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Bianco G, Boattini M, Comini S, Bondi A, Curtoni A, Piccinini G, Musso T, Broccolo F, Cavallo R, Nordmann P, Costa C. Detection of volatile organic compounds as new paradigm to accelerate antimicrobial susceptibility testing: performance evaluation of VITEK® REVEAL™. J Antimicrob Chemother 2024:dkae219. [PMID: 38958300 DOI: 10.1093/jac/dkae219] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2024] [Accepted: 06/13/2024] [Indexed: 07/04/2024] Open
Abstract
OBJECTIVES The measurement of VOCs release in the headspace of a bacterial culture represents a new approach to rapidly assess antimicrobial susceptibility. Herein, we evaluated the diagnostic performance of the VITEK® REVEAL™ system directly from a collection of Gram-negative positive blood cultures. MATERIALS AND METHODS One hundred and twenty-eight positive blood cultures were included in the analysis (Enterobacterales, n = 95; Pseudomonas aeruginosa, n = 21; Acinetobacter baumannii complex, n = 12). Samples were processed using VITEK® REVEAL™ according to the manufacturer's recommendations, and MICs of 22 antimicrobials were compared with those obtained using reference methods. Categorical agreement (CA), essential agreement (EA) and categorical errors were calculated. RESULTS Overall, 2220 strain/antibiotic pair combinations were analysed. Of these, most were classified as resistant by reference antimicrobial susceptibility testing (1091/2220; 48.7%). The overall CA and EA were 97.6% and 97.7%, respectively. CA ranged from 97.5% in Enterobacterales to 97.9% in both P. aeruginosa and A. baumannii complex. The overall number of categorical discrepancies were: 18 very major errors (1.6%), 13 major errors (1.2%) and 22 minor errors (2.4%). EA ranged from 95.2% in P. aeruginosa to 98.1% in Enterobacterales. Screening test for ESBL phenotype was positive, indeterminate and negative in 13.7%, 32.6% and 27.4% of Enterobacterales isolates tested by both VITEK® REVEAL™ and the reference method, showing 100% CA. CONCLUSIONS VITEK® REVEAL™ represents a reliable tool to obtain antimicrobial susceptibility results of the main Gram-negative species directly from positive blood cultures with time to results of less than 8 h.
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Affiliation(s)
- Gabriele Bianco
- Department of Experimental Medicine, University of Salento, Lecce, Italy
- Microbiology and Virology Unit, University Hospital Città della Salute e della Scienza di Torino, Turin, Italy
| | - Matteo Boattini
- Microbiology and Virology Unit, University Hospital Città della Salute e della Scienza di Torino, Turin, Italy
- Department of Public Health and Paediatrics, University of Turin, Turin, Italy
- Lisbon Academic Medical Centre, Lisbon, Portugal
| | - Sara Comini
- Operative Unit of Clinical Pathology, Carlo Urbani Hospital, Ancona, Italy
| | - Alessandro Bondi
- Microbiology and Virology Unit, University Hospital Città della Salute e della Scienza di Torino, Turin, Italy
- Department of Public Health and Paediatrics, University of Turin, Turin, Italy
| | - Antonio Curtoni
- Microbiology and Virology Unit, University Hospital Città della Salute e della Scienza di Torino, Turin, Italy
- Department of Public Health and Paediatrics, University of Turin, Turin, Italy
| | - Giorgia Piccinini
- Department of Public Health and Paediatrics, University of Turin, Turin, Italy
- PhD National Programme in One Health Approaches to Infectious Diseases and Life Science Research, Department of Public Health, Experimental and Forensic Medicine, University of Pavia, Pavia 27100, Italy
| | - Tiziana Musso
- Department of Public Health and Paediatrics, University of Turin, Turin, Italy
| | - Francesco Broccolo
- Department of Experimental Medicine, University of Salento, Lecce, Italy
| | - Rossana Cavallo
- Microbiology and Virology Unit, University Hospital Città della Salute e della Scienza di Torino, Turin, Italy
- Department of Public Health and Paediatrics, University of Turin, Turin, Italy
| | - Patrice Nordmann
- Medical and Molecular Microbiology, Faculty of Science and Medicine, University of Fribourg, 1700 Fribourg, Switzerland
- Swiss National Reference Center for Emerging Antibiotic Resistance (NARA), University of Fribourg, 1700 Fribourg, Switzerland
- INSERM European Unit (IAME), University of Fribourg, 1700 Fribourg, Switzerland
- Institute for Microbiology, University of Lausanne and University Hospital Centre, 1011 Lausanne, Switzerland
| | - Cristina Costa
- Microbiology and Virology Unit, University Hospital Città della Salute e della Scienza di Torino, Turin, Italy
- Department of Public Health and Paediatrics, University of Turin, Turin, Italy
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Spoelstra GB, Blok SN, Reali Nazario L, Noord L, Fu Y, Simeth NA, IJpma FFA, van Oosten M, van Dijl JM, Feringa BL, Szymanski W, Elsinga PH. Synthesis and preclinical evaluation of novel 18F-vancomycin-based tracers for the detection of bacterial infections using positron emission tomography. Eur J Nucl Med Mol Imaging 2024; 51:2583-2596. [PMID: 38644432 PMCID: PMC11224109 DOI: 10.1007/s00259-024-06717-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Accepted: 04/14/2024] [Indexed: 04/23/2024]
Abstract
INTRODUCTION Bacterial infections are a major problem in medicine, and the rapid and accurate detection of such infections is essential for optimal patient outcome. Bacterial infections can be diagnosed by nuclear imaging, but most currently available modalities are unable to discriminate infection from sterile inflammation. Bacteria-targeted positron emission tomography (PET) tracers have the potential to overcome this hurdle. In the present study, we compared three 18F-labelled PET tracers based on the clinically applied antibiotic vancomycin for targeted imaging of Gram-positive bacteria. METHODS [18F]FB-NHS and [18F]BODIPY-FL-NHS were conjugated to vancomycin. The resulting conjugates, together with our previously developed [18F]PQ-VE1-vancomycin, were tested for stability, lipophilicity, selective binding to Gram-positive bacteria, antimicrobial activity and biodistribution. For the first time, the pharmacokinetic properties of all three tracers were compared in healthy animals to identify potential binding sites. RESULTS [18F]FB-vancomycin, [18F]BODIPY-FL-vancomycin, and [18F]PQ-VE1-vancomycin were successfully synthesized with radiochemical yields of 11.7%, 2.6%, and 0.8%, respectively. [18F]FB-vancomycin exhibited poor in vitro and in vivo stability and, accordingly, no bacterial binding. In contrast, [18F]BODIPY-FL-vancomycin and [18F]PQ-VE1-vancomycin showed strong and specific binding to Gram-positive bacteria, including methicillin-resistant Staphylococcus aureus (MRSA), which was outcompeted by unlabeled vancomycin only at concentrations exceeding clinically relevant vancomycin blood levels. Biodistribution showed renal clearance of [18F]PQ-VE1-vancomycin and [18F]BODIPY-FL-vancomycin with low non-specific accumulation in muscles, fat and bones. CONCLUSION Here we present the synthesis and first evaluation of the vancomycin-based PET tracers [18F]BODIPY-FL-vancomycin and [18F]PQ-VE1-vancomycin for image-guided detection of Gram-positive bacteria. Our study paves the way towards real-time bacteria-targeted diagnosis of soft tissue and implant-associated infections that are oftentimes caused by Gram-positive bacteria, even after prophylactic treatment with vancomycin.
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Affiliation(s)
- G B Spoelstra
- Department of Nuclear Medicine and Molecular Imaging, University of Groningen, University Medical Center Groningen, Hanzeplein 1, Groningen, 9713GZ, The Netherlands
| | - S N Blok
- Department of Nuclear Medicine and Molecular Imaging, University of Groningen, University Medical Center Groningen, Hanzeplein 1, Groningen, 9713GZ, The Netherlands
| | - L Reali Nazario
- Department of Nuclear Medicine and Molecular Imaging, University of Groningen, University Medical Center Groningen, Hanzeplein 1, Groningen, 9713GZ, The Netherlands
| | - L Noord
- Department of Nuclear Medicine and Molecular Imaging, University of Groningen, University Medical Center Groningen, Hanzeplein 1, Groningen, 9713GZ, The Netherlands
| | - Y Fu
- Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 7, Groningen, 9747AG, The Netherlands
| | - N A Simeth
- Institute for Organic and Biomolecular Chemistry, Department of Chemistry, University of Göttingen, Tammannstraβe 2, 37077, Göttingen, Germany
| | - F F A IJpma
- Department of Trauma Surgery, University of Groningen, University Medical Center Groningen, Hanzeplein 1, Groningen, 9713GZ, The Netherlands
| | - M van Oosten
- Department of Medical Microbiology and Infection Prevention, University of Groningen, University Medical Center Groningen, Hanzeplein 1, Groningen, 9713GZ, The Netherlands
| | - J M van Dijl
- Department of Medical Microbiology and Infection Prevention, University of Groningen, University Medical Center Groningen, Hanzeplein 1, Groningen, 9713GZ, The Netherlands
| | - B L Feringa
- Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 7, Groningen, 9747AG, The Netherlands
| | - W Szymanski
- Department of Radiology, University of Groningen, University Medical Center Groningen, Hanzeplein 1, Groningen, 9713GZ, The Netherlands
- Department of Medicinal Chemistry, Photopharmacology and Imaging, University of Groningen, Groningen Research Institute of Pharmacy, Antonius Deusinglaan 1, Groningen, 9713AV, The Netherlands
| | - P H Elsinga
- Department of Nuclear Medicine and Molecular Imaging, University of Groningen, University Medical Center Groningen, Hanzeplein 1, Groningen, 9713GZ, The Netherlands.
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Thomas JK, Clark J, Arora V, Burgess DS, Burgess DR, Mynatt RP, VanHoose JD, Wallace KL, Cotner SE. Performance of ePlex® blood culture identification panels in clinical isolates and characterization of antimicrobial stewardship opportunities. Diagn Microbiol Infect Dis 2024; 109:116269. [PMID: 38692201 DOI: 10.1016/j.diagmicrobio.2024.116269] [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: 08/03/2023] [Revised: 03/08/2024] [Accepted: 03/14/2024] [Indexed: 05/03/2024]
Abstract
We assessed the performance of GenMark's ePlex® Blood Culture Identification (BCID) Panels for overall agreement of organism identification and resistance mechanism detection with standard microbiologic methods. This study included patients with a positive blood culture from May 2020 to January 2021. The primary outcomes were to assess concordance of ePlex® organism identification with standard identification methods and concordance of ePlex® genotypic resistance mechanism detection with standard phenotypic susceptibility testing. Secondary outcomes included panel specific performance and characterization of antimicrobial stewardship opportunities. The overall identification concordance rate in 1276 positive blood cultures was 98.1%. The overall concordance for the presence of resistance markers was 98.2% and concordance for the absence of resistance markers was 100%. A majority of ePlex® results (69.5%) represented opportunities for potential antimicrobial stewardship intervention. High concordance rates between the ePlex® BCID panels and standard identification and susceptibility methods enable utilization of results to guide rapid antimicrobial optimization.
