in the studies conducted until 2016. We searched Google Scholar, Scopus, ScienceDirect, Cochrane, PubMed, and Medline electronic databases without any time limitations up to December 2016 for English studies reporting microorganisms involved in infective endocarditis microbiology using PCR and real-time PCR. Most studies were prospective. Eleven out of 12 studies used valve tissue samples and blood cultures while only 1 study used whole blood. Also, 10 studies used the molecular method of PCR while 2 studies used real-time PCR. Most studies used 16S rDNA gene as the target gene. The bacteria were identified as the most common microorganisms involved in infective endocarditis. Streptococcus spp. and Staphylococcus spp. were, by far, the most predominant bacteria detected. In all studies, PCR and real-time PCR identified more pathogens than blood and tissue cultures; moreover, the sensitivity and specificity of PCR and real-time PCR were more than cultures in most of the studies. The highest sensitivity and specificity were 96% and 100%, respectively. The gram positive bacteria were the most frequent cause of infective endocarditis. The molecular methods enjoy a greater sensitivity compared to the conventional blood culture methods; yet, they are applicable only to the valve tissue of the patients undergoing cardiac valve surgery.
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Affiliation(s)
- Reza Faraji
- Yazd Cardiovascular Research Center, Shahid Sadoughi University of Medical Sciences, Yazd, Iran
| | | | | | - Seyed Mehdi Kalantar
- Medical Genetic Research and Clinical Centre for Infertility, Shahid Sadoughi University of Medical Sciences, Yazd, Iran
| | | | - Mohammadhossien Soltani
- Yazd Cardiovascular Research Center, Shahid Sadoughi University of Medical Sciences, Yazd, Iran
| | - Mahmood Emami
- Yazd Cardiovascular Research Center, Shahid Sadoughi University of Medical Sciences, Yazd, Iran
| | - Hengameh Zandi
- Department of Microbiology, Faculty of Medicine, Shahid Sadoughi University of Medical Sciences, Yazd, Iran
| | - Ali Dehghani Firoozabadi
- Yazd Cardiovascular Research Center, Shahid Sadoughi University of Medical Sciences, Yazd, Iran.
| | - Mahmood Kazeminasab
- Student Research Committee, Shahid Sadoughi University of Medical Sciences, Yazd, Iran
| | - Nastaran Ahmadi
- Yazd Cardiovascular Research Center, Shahid Sadoughi University of Medical Sciences, Yazd, Iran
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Comparison of PCR-Electrospray Ionization Mass Spectrometry with 16S rRNA PCR and Amplicon Sequencing for Detection of Bacteria in Excised Heart Valves. J Clin Microbiol 2016; 54:2825-2831. [PMID: 27629895 DOI: 10.1128/jcm.01240-16] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2016] [Accepted: 09/02/2016] [Indexed: 12/27/2022] Open
Abstract
Identification of the causative pathogen of infective endocarditis (IE) is crucial for adequate management and therapy. A broad-range PCR-electrospray ionization mass spectrometry (PCR-ESI-MS) technique was compared with broad-spectrum 16S rRNA PCR and amplicon sequencing (16S rRNA PCR) for the detection of bacterial pathogens in 40 heart valves obtained from 34 definite infective endocarditis patients according to the modified Duke criteria and six nonendocarditis patients. Concordance between the two molecular techniques was 98% for being positive or negative, 97% for concordant identification up to the genus level, and 77% for concordant identification up to the species level. Sensitivity for detecting the causative pathogen (up to the genus level) in excised heart valves was 88% for 16S rRNA PCR and 85% for PCR-ESI-MS; the specificity was 83% for both methods. The two molecular techniques were significantly more sensitive than valve culture (18%) and accurately identified bacteria in excised heart valves. In eight patients with culture-negative IE, the following results were obtained: concordant detection of Coxiella burnetii (n = 2), Streptococcus gallolyticus (n = 1), Propionibacterium acnes (n = 1), and viridans group streptococci (n = 1) by both molecular tests, detection of P. acnes by PCR-ESI-MS whereas the 16S rRNA PCR was negative (n = 1), and a false-negative result by both molecular techniques (n = 2). In one case of IE caused by viridans streptococci, PCR-ESI-MS was positive for Enterococcus spp. The advantages of PCR-ESI-MS compared to 16S rRNA PCR are its automated workflow and shorter turnaround times.
