1
|
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.
Collapse
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
| |
Collapse
|
2
|
Flurin L, Fisher CR, Wolf MJ, Pritt BS, DeSimone DC, Patel R. Comparison of Blood-Based Shotgun and Targeted Metagenomic Sequencing for Microbiological Diagnosis of Infective Endocarditis. Open Forum Infect Dis 2023; 10:ofad546. [PMID: 38075017 PMCID: PMC10709542 DOI: 10.1093/ofid/ofad546] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2023] Open
Abstract
Background Shotgun and targeted metagenomic sequencing have been shown in separate studies to be potentially useful for culture-free pathogen identification in blood and/or plasma of patients with infective endocarditis (IE). However, the 2 approaches have not been directly compared. The aim of this study was to compare shotgun metagenomic sequencing with targeted metagenomic sequencing (tMGS) for organism identification in blood or plasma of patients with IE. Methods Patients with possible or definite IE were prospectively enrolled from October 2020 to July 2021. Shotgun metagenomic sequencing was performed with the Karius test, which uses microbial cell-free DNA (mcfDNA) sequencing to detect, identify, and quantitate DNA-based pathogens in plasma. tMGS was performed using a 16S ribosomal RNA (rRNA) polymerase chain reaction assay targeting the V1 to V3 regions of the 16S rRNA gene. Results were compared using the McNemar test of paired proportions. Results Samples from 34 patients were investigated. The Karius test was positive in 24/34 (71%), including 3/6 (50%) with blood culture-negative endocarditis (BCNE), which was not significantly different from the positivity rate of tMGS (P = .41). Results of the Karius test were concordant with tMGS in 75% of cases. The Karius test detected 2 cases of methicillin-resistant Staphylococcus aureus among the 7 S. aureus detections, in accordance with results of phenotypic susceptibility testing. The combination of blood cultures, the Karius test, and tMGS found a potential causative pathogen in 33/34 (97%), including 5/6 with BCNE. Conclusions The Karius test and tMGS yielded comparable detection rates; however, beyond organism identification, the Karius test generated potentially useful antibiotic resistance data.
Collapse
Affiliation(s)
- Laure Flurin
- Divisions of Clinical Microbiology, Mayo Clinic, Rochester, Minnesota, USA
- Department of Intensive Care, University Hospital of Guadeloupe, Pointe-à-Pitre, France
- Division of Infectious Diseases, Mayo Clinic, Rochester, Minnesota, USA
| | - Cody R Fisher
- Divisions of Clinical Microbiology, Mayo Clinic, Rochester, Minnesota, USA
- Division of Infectious Diseases, Mayo Clinic, Rochester, Minnesota, USA
| | - Matthew J Wolf
- Divisions of Clinical Microbiology, Mayo Clinic, Rochester, Minnesota, USA
- Division of Infectious Diseases, Mayo Clinic, Rochester, Minnesota, USA
| | - Bobbi S Pritt
- Division of Infectious Diseases, Mayo Clinic, Rochester, Minnesota, USA
| | - Daniel C DeSimone
- Division of Infectious Diseases, Mayo Clinic, Rochester, Minnesota, USA
| | - Robin Patel
- Divisions of Clinical Microbiology, Mayo Clinic, Rochester, Minnesota, USA
- Division of Infectious Diseases, Mayo Clinic, Rochester, Minnesota, USA
| |
Collapse
|
3
|
Dumm RE, Glaser LJ, Rodino KG. Development of a scoring system to identify high-yield specimens for bacterial broad-range 16S rRNA gene PCR with sequencing at a tertiary care medical center. Am J Clin Pathol 2023; 160:477-482. [PMID: 37458096 DOI: 10.1093/ajcp/aqad074] [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: 04/06/2023] [Accepted: 05/25/2023] [Indexed: 07/18/2023] Open
Abstract
OBJECTIVES Broad-range bacterial polymerase chain reaction with sequencing (BRBPS) provides valuable diagnostic data, especially in cases of culture-negative infections. However, as BRBPS testing demonstrates generally low positivity, cost per impactful result can be high and commonly involves longer turnaround times compared with other methods, targeting use of this assay to high-yield situations remains a challenging goal. Diagnostic stewardship can help alleviate these challenges and increase clinical utility, yet not all laboratories have a dedicated stewardship team, and little formal guidance exists on identifying high-yield samples outside of specific clinical syndromes. In this study, we performed a retrospective review of 86 BRBPS orders from a tertiary care medical center, with a focus on identifying high-yield cases using an infectious markers scoring system, visualized inflammation or organism (VIO) score, to predict return of actionable diagnostic data. METHODS Using chart review, we evaluated how results from high VIO score or low VIO score specimens contributed to clinical management. RESULTS Testing low VIO score samples identified an organism in only 10% of samples, and of these positive results, 33% were considered to represent contamination. Despite negative routine workup and no identified pathogen via BRBPS, broad antimicrobial treatment was continued in 85% of cases with a low VIO score. In contrast, specimens with high VIO scores were more predictably positive by BRBPS, identified organisms that were universally considered pathogens, and provided opportunities to target or de-escalate antimicrobial therapy. CONCLUSIONS This study describes the VIO scoring system to guide the identification of high-yield samples and steward the appropriate use of BRBPS testing.