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Affiliation(s)
- Jenni K Thomas
- Department of Pharmacy Services, University of Kentucky HealthCare, Lexington, KY, USA
| | - Justin Clark
- University of Kentucky College of Pharmacy, Lexington, KY, USA
| | - Vaneet Arora
- University of Kentucky College of Medicine, Lexington, KY, USA; Department of Pathology and Laboratory Medicine, University of Kentucky HealthCare, Lexington, KY, USA
| | - David S Burgess
- University of Kentucky College of Pharmacy, Lexington, KY, USA
| | - Donna R Burgess
- Department of Pharmacy Services, University of Kentucky HealthCare, Lexington, KY, USA; University of Kentucky College of Pharmacy, Lexington, KY, USA
| | - Ryan P Mynatt
- Department of Pharmacy Services, University of Kentucky HealthCare, Lexington, KY, USA
| | - Jeremy D VanHoose
- Department of Pharmacy Services, University of Kentucky HealthCare, Lexington, KY, USA
| | - Katie L Wallace
- Department of Pharmacy Services, University of Kentucky HealthCare, Lexington, KY, USA; University of Kentucky College of Pharmacy, Lexington, KY, USA
| | - Sarah E Cotner
- Department of Pharmacy Services, University of Kentucky HealthCare, Lexington, KY, USA; University of Kentucky College of Pharmacy, Lexington, KY, USA.
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Sartelli M, Tascini C, Coccolini F, Dellai F, Ansaloni L, Antonelli M, Bartoletti M, Bassetti M, Boncagni F, Carlini M, Cattelan AM, Cavaliere A, Ceresoli M, Cipriano A, Cortegiani A, Cortese F, Cristini F, Cucinotta E, Dalfino L, De Pascale G, De Rosa FG, Falcone M, Forfori F, Fugazzola P, Gatti M, Gentile I, Ghiadoni L, Giannella M, Giarratano A, Giordano A, Girardis M, Mastroianni C, Monti G, Montori G, Palmieri M, Pani M, Paolillo C, Parini D, Parruti G, Pasero D, Pea F, Peghin M, Petrosillo N, Podda M, Rizzo C, Rossolini GM, Russo A, Scoccia L, Sganga G, Signorini L, Stefani S, Tumbarello M, Tumietto F, Valentino M, Venditti M, Viaggi B, Vivaldi F, Zaghi C, Labricciosa FM, Abu-Zidan F, Catena F, Viale P. Management of intra-abdominal infections: recommendations by the Italian council for the optimization of antimicrobial use. World J Emerg Surg 2024; 19:23. [PMID: 38851757 PMCID: PMC11162065 DOI: 10.1186/s13017-024-00551-w] [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: 03/26/2024] [Accepted: 06/01/2024] [Indexed: 06/10/2024] Open
Abstract
Intra-abdominal infections (IAIs) are common surgical emergencies and are an important cause of morbidity and mortality in hospital settings, particularly if poorly managed. The cornerstones of effective IAIs management include early diagnosis, adequate source control, appropriate antimicrobial therapy, and early physiologic stabilization using intravenous fluids and vasopressor agents in critically ill patients. Adequate empiric antimicrobial therapy in patients with IAIs is of paramount importance because inappropriate antimicrobial therapy is associated with poor outcomes. Optimizing antimicrobial prescriptions improves treatment effectiveness, increases patients' safety, and minimizes the risk of opportunistic infections (such as Clostridioides difficile) and antimicrobial resistance selection. The growing emergence of multi-drug resistant organisms has caused an impending crisis with alarming implications, especially regarding Gram-negative bacteria. The Multidisciplinary and Intersociety Italian Council for the Optimization of Antimicrobial Use promoted a consensus conference on the antimicrobial management of IAIs, including emergency medicine specialists, radiologists, surgeons, intensivists, infectious disease specialists, clinical pharmacologists, hospital pharmacists, microbiologists and public health specialists. Relevant clinical questions were constructed by the Organizational Committee in order to investigate the topic. The expert panel produced recommendation statements based on the best scientific evidence from PubMed and EMBASE Library and experts' opinions. The statements were planned and graded according to the Grading of Recommendations Assessment, Development and Evaluation (GRADE) hierarchy of evidence. On November 10, 2023, the experts met in Mestre (Italy) to debate the statements. After the approval of the statements, the expert panel met via email and virtual meetings to prepare and revise the definitive document. This document represents the executive summary of the consensus conference and comprises three sections. The first section focuses on the general principles of diagnosis and treatment of IAIs. The second section provides twenty-three evidence-based recommendations for the antimicrobial therapy of IAIs. The third section presents eight clinical diagnostic-therapeutic pathways for the most common IAIs. The document has been endorsed by the Italian Society of Surgery.
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Affiliation(s)
- Massimo Sartelli
- Department of Surgery, Macerata Hospital, Via Santa Lucia 2, 62100, Macerata, Italy.
| | - Carlo Tascini
- Infectious Diseases Clinic, Santa Maria Della Misericordia University Hospital of Udine, ASUFC, Udine, Italy
- Infectious Diseases Clinic, Department of Medicine (DAME), University of Udine, Udine, Italy
| | - Federico Coccolini
- Department of General, Emergency and Trauma Surgery, Azienda Ospedaliero Universitaria Pisana, University Hospital, Pisa, Italy
| | - Fabiana Dellai
- Infectious Diseases Clinic, Department of Medicine (DAME), University of Udine, Udine, Italy
| | - Luca Ansaloni
- Division of General Surgery, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
- Department of Clinical, Diagnostic and Pediatric Sciences, University of Pavia, Pavia, Italy
| | - Massimo Antonelli
- Dipartimento di Scienze Biotecnologiche di Base, Cliniche Intensivologiche e Perioperatorie, Università Cattolica del Sacro Cuore, Rome, Italy
- Dipartimento di Scienze Dell'Emergenza, Anestesiologiche e Della Rianimazione, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
| | - Michele Bartoletti
- Department of Biomedical Sciences, Humanitas University, Milan, Italy
- Infectious Disease Unit, IRCCS Humanitas Research Hospital, Milan, Italy
| | - Matteo Bassetti
- Division of Infectious Diseases, Department of Health Sciences, University of Genova, Genoa, Italy
- Division of Infectious Diseases, IRCCS Ospedale Policlinico San Martino, Genoa, Italy
| | - Federico Boncagni
- Anesthesiology and Intensive Care Unit, Macerata Hospital, Macerata, Italy
| | - Massimo Carlini
- Department of General Surgery, S. Eugenio Hospital, Rome, Italy
| | - Anna Maria Cattelan
- Infectious and Tropical Diseases Unit, Padua University Hospital, Padua, Italy
- Department of Molecular Medicine, University of Padua, Padua, Italy
| | - Arturo Cavaliere
- Unit of Hospital Pharmacy, Viterbo Local Health Authority, Viterbo, Italy
| | - Marco Ceresoli
- General and Emergency Surgery, Milano-Bicocca University, School of Medicine and Surgery, Monza, Italy
| | - Alessandro Cipriano
- Department of Emergency Medicine, Azienda Ospedaliero Universitaria Pisana, University of Pisa, Pisa, Italy
| | - Andrea Cortegiani
- Department of Precision Medicine in Medical Surgical and Critical Care, University of Palermo, Palermo, Italy
- Department of Anesthesia, Intensive Care and Emergency, Policlinico Paolo Giaccone, University of Palermo, Palermo, Italy
| | | | - Francesco Cristini
- Infectious Diseases Unit, AUSL Romagna, Forlì and Cesena Hospitals, Forlì, Italy
- Department of Medical and Surgical Sciences, Alma Mater Studiorum University of Bologna, Bologna, Italy
| | - Eugenio Cucinotta
- Department of Human Pathology of the Adult and Evolutive Age "Gaetano Barresi", Section of General Surgery, University of Messina, Messina, Italy
| | - Lidia Dalfino
- Anesthesia and Intensive Care Unit, Department of Precision and Regenerative Medicine and Ionian Area, Polyclinic of Bari, University of Bari, Bari, Italy
| | - Gennaro De Pascale
- Dipartimento di Scienze Biotecnologiche di Base, Cliniche Intensivologiche e Perioperatorie, Università Cattolica del Sacro Cuore, Rome, Italy
- Dipartimento di Scienze Dell'Emergenza, Anestesiologiche e Della Rianimazione, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
| | | | - Marco Falcone
- Infectious Diseases Unit, Department of Clinical and Experimental Medicine, Azienda Ospedaliero Universitaria Pisana, University of Pisa, Pisa, Italy
| | - Francesco Forfori
- Anesthesia and Intensive Care, Anesthesia and Resuscitation Department, Azienda Ospedaliero Universitaria Pisana, University of Pisa, Pisa, Italy
| | - Paola Fugazzola
- Division of General Surgery, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
- Department of Clinical, Diagnostic and Pediatric Sciences, University of Pavia, Pavia, Italy
| | - Milo Gatti
- Department of Medical and Surgical Sciences, Alma Mater Studiorum University of Bologna, Bologna, Italy
- Clinical Pharmacology Unit, Department for Integrated Infectious Risk Management, IRCCS Azienda Ospedaliero-Universitaria Di Bologna, Bologna, Italy
| | - Ivan Gentile
- Section of Infectious Diseases, Department of Clinical Medicine and Surgery, University of Naples Federico II, Naples, Italy
| | - Lorenzo Ghiadoni
- Department of Emergency Medicine, Azienda Ospedaliero Universitaria Pisana, University of Pisa, Pisa, Italy
- Department on Clinical and Experimental Medicine, University of Pisa, Pisa, Italy
| | - Maddalena Giannella
- Department of Medical and Surgical Sciences, Alma Mater Studiorum University of Bologna, Bologna, Italy
- Infectious Diseases Unit, Department for Integrated Infectious Risk Management, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italy
| | - Antonino Giarratano
- Department of Precision Medicine in Medical Surgical and Critical Care, University of Palermo, Palermo, Italy
- Department of Anesthesia, Intensive Care and Emergency, Policlinico Paolo Giaccone, University of Palermo, Palermo, Italy
| | - Alessio Giordano
- Unit of Emergency Surgery, Careggi University Hospital, Florence, Italy
| | - Massimo Girardis
- Anesthesia and Intensive Care Medicine, Policlinico di Modena, University of Modena and Reggio Emilia, Modena, Italy
| | - Claudio Mastroianni
- Department of Public Health and Infectious Diseases, AOU Policlinico Umberto 1, Sapienza University of Rome, Rome, Italy
| | - Gianpaola Monti
- Department of Anesthesia and Intensive Care, ASST GOM Niguarda Ca' Granda, Milan, Italy
| | - Giulia Montori
- Unit of General and Emergency Surgery, Vittorio Veneto Hospital, Vittorio Veneto, Italy
| | - Miriam Palmieri
- Department of Surgery, Macerata Hospital, Via Santa Lucia 2, 62100, Macerata, Italy
| | - Marcello Pani
- Hospital Pharmacy Unit, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
| | - Ciro Paolillo
- Emergency Department, University of Verona, Verona, Italy
| | - Dario Parini
- General Surgery Department, Santa Maria Della Misericordia Hospital, Rovigo, Italy
| | - Giustino Parruti
- Infectious Diseases Unit, Pescara General Hospital, Pescara, Italy
| | - Daniela Pasero
- Department of Emergency, Anaesthesia and Intensive Care Unit, ASL1 Sassari, Sassari, Italy
- Department of Medicine, Surgery and Pharmacy, University of Sassari, Sassari, Italy
| | - Federico Pea
- Department of Medical and Surgical Sciences, Alma Mater Studiorum University of Bologna, Bologna, Italy
- Clinical Pharmacology Unit, Department for Integrated Infectious Risk Management, IRCCS Azienda Ospedaliero-Universitaria Di Bologna, Bologna, Italy
| | - Maddalena Peghin