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TB or Not TB. INFECTIOUS DISEASES IN CLINICAL PRACTICE 2016. [DOI: 10.1097/ipc.0000000000000347] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Miller RJH, Chow B, Pillai D, Church D. Development and evaluation of a novel fast broad-range 16S ribosomal DNA PCR and sequencing assay for diagnosis of bacterial infective endocarditis: multi-year experience in a large Canadian healthcare zone and a literature review. BMC Infect Dis 2016; 16:146. [PMID: 27066823 PMCID: PMC4828839 DOI: 10.1186/s12879-016-1476-4] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2015] [Accepted: 03/22/2016] [Indexed: 11/29/2022] Open
Abstract
Background The study aimed to explore the sensitivity and specificity of a novel fast 16S rDNA PCR and sequencing assay for the improved diagnosis of infective endocarditis (IE) in patients with suspected native or prosthetic heart valve (HV) infection over a multi-year period at our cardiovascular center. Methods Sixty-eight patients were prospectively enrolled who underwent HV replacement for suspected or confirmed IE between February 1, 2009 and September 1, 2014. Patient demographics, medical co-morbidities, Duke’s criteria, culture results, and antibiotic therapy were collected by detailed chart reviews. Dual-priming oligonucleotide primers targeted to 500 bps of the V1-V3 region of the 16S rRNA gene were used to perform fast broad-range 16S rDNA PCR and Sanger sequencing on ribosomal DNA extracted from HV tissues. The performance/diagnostic efficiency of the molecular test was evaluated against blood cultures and Gram stain and culture of HV tissue in patients’ with definite IE according to Duke’s criteria. Results Fifty patients (73.5 %) had definite IE and another 8 (11.8 %) had possible IE according to Duke’s criteria. Cardiac surgery was delayed an average of 15.4 days from the time of the patient’s last positive blood culture, and appropriate antibiotic therapy was given in the pre-operative period. While 44/50 (88 %) patients had a positive blood culture, HV tissue culture was only positive in 23 (46 %) of them. Molecular testing of all HV tissues had sensitivity, specificity, NPV and PPV of 92, 77.8, 77.8 and 92 % compared to 44, 100, 39.1 and 100 % respectively for culture for diagnosis of definite IE. For prosthetic HV tissue, 16S rDNA PCR had sensitivity of 93 % and specificity of 83 % compared to 35 and 100 % respectively for culture. A literature review showed that the diagnostic accuracy of our novel fast broad-range 16S rDNA PCR assay was similar or better than that of previously published studies. Conclusions This novel fast broad-range 16S rDNA PCR/sequencing test had superior sensitivity compared to tissue Gram stain and culture for identifying underlying bacterial pathogen in both native and prosthetic valve endocarditis.
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Affiliation(s)
- Robert J H Miller
- Department of Cardiac Sciences, University of Calgary, Calgary, Alberta, T2N 2T9, Canada
| | - Barbara Chow
- Calgary Laboratory Services, Calgary, Alberta, T2L 2K8, Canada
| | - Dylan Pillai
- Departments of Pathology & Laboratory Medicine and Medicine, University of Calgary, and Calgary Laboratory Services, 9-3535 Research Rd. NW, Calgary, Alberta, T2L 2K8, Canada
| | - Deirdre Church
- Departments of Pathology & Laboratory Medicine and Medicine, University of Calgary, and Calgary Laboratory Services, 9-3535 Research Rd. NW, Calgary, Alberta, T2L 2K8, Canada.