Collapse
Affiliation(s)
- Rebekah E Dumm
- Pathology and Immunology, Division of Laboratory and Genomic Medicine, Washington University School of Medicine, Washington University, St Louis, MO, US
| | - Laurel J Glaser
- Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, US
| | - Kyle G Rodino
- Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, US
| |
Collapse
|
4
|
Drevinek P, Hollweck R, Lorenz MG, Lustig M, Bjarnsholt T. Direct 16S/18S rRNA Gene PCR Followed by Sanger Sequencing as a Clinical Diagnostic Tool for Detection of Bacterial and Fungal Infections: a Systematic Review and Meta-Analysis. J Clin Microbiol 2023; 61:e0033823. [PMID: 37367430 PMCID: PMC10575125 DOI: 10.1128/jcm.00338-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/28/2023] Open
Abstract
rRNA gene Sanger sequencing is being used for the identification of cultured pathogens. A new diagnostic approach is sequencing of uncultured samples by using the commercial DNA extraction and sequencing platform SepsiTest (ST). The goal was to analyze the clinical performance of ST with a focus on nongrowing pathogens and the impact on antibiotic therapy. A literature search used PubMed/Medline, Cochrane, Science Direct, and Google Scholar. Eligibility followed PRISMA-P criteria. Quality and risk of bias were assessed drawing on QUADAS-2 (quality assessment of diagnostic accuracy studies, revised) criteria. Meta-analyses were performed regarding accuracy metrics compared to standard references and the added value of ST in terms of extra found pathogens. We identified 25 studies on sepsis, infectious endocarditis, bacterial meningitis, joint infections, pyomyositis, and various diseases from routine diagnosis. Patients with suspected infections of purportedly sterile body sites originated from various hospital wards. The overall sensitivity (79%; 95% confidence interval [CI], 73 to 84%) and specificity (83%; 95% CI, 72 to 90%) were accompanied by large effect sizes. ST-related positivity was 32% (95% CI, 30 to 34%), which was significantly higher than the culture positivity (20%; 95% CI, 18 to 22%). The overall added value of ST was 14% (95% CI, 10 to 20%) for all samples. With 130 relevant taxa, ST uncovered high microbial richness. Four studies demonstrated changes of antibiotic treatment at 12% (95% CI, 9 to 15%) of all patients upon availability of ST results. ST appears to be an approach for the diagnosis of nongrowing pathogens. The potential clinical role of this agnostic molecular diagnostic tool is discussed regarding changes of antibiotic treatment in cases where culture stays negative.
Collapse
Affiliation(s)
- Pavel Drevinek
- Department of Medical Microbiology, 2nd Faculty of Medicine, Charles University and Motol University Hospital, Prague, Czech Republic
| | | | | | | | - Thomas Bjarnsholt
- Department of Clinical Microbiology, Centre for Diagnostics, Rigshospitalet, Copenhagen, Denmark
- Costerton Biofilm Center, University of Copenhagen, Copenhagen, Denmark
| |
Collapse
|
5
|
McHugh J, Saleh OA. Updates in Culture-Negative Endocarditis. Pathogens 2023; 12:1027. [PMID: 37623987 PMCID: PMC10459830 DOI: 10.3390/pathogens12081027] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2023] [Revised: 08/08/2023] [Accepted: 08/09/2023] [Indexed: 08/26/2023] Open
Abstract
Blood culture-negative infective endocarditis (BCNE) is a challenging condition associated with significant morbidity and mortality. This review discusses the epidemiology, microbiology, diagnosis, and treatment of BCNE considering advancements in molecular diagnostics and increased access to cardiac surgery. BCNE can be categorized into bacterial endocarditis with sterilized blood cultures due to previous antibiotic treatment, endocarditis caused by fastidious microorganisms, and true BCNE caused by intracellular organisms that cannot be cultured using traditional techniques. Non-infectious causes such as nonbacterial thrombotic endocarditis should also be considered. Diagnostic approaches involve thorough patient history; blood and serum testing, including appropriate handling of blood cultures; serological testing; and molecular techniques such as targeted and shotgun metagenomic sequencing. Where available, evaluation of explanted cardiac tissue through histopathology and molecular techniques is crucial. The therapy for BCNE depends on the likely causative agent and the presence of prosthetic material, with surgical intervention often required.