- Infectious and Tropical Diseases Unit, Department of Medicine and Surgery, University of Insubria-ASST-Sette Laghi, Varese, Italy
| | - Nicola Petrosillo
- Infection Prevention and Control Service, Fondazione Policlinico Universitario Campus Bio-Medico, Rome, Italy
| | - Mauro Podda
- Department of Surgical Science, University of Cagliari, Cagliari, Italy
| | - Caterina Rizzo
- Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, Pisa, Italy
| | - Gian Maria Rossolini
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy
- Microbiology and Virology Unit, Florence Careggi University Hospital, Florence, Italy
| | - Alessandro Russo
- Department of Medical and Surgical Sciences, "Magna Graecia" University, Catanzaro, Italy
- Infectious and Tropical Disease Unit, "Renato Dulbecco" Teaching Hospital, Catanzaro, Italy
| | - Loredana Scoccia
- Hospital Pharmacy Unit, Macerata Hospital, AST Macerata, Macerata, Italy
| | - Gabriele Sganga
- Emergency and Trauma Surgery Unit, Fondazione Policlinico Universitario A Gemelli IRCCS, Rome, Italy
- Department of Medical and Surgical Sciences, Università Cattolica del Sacro Cuore, Rome, Italy
| | - Liana Signorini
- Unit of Infectious and Tropical Diseases, ASST Spedali Civili Di Brescia, Brescia, Italy
| | - Stefania Stefani
- Department of Biomedical and Biotechnological Sciences (BIOMETEC), University of Catania, Catania, Italy
| | - Mario Tumbarello
- Department of Medical Biotechnologies, University of Siena, Siena, Italy
- Infectious and Tropical Diseases Unit, Azienda Ospedaliero-Universitaria Senese, Siena, Italy
| | - Fabio Tumietto
- UO Antimicrobial Stewardship-AUSL Bologna, Bologna, Italy
| | | | - Mario Venditti
- Department of Public Health and Infectious Diseases, Sapienza University of Rome, Rome, Italy
| | - Bruno Viaggi
- Intensive Care Department, Careggi Hospital, Florence, Italy
| | | | - Claudia Zaghi
- General, Emergency and Trauma Surgery Department, Vicenza Hospital, Vicenza, Italy
| | | | - Fikri Abu-Zidan
- Statistics and Research Methodology, The Research Office, College of Medicine and Health Sciences, United Arab Emirates University, Al-Ain, United Arab Emirates
| | - Fausto Catena
- Emergency and General Surgery Department, Bufalini Hospital, Cesena, Italy
| | - Pierluigi Viale
- Department of Medical and Surgical Sciences, Alma Mater Studiorum University of Bologna, Bologna, Italy
- Infectious Diseases Unit, Department for Integrated Infectious Risk Management, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italy
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Jiang S, Zhao D, Wang C, Liu X, Yang Q, Bao X, Dong T, Li G, Gu Y, Ye Y, Sun B, Xu S, Zhou X, Fan L, Tang L. Clinical evaluation of droplet digital PCR in the early identification of suspected sepsis patients in the emergency department: a prospective observational study. Front Cell Infect Microbiol 2024; 14:1358801. [PMID: 38895732 PMCID: PMC11183271 DOI: 10.3389/fcimb.2024.1358801] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Accepted: 05/07/2024] [Indexed: 06/21/2024] Open
Abstract
Background Rapid and accurate diagnosis of the causative agents is essential for clinical management of bloodstream infections (BSIs) that might induce sepsis/septic shock. A considerable number of suspected sepsis patients initially enter the health-care system through an emergency department (ED), hence it is vital to establish an early strategy to recognize sepsis and initiate prompt care in ED. This study aimed to evaluate the diagnostic performance and clinical value of droplet digital PCR (ddPCR) assay in suspected sepsis patients in the ED. Methods This was a prospective single-centered observational study including patients admitted to the ED from 25 October 2022 to 3 June 2023 with suspected BSIs screened by Modified Shapiro Score (MSS) score. The comparison between ddPCR and blood culture (BC) was performed to evaluate the diagnostic performance of ddPCR for BSIs. Meanwhile, correlative analysis between ddPCR and the inflammatory and prognostic-related biomarkers were conducted to explore the relevance. Further, the health economic evaluation of the ddPCR was analyzed. Results 258 samples from 228 patients, with BC and ddPCR performed simultaneously, were included in this study. We found that ddPCR results were positive in 48.13% (103 of 214) of episodes, with identification of 132 pathogens. In contrast, BC only detected 18 positives, 88.89% of which were identified by ddPCR. When considering culture-proven BSIs, ddPCR shows an overall sensitivity of 88.89% and specificity of 55.61%, the optimal diagnostic power for quantifying BSI through ddPCR is achieved with a copy cutoff of 155.5. We further found that ddPCR exhibited a high accuracy especially in liver abscess patients. Among all the identified virus by ddPCR, EBV has a substantially higher positive rate with a link to immunosuppression. Moreover, the copies of pathogens in ddPCR were positively correlated with various markers of inflammation, coagulation, immunity as well as prognosis. With high sensitivity and specificity, ddPCR facilitates precision antimicrobial stewardship and reduces health care costs. Conclusions The multiplexed ddPCR delivers precise and quantitative load data on the causal pathogen, offers the ability to monitor the patient's condition and may serve as early warning of sepsis in time-urgent clinical situations as ED. Importance Early detection and effective administration of antibiotics are essential to improve clinical outcomes for those with life-threatening infection in the emergency department. ddPCR, an emerging tool for rapid and sensitive pathogen identification used as a precise bedside test, has developed to address the current challenges of BSI diagnosis and precise treatment. It characterizes sensitivity, specificity, reproducibility, and absolute quantifications without a standard curve. ddPCR can detect causative pathogens and related resistance genes in patients with suspected BSIs within a span of three hours. In addition, it can identify polymicrobial BSIs and dynamically monitor changes in pathogenic microorganisms in the blood and can be used to evaluate antibiotic efficacy and survival prognosis. Moreover, the copies of pathogens in ddPCR were positively correlated with various markers of inflammation, coagulation, immunity. With high sensitivity and specificity, ddPCR facilitates precision antimicrobial stewardship and reduces health care costs.
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Affiliation(s)
- Sen Jiang
- Department of Internal Emergency Medicine, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
- School of Medicine, Tongji University, Shanghai, China
| | - Dongyang Zhao
- Department of Internal Emergency Medicine, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
- School of Medicine, Tongji University, Shanghai, China
| | - Chunxue Wang
- Department of Internal Emergency Medicine, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
- School of Medicine, Tongji University, Shanghai, China
| | - Xiandong Liu
- Department of Internal Emergency Medicine, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
- School of Medicine, Tongji University, Shanghai, China
| | - Qian Yang
- Department of Internal Emergency Medicine, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
- School of Medicine, Tongji University, Shanghai, China
| | - Xiaowei Bao
- Department of Internal Emergency Medicine, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
- School of Medicine, Tongji University, Shanghai, China
| | - Tiancao Dong
- Department of Internal Emergency Medicine, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
- School of Medicine, Tongji University, Shanghai, China
| | - Gen Li
- School of Medicine, Tongji University, Shanghai, China
- Department of Clinical Laboratory, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
| | - Yi Gu
- Department of Internal Emergency Medicine, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
- School of Medicine, Tongji University, Shanghai, China
| | - Yangqin Ye
- School of Medicine, Tongji University, Shanghai, China
- Department of Clinical Laboratory, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
| | - Bingke Sun
- Department of Internal Emergency Medicine, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
- School of Medicine, Tongji University, Shanghai, China
| | - Shumin Xu
- Department of Internal Emergency Medicine, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
- School of Medicine, Tongji University, Shanghai, China
| | - Xiaohui Zhou
- School of Medicine, Tongji University, Shanghai, China
- Research Center for Translational Medicine, Shanghai Heart Failure Research Center, Shanghai East Hospital, Tongji University, Shanghai, China
| | - Lieying Fan
- School of Medicine, Tongji University, Shanghai, China
- Department of Clinical Laboratory, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
| | - Lunxian Tang
- Department of Internal Emergency Medicine, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
- School of Medicine, Tongji University, Shanghai, China
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Ishikawa T, Uejima Y, Okai M, Shiga K, Shoji K, Miyairi I, Kato M, Morooka S, Kubota M, Tagaya T, Tsuji S, Aoki S, Ide K, Niimi H, Uchiyama T, Onodera M, Kawai T. Melting temperature mapping method in children: Rapid identification of pathogenic microbes. J Infect Chemother 2024; 30:475-480. [PMID: 38036030 DOI: 10.1016/j.jiac.2023.11.024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Revised: 11/16/2023] [Accepted: 11/23/2023] [Indexed: 12/02/2023]
Abstract
INTRODUCTION The melting temperature (Tm) mapping method (TM) identifies bacterial species by intrinsic patterns of Tm values in the 16S ribosomal RNA gene (16S rDNA) extracted directly from whole blood. We examined potential clinical application of TM in children with bloodstream infection (BSI). METHODS This was a prospective observational study at a children's hospital in Japan from 2018 to 2021. In patients with diagnosed or suspected BSI, we investigated the match rates of pathogenic bacteria identified by TM and blood culture (BC), the inspection time to identification of TM, and the amount of bacterial DNA in blood samples. RESULTS The median age of 81 patients (93 samples) was 3.6 years. Of 23 samples identified by TM, 11 samples matched the bacterial species with BC (positive-match rate, 48 %). Of 64 TM-negative samples, 62 samples were negative for BC (negative-match rate, 97 %). Six samples, including one containing two pathogenic bacterial species, were not suitable for TM identification. In total, the matched samples were 73 of 93 samples (match rate, 78 %). There were seven samples identified by TM in BC-negative samples from blood collected after antibiotic therapy. Interestingly, the bacteria were matched with BC before antibiotic administration. These TM samples contained as many 16S rDNA copies as the BC-positive samples. The median inspection time to identification using TM was 4.7 h. CONCLUSIONS In children with BSI, TM had high negative-match rates with BC, the potential to identify the pathogenic bacteria even in patients on antibiotic therapy, and more rapid identification compared to BC. REGISTERING CLINICAL TRIALS UMIN000041359https://center6.umin.ac.jp/cgi-open-bin/ctr/ctr_view.cgi?recptno=R000047220.
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Affiliation(s)
- Takashi Ishikawa
- Division of Immunology, National Center for Child Health and Development, Tokyo, Japan; Department of Pediatrics, Jikei University School of Medicine, Tokyo, Japan.