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Abstract
Infective endocarditis occurs worldwide, and is defined by infection of a native or prosthetic heart valve, the endocardial surface, or an indwelling cardiac device. The causes and epidemiology of the disease have evolved in recent decades with a doubling of the average patient age and an increased prevalence in patients with indwelling cardiac devices. The microbiology of the disease has also changed, and staphylococci, most often associated with health-care contact and invasive procedures, have overtaken streptococci as the most common cause of the disease. Although novel diagnostic and therapeutic strategies have emerged, 1 year mortality has not improved and remains at 30%, which is worse than for many cancers. Logistical barriers and an absence of randomised trials hinder clinical management, and longstanding controversies such as use of antibiotic prophylaxis remain unresolved. In this Seminar, we discuss clinical practice, controversies, and strategies needed to target this potentially devastating disease.
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Affiliation(s)
- Thomas J Cahill
- Department of Cardiology, Oxford University Hospitals, Oxford, UK
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Affiliation(s)
- B Cherie Millar
- Northern Ireland Public Health Laboratory, Department of Bacteriology, Belfast City Hospital, Belfast, UK
| | - Gilbert Habib
- Aix-Marseille Université, Marseille, France Cardiology Department, APHM, La Timone Hospital, Marseille, France
| | - John E Moore
- Northern Ireland Public Health Laboratory, Department of Bacteriology, Belfast City Hospital, Belfast, UK
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Faria MMP, Conly JM, Surette MG. The development and application of a molecular community profiling strategy to identify polymicrobial bacterial DNA in the whole blood of septic patients. BMC Microbiol 2015; 15:215. [PMID: 26474751 PMCID: PMC4609058 DOI: 10.1186/s12866-015-0557-7] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2015] [Accepted: 10/08/2015] [Indexed: 02/08/2023] Open
Abstract
Background The application of molecular based diagnostics in sepsis has had limited success to date. Molecular community profiling methods have indicated that polymicrobial infections are more common than suggested by standard clinical culture. A molecular profiling approach was developed to investigate the propensity for polymicrobial infections in patients predicted to have bacterial sepsis. Results Disruption of blood cells with saponin and hypotonic shock enabled the recovery of microbial cells with no significant changes in microbial growth when compared to CFU/ml values immediately prior to the addition of saponin. DNA extraction included a cell-wall digestion step with both lysozyme and mutanolysin, which increased the recovery of terminal restriction fragments by 2.4 fold from diverse organisms. Efficiencies of recovery and limits of detection using Illumina sequencing of the 16S rRNA V3 region were determined for both viable cells and DNA using mock bacterial communities inoculated into whole blood. Bacteria from pre-defined communities could be recovered following lysis and removal of host cells with > 97 % recovery of total DNA present. Applying the molecular profiling methodology to three septic patients in the intensive care unit revealed microbial DNA from blood had consistent alignment with cultured organisms from the primary infection site providing evidence for a bloodstream infection in the absence of a clinical lab positive blood culture result in two of the three cases. In addition, the molecular profiling indicated greater diversity was present in the primary infection sample when compared to clinical diagnostic culture. Conclusions A method for analyzing bacterial DNA from whole blood was developed in order to characterize the bacterial DNA profile of sepsis infections. Preliminary results indicated that sepsis infections were polymicrobial in nature with the bacterial DNA recovered suggesting a more complex etiology when compared to blood culture data.
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Affiliation(s)
- M M P Faria
- Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, AB, T2N 4 N1, Canada. .,Department of Calvin, Phoebe and Joan Snyder Institute for Chronic Diseases, University of Calgary, Calgary, AB, T2N 4 N1, Canada. .,Farncombe Family Digestive Health Research Institute, Departments of Medicine and Biochemistry and Biomedical Sciences, Faculty of Health Sciences, McMaster University, 1280 Main Street, HSC 3 N 8 F, Hamilton, ON, L8S 4 K1, Canada.
| | - J M Conly
- Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, AB, T2N 4 N1, Canada. .,Department of Medicine, University of Calgary, Calgary, AB, T2N 4 N1, Canada. .,Department of Pathology and Laboratory Medicine, University of Calgary, Calgary, AB, T2N 4 N1, Canada. .,Department of Calvin, Phoebe and Joan Snyder Institute for Chronic Diseases, University of Calgary, Calgary, AB, T2N 4 N1, Canada.