Collapse
Affiliation(s)
- Jack McHugh
- Division of Public Health, Infectious Diseases, Occupational Medicine, Mayo Clinic, Rochester, MN 55901, USA;
| | | |
Collapse
|
6
|
Coxiella burnetii and Bartonella Endocarditis Diagnosed by Metagenomic Next-Generation Sequencing. J Clin Med 2022; 11:jcm11237150. [PMID: 36498724 PMCID: PMC9736278 DOI: 10.3390/jcm11237150] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2022] [Revised: 11/07/2022] [Accepted: 11/24/2022] [Indexed: 12/05/2022] Open
Abstract
(1) Background: Culture-negative endocarditis is challenging to diagnose. Here, we retrospectively identified 23 cases of Coxiella burnetii and Bartonella endocarditis by metagenomic next-generation sequencing. (2) Methods: Twenty-three patients with culture-negative endocarditis were retrospectively enrolled from Guangdong Provincial People's Hospital (n = 23) between April 2019 and December 2021. Metagenomic next-generation sequencing was performed on blood (n = 22) and excised cardiac valvular tissue samples (n = 22) for etiological identification, and Sanger sequencing was performed for pathogenic diagnostic verification. The demographic and clinical data of the 23 patients were obtained from hospital electronic health records. (3) Results: A total of 23 male patients (median age, 56 years (interquartile range, 16)) with culture-negative endocarditis were diagnosed with Coxiella burnetii (n = 21) or Bartonella (n = 2) species infection by metagenomic next-generation sequencing. All patients underwent cardiac surgery. The resected tissue exhibited both a significantly higher number of unique suspected pathogen read-pairs and more unique pathogen read-pairs than the blood specimens. The results of Sanger sequencing tests on all remaining tissue and blood specimens were positive. Oral doxycycline was added to the antibiotic regimen for at least 1.5 years according to etiology. A total of 21 patients (91%) were discharged, and 20 patients were healthy at the 21-month (interquartile range, 15) follow-up visit. One patient exhibited endocarditis relapse with the same pathogen from inadequate antibiotic administration. The last 2 patients (9%) developed septic shock and multiple organ dysfunction syndrome postoperatively and died shortly after discharge. (4) Conclusions: CNE caused by C. burnetii and Bartonella species is challenging to diagnose and exhibits poor outcome due to delayed treatment. In response, mNGS, characterized by high sensitivity and rapid results, is an effective alternative for the etiological identification of C. burnetii and Bartonella endocarditis.
Collapse
|
7
|
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.
Collapse
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
| | | |
Collapse
|
8
|
Fida M, Khalil S, Abu Saleh O, Challener DW, Sohail MR, Yang JN, Pritt BS, Schuetz AN, Patel R. Diagnostic Value of 16S Ribosomal RNA Gene Polymerase Chain Reaction/Sanger Sequencing in Clinical Practice. Clin Infect Dis 2021; 73:961-968. [PMID: 34407178 DOI: 10.1093/cid/ciab167] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Accurate microbiologic diagnosis is important for appropriate management of infectious diseases. Sequencing-based molecular diagnostics are increasingly used for precision diagnosis of infections. However, their clinical utility is unclear. METHODS We conducted a retrospective analysis of specimens that underwent 16S ribosomal RNA (rRNA) gene polymerase chain reaction (PCR) followed by Sanger sequencing at our institution from April 2017 through March 2019. RESULTS A total of 566 specimens obtained from 460 patients were studied. Patients were considered clinically infected or noninfected based on final diagnosis and management. In 17% of patients, 16S rRNA PCR/sequencing was positive and in 5% of patients, this test led to an impact on clinical care. In comparison, bacterial cultures were positive in 21% of patients. Specimens with a positive Gram stain had 12 times greater odds of having a positive molecular result than those with a negative Gram stain (95% confidence interval for odds ratio, 5.2-31.4). Overall, PCR positivity was higher in cardiovascular specimens (37%) obtained from clinically infected patients, with bacterial cultures being more likely to be positive for musculoskeletal specimens (P < .001). 16S rRNA PCR/sequencing identified a probable pathogen in 10% culture-negative specimens. CONCLUSION 16S rRNA PCR/sequencing can play a role in the diagnostic evaluation of patients with culture-negative infections, especially those with cardiovascular infections.
Collapse
Affiliation(s)
- Madiha Fida
- Division of Infectious Diseases, Department of Medicine, Mayo Clinic, Rochester, Minnesota, USA.,Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
| | - Sarwat Khalil
- Division of Infectious Diseases, Department of Medicine, Mayo Clinic, Rochester, Minnesota, USA.,Division of Infectious Disease and International Medicine, Department of Medicine, University of Minnesota, Minneapolis, MN, USA
| | - Omar Abu Saleh
- Division of Infectious Diseases, Department of Medicine, Mayo Clinic, Rochester, Minnesota, USA
| | - Douglas W Challener
- Division of Infectious Diseases, Department of Medicine, Mayo Clinic, Rochester, Minnesota, USA
| | - Muhammad Rizwan Sohail
- Division of Infectious Diseases, Department of Medicine, Mayo Clinic, Rochester, Minnesota, USA.,Division of Infectious Disease, Department of Medicine, Baylor College of Medicine, Houston, Texas, USA
| | - Joshua N Yang
- Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
| | - Bobbi S Pritt
- Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
| | - Audrey N Schuetz
- Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
| | - Robin Patel
- Division of Infectious Diseases, Department of Medicine, Mayo Clinic, Rochester, Minnesota, USA.,Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
| |
Collapse
|
9
|
Van Belkum A, Gros MF, Ferry T, Lustig S, Laurent F, Durand G, Jay C, Rochas O, Ginocchio CC. Novel strategies to diagnose prosthetic or native bone and joint infections. Expert Rev Anti Infect Ther 2021; 20:391-405. [PMID: 34384319 DOI: 10.1080/14787210.2021.1967745] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
INTRODUCTION Bone and Joint Infections (BJI) are medically important, costly and occur in native and prosthetic joints. Arthroplasties will increase significantly in absolute numbers over time as well as the incidence of Prosthetic Joint Infections (PJI). Diagnosis of BJI and PJI is sub-optimal. The available diagnostic tests have variable effectiveness, are often below standard in sensitivity and/or specificity, and carry significant contamination risks during the collection of clinical samples. Improvement of diagnostics is urgently needed. AREAS COVERED We provide a narrative review on current and future diagnostic microbiology technologies. Pathogen identification, antibiotic resistance detection, and assessment of the epidemiology of infections via bacterial typing are considered useful for improved patient management. We confirm the continuing importance of culture methods and successful introduction of molecular, mass spectrometry-mediated and next-generation genome sequencing technologies. The diagnostic algorithms for BJI must be better defined, especially in the context of diversity of both disease phenotypes and clinical specimens rendered available. EXPERT OPINION Whether interventions in BJI or PJI are surgical or chemo-therapeutic (antibiotics and bacteriophages included), prior sensitive and specific pathogen detection remains a therapy-substantiating necessity. Innovative tests for earlier and more sensitive and specific detection of bacterial pathogens in BJI are urgently needed.