| | - Yoji Uejima
- Division of Infectious Diseases and Immunology, Saitama Children's Medical Center, Saitama, Japan; Department of Clinical Laboratory and Molecular Pathology, Toyama University Hospital, Toyama, Japan
| | - Masashi Okai
- Division of Immunology, National Center for Child Health and Development, Tokyo, Japan; Department of Pediatrics, Jikei University School of Medicine, Tokyo, Japan
| | - Kyoko Shiga
- Division of Immunology, National Center for Child Health and Development, Tokyo, Japan
| | - Kensuke Shoji
- Division of Infectious Diseases, National Center for Child Health and Development, Tokyo, Japan
| | - Isao Miyairi
- Division of Infectious Diseases, National Center for Child Health and Development, Tokyo, Japan
| | - Motohiro Kato
- Department of Pediatric Hematology and Oncology Research, National Center for Child Health and Development, Tokyo, Japan
| | - Shintaro Morooka
- Department of General Pediatrics & Interdisciplinary Medicine, National Center for Child Health and Development, Tokyo, Japan
| | - Mitsuru Kubota
- Department of General Pediatrics & Interdisciplinary Medicine, National Center for Child Health and Development, Tokyo, Japan
| | - Takashi Tagaya
- Division of Pediatric Emergency and Transport Services, National Center for Child Health and Development, Tokyo, Japan
| | - Satoshi Tsuji
- Division of Pediatric Emergency and Transport Services, National Center for Child Health and Development, Tokyo, Japan
| | - Satoshi Aoki
- Division of Critical Care Medicine, National Center for Child Health and Development, Tokyo, Japan
| | - Kentaro Ide
- Division of Critical Care Medicine, National Center for Child Health and Development, Tokyo, Japan
| | - Hideki Niimi
- Department of Clinical Laboratory and Molecular Pathology, Toyama University Hospital, Toyama, Japan
| | - Toru Uchiyama
- Division of Immunology, National Center for Child Health and Development, Tokyo, Japan; Department of Human Genetics, National Center for Child Health and Development, Tokyo, Japan
| | - Masafumi Onodera
- Division of Immunology, National Center for Child Health and Development, Tokyo, Japan; Gene & Cell Therapy Promotion Center, National Center for Child Health and Development, Tokyo, Japan
| | - Toshinao Kawai
- Division of Immunology, National Center for Child Health and Development, Tokyo, Japan; Department of Pediatrics, Jikei University School of Medicine, Tokyo, Japan
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7
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Han D, Yu F, Zhang D, Hu J, Zhang X, Xiang D, Lou B, Chen Y, Zheng S. Molecular rapid diagnostic testing for bloodstream infections: Nanopore targeted sequencing with pathogen-specific primers. J Infect 2024; 88:106166. [PMID: 38670268 DOI: 10.1016/j.jinf.2024.106166] [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: 02/10/2024] [Revised: 04/01/2024] [Accepted: 04/20/2024] [Indexed: 04/28/2024]
Abstract
BACKGROUND Nanopore sequencing, known for real-time analysis, shows promise for rapid clinical infection diagnosis but lacks effective assays for bloodstream infections (BSIs). METHODS We prospectively assessed the performance of a novel nanopore targeted sequencing (NTS) assay in identifying pathogens and predicting antibiotic resistance in BSIs, analyzing 387 blood samples from December 2021 to April 2023. RESULTS The positivity rate for NTS (69.5 %, 269/387) nearly matches that of metagenomic next-generation sequencing (mNGS) (74.7 %, 289/387; p = 0.128) and surpasses the positivity rate of conventional blood culture (BC) (33.9 %, 131/387; p < 0.01). Frequent pathogens detected by NTS included Klebsiella pneumoniae (n = 54), Pseudomonas aeruginosa (n = 36), Escherichia coli (n = 36), Enterococcus faecium(n = 30), Acinetobacter baumannii(n = 26), Staphylococcus aureus(n = 23), and Human cytomegalovirus (n = 37). Against a composite BSI diagnostic standard, NTS demonstrated a sensitivity and specificity of 84.0 % (95 % CI 79.5 %-87.7 %) and 90.1 % (95 % CI 81.7 %-88.5 %), respectively. The concordance between NTS and mNGS results (the percentage of total cases where both either detected BSI-related pathogens or were both negative) was 90.2 % (359/387), whereas the consistency between NTS and BC was only 60.2 % (233/387). In 80.6 % (50/62) of the samples with identical pathogens identified by both NTS tests and BCs, the genotypic resistance identified by NTS correlated with culture-confirmed phenotypic resistance. Using NTS, 95 % of samples can be tested and analyzed in approximately 7 h, allowing for early patient diagnosis. CONCLUSIONS NTS is rapid, sensitive, and efficient for detecting BSIs and drug-resistant genes, making it a potential preferred diagnostic tool for early infection identification in critically ill patients.
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Affiliation(s)
- Dongsheng Han
- Department of Laboratory Medicine, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310003, China; Zhejiang Key Laboratory of Clinical In Vitro Diagnostic Techniques, Hangzhou, Zhejiang 310003, China; Institute of Laboratory Medicine, Zhejiang University, Hangzhou, Zhejiang 310003, China
| | - Fei Yu
- Department of Laboratory Medicine, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310003, China; Zhejiang Key Laboratory of Clinical In Vitro Diagnostic Techniques, Hangzhou, Zhejiang 310003, China; Institute of Laboratory Medicine, Zhejiang University, Hangzhou, Zhejiang 310003, China
| | - Dan Zhang
- Department of Laboratory Medicine, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310003, China; Zhejiang Key Laboratory of Clinical In Vitro Diagnostic Techniques, Hangzhou, Zhejiang 310003, China; Institute of Laboratory Medicine, Zhejiang University, Hangzhou, Zhejiang 310003, China
| | - Juan Hu
- Department of Critical Care Units, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang 310003, China
| | - Xuan Zhang
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310003, China
| | - Dairong Xiang
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310003, China
| | - Bin Lou
- Department of Laboratory Medicine, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310003, China; Zhejiang Key Laboratory of Clinical In Vitro Diagnostic Techniques, Hangzhou, Zhejiang 310003, China; Institute of Laboratory Medicine, Zhejiang University, Hangzhou, Zhejiang 310003, China
| | - Yu Chen
- Department of Laboratory Medicine, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310003, China; Zhejiang Key Laboratory of Clinical In Vitro Diagnostic Techniques, Hangzhou, Zhejiang 310003, China; Institute of Laboratory Medicine, Zhejiang University, Hangzhou, Zhejiang 310003, China.
| | - Shufa Zheng
- Department of Laboratory Medicine, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310003, China; Zhejiang Key Laboratory of Clinical In Vitro Diagnostic Techniques, Hangzhou, Zhejiang 310003, China; Institute of Laboratory Medicine, Zhejiang University, Hangzhou, Zhejiang 310003, China.
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Um YW, Park I, Lee JH, Kim HE, Han D, Kang SH, Kim S, Jo YH. Dynamic Changes in Soluble Triggering Receptor Expressed on Myeloid Cells-1 in Sepsis with Respect to Antibiotic Susceptibility. Infect Drug Resist 2024; 17:2141-2147. [PMID: 38828372 PMCID: PMC11143990 DOI: 10.2147/idr.s464286] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2024] [Accepted: 05/22/2024] [Indexed: 06/05/2024] Open
Abstract
Purpose Proper antibiotic administration is crucial for sepsis management. Given the escalating incidence of antimicrobial resistance, there is a pressing need for indicators of antimicrobial susceptibility with short turnaround times. This study aimed to investigate the potential of soluble triggering receptor expressed on myeloid cells-1 (sTREM-1) as an early biomarker for in vivo antibiotic susceptibility in patients with sepsis. Patients and Methods We conducted a retrospective analysis of plasma samples from patients enrolled in a pre-established study designed to investigate prognostic biomarkers in patients with sepsis or septic shock. Baseline and 6 h sTREM-1 levels were examined using enzyme-linked immunosorbent assays. The primary outcome of the study was the comparison of percentage changes in sTREM-1 levels at the 6 h relative to baseline with respect to antibiotic susceptibility. Results Of the 596 patients enrolled in the pre-established study, 29 with a median age of 75.8 and a 28-day mortality rate of 17.2% were included in the present analysis. Among these patients, 24 were classified into the susceptible group, whereas the remaining five were classified into the resistant group. The trend in plasma sTREM-1 levels differed with respect to antibiotic susceptibility. Moreover, percentage change in sTREM-1 levels at the 6 h relative to baseline was significantly higher in the resistant group (P = 0.028). Conclusion The trend in plasma sTREM-1 levels in patients with sepsis differed with respect to antibiotic susceptibility, with a higher percentage change in patients treated with inappropriate antibiotics. These findings indicate the potential utility of sTREM-1 as an early biomarker of antibiotic susceptibility.
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Affiliation(s)
- Young Woo Um
- Department of Emergency Medicine, Seoul National University Bundang Hospital, Seongnam-si, Gyeonggi-do, Korea
| | - Inwon Park
- Department of Emergency Medicine, Seoul National University Bundang Hospital, Seongnam-si, Gyeonggi-do, Korea
| | - Jae Hyuk Lee
- Department of Emergency Medicine, Seoul National University Bundang Hospital, Seongnam-si, Gyeonggi-do, Korea
| | - Hee Eun Kim
- Department of Emergency Medicine, Seoul National University Bundang Hospital, Seongnam-si, Gyeonggi-do, Korea
| | - Dongkwan Han
- Department of Emergency Medicine, Seoul National University Bundang Hospital, Seongnam-si, Gyeonggi-do, Korea
| | - Seung Hyun Kang
- Department of Emergency Medicine, Seoul National University Bundang Hospital, Seongnam-si, Gyeonggi-do, Korea
| | - Seonghye Kim
- Department of Emergency Medicine, Seoul National University Bundang Hospital, Seongnam-si, Gyeonggi-do, Korea
| | - You Hwan Jo
- Department of Emergency Medicine, Seoul National University Bundang Hospital, Seongnam-si, Gyeonggi-do, Korea
- Department of Emergency Medicine, Seoul National University College of Medicine, Seoul, Korea
- Disaster Medicine Research Center, Seoul National University Medical Research Center, Seoul, Korea
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9
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Kim KJ, Yun SG, Cho Y, Lee CK, Nam MH. Rapid Direct Identification of Microbial Pathogens and Antimicrobial Resistance Genes in Positive Blood Cultures Using a Fully Automated Multiplex PCR Assay. J Korean Med Sci 2024; 39:e157. [PMID: 38711319 DOI: 10.3346/jkms.2024.39.e157] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Accepted: 04/22/2024] [Indexed: 05/08/2024] Open
Abstract
This study assessed the performance of the BioFire Blood Culture Identification 2 (BCID2) panel in identifying microorganisms and antimicrobial resistance (AMR) profiles in positive blood cultures (BCs) and its influence on turnaround time (TAT) compared with conventional culture methods. We obtained 117 positive BCs, of these, 102 (87.2%) were correctly identified using BCID2. The discordance was due to off-panel pathogens detected by culture (n = 13), and additional pathogens identified by BCID2 (n = 2). On-panel pathogen concordance between the conventional culture and BCID2 methods was 98.1% (102/104). The conventional method detected 19 carbapenemase-producing organisms, 14 extended-spectrum beta-lactamase-producing Enterobacterales, 18 methicillin-resistant Staphylococcus spp., and four vancomycin-resistant Enterococcus faecium. BCID2 correctly predicted 53 (96.4%) of 55 phenotypic resistance patterns by detecting AMR genes. The TAT for BCID2 was significantly lower than that for the conventional method. BCID2 rapidly identifies pathogens and AMR genes in positive BCs.
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Affiliation(s)
- Keun Ju Kim
- Department of Laboratory Medicine, Korea University College of Medicine, Seoul, Korea
| | - Seung Gyu Yun
- Department of Laboratory Medicine, Korea University College of Medicine, Seoul, Korea
| | - Yunjung Cho
- Department of Laboratory Medicine, Korea University College of Medicine, Seoul, Korea
| | - Chang Kyu Lee
- Department of Laboratory Medicine, Korea University College of Medicine, Seoul, Korea
| | - Myung-Hyun Nam
- Department of Laboratory Medicine, Korea University College of Medicine, Seoul, Korea.
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Pinto D, Themudo G, Pereira AC, Botelho A, Cunha MV. Rescue of Mycobacterium bovis DNA Obtained from Cultured Samples during Official Surveillance of Animal TB: Key Steps for Robust Whole Genome Sequence Data Generation. Int J Mol Sci 2024; 25:3869. [PMID: 38612679 PMCID: PMC11011339 DOI: 10.3390/ijms25073869] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2024] [Revised: 03/28/2024] [Accepted: 03/28/2024] [Indexed: 04/14/2024] Open
Abstract
Epidemiological surveillance of animal tuberculosis (TB) based on whole genome sequencing (WGS) of Mycobacterium bovis has recently gained track due to its high resolution to identify infection sources, characterize the pathogen population structure, and facilitate contact tracing. However, the workflow from bacterial isolation to sequence data analysis has several technical challenges that may severely impact the power to understand the epidemiological scenario and inform outbreak response. While trying to use archived DNA from cultured samples obtained during routine official surveillance of animal TB in Portugal, we struggled against three major challenges: the low amount of M. bovis DNA obtained from routinely processed animal samples; the lack of purity of M. bovis DNA, i.e., high levels of contamination with DNA from other organisms; and the co-occurrence of more than one M. bovis strain per sample (within-host mixed infection). The loss of isolated genomes generates missed links in transmission chain reconstruction, hampering the biological and epidemiological interpretation of data as a whole. Upon identification of these challenges, we implemented an integrated solution framework based on whole genome amplification and a dedicated computational pipeline to minimize their effects and recover as many genomes as possible. With the approaches described herein, we were able to recover 62 out of 100 samples that would have otherwise been lost. Based on these results, we discuss adjustments that should be made in official and research laboratories to facilitate the sequential implementation of bacteriological culture, PCR, downstream genomics, and computational-based methods. All of this in a time frame supporting data-driven intervention.