| | - M G Surette
- Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, AB, T2N 4 N1, Canada. .,Department of Calvin, Phoebe and Joan Snyder Institute for Chronic Diseases, University of Calgary, Calgary, AB, T2N 4 N1, Canada. .,Farncombe Family Digestive Health Research Institute, Departments of Medicine and Biochemistry and Biomedical Sciences, Faculty of Health Sciences, McMaster University, 1280 Main Street, HSC 3 N 8 F, Hamilton, ON, L8S 4 K1, Canada. .,Department of Medicine, McMaster University, Hamilton, ON, L8S 4 K1, Canada. .,Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, L8S 4 K1, Canada.
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Baltimore RS, Gewitz M, Baddour LM, Beerman LB, Jackson MA, Lockhart PB, Pahl E, Schutze GE, Shulman ST, Willoughby R. Infective Endocarditis in Childhood: 2015 Update. Circulation 2015; 132:1487-515. [DOI: 10.1161/cir.0000000000000298] [Citation(s) in RCA: 201] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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Harshman DK, Rao BM, McLain JE, Watts GS, Yoon JY. Innovative qPCR using interfacial effects to enable low threshold cycle detection and inhibition relief. SCIENCE ADVANCES 2015; 1:e1400061. [PMID: 26601245 PMCID: PMC4643774 DOI: 10.1126/sciadv.1400061] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2014] [Accepted: 06/12/2015] [Indexed: 05/11/2023]
Abstract
Molecular diagnostics offers quick access to information but fails to operate at a speed required for clinical decision-making. Our novel methodology, droplet-on-thermocouple silhouette real-time polymerase chain reaction (DOTS qPCR), uses interfacial effects for droplet actuation, inhibition relief, and amplification sensing. DOTS qPCR has sample-to-answer times as short as 3 min 30 s. In infective endocarditis diagnosis, DOTS qPCR demonstrates reproducibility, differentiation of antibiotic susceptibility, subpicogram limit of detection, and thermocycling speeds of up to 28 s/cycle in the presence of tissue contaminants. Langmuir and Gibbs adsorption isotherms are used to describe the decreasing interfacial tension upon amplification. Moreover, a log-linear relationship with low threshold cycles is presented for real-time quantification by imaging the droplet-on-thermocouple silhouette with a smartphone. DOTS qPCR resolves several limitations of commercially available real-time PCR systems, which rely on fluorescence detection, have substantially higher threshold cycles, and require expensive optical components and extensive sample preparation. Due to the advantages of low threshold cycle detection, we anticipate extending this technology to biological research applications such as single cell, single nucleus, and single DNA molecule analyses. Our work is the first demonstrated use of interfacial effects for sensing reaction progress, and it will enable point-of-care molecular diagnosis of infections.
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Affiliation(s)
- Dustin K. Harshman
- Biomedical Engineering Graduate Interdisciplinary Program, The University of Arizona, Tucson, AZ 85721, USA
| | - Brianna M. Rao
- Department of Biomedical Engineering, The University of Arizona, Tucson, AZ 85721, USA
| | - Jean E. McLain
- Water Resources Research Center and Department of Soil, Water and Environmental Science, The University of Arizona, Tucson, AZ 85721, USA
| | - George S. Watts
- Arizona Cancer Center and Department of Pharmacology, The University of Arizona, Tucson, AZ 85721, USA
| | - Jeong-Yeol Yoon
- Biomedical Engineering Graduate Interdisciplinary Program, The University of Arizona, Tucson, AZ 85721, USA
- Department of Biomedical Engineering, The University of Arizona, Tucson, AZ 85721, USA
- Department of Agricultural and Biosystems Engineering, The University of Arizona, Tucson, AZ 85721, USA
- Corresponding author. E-mail:
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Le Guern R, Loïez C, Armand S, Marceau L, Courcol R, Wallet F. Infective endocarditis: does a new 16S rDNA set of primers improve the microbiological diagnosis? Infect Dis (Lond) 2015; 47:896-901. [PMID: 26305496 DOI: 10.3109/23744235.2015.1075661] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND In infective endocarditis (IE), blood cultures are negative in 2.5-31% of cases because of a previously prescribed antimicrobial treatment. Molecular methods may represent an alternative to conventional microbiological techniques to identify the causative agent. The aim of this prospective study was to evaluate the performance of a new primer pair (341F/785R) for 16S rDNA amplification in heart valves compared with primers 91E/13BS already used for the diagnosis of IE. The primer pair 341F/785R was previously selected in silico to allow 16S rDNA amplification for a large coverage of bacterial species. RESULTS A total of 74 patients suspected of having IE were included in this study. IE was diagnosed in 55 of these patients using the modified Duke criteria, which was the gold standard here. 91E/13BS primers were more sensitive than 341F/785R primers: 38/55 (69.1%) samples were positive using 91E/13BS primers against 28/55 (50.9%) with 341F/785R (p = 0.013). When at least one of the two molecular methods was positive, the sensitivity and specificity of 16S rDNA amplification was 72.7% and 94.7%, respectively. CONCLUSION Even if the new primer pair 341F/785R seemed promising in silico, it was less sensitive for 16S rDNA amplification in heart valves than the 91E/13BS pair already used. This study underlines a lack of standardization for 16S rDNA amplification for clinical samples.
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Affiliation(s)
- Rémi Le Guern
- a From the Laboratoire de Bactériologie-Hygiène, Centre de Biologie Pathologie, CHRU de Lille, Université de Lille 2 , Lille , France
| | - Caroline Loïez
- a From the Laboratoire de Bactériologie-Hygiène, Centre de Biologie Pathologie, CHRU de Lille, Université de Lille 2 , Lille , France
| | - Sylvie Armand
- a From the Laboratoire de Bactériologie-Hygiène, Centre de Biologie Pathologie, CHRU de Lille, Université de Lille 2 , Lille , France
| | - Laure Marceau
- a From the Laboratoire de Bactériologie-Hygiène, Centre de Biologie Pathologie, CHRU de Lille, Université de Lille 2 , Lille , France
| | - René Courcol
- a From the Laboratoire de Bactériologie-Hygiène, Centre de Biologie Pathologie, CHRU de Lille, Université de Lille 2 , Lille , France
| | - Frédéric Wallet
- a From the Laboratoire de Bactériologie-Hygiène, Centre de Biologie Pathologie, CHRU de Lille, Université de Lille 2 , Lille , France
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Impact of serology and molecular methods on improving the microbiologic diagnosis of infective endocarditis in Egypt. Infection 2015; 43:523-9. [DOI: 10.1007/s15010-015-0761-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2014] [Accepted: 03/12/2015] [Indexed: 12/13/2022]
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Tattevin P, Watt G, Revest M, Arvieux C, Fournier PE. Update on blood culture-negative endocarditis. Med Mal Infect 2015; 45:1-8. [PMID: 25480453 DOI: 10.1016/j.medmal.2014.11.003] [Citation(s) in RCA: 92] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2014] [Accepted: 11/04/2014] [Indexed: 12/13/2022]
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Leli C, Moretti A, Pasticci MB, Cenci E, Bistoni F, Mencacci A. A commercially available multiplex real-time PCR for detection of pathogens in cardiac valves from patients with infective endocarditis. Diagn Microbiol Infect Dis 2014; 79:98-101. [DOI: 10.1016/j.diagmicrobio.2013.12.011] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2013] [Revised: 12/13/2013] [Accepted: 12/13/2013] [Indexed: 01/15/2023]
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Kemp M, Bangsborg J, Kjerulf A, Schmidt TA, Christensen J, Irmukhamedov A6, Bruun NE, Dargis R, Andresen K, Christensen JJ. Advantages and limitations of ribosomal RNA PCR and DNA sequencing for identification of bacteria in cardiac valves of danish patients. Open Microbiol J 2013; 7:146-51. [PMID: 24403979 PMCID: PMC3883160 DOI: 10.2174/1874285801307010146] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2013] [Revised: 11/14/2013] [Accepted: 11/14/2013] [Indexed: 11/29/2022] Open
Abstract
Studies on the value of culture-independent molecular identification of bacteria in cardiac valves are mostly restricted to comparing agreement of identification to what is obtained by culture to the number of identified bacteria in culture-negative cases. However, evaluation of the usefulness of direct molecular identification should also address weaknesses, their relevance in the given setting, and possible improvements. In this study cardiac valves from 56 Danish patients referred for surgery for infective endocarditis were analysed by microscopy and culture as well as by PCR targeting part of the bacterial 16S rRNA gene followed by DNA sequencing of the PCR product. PCR and DNA sequencing identified significant bacteria in 49 samples from 43 patients, including five out of 13 culture-negative cases. No rare, exotic, or intracellular bacteria were identified. There was a general agreement between bacterial identity obtained by ribosomal PCR and DNA sequencing from the valves and bacterial isolates from blood culture. However, DNA sequencing of the 16S rRNA gene did not discriminate well among non-haemolytic streptococci, especially within the Streptococcus mitis group. Ribosomal PCR with subsequent DNA sequencing is an efficient and reliable method of identifying the cause of IE, but exact species identification of some of the most common causes, i.e. non-haemolytic streptococci, may be improved with other molecular methods.
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Affiliation(s)
- Michael Kemp
- Microbiological Surveillance & Research, Statens Serum Institut, Copenhagen, Denmark ; Department of Clinical Microbiology, Odense University Hospital, Odense, Denmark
| | - Jette Bangsborg
- Department of Clinical Microbiology, Herlev University hospital, Copenhagen, Denmark
| | - Anne Kjerulf
- Department of Clinical Microbiology, Herlev University hospital, Copenhagen, Denmark
| | | | - John Christensen
- Department of Cardiothoracic Surgery, Gentofte University Hospital, Copenhagen, Denmark
| | | | - Niels Eske Bruun
- Department of Cardiology, Gentofte University Hospital, Copenhagen, Denmark
| | - Rimtas Dargis
- Microbiological Surveillance & Research, Statens Serum Institut, Copenhagen, Denmark ; Department of Clinical Microbiology, Slagelse Hospital, Slagelse, Denmark
| | - Keld Andresen
- Microbiological Surveillance & Research, Statens Serum Institut, Copenhagen, Denmark
| | - Jens Jørgen Christensen
- Microbiological Surveillance & Research, Statens Serum Institut, Copenhagen, Denmark ; Department of Clinical Microbiology, Slagelse Hospital, Slagelse, Denmark
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Broad-range PCR: past, present, or future of bacteriology? Med Mal Infect 2013; 43:322-30. [PMID: 23876208 DOI: 10.1016/j.medmal.2013.06.003] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2013] [Revised: 04/08/2013] [Accepted: 06/17/2013] [Indexed: 11/20/2022]
Abstract
PCR targeting the gene encoding 16S ribosomal RNA (commonly named broad-range PCR or 16S PCR) has been used for 20 years as a polyvalent tool to study prokaryotes. Broad-range PCR was first used as a taxonomic tool, then in clinical microbiology. We will describe the use of broad-range PCR in clinical microbiology. The first application was identification of bacterial strains obtained by culture but whose phenotypic or proteomic identification remained difficult or impossible. This changed bacterial taxonomy and allowed discovering many new species. The second application of broad-range PCR in clinical microbiology is the detection of bacterial DNA from clinical samples; we will review the clinical settings in which the technique proved useful (such as endocarditis) and those in which it did not (such as characterization of bacteria in ascites, in cirrhotic patients). This technique allowed identifying the etiological agents for several diseases, such as Whipple disease. This review is a synthesis of data concerning the applications, assets, and drawbacks of broad-range PCR in clinical microbiology.
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PCR-electrospray ionization mass spectrometry for direct detection of pathogens and antimicrobial resistance from heart valves in patients with infective endocarditis. J Clin Microbiol 2013; 51:2040-6. [PMID: 23596241 DOI: 10.1128/jcm.00304-13] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Microbiological diagnosis is pivotal to the appropriate management and treatment of infective endocarditis. We evaluated PCR-electrospray ionization mass spectrometry (PCR/ESI-MS) for bacterial and candidal detection using 83 formalin-fixed paraffin-embedded heart valves from subjects with endocarditis who had positive valve and/or blood cultures, 63 of whom had positive valvular Gram stains. PCR/ESI-MS yielded 55% positivity with concordant microbiology at the genus/species or organism group level (e.g., viridans group streptococci), 11% positivity with discordant microbiology, and 34% with no detection. PCR/ESI-MS detected all antimicrobial resistance encoded by mecA or vanA/B and identified a case of Tropheryma whipplei endocarditis not previously recognized.
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Wallet F, Herwegh S, Decoene C, Courcol RJ. PCR-electrospray ionization time-of-flight mass spectrometry: a new tool for the diagnosis of infective endocarditis from heart valves. Diagn Microbiol Infect Dis 2013; 76:125-8. [PMID: 23523601 DOI: 10.1016/j.diagmicrobio.2013.02.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2012] [Revised: 01/31/2013] [Accepted: 02/11/2013] [Indexed: 01/06/2023]
Abstract
A polymerase chain reaction with an injection of the amplicons in an electrospray ionization mass spectrometry (PCR-ESI-MS) technique was evaluated for the diagnosis of bacterial and yeast pathogens on 13 cardiac valves with suspected endocarditis. At the moment of surgery, 3/13 PCR-ESI-MS results matched with microbiological documentation. Nine PCR-ESI-MS results correlated with Duke's criteria, leukocytes, C-reactive protein and blood cultures before surgery. The PCR-ESI-MS result of the last valve failed to confirm the blood culture result obtained fifteen days before. With speed and accuracy, this method may be useful to assert microbiological identification and adapt treatment.
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Molecular Characterization and Virulence Genes of Aeromonas hydrophila Isolated from the Chinese Giant Salamander ( Andrias davidianus). ASIAN HERPETOL RES 2013. [DOI: 10.3724/sp.j.1245.2012.00303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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42
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Diagnosis and management of prosthetic vascular graft infections. Med Mal Infect 2012; 42:102-9. [DOI: 10.1016/j.medmal.2012.01.003] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2011] [Accepted: 01/03/2012] [Indexed: 01/15/2023]
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Value of PCR in surgically treated patients with staphylococcal infective endocarditis: a 4-year retrospective study. Eur J Clin Microbiol Infect Dis 2011; 31:1187-94. [DOI: 10.1007/s10096-011-1427-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2011] [Accepted: 09/12/2011] [Indexed: 12/20/2022]
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Wolff TY, Moser C, Bundgaard H, Høiby N, Nielsen PH, Thomsen TR. Detection of microbial diversity in endocarditis using cultivation-independent molecular techniques. ACTA ACUST UNITED AC 2011; 43:857-69. [PMID: 21867468 DOI: 10.3109/00365548.2011.598877] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
BACKGROUND The aim of this study was to investigate whether the diagnosis of infective endocarditis (IE) could be improved using molecular tools in addition to standard microscopy and cultivation methods. METHODS Cultivation was performed on blood or tissue samples as recommended in the modified Duke criteria. The molecular tools included a broad-range polymerase chain reaction (PCR)-based denaturant gradient gel electrophoresis and a more detailed identification by constructing clone libraries followed by sequencing. RESULTS Of 14 patients, 12 were positive by blood or tissue cultivation and all were monomicrobial. Molecular methods showed the presence of DNA from multiple bacterial species in 6 of the samples and indicated a larger variety of bacteria in the different samples than identified by cultivation. For 8 of the patients there was a good correlation between the results of cultivation and molecular methods, and for these samples the identified bacteria are known to be frequently involved with IE. Many of the additional bacteria only identified by the molecular methods are not reported as common causes of IE. CONCLUSIONS Application of molecular tools in addition to cultivation indicated that polymicrobial infections might be of importance in IE. However, the significance of the more unknown microorganisms needs to be investigated further.
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Affiliation(s)
- Tine Y Wolff
- Life Science Division, The Danish Technological Institute, Århus
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