Collapse
Affiliation(s)
- Alex Van Belkum
- bioMérieux, Open Innovation and Partnerships, 3 Route De Port Michaud, La Balme Les Grottes, France
| | | | - Tristan Ferry
- Service Des Maladies Infectieuses Et Tropicales, Hospices Civils De Lyon, Hôpital De La Croix-Rousse, Lyon, France.,Maladies Infectieuses, Université Claude Bernard Lyon 1, Villeurbanne, France.,Centre Interrégional De Référence Pour La Prise En Charge Des Infections Ostéo-articulaires Complexes (Crioac Lyon), Hôpital De La Croix-Rousse, Lyon, France.,Ciri - Centre International De Recherche En Infectiologie, Inserm, U1111, Université́ Claude Bernard Lyon 1CNRS, UMR5308, Ecole Normale Supérieure De Lyon, Univ Lyon, Lyon, France
| | - Sebastien Lustig
- Maladies Infectieuses, Université Claude Bernard Lyon 1, Villeurbanne, France.,Service De Chirurgie Orthopédique, Hôpital De La Croix-Rousse, Lyon, France
| | - Frédéric Laurent
- Service Des Maladies Infectieuses Et Tropicales, Hospices Civils De Lyon, Hôpital De La Croix-Rousse, Lyon, France.,Ciri - Centre International De Recherche En Infectiologie, Inserm, U1111, Université́ Claude Bernard Lyon 1CNRS, UMR5308, Ecole Normale Supérieure De Lyon, Univ Lyon, Lyon, France
| | | | - Corinne Jay
- bioMérieux, BioFire Development Emea, Grenoble, France
| | - Olivier Rochas
- Corporate Business Development, bioMérieux, Marcy-l'Étoile, France
| | | |
Collapse
|
10
|
Identification of Leptotrichia goodfellowii infective endocarditis by next-generation sequencing of 16S rDNA amplicons. Cold Spring Harb Mol Case Stud 2021; 7:mcs.a005876. [PMID: 33288524 PMCID: PMC7903886 DOI: 10.1101/mcs.a005876] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Accepted: 11/23/2020] [Indexed: 12/02/2022] Open
Abstract
The oral aerotolerant anaerobe Leptotrichia goodfellowii is an unusual cause of endocarditis and is amenable to treatment with β-lactam antibiotics. Because this organism is difficult to identify by conventional methods, molecular detection is a key diagnostic modality. Broad-range 16S rDNA PCR followed by Sanger sequencing constitute the first-line molecular approach, yet poor DNA quality, contaminating DNA, or low template quantity make identification challenging. Here we report a case of culture-negative, aortic and mitral valve endocarditis in a 66-yr-old woman with a history of cardiomyopathy, atrial fibrillation with intracardiac pacer, poor dentition, and recent tooth infection. In this case, 16S rDNA amplicon Sanger sequencing was not sufficient for pathogen identification because of interfering DNA, but deconvolution of the clinical sample using reflexive next-generation amplicon sequencing enabled confident identification of a single pathogenic organism, L. goodfellowii. The patient developed a sigmoid colon perforation and died despite additional surgical treatment. Most Leptotrichia endocarditis cases have been subacute and have been successfully treated with antibiotics, with or without valve replacement. This case highlights both an unusual etiologic agent of endocarditis, as well as the rational utilization of advanced molecular diagnostics tools for characterizing serious infections.
Collapse
|
11
|
Ursenbach A, Schramm F, Séverac F, Hansmann Y, Lefebvre N, Ruch Y, Argemi X. Revised version (INFD-D-20-00242): impact of 16S rDNA sequencing on clinical treatment decisions: a single center retrospective study. BMC Infect Dis 2021; 21:190. [PMID: 33602178 PMCID: PMC7890971 DOI: 10.1186/s12879-021-05892-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Accepted: 02/12/2021] [Indexed: 11/23/2022] Open
Abstract
Background PCRs targeting 16S ribosomal DNA (16S PCR) followed by Sanger’s sequencing can identify bacteria from normally sterile sites and complement standard analyzes, but they are expensive. We conducted a retrospective study in the Strasbourg University Hospital to assess the clinical impact of 16S PCR sequencing on patients’ treatments according to different sample types. Methods From 2014 to 2018, 806 16S PCR samples were processed, and 191 of those were positive. Results Overall, the test impacted the treatment of 62 of the 191 patients (32%). The antibiotic treatment was rationalized in 31 patients (50%) and extended in 24 patients (39%), and an invasive procedure was chosen for 7 patients (11%) due to the 16S PCR sequencing results. Positive 16S PCR sequencing results on cerebrospinal fluid (CSF) had a greater impact on patients’ management than positive ones on cardiac valves (p = 0.044). The clinical impact of positive 16S PCR sequencing results were significantly higher when blood cultures were negative (p < 0.001), and this difference appeared larger when both blood and sample cultures were negative (p < 0.001). The diagnostic contribution of 16S PCR was higher in patients with previous antibiotic treatment (p < 0.001). Conclusion In all, 16S PCR analysis has a significant clinical impact on patient management, particularly for suspected CSF infections, for patients with culture-negative samples and for those with previous antibiotic treatments. Supplementary Information The online version contains supplementary material available at 10.1186/s12879-021-05892-4.
Collapse
Affiliation(s)
- Axel Ursenbach
- Laboratoire de bactériologie, Faculté de Médecine, Université de Strasbourg, 3 rue Koeberlé, 67000, Strasbourg, France.
| | - Frédéric Schramm
- Laboratoire de bactériologie, Faculté de Médecine, Université de Strasbourg, 3 rue Koeberlé, 67000, Strasbourg, France
| | - François Séverac
- Service de Santé Publique, Hôpitaux Universitaires de Strasbourg, Strasbourg, France
| | - Yves Hansmann
- Maladies Infectieuses et Tropicales, Hôpitaux Universitaires de Strasbourg, Strasbourg, France
| | - Nicolas Lefebvre
- Maladies Infectieuses et Tropicales, Hôpitaux Universitaires de Strasbourg, Strasbourg, France
| | - Yvon Ruch
- Maladies Infectieuses et Tropicales, Hôpitaux Universitaires de Strasbourg, Strasbourg, France
| | - Xavier Argemi
- Maladies Infectieuses et Tropicales, Hôpitaux Universitaires de Strasbourg, Strasbourg, France
| |
Collapse
|
12
|
Esquer Garrigos Z, Sohail MR, Greenwood-Quaintance KE, Cunningham SA, Vijayvargiya P, Fida M, Friedman PA, Mandrekar J, DeSimone DC, Baddour LM, Patel R. Molecular Approach to Diagnosis of Cardiovascular Implantable Electronic Device Infection. Clin Infect Dis 2021; 70:898-906. [PMID: 30944928 DOI: 10.1093/cid/ciz266] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2018] [Accepted: 03/26/2019] [Indexed: 12/27/2022] Open
Abstract
BACKGROUND Sonicate fluid (SF), a solution derived from vortexing and sonication of explanted cardiovascular implantable electronic devices (CIEDs), is a higher-yield specimen compared with swabs or tissues for culture-based detection of microorganisms associated with CIED infection. Despite this, SF culture fails to identify a causative organism in ~50% of cases. We aimed to evaluate the diagnostic performance of 16S ribosomal RNA gene (rRNA) polymerase chain reaction (PCR)/sequencing of SF and compare it with that of SF culture. METHODS We identified 322 SF specimens from extracted CIEDs and reviewed clinical data for each patient. Subjects were classified as having or not having CIED infection. Cases were subcategorized as culture negative if no significant growth was reported from SF cultures and as culture positive if an organism was detected above predefined thresholds. 16S rRNA PCR/sequencing was performed, with the organisms identified reported according to Clinical and Laboratory Standards Institute guidelines for sequence data interpretation. RESULTS A total of 278 SF samples corresponded to infected cases, of which 160 were culture positive and 118 culture negative. The remaining 44 were from noninfected cases, of which 2 were culture positive. Compared with SF culture, the sensitivity of 16S rRNA PCR/sequencing was higher (64% vs 57.5%, P = .003). 16S rRNA PCR/sequencing detected a potential pathogen in 28 of 118 culture-negative cases, identifying staphylococci in the majority (18/28). CONCLUSIONS 16S rRNA PCR/sequencing has higher sensitivity to detect bacteria in SF from extracted CIEDs than does SF culture.
Collapse
Affiliation(s)
- Zerelda Esquer Garrigos
- Division of Infectious Diseases Mayo Clinic College of Medicine and Science, Rochester, Minnesota
| | - M Rizwan Sohail
- Division of Infectious Diseases Mayo Clinic College of Medicine and Science, Rochester, Minnesota.,Department of Cardiovascular Diseases, Mayo Clinic College of Medicine and Science, Rochester, Minnesota
| | | | - Scott A Cunningham
- Division of Infectious Diseases Mayo Clinic College of Medicine and Science, Rochester, Minnesota
| | - Prakhar Vijayvargiya
- Division of Infectious Diseases Mayo Clinic College of Medicine and Science, Rochester, Minnesota
| | - Madiha Fida
- Division of Infectious Diseases Mayo Clinic College of Medicine and Science, Rochester, Minnesota
| | - Paul A Friedman
- Department of Cardiovascular Diseases, Mayo Clinic College of Medicine and Science, Rochester, Minnesota
| | - Jayawant Mandrekar
- Department of Health Sciences Research, Mayo Clinic College of Medicine and Science, Rochester, Minnesota
| | - Daniel C DeSimone
- Division of Infectious Diseases Mayo Clinic College of Medicine and Science, Rochester, Minnesota.,Department of Cardiovascular Diseases, Mayo Clinic College of Medicine and Science, Rochester, Minnesota
| | - Larry M Baddour
- Division of Infectious Diseases Mayo Clinic College of Medicine and Science, Rochester, Minnesota.,Department of Cardiovascular Diseases, Mayo Clinic College of Medicine and Science, Rochester, Minnesota
| | - Robin Patel
- Division of Infectious Diseases Mayo Clinic College of Medicine and Science, Rochester, Minnesota
| |
Collapse
|
13
|
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
|
14
|
Added diagnostic value and impact on antimicrobial therapy of 16S rRNA PCR and amplicon sequencing on resected heart valves in infective endocarditis: a prospective cohort study. Clin Microbiol Infect 2017. [DOI: 10.1016/j.cmi.2017.06.008] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
|
15
|
Abstract
Infective endocarditis is life-threatening; identification of the underlying etiology informs optimized individual patient management. Changing epidemiology, advances in blood culture techniques, and new diagnostics guide the application of laboratory testing for diagnosis of endocarditis. Blood cultures remain the standard test for microbial diagnosis, with directed serological testing (i.e., Q fever serology, Bartonella serology) in culture-negative cases. Histopathology and molecular diagnostics (e.g., 16S rRNA gene PCR/sequencing, Tropheryma whipplei PCR) may be applied to resected valves to aid in diagnosis. Herein, we summarize recent knowledge in this area and propose a microbiologic and pathological algorithm for endocarditis diagnosis.
Collapse
|
16
|
Laboratory Approach to the Diagnosis of Culture-Negative Infective Endocarditis. Heart Lung Circ 2017; 26:763-771. [PMID: 28372886 DOI: 10.1016/j.hlc.2017.02.009] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2017] [Accepted: 02/01/2017] [Indexed: 12/31/2022]
Abstract
Blood-culture negative endocarditis (BCNE) accounts for up to 35% of all cases of infective endocarditis (IE) and is a serious life-threatening condition with considerable morbidity and mortality. Rapid detection and identification of the causative pathogen is essential for timely, directed therapy. Blood-culture negative endocarditis presents a diagnostic and therapeutic challenge. Causes of BCNE are varied including: treatment with antibiotic agents prior to blood culture collection; sub-optimal specimen collection; and/or infection due to fastidious (eg. nutritionally variant streptococci), intracellular (eg. Coxiella burnetii, Bartonella species) or non-culturable or difficult to culture organisms (eg. Mycobacteria, Tropheryma whipplei and fungi); as well as non-infective aetiologies. Here, we review aetiological and diagnostic approaches to BCNE including newer molecular based techniques, with a brief summary of imaging investigation and treatment principles.
Collapse
|
17
|
Akram A, Maley M, Gosbell I, Nguyen T, Chavada R. Utility of 16S rRNA PCR performed on clinical specimens in patient management. Int J Infect Dis 2017; 57:144-149. [PMID: 28216180 DOI: 10.1016/j.ijid.2017.02.006] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2016] [Revised: 02/07/2017] [Accepted: 02/08/2017] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND Broad-range 16S rRNA PCR can be used for the detection and identification of bacteria from clinical specimens in patients for whom there is a high suspicion of infection and cultures are negative. The aims of this study were (1) to compare 16S rRNA PCR results with microbiological culture results, (2) to assess the utility of 16S rRNA PCR with regard to antimicrobial therapy, and (3) to compare the yield of 16S rRNA PCR for different types of clinical specimen and to perform a cost analysis of the test. METHODS A retrospective study was performed on different clinical specimens which had 16S performed over 3 years (2012-2015). Standard microbiological cultures were performed on appropriate media, as per the laboratory protocol. Patient clinical and microbiological data were obtained from the electronic medical records and laboratory information system, respectively. 16S rRNA PCR was performed in a reference laboratory using a validated method for amplification and sequencing. The outcomes assessed were the performance of 16S rRNA PCR, change of antimicrobials (rationalization, cessation, or addition), and duration of therapy. Concordance of 16S rRNA PCR with bacterial cultures was also determined for tissue specimens. RESULTS Thirty-two patients were included in the study, for whom an equal number of specimens (n=32) were sent for 16S rRNA PCR. 16S rRNA PCR could identify an organism in 10 of 32 cases (31.2%), of which seven were culture-positive and three were culture-negative. The sensitivity was 58% (confidence interval (CI) 28.59-83.5%) and specificity was 85% (CI 61.13-96%), with a positive predictive value of 70% (CI 35.3-91.9%) and negative predictive value of 77.2% (CI 54.17-91.3%). Antimicrobial therapy was rationalized after 16S rRNA PCR results in five patients (15.6%) and was ceased in four based on negative results (12.5%). Overall the 16S rRNA PCR result had an impact on antimicrobial therapy in 28% of patients (9/32). The highest concordance of 16S rRNA PCR with bacterial culture was found for heart valve tissue (80%), followed by joint fluid/tissue (50%). CONCLUSIONS Despite the low diagnostic yield, results of 16S rRNA PCR can still have a significant impact on patient management due to rationalization or cessation of the antimicrobial therapy. The yield of 16S rRNA PCR was highest for heart valves.
Collapse
Affiliation(s)
- A Akram
- Department of Microbiology and Infectious Diseases, Sydney South West Pathology Services, Liverpool Hospital, Liverpool, NSW, Australia
| | - M Maley
- Department of Microbiology and Infectious Diseases, Sydney South West Pathology Services, Liverpool Hospital, Liverpool, NSW, Australia
| | - I Gosbell
- Department of Microbiology and Infectious Diseases, Sydney South West Pathology Services, Liverpool Hospital, Liverpool, NSW, Australia; Antibiotic Resistance and Mobile Elements Group, Ingham Institute for Applied Medical Research, Liverpool, NSW, Australia; Molecular Medicine Research Group, School of Medicine, University of Western Sydney, Campbelltown, NSW, Australia
| | - T Nguyen
- Institute of Clinical Pathology and Medical Research, Westmead Hospital, Westmead, NSW, Australia
| | - R Chavada
- Department of Microbiology and Infectious Diseases, Pathology North, Gosford/Wyong Hospitals, Gosford, NSW, Australia.
| |
Collapse
|
18
|
Hirano K, Tokui T, Inagaki M, Fujii T, Maze Y, Toyoshima H. Aggregatibacter aphrophilus infective endocarditis confirmed by broad-range PCR diagnosis: A case report. Int J Surg Case Rep 2017; 31:150-153. [PMID: 28152491 PMCID: PMC5288324 DOI: 10.1016/j.ijscr.2017.01.041] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2016] [Revised: 01/17/2017] [Accepted: 01/17/2017] [Indexed: 12/16/2022] Open
Abstract
INTRODUCTION Aggregatibacter aphrophilus is a rare cause of infective endocarditis. This pathogen is difficult to identify with common culture methods, which can lead to incorrect diagnosis and treatment. PRESENTATION OF CASE A 72-year-old woman was admitted to a community hospital with a persistent high fever and deteriorating renal function. Based on negative blood culture and positive serum proteinase 3 anti-neutrophil cytoplasmic antibody (PR3-ANCA), acute renal failure associated with ANCA-rerated vasculitis was initially suspected. However, the patient developed heart failure soon afterward; echocardiography showed mitral insufficiency with mobile vegetation attached to the mitral valve, indicating infective endocarditis. After transfer to our hospital, the patient underwent mitral valve repair. Broad-range polymerase chain reaction (br-PCR) and sequencing identified Aggregatibacter aphrophilus in the excised vegetation. The patient had a good postoperative course, with recovery of renal function. CONCLUSION A rare disease, Aggregatibacter aphrophilus infective endocarditis was successfully treated with surgical repair and appropriate antibiotic therapy. To avoid misdiagnosis, br-PCR testing should be performed in patients with blood culture-negative endocarditis.
Collapse
Affiliation(s)
- Koji Hirano
- Department of Thoracic and Cardiovascular Surgery, Japan Red Cross Ise Hospital, Ise, Japan.
| | - Toshiya Tokui
- Department of Thoracic and Cardiovascular Surgery, Japan Red Cross Ise Hospital, Ise, Japan
| | - Masahiro Inagaki
- Department of Thoracic and Cardiovascular Surgery, Japan Red Cross Ise Hospital, Ise, Japan
| | - Taro Fujii
- Department of Thoracic and Cardiovascular Surgery, Japan Red Cross Ise Hospital, Ise, Japan
| | - Yasumi Maze
- Department of Thoracic and Cardiovascular Surgery, Japan Red Cross Ise Hospital, Ise, Japan
| | - Hirokazu Toyoshima
- Department of Infectious Diseases, Japan Red Cross Ise Hospital, Ise, Japan
| |
Collapse
|
19
|
Kotova EO, Domonova EA, Karaulova YL, Milto AS, Pisaryuk AS, Silveistrova OY, Shipulina OY, Shipulin GA, Moiseev VS. [Infective endocarditis: Importance of molecular biological techniques in etiological diagnosis]. TERAPEVT ARKH 2016; 88:62-67. [PMID: 28005033 DOI: 10.17116/terarkh2016881162-67] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
AIM To investigate the specific features of conventional bacteriological methods and current molecular biological techniques for the etiological diagnosis of infective endocarditis (IE). SUBJECTS AND METHODS Examinations were made in 53 patients treated at City Clinical Hospital Sixty-Four, Moscow Healthcare Department, in 2012-2015 who underwent simultaneous bacteriological and molecular biological (polymerase chain reaction (PCR) or PCR with further sequencing) examinations of blood or resected cardiac valve tissues. RESULTS The investigation included 53 patients (31 men; median age, 62 years) with IE (Duke 2009); its primary form was observed in 32 (60.4%) patients. Blood bacteriological tests and PCR assays were positive in 28 (52.8%) and 34 (64.2%) patients, respectively. There were concordant results in 21 of the 28 positive blood culture cases and discordant results in 7 (25%); at the same time 3 cases showed a compete discordance in the detected causative agents (the growth of Enterococcus spp. was revealed by bacteriological examination and that of Staphylococcus spp., Streptococcus spp., and Escherichia coli by DNA PCR) and a pathogen could not be identified by DNA PCR in 4 patients who had positive blood bacteriological results. The positive PCR results for cocci and fungi were obtained in 10 of the 25 (47.2%) examinees with culture-negative IE. Rare causative agents were not revealed. The tissues obtained from 8 resected damaged heart valves displayed a wider spectrum of pathogens than did blood samples, which was associated with the formation of bacterial films. CONCLUSION The etiological agent of IE was revealed in venous blood by bacteriological examination in 52.8% of the examinees, by PCR in 64.2%, and by either in 71.7%. There were concordant and discordant results in 67.9 and 32.1% of the patients, respectively; among whom 18.9% were found to have pathogen DNA revealed by PCR in culture-negative IE.
Collapse
Affiliation(s)
- E O Kotova
- Peoples' Friendship University of Russia, Ministry of Education and Science of Russia, Moscow, Russia
| | - E A Domonova
- Central Research Institute of Epidemiology, Russian Federal Service for Supervision of Consumer Rights Protection and Human Welfare, Moscow, Russia
| | - Yu L Karaulova
- Peoples' Friendship University of Russia, Ministry of Education and Science of Russia, Moscow, Russia; City Clinical Hospital Sixty-Four, Moscow Healthcare Department, Moscow, Russia
| | - A S Milto
- City Clinical Hospital Sixty-Four, Moscow Healthcare Department, Moscow, Russia
| | - A S Pisaryuk
- Peoples' Friendship University of Russia, Ministry of Education and Science of Russia, Moscow, Russia
| | - O Yu Silveistrova
- Central Research Institute of Epidemiology, Russian Federal Service for Supervision of Consumer Rights Protection and Human Welfare, Moscow, Russia
| | - O Yu Shipulina
- Central Research Institute of Epidemiology, Russian Federal Service for Supervision of Consumer Rights Protection and Human Welfare, Moscow, Russia
| | - G A Shipulin
- Central Research Institute of Epidemiology, Russian Federal Service for Supervision of Consumer Rights Protection and Human Welfare, Moscow, Russia
| | - V S Moiseev
- Peoples' Friendship University of Russia, Ministry of Education and Science of Russia, Moscow, Russia
| |
Collapse
|
20
|
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.
Collapse
|
21
|
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.
Collapse
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.
| |
Collapse
|
22
|
Advantages and Limitations of Direct PCR Amplification of Bacterial 16S-rDNA from Resected Heart Tissue or Swabs Followed by Direct Sequencing for Diagnosing Infective Endocarditis: A Retrospective Analysis in the Routine Clinical Setting. BIOMED RESEARCH INTERNATIONAL 2016; 2016:7923874. [PMID: 27110570 PMCID: PMC4823489 DOI: 10.1155/2016/7923874] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/30/2015] [Revised: 02/24/2016] [Accepted: 03/03/2016] [Indexed: 12/20/2022]
Abstract
Infective endocarditis (IE) is a life-threatening disease that is associated with high morbidity and mortality. Its long-term prognosis strongly depends on a timely and optimized antibiotic treatment. Therefore, identification of the causative pathogen is crucial and currently based on blood cultures followed by characterization and susceptibility testing of the isolate. However, antibiotic treatment starting prior to blood sampling or IE caused by fastidious or intracellular microorganisms may cause negative culture results. Here we investigate the additional diagnostic value of broad-range PCR in combination with direct sequencing on resected heart tissue or swabs in patients with tissue or swab culture-negative IE in a routine clinical setting. Sensitivity, specificity, and positive and negative predictive values of broad-range PCR from diagnostic material in our patients were 33.3%, 76.9%, 90.9%, and 14.3%, respectively. We identified a total of 20 patients (21.5%) with tissue or culture-negative IE who profited by the additional application of broad-range PCR. We conclude that broad-range PCR on resected heart tissue or swabs is an important complementary diagnostic approach. It should be seen as an indispensable new tool for both the therapeutic and diagnostic management of culture-negative IE and we thus propose its possible inclusion in Duke's diagnostic classification scheme.
Collapse
|