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Affiliation(s)
- Daniela Pinto
- Centre for Ecology, Evolution and Environmental Changes (cE3c) & CHANGE—Global Change and Sustainability Institute, Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisboa, Portugal; (D.P.); (A.C.P.)
- Biosystems & Integrative Sciences Institute (BioISI), Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisboa, Portugal
| | - Gonçalo Themudo
- Centre for Ecology, Evolution and Environmental Changes (cE3c) & CHANGE—Global Change and Sustainability Institute, Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisboa, Portugal; (D.P.); (A.C.P.)
| | - André C. Pereira
- Centre for Ecology, Evolution and Environmental Changes (cE3c) & CHANGE—Global Change and Sustainability Institute, Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisboa, Portugal; (D.P.); (A.C.P.)
- Biosystems & Integrative Sciences Institute (BioISI), Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisboa, Portugal
| | - Ana Botelho
- National Institute for Agrarian and Veterinary Research (INIAV IP), Av. da República, Quinta do Marquês, 2780-157 Oeiras, Portugal;
| | - Mónica V. Cunha
- Centre for Ecology, Evolution and Environmental Changes (cE3c) & CHANGE—Global Change and Sustainability Institute, Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisboa, Portugal; (D.P.); (A.C.P.)
- Biosystems & Integrative Sciences Institute (BioISI), Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisboa, Portugal
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Gillis VELM, Dalloyaux D, Te Morsche RHM, van Ingen J, Sir Ö, Rovers CP, Wouters Y, Wanten GJA. ddPCR enables rapid detection of bloodstream infections in patients on home parenteral nutrition: A prospective cohort study. JOURNAL OF MICROBIOLOGY, IMMUNOLOGY, AND INFECTION = WEI MIAN YU GAN RAN ZA ZHI 2024:S1684-1182(24)00049-5. [PMID: 38575399 DOI: 10.1016/j.jmii.2024.03.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Revised: 11/21/2023] [Accepted: 03/12/2024] [Indexed: 04/06/2024]
Abstract
INTRODUCTION Chronic intestinal failure patients (CIF) require a central venous access device (CVAD) to administer parenteral nutrition. Most serious complication related to a CVAD is a central line-associated bloodstream infection (CLABSI). The golden standard to diagnose a CLABSI are blood cultures, however, they may require 1-5 days before getting a result. Droplet digital polymerase chain reaction (ddPCR) for the detection of pathogen 16S/28S rRNA is a novel culture-independent molecular technique that has been developed to enhance and expedite infection diagnostics within two and a half hours. In this study, we prospectively compared ddPCR with blood cultures to detect pathogens in whole blood. METHODS We included adult CIF patients with a clinical suspicion of CLABSI in this prospective single-blinded clinical study. Blood cultures were routinely collected and subsequently two central samples from the CVAD and two peripheral samples from a peripheral venous access point. Primary outcome was the sensitivity and specificity of ddPCR. RESULTS In total, 75 patients with 126 suspected CLABSI episodes were included, with 80 blood samples from the CVAD and 114 from peripheral veins. The central ddPCR samples showed a sensitivity of 91% (95%CI 77-98), and specificity of 96% (95%CI 85-99). Peripheral ddPCR samples had a sensitivity of 63% (95%CI 46-77) and specificity of 99% (95%CI 93-100). CONCLUSION ddPCR showed a high sensitivity and specificity relative to blood cultures and enables rapid pathogen detection and characterization. Clinical studies should explore if integrated ddPCR and blood culture outcomes enables a more rapid pathogen guided CLABSI treatment and enhancing patient outcomes.
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Affiliation(s)
- Veerle E L M Gillis
- Department of Gastroenterology and Hepatology, Radboud University Medical Center, Nijmegen, the Netherlands.
| | - Daisy Dalloyaux
- Department of Gastroenterology and Hepatology, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Rene H M Te Morsche
- Department of Gastroenterology and Hepatology, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Jakko van Ingen
- Department of Medical Microbiology, Radboudumc Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Özcan Sir
- Department of Emergency Medicine, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Chantal P Rovers
- Department of Internal Medicine, Division of Infectious Diseases, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Yannick Wouters
- Department of Gastroenterology and Hepatology, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Geert J A Wanten
- Department of Gastroenterology and Hepatology, Radboud University Medical Center, Nijmegen, the Netherlands
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Moragues-Solanas L, Le-Viet T, McSorley E, Halford C, Lockhart DS, Aydin A, Kay GL, Elumogo N, Mullen W, O'Grady J, Gilmour MW. Development and proof-of-concept demonstration of a clinical metagenomics method for the rapid detection of bloodstream infection. BMC Med Genomics 2024; 17:71. [PMID: 38443925 PMCID: PMC10916079 DOI: 10.1186/s12920-024-01835-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Accepted: 02/13/2024] [Indexed: 03/07/2024] Open
Abstract
BACKGROUND The timely and accurate diagnosis of bloodstream infection (BSI) is critical for patient management. With longstanding challenges for routine blood culture, metagenomics is a promising approach to rapidly provide sequence-based detection and characterisation of bloodborne bacteria. Long-read sequencing technologies have successfully supported the use of clinical metagenomics for syndromes such as respiratory illness, and modified approaches may address two requisite factors for metagenomics to be used as a BSI diagnostic: depletion of the high level of host DNA to then detect the low abundance of microbes in blood. METHODS Blood samples from healthy donors were spiked with different concentrations of four prevalent causative species of BSI. All samples were then subjected to a modified saponin-based host DNA depletion protocol and optimised DNA extraction, whole genome amplification and debranching steps in preparation for sequencing, followed by bioinformatical analyses. Two related variants of the protocol are presented: 1mL of blood processed without bacterial enrichment, and 5mL of blood processed following a rapid bacterial enrichment protocol-SepsiPURE. RESULTS After first identifying that a large proportion of host mitochondrial DNA remained, the host depletion process was optimised by increasing saponin concentration to 3% and scaling the reaction to allow more sample volume. Compared to non-depleted controls, the 3% saponin-based depletion protocol reduced the presence of host chromosomal and mitochondrial DNA < 106 and < 103 fold respectively. When the modified depletion method was further combined with a rapid bacterial enrichment method (SepsiPURE; with 5mL blood samples) the depletion of mitochondrial DNA improved by a further > 10X while also increasing detectable bacteria by > 10X. Parameters during DNA extraction, whole genome amplification and long-read sequencing were also adjusted, and subsequently amplicons were detected for each input bacterial species at each of the spiked concentrations, ranging from 50-100 colony forming units (CFU)/mL to 1-5 CFU/mL. CONCLUSION In this proof-of-concept study, four prevalent BSI causative species were detected in under 12 h to species level (with antimicrobial resistance determinants) at concentrations relevant to clinical blood samples. The use of a rapid and precise metagenomic protocols has the potential to advance the diagnosis of BSI.
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Affiliation(s)
- Lluis Moragues-Solanas
- Quadram Institute Bioscience, Norwich Research Park, Rosalind Franklin Road, Norwich, Norfolk, NR4 7UQ, UK
- University of East Anglia, Norwich, Norfolk, UK
| | - Thanh Le-Viet
- Quadram Institute Bioscience, Norwich Research Park, Rosalind Franklin Road, Norwich, Norfolk, NR4 7UQ, UK
| | - Elinor McSorley
- Momentum Bioscience Ltd, Blenheim Office Park, Witney, Oxfordshire, UK
| | - Carl Halford
- University of East Anglia, Norwich, Norfolk, UK
- Defence Science and Technology Laboratory, Porton Down, Salisbury, Wiltshire, UK
| | - Daniel S Lockhart
- Momentum Bioscience Ltd, Blenheim Office Park, Witney, Oxfordshire, UK
| | - Alp Aydin
- Quadram Institute Bioscience, Norwich Research Park, Rosalind Franklin Road, Norwich, Norfolk, NR4 7UQ, UK
- Oxford Nanopore Technologies Plc, Quadram Institute Bioscience, Norwich, UK
| | - Gemma L Kay
- Quadram Institute Bioscience, Norwich Research Park, Rosalind Franklin Road, Norwich, Norfolk, NR4 7UQ, UK
- Oxford Nanopore Technologies Plc, Quadram Institute Bioscience, Norwich, UK
| | - Ngozi Elumogo
- Quadram Institute Bioscience, Norwich Research Park, Rosalind Franklin Road, Norwich, Norfolk, NR4 7UQ, UK
- Norfolk and Norwich University Hospital, Colney Lane, Norwich, UK
| | - William Mullen
- Momentum Bioscience Ltd, Blenheim Office Park, Witney, Oxfordshire, UK
| | - Justin O'Grady
- University of East Anglia, Norwich, Norfolk, UK
- Oxford Nanopore Technologies Plc, Quadram Institute Bioscience, Norwich, UK
| | - Matthew W Gilmour
- Quadram Institute Bioscience, Norwich Research Park, Rosalind Franklin Road, Norwich, Norfolk, NR4 7UQ, UK.
- University of East Anglia, Norwich, Norfolk, UK.
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13
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Jung N, Schommers P, Leisse C. [Precision medicine in infectious diseases]. INNERE MEDIZIN (HEIDELBERG, GERMANY) 2024; 65:220-227. [PMID: 38038764 DOI: 10.1007/s00108-023-01620-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 10/19/2023] [Indexed: 12/02/2023]
Abstract
Infectious medicine faces a variety of challenges, such as the increase in antibiotic resistance and the emergence and spread of infectious diseases fueled by climate change and globalization. Precision medicine can provide solutions to many of these challenges. Since an untargeted request for diagnostic tests can lead to test results without clinical relevance, which can increase the use of non-indicated antibiotics, the principle aimed at is: targeted diagnostics (the right test) and consideration of patient characteristics (the right person) to optimize management (the right action). At the same time, one must always decide whether empirical therapy must be immediately initiated, even if the results of the initiated diagnostics are not yet available. In addition, many new diagnostics as well as therapies have recently been developed for the rapid detection and more specific treatment of bacterial infections. Molecular genetic methods, which offer more rapid results than classical bacterial cultures, are gaining ground as new diagnostics. New therapeutics such as bacteriophages, antibodies or antibacterial peptides allow increasingly precise treatment of certain bacterial infections. Precision medicine will also play an increasingly important role in infectious medicine in the future.
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Affiliation(s)
- N Jung
- Universität zu Köln, Medizinische Fakultät und Uniklinik Köln, Klinik I für Innere Medizin, Infektiologie, Köln, Deutschland.
| | - P Schommers
- Universität zu Köln, Medizinische Fakultät und Uniklinik Köln, Klinik I für Innere Medizin, Infektiologie, Köln, Deutschland
| | - C Leisse
- Universität zu Köln, Medizinische Fakultät und Uniklinik Köln, Klinik I für Innere Medizin, Infektiologie, Köln, Deutschland
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14
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Lehnert T, Gijs MAM. Microfluidic systems for infectious disease diagnostics. LAB ON A CHIP 2024; 24:1441-1493. [PMID: 38372324 DOI: 10.1039/d4lc00117f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/20/2024]
Abstract
Microorganisms, encompassing both uni- and multicellular entities, exhibit remarkable diversity as omnipresent life forms in nature. They play a pivotal role by supplying essential components for sustaining biological processes across diverse ecosystems, including higher host organisms. The complex interactions within the human gut microbiota are crucial for metabolic functions, immune responses, and biochemical signalling, particularly through the gut-brain axis. Viruses also play important roles in biological processes, for example by increasing genetic diversity through horizontal gene transfer when replicating inside living cells. On the other hand, infection of the human body by microbiological agents may lead to severe physiological disorders and diseases. Infectious diseases pose a significant burden on global healthcare systems, characterized by substantial variations in the epidemiological landscape. Fast spreading antibiotic resistance or uncontrolled outbreaks of communicable diseases are major challenges at present. Furthermore, delivering field-proven point-of-care diagnostic tools to the most severely affected populations in low-resource settings is particularly important and challenging. New paradigms and technological approaches enabling rapid and informed disease management need to be implemented. In this respect, infectious disease diagnostics taking advantage of microfluidic systems combined with integrated biosensor-based pathogen detection offers a host of innovative and promising solutions. In this review, we aim to outline recent activities and progress in the development of microfluidic diagnostic tools. Our literature research mainly covers the last 5 years. We will follow a classification scheme based on the human body systems primarily involved at the clinical level or on specific pathogen transmission modes. Important diseases, such as tuberculosis and malaria, will be addressed more extensively.
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Affiliation(s)
- Thomas Lehnert
- Laboratory of Microsystems, École Polytechnique Fédérale de Lausanne, Lausanne, CH-1015, Switzerland.
| | - Martin A M Gijs
- Laboratory of Microsystems, École Polytechnique Fédérale de Lausanne, Lausanne, CH-1015, Switzerland.
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15
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Peri AM, O’Callaghan K, Rafiei N, Graves B, Sinclair H, Brischetto A, Lim K, Parkes-Smith J, Eustace M, Davidson N, Tabah A, Stewart A, Chatfield MD, Harris PNA, Paterson DL. Persistence of Detectable Pathogens by Culture-Independent Systems (T2 Magnetic Resonance) in Patients With Bloodstream Infection: Prognostic Role and Possible Clinical Implications. Clin Infect Dis 2024; 78:283-291. [PMID: 37890109 PMCID: PMC10874273 DOI: 10.1093/cid/ciad663] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Revised: 10/13/2023] [Accepted: 10/25/2023] [Indexed: 10/29/2023] Open
Abstract
BACKGROUND Persistent Staphylococcus aureus bacteremia is associated with metastatic infection and adverse outcomes, whereas gram-negative bacteremia is normally transient and shorter course therapy is increasingly advocated for affected patients. Whether the prolonged detection of pathogen DNA in blood by culture-independent systems could have prognostic value and guide management decisions is unknown. METHODS We performed a multicenter, prospective, observational study on 102 patients with bloodstream infection (BSI) to compare time to bloodstream clearance according to T2 magnetic resonance and blood cultures over a 4-day follow-up. We also explored the association between duration of detectable pathogens according to T2 magnetic resonance (magnetic resonance-DNAemia [MR-DNAemia]) and clinical outcomes. RESULTS Time to bloodstream clearance according to T2 magnetic resonance was significantly longer than blood culture clearance (HR, .54; 95% CI, .39-.75) and did not differ according to the causative pathogen (P = .5). Each additional day of MR-DNAemia increased the odds of persistent infection (defined as metastatic infection or delayed source control) both in the overall population (OR, 1.98; 95% CI, 1.45-2.70) and in S. aureus (OR, 1.92; 95% CI, 1.12-3.29) and gram-negative bacteremia (OR, 2.21; 95% CI, 1.35-3.60). MR-DNAemia duration was also associated with no improvement in Sequential Organ Failure Assessment score at day 7 from infection onset (OR, 1.76; 95% CI, 1.21-2.56). CONCLUSIONS T2 magnetic resonance may help diagnose BSI in patients on antimicrobials with negative blood cultures as well as to identify patients with metastatic infection, source control failure, or adverse short-term outcome. Future studies may inform its usefulness within the setting of antimicrobial stewardship programs.
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Affiliation(s)
- Anna Maria Peri
- UQ Centre for Clinical Research, The University of Queensland, Brisbane, Queensland, Australia
| | - Kevin O’Callaghan
- Infectious Diseases Unit, Redcliffe Hospital, Redcliffe, Queensland, Australia
| | - Nastaran Rafiei
- Infectious Diseases Unit, Caboolture Hospital, Caboolture, Queensland, Australia
| | - Bianca Graves
- Herston Infectious Diseases Institute, Herston, Brisbane, Queensland, Australia
| | - Holly Sinclair
- Infectious Diseases Unit, Royal Brisbane and Women’s Hospital, Brisbane, Queensland, Australia
| | - Anna Brischetto
- Infectious Diseases Unit, Redcliffe Hospital, Redcliffe, Queensland, Australia
| | - Karen Lim
- Infectious Diseases Unit, Redcliffe Hospital, Redcliffe, Queensland, Australia
| | - Jill Parkes-Smith
- Infectious Diseases Unit, Redcliffe Hospital, Redcliffe, Queensland, Australia
| | - Matthew Eustace
- Infectious Diseases Unit, Redcliffe Hospital, Redcliffe, Queensland, Australia
| | - Natalie Davidson
- Infectious Diseases Unit, Redcliffe Hospital, Redcliffe, Queensland, Australia
| | - Alexis Tabah
- Intensive Care Unit, Redcliffe Hospital, Redcliffe, Queensland, Australia
| | - Adam Stewart
- Central Microbiology, Pathology Queensland, Royal Brisbane and Women's Hospital, Brisbane, Queensland, Australia
| | - Mark D Chatfield
- UQ Centre for Clinical Research, The University of Queensland, Brisbane, Queensland, Australia
| | - Patrick N A Harris
- UQ Centre for Clinical Research, The University of Queensland, Brisbane, Queensland, Australia
- Herston Infectious Diseases Institute, Herston, Brisbane, Queensland, Australia
- Central Microbiology, Pathology Queensland, Royal Brisbane and Women's Hospital, Brisbane, Queensland, Australia
| | - David L Paterson
- UQ Centre for Clinical Research, The University of Queensland, Brisbane, Queensland, Australia
- Infectious Diseases Unit, Royal Brisbane and Women’s Hospital, Brisbane, Queensland, Australia
- ADVANCE-ID, Saw Swee Hock School of Public Health, National University of Singapore, Singapore
- Infectious Diseases Translational Research Program, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
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16
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Reinicke M, Braun SD, Diezel C, Lemuth O, Engelmann I, Liebe T, Ehricht R. From Shadows to Spotlight: Enhancing Bacterial DNA Detection in Blood Samples through Cutting-Edge Molecular Pre-Amplification. Antibiotics (Basel) 2024; 13:161. [PMID: 38391548 PMCID: PMC10886392 DOI: 10.3390/antibiotics13020161] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Revised: 01/29/2024] [Accepted: 01/30/2024] [Indexed: 02/24/2024] Open
Abstract
One of the greatest challenges to the use of molecular methods for diagnostic purposes is the detection of target DNA that is present only in low concentrations. One major factor that negatively impacts accuracy, diagnostic sensitivity, and specificity is the sample matrix, which hinders the attainment of the required detection limit due to the presence of residual background DNA. To address this issue, various methods have been developed to enhance sensitivity through targeted pre-amplification of marker sequences. Diagnostic sensitivity to the single molecular level is critical, particularly when identifying bloodstream infections. In cases of clinically manifest sepsis, the concentration of bacteria in the blood may reach as low as one bacterial cell/CFU per mL of blood. Therefore, it is crucial to achieve the highest level of sensitivity for accurate detection. In the present study, we have established a method that fills the analytical gap between low concentrations of molecular markers and the minimum requirements for molecular testing. For this purpose, a sample preparation of whole blood samples with a directly downstream pre-amplification was developed, which amplifies specific species and resistance markers in a multiplex procedure. When applying pre-amplification techniques, the sensitivity of the pathogen detection in whole blood samples was up to 100 times higher than in non-pre-amplified samples. The method was tested with blood samples that were spiked with several Gram-positive and Gram-negative bacterial pathogens. By applying this method to artificial spiked blood samples, it was possible to demonstrate a sensitivity of 1 colony-forming unit (CFU) per millilitre of blood for S. aureus and E. faecium. A detection limit of 28 and 383 CFU per ml of blood was achieved for E. coli and K. pneumoniae, respectively. If the sensitivity is also confirmed for real clinical blood samples from septic patients, the novel technique can be used for pathogen detection without cultivation, which might help to accelerate diagnostics and, thus, to decrease sepsis mortality rates.
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Affiliation(s)
- Martin Reinicke
- Leibniz Institute of Photonic Technology (IPHT), Leibniz Centre for Photonics in Infection Research (LPI), 07745 Jena, Germany
- InfectoGnostics Research Campus, 07743 Jena, Germany
| | - Sascha Daniel Braun
- Leibniz Institute of Photonic Technology (IPHT), Leibniz Centre for Photonics in Infection Research (LPI), 07745 Jena, Germany
- InfectoGnostics Research Campus, 07743 Jena, Germany
| | - Celia Diezel
- Leibniz Institute of Photonic Technology (IPHT), Leibniz Centre for Photonics in Infection Research (LPI), 07745 Jena, Germany
- InfectoGnostics Research Campus, 07743 Jena, Germany
| | - Oliver Lemuth
- InfectoGnostics Research Campus, 07743 Jena, Germany
- BLINK AG, 07747 Jena, Germany
| | - Ines Engelmann
- InfectoGnostics Research Campus, 07743 Jena, Germany
- BLINK AG, 07747 Jena, Germany
| | - Theresa Liebe
- InfectoGnostics Research Campus, 07743 Jena, Germany
- BLINK AG, 07747 Jena, Germany
| | - Ralf Ehricht
- Leibniz Institute of Photonic Technology (IPHT), Leibniz Centre for Photonics in Infection Research (LPI), 07745 Jena, Germany
- InfectoGnostics Research Campus, 07743 Jena, Germany
- Institute of Physical Chemistry, Friedrich-Schiller University, 07743 Jena, Germany
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17
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Shigemori H, Fujita S, Tamiya E, Nagai H. Miniaturization of CRISPR/Cas12-Based DNA Sensor Array by Non-Contact Printing. MICROMACHINES 2024; 15:144. [PMID: 38258263 PMCID: PMC10818962 DOI: 10.3390/mi15010144] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 01/10/2024] [Accepted: 01/11/2024] [Indexed: 01/24/2024]
Abstract
DNA microarrays have been applied for comprehensive genotyping, but remain a drawback in complicated operations. As a solution, we previously reported the solid-phase collateral cleavage (SPCC) system based on the clustered regularly interspaced short palindromic repeat/CRISPR-associated protein 12 (CRISPR/Cas12). Surface-immobilized Cas12-CRISPR RNA (crRNA) can directly hybridize target double-stranded DNA (dsDNA) and subsequently produce a signal via the cleavage of single-stranded DNA (ssDNA) reporter immobilized on the same spot. Therefore, SPCC-based multiplex dsDNA detection can be performed easily. This study reports the miniaturization of SPCC-based spots patterned by a non-contact printer and its performance in comprehensive genotyping on a massively accumulated array. Initially, printing, immobilization, and washing processes of Cas12-crRNA were established to fabricate the non-contact-patterned SPCC-based sensor array. A target dsDNA concentration response was obtained based on the developed sensor array, even with a spot diameter of 0.64 ± 0.05 mm. Also, the limit of detection was 572 pM, 531 pM, and 3.04 nM with 40, 20, and 10 nL-printing of Cas12-crRNA, respectively. Furthermore, the sensor array specifically detected three dsDNA sequences in one-pot multiplexing; therefore, the feasibility of comprehensive genotyping was confirmed. These results demonstrate that our technology can be miniaturized as a CRISPR/Cas12-based microarray by using non-contact printing. In the future, the non-contact-patterned SPCC-based sensor array can be applied as an alternative tool to DNA microarrays.
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Affiliation(s)
- Hiroki Shigemori
- Advanced Photonics and Biosensing Open Innovation Laboratory (PhotoBIO-OIL), National Institute of Advanced Industrial Science and Technology (AIST), Photonics Center Osaka University, 2-1 Yamada-Oka, Suita 565-0871, Osaka, Japan; (H.S.); (S.F.); (E.T.)
- Graduate School of Human Development and Environment, Kobe University, 3-11 Tsurukabuto, Nada-ku, Kobe 657-0011, Hyogo, Japan
| | - Satoshi Fujita
- Advanced Photonics and Biosensing Open Innovation Laboratory (PhotoBIO-OIL), National Institute of Advanced Industrial Science and Technology (AIST), Photonics Center Osaka University, 2-1 Yamada-Oka, Suita 565-0871, Osaka, Japan; (H.S.); (S.F.); (E.T.)
| | - Eiichi Tamiya
- Advanced Photonics and Biosensing Open Innovation Laboratory (PhotoBIO-OIL), National Institute of Advanced Industrial Science and Technology (AIST), Photonics Center Osaka University, 2-1 Yamada-Oka, Suita 565-0871, Osaka, Japan; (H.S.); (S.F.); (E.T.)
- Institute of Scientific and Industrial Research (SANKEN), Osaka University, 8-1 Mihogaoka, Ibaraki 567-0047, Osaka, Japan
| | - Hidenori Nagai
- Advanced Photonics and Biosensing Open Innovation Laboratory (PhotoBIO-OIL), National Institute of Advanced Industrial Science and Technology (AIST), Photonics Center Osaka University, 2-1 Yamada-Oka, Suita 565-0871, Osaka, Japan; (H.S.); (S.F.); (E.T.)
- Graduate School of Human Development and Environment, Kobe University, 3-11 Tsurukabuto, Nada-ku, Kobe 657-0011, Hyogo, Japan
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18
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Song J, Lin S, Zhu L, Lin Y, An W, Zhang J, Wang H, Yang Z, Liao Y, Xu Y, Li Q. Direct identification of pathogens via microbial cellular DNA in whole blood by MeltArray. Microb Biotechnol 2024; 17:e14380. [PMID: 38084800 PMCID: PMC10832520 DOI: 10.1111/1751-7915.14380] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Revised: 10/27/2023] [Accepted: 11/16/2023] [Indexed: 02/03/2024] Open
Abstract
Rapid identification of pathogens is critical for early and appropriate treatment of bloodstream infections. The various culture-independent assays that have been developed often have long turnaround times, low sensitivity and narrow pathogen coverage. Here, we propose a new multiplex PCR assay, MeltArray, which uses intact microbial cells as the source of genomic DNA (gDNA). The successive steps of the MeltArray assay, including selective lysis of human cells, microbial cell sedimentation, microbial cellular DNA extraction, target-specific pre-amplification and multiplex PCR detection, allowed the detection of 35 major bloodstream infectious pathogens in whole blood within 5.5 h. The limits of detection varied depending on the pathogen and ranged from 1 to 5 CFU/mL. Of 443 blood culture samples, including 373 positive blood culture samples and 70 negative blood culture samples, the MeltArray assay showed a sensitivity of 93.8% (350/373, 95% confidence interval [CI] = 90.7%-96.0%), specificity of 98.6% (69/70, 95% CI = 91.2%-99.9%), positive predictive value of 99.7% (95% CI = 98.1%-99.9%), and negative predictive value of 75.0% (95% CI = 64.7%-83.2%). The MeltArray detection results of 16 samples differed from MALDI-TOF and were confirmed by Sanger sequencing. Further testing of 110 whole blood samples from patients with suspected bloodstream infections using blood culture results revealed that the MeltArray assay had a clinical sensitivity of 100% (9/9, 95% CI = 62.8%-100.0%), clinical specificity of 74.5% (70/94, 95% CI = 64.2%-82.7%), positive predictive value of 27.3% (95% CI = 13.9%-45.8%), and negative predictive value of 100.0% (95% CI = 93.5%-100.0%). Compared with metagenomic next-generation sequencing, the MeltArray assay displayed a positive agreement of 85.7% (6/7, 95% CI = 42.0%-99.2%) and negative agreement of 100.0% (4/4, 95% CI = 39.6%-100.0%). We conclude that the MeltArray assay can be used as a rapid and reliable tool for direct identification of pathogens in bloodstream infections.
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Affiliation(s)
- Jiabao Song
- Engineering Research Centre of Molecular Diagnostics of the Ministry of Education, State Key Laboratory of Cellular Stress Biology, State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Life SciencesXiamen UniversityXiamenChina
| | - Su Lin
- Engineering Research Centre of Molecular Diagnostics of the Ministry of Education, State Key Laboratory of Cellular Stress Biology, State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Life SciencesXiamen UniversityXiamenChina
| | - Lin Zhu
- Engineering Research Centre of Molecular Diagnostics of the Ministry of Education, State Key Laboratory of Cellular Stress Biology, State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Life SciencesXiamen UniversityXiamenChina
| | - Yong Lin
- Zhongshan HospitalXiamen UniversityXiamenChina
| | - Wenbin An
- Xiang'an HospitalXiamen UniversityXiamenChina
| | - Jinding Zhang
- Engineering Research Centre of Molecular Diagnostics of the Ministry of Education, State Key Laboratory of Cellular Stress Biology, State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Life SciencesXiamen UniversityXiamenChina
| | - Haohao Wang
- Engineering Research Centre of Molecular Diagnostics of the Ministry of Education, State Key Laboratory of Cellular Stress Biology, State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Life SciencesXiamen UniversityXiamenChina
| | - Zhuan Yang
- Engineering Research Centre of Molecular Diagnostics of the Ministry of Education, State Key Laboratory of Cellular Stress Biology, State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Life SciencesXiamen UniversityXiamenChina
| | - Yiqun Liao
- Engineering Research Centre of Molecular Diagnostics of the Ministry of Education, State Key Laboratory of Cellular Stress Biology, State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Life SciencesXiamen UniversityXiamenChina
| | - Ye Xu
- Engineering Research Centre of Molecular Diagnostics of the Ministry of Education, State Key Laboratory of Cellular Stress Biology, State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Life SciencesXiamen UniversityXiamenChina
| | - Qingge Li
- Engineering Research Centre of Molecular Diagnostics of the Ministry of Education, State Key Laboratory of Cellular Stress Biology, State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Life SciencesXiamen UniversityXiamenChina
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19
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Wang ZY, Li LL, Cao XL, Li P, Du J, Zou MJ, Wang LL. Clinical application of amplification-based versus amplification-free metagenomic next-generation sequencing test in infectious diseases. Front Cell Infect Microbiol 2023; 13:1138174. [PMID: 38094744 PMCID: PMC10716234 DOI: 10.3389/fcimb.2023.1138174] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Accepted: 11/07/2023] [Indexed: 12/18/2023] Open
Abstract
Background Recently, metagenomic next-generation sequencing (mNGS) has been used in the diagnosis of infectious diseases (IDs) as an emerging and powerful tool. However, whether the complicated methodological variation in mNGS detections makes a difference in their clinical performance is still unknown. Here we conducted a method study on the clinical application of mNGS tests in the DNA detection of IDs. Methods We analyzed the effect of several potential factors in the whole process of mNGS for DNA detection on microorganism identification in 98 samples of suspected ID patients by amplification-based mNGS. The amplification-based and amplification-free mNGS tests were successfully performed in 41 samples. Then we compared the clinical application of the two mNGS methods in the DNA detection of IDs. Results We found that a higher concentration of extracted nucleic acid was more conducive to detecting microorganisms. Other potential factors, such as read depth and proportion of human reads, might not be attributed to microorganism identification. The concordance rate of amplification-based and amplification-free mNGS results was 80.5% (33/41) in the patients with suspected IDs. Amplification-based mNGS showed approximately 16.7% higher sensitivity than amplification-free mNGS. However, 4 cases with causative pathogens only detected by amplification-based mNGS were finally proved false-positive. In addition, empirical antibiotic treatments were adjusted in 18 patients following mNGS testing with unexpected pathogens. Conclusions Amplification-based and amplification-free mNGS tests showed their specific advantages and disadvantages in the diagnosis of IDs. The clinical application of mNGS still needs more exploration from a methodological perspective. With advanced technology and standardized procedure, mNGS will play a promising role in the diagnosis of IDs and help guide the use of antibiotics.
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Affiliation(s)
- Zhe-Ying Wang
- Department of Clinical Laboratory, Qilu Hospital of Shandong University, Jinan, Shandong, China
- Shandong Engineering Research Center of Biomarker and Artificial Intelligence Application, Jinan, Shandong, China
| | - Lu-Lu Li
- Department of Clinical Laboratory, Qilu Hospital of Shandong University, Jinan, Shandong, China
| | - Xue-Lei Cao
- Department of Clinical Laboratory, Qilu Hospital of Shandong University, Jinan, Shandong, China
- Shandong Engineering Research Center of Biomarker and Artificial Intelligence Application, Jinan, Shandong, China
| | - Ping Li
- Department of Clinical Laboratory, Qilu Hospital of Shandong University, Jinan, Shandong, China
- Shandong Engineering Research Center of Biomarker and Artificial Intelligence Application, Jinan, Shandong, China
| | - Jian Du
- Department of Urology, The First Affiliated Hospital of Shandong First Medical University, Jinan, Shandong, China
| | - Ming-Jin Zou
- Department of Clinical Laboratory, Qilu Hospital of Shandong University, Jinan, Shandong, China
| | - Li-Li Wang
- Department of Clinical Laboratory, Qilu Hospital of Shandong University, Jinan, Shandong, China
- Shandong Engineering Research Center of Biomarker and Artificial Intelligence Application, Jinan, Shandong, China
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20
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Bloomfield DA, Akhter S, Aguayza E. Routine blood culture in the emergency department: Worthy or waste? Acad Emerg Med 2023; 30:1168-1169. [PMID: 37042350 DOI: 10.1111/acem.14736] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Revised: 02/24/2023] [Accepted: 03/07/2023] [Indexed: 04/13/2023]
Affiliation(s)
| | - Shahnaz Akhter
- Department of Medicine, Richmond University Medical Center, New York City, New York, USA
| | - Erica Aguayza
- Richmond University Medical Center, New York City, New York, USA
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21
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Chu PY, Yang CM, Huang KL, Wu AY, Hsieh CH, Chao AC, Wu MH. Development of an Optically Induced Dielectrophoresis (ODEP) Microfluidic System for High-Performance Isolation and Purification of Bacteria. BIOSENSORS 2023; 13:952. [PMID: 37998128 PMCID: PMC10669672 DOI: 10.3390/bios13110952] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Revised: 10/13/2023] [Accepted: 10/24/2023] [Indexed: 11/25/2023]
Abstract
For the rapid detection of bacteria in a blood sample, nucleic acid amplification-based assays are believed to be promising. Nevertheless, the nucleic acids released from the dead blood cells or bacteria could affect the assay performance. This highlights the importance of the isolation of live bacteria from blood samples. To address this issue, this study proposes a two-step process. First, a blood sample was treated with the immuno-magnetic microbeads-based separation to remove the majority of blood cells. Second, an optically induced dielectrophoresis (ODEP) microfluidic system with an integrated dynamic circular light image array was utilized to further isolate and purify the live bacteria from the remaining blood cells based on their size difference. In this work, the ODEP microfluidic system was developed. Its performance for the isolation and purification of bacteria was evaluated. The results revealed that the method was able to harvest the live bacteria in a high purity (90.5~99.2%) manner. Overall, the proposed method was proven to be capable of isolating and purifying high-purity live bacteria without causing damage to the co-existing cells. This technical feature was found to be valuable for the subsequent nucleic-acid-based bacteria detection, in which the interferences caused by the nontarget nucleic acids could be eliminated.
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Affiliation(s)
- Po-Yu Chu
- Graduate Institute of Biomedical Engineering, Chang Gung University, Taoyuan City 33302, Taiwan; (P.-Y.C.); (K.-L.H.); (A.-Y.W.)
| | - Chia-Ming Yang
- Department of Electronic Engineering, Chang Gung University, Taoyuan City 33302, Taiwan;
- Institute of Electro-Optical Engineering, Chang Gung University, Taoyuan City 33302, Taiwan
- Biosensor Group, Biomedical Engineering Research Center, Chang Gung University, Taoyuan City 33302, Taiwan
- Department of Neurosurgery, Chang Gung Memorial Hospital at Linkou, Taoyuan City 33302, Taiwan
- Department of Materials Engineering, Ming Chi University of Technology, New Taipei City 243303, Taiwan
| | - Kai-Lin Huang
- Graduate Institute of Biomedical Engineering, Chang Gung University, Taoyuan City 33302, Taiwan; (P.-Y.C.); (K.-L.H.); (A.-Y.W.)
| | - Ai-Yun Wu
- Graduate Institute of Biomedical Engineering, Chang Gung University, Taoyuan City 33302, Taiwan; (P.-Y.C.); (K.-L.H.); (A.-Y.W.)
| | - Chia-Hsun Hsieh
- Division of Hematology/Oncology, Department of Internal Medicine, Chang Gung Memorial Hospital at Linkou, Taoyuan City 33302, Taiwan;
- Division of Hematology/Oncology, Department of Internal Medicine, New Taipei Municipal TuCheng Hospital, New Taipei City 236017, Taiwan
| | - A-Ching Chao
- Department of Neurology, Kaohsiung Medical University Hospital, Kaohsiung City 80756, Taiwan
- Department of Neurology, College of Medicine, Kaohsiung Medical University, Kaohsiung City 80756, Taiwan
| | - Min-Hsien Wu
- Graduate Institute of Biomedical Engineering, Chang Gung University, Taoyuan City 33302, Taiwan; (P.-Y.C.); (K.-L.H.); (A.-Y.W.)
- Division of Hematology/Oncology, Department of Internal Medicine, Chang Gung Memorial Hospital at Linkou, Taoyuan City 33302, Taiwan;
- Division of Hematology/Oncology, Department of Internal Medicine, New Taipei Municipal TuCheng Hospital, New Taipei City 236017, Taiwan
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22
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Liu CG, Liao AJ. [Feature analysis of different neutrophil levels on the distribution of pathogens in bloodstream infection in patients with hematologic malignancy]. ZHONGHUA XUE YE XUE ZA ZHI = ZHONGHUA XUEYEXUE ZAZHI 2023; 44:857-860. [PMID: 38049340 PMCID: PMC10694080 DOI: 10.3760/cma.j.issn.0253-2727.2023.10.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Indexed: 12/06/2023]
Affiliation(s)
- C G Liu
- Department of Hematology, Shengjing Hospital of China Medical University, Shenyang 110004, China
| | - A J Liao
- Department of Hematology, Shengjing Hospital of China Medical University, Shenyang 110004, China
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Li M, Zhao L, Zhu Y, Ou M, Xu H, Hu X, Wei H, Chen Y, Shen H. Clinical value of droplet digital PCR in the diagnosis and dynamic monitoring of suspected bacterial bloodstream infections. Clin Chim Acta 2023; 550:117566. [PMID: 37776990 DOI: 10.1016/j.cca.2023.117566] [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: 08/05/2023] [Revised: 09/20/2023] [Accepted: 09/22/2023] [Indexed: 10/02/2023]
Abstract
BACKGROUND Bloodstream infections (BSIs) represent a significant public health challenge due to their high morbidity and mortality. The clinical prognosis of BSIs is closely related to the timely and accurate diagnosis and the rational use of initial antimicrobials. We aimed to evaluate the clinical value of droplet digital PCR (ddPCR) in rapid diagnosis and dynamic monitoring of BSIs. METHODS In this prospective study, using a ddPCR-based approach which detects 18 common pathogens, we compared the detection results and clinical concordance rates of ddPCR with blood culture (BC) in 211 patients with suspected BSIs. Further, the inflammatory profile of BSIs with Gram-negative bacteria was analyzed by Olink proteomics platform. RESULTS Our data showed that the positive detection rate of ddPCR was 48.82%, which was higher than that of BC (9.48%). For BC-validated BSIs, ddPCR had a sensitivity of 90.00% and a specificity of 55.50%. When considering clinically-validated BSIs, the diagnostic value of ddPCR improved with a sensitivity of 92.59% and a specificity of 78.46%.The bacterial load detected by ddPCR was correlated with traditional clinical inflammatory indicators such as interleukin-6 (IL-6) and C-reactive protein (CRP). In addition, using Olink proteomics platform, we revealed that serological osteoprotegerin (OPG), interleukin-8 (IL-8), interleukin-18 receptor 1 (IL-18R1), C-C motif chemokine 20 (CCL20) and IL-6 were substantially elevated in Gram-negative bacteria-associated BSIs, which could serve as novel auxiliary diagnostic indicators for Gram-negative bacteria BSIs. CONCLUSION ddPCR has the potential to provide early pathogen diagnosis, dynamic monitoring, and treatment regimen optimization for patients with BSIs.
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Affiliation(s)
- Miao Li
- Department of Laboratory Medicine, Nanjing Drum Tower Hospital Clinical College of Nanjing University of Chinese Medicine, Jiangsu, China
| | - Liwei Zhao
- Department of Laboratory Medicine, Nanjing Drum Tower Hospital Clinical College of Nanjing University of Chinese Medicine, Jiangsu, China
| | - Yijia Zhu
- Department of Laboratory Medicine, Nanjing Drum Tower Hospital Clinical College of Nanjing University of Chinese Medicine, Jiangsu, China
| | - Mingrong Ou
- Department of Laboratory Medicine, Nanjing Drum Tower Hospital Clinical College of Nanjing Medical University, Jiangsu, China
| | - Hongpan Xu
- Department of Laboratory Medicine, Nanjing Drum Tower Hospital Clinical College of Nanjing University of Chinese Medicine, Jiangsu, China
| | - Xiaohan Hu
- Department of Laboratory Medicine, Nanjing Drum Tower Hospital Clinical College of Nanjing University of Chinese Medicine, Jiangsu, China
| | - Hongxia Wei
- Department of Laboratory Medicine, Nanjing Drum Tower Hospital Clinical College of Nanjing University of Chinese Medicine, Jiangsu, China
| | - Yuxin Chen
- Department of Laboratory Medicine, Nanjing Drum Tower Hospital Clinical College of Nanjing University of Chinese Medicine, Jiangsu, China.
| | - Han Shen
- Department of Laboratory Medicine, Nanjing Drum Tower Hospital Clinical College of Nanjing University of Chinese Medicine, Jiangsu, China.
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24
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Uechi A, Uechi K, Nakano A, Yogi S, Shimoji M, Maeda S. Evaluation of the feasibility of EUCAST RAST using antimicrobial disks available in Japan. J Infect Chemother 2023; 29:978-984. [PMID: 37400015 DOI: 10.1016/j.jiac.2023.06.016] [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] [Revised: 06/04/2023] [Accepted: 06/23/2023] [Indexed: 07/05/2023]
Abstract
BACKGROUND In November 2018, the European Committee for Antimicrobial Susceptibility Testing (EUCAST) established rapid antimicrobial susceptibility testing (RAST), which could be performed directly on positive blood culture samples. Although concentrations of antimicrobial agents in several antimicrobial disks available in Japan are different from those recommended by the EUCAST, the feasibility of EUCAST RAST using antimicrobial disks available in Japan remains to be evaluated. METHODS Blood culture bottles spiked with 127 clinical isolates (65 Escherichia coli and 62 Klebsiella pneumoniae) were tested by RAST for cefotaxime (CTX), ceftazidime (CAZ), meropenem, and ciprofloxacin using antimicrobial disks available in Japan, and compared with a reference AST method using automated AST instrument (VITEK®2). RESULTS The overall category agreement (CA) for RAST using antimicrobial disks available in Japan was 96.3%, 96.8%, and 95.6% after 4, 6, and 8 h of incubations, respectively. However, the CAZ RAST for E. coli showed major error of 8.2% (8 h incubation) for the Sensi disk, 14.3% (6 h incubation), and 24.5% (8 h incubation) for the KB disk. The CTX RAST for K. pneumoniae showed 25% (4 h incubation) and 31.3% (4 h incubation) of very major error for the Sensi and KB disks, respectively. CONCLUSIONS The EUCAST RAST results for E. coli and K. pneumoniae using antimicrobial disks available in Japan suggest their usefulness, although modified RAST breakpoints are required for several antimicrobial agents.
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Affiliation(s)
- Ayumi Uechi
- Division of Clinical Laboratory and Blood Transfusion, University of the Ryukyus Hospital, Okinawa, Japan.
| | - Kohei Uechi
- Division of Clinical Laboratory and Blood Transfusion, University of the Ryukyus Hospital, Okinawa, Japan
| | - Ami Nakano
- Division of Clinical Laboratory and Blood Transfusion, University of the Ryukyus Hospital, Okinawa, Japan
| | - Shohei Yogi
- Department of Morphological Pathology, School of Health Sciences, Faculty of Medicine and Graduate School of Health Sciences, University of the Ryukyus, Okinawa, Japan
| | - Maria Shimoji
- Division of Clinical Laboratory and Blood Transfusion, University of the Ryukyus Hospital, Okinawa, Japan
| | - Shiro Maeda
- Division of Clinical Laboratory and Blood Transfusion, University of the Ryukyus Hospital, Okinawa, Japan; Department of Advanced Genomic and Laboratory Medicine, Graduate School of Medicine, University of the Ryukyus, Okinawa, Japan
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25
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Smith RD, Johnson JK, Ernst RK. Comparison of 3 diagnostic platforms for identification of bacteria and yeast from positive blood culture bottles. Diagn Microbiol Infect Dis 2023; 107:116018. [PMID: 37478505 DOI: 10.1016/j.diagmicrobio.2023.116018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Revised: 04/26/2023] [Accepted: 07/03/2023] [Indexed: 07/23/2023]
Abstract
Managing bloodstream infections requires fast and accurate diagnostics. Culture-based diagnostic methods for identification from positive blood culture require 24-hour subculture, potentially delaying time to appropriate therapy. Positive blood cultures were collected (n = 301) from September 2021 to August 2022 at the University of Maryland Medical Center. Platforms compared were BioFire® BCID2, Sepsityper®, and short-term culture. For monomicrobial cultures, FilmArray® BCID2 identified 88.3% (241/273) of pathogens. Rapid Sepsityper® identified 76.9% (210/273) of pathogens. Sepsityper® extraction identified 82.4% (225/273) of pathogens. Short-term culture identified 83.5% (228/273) of pathogens. For polymicrobial cultures, Sepsityper®, short-term culture, and BioFire® BCID2 had complete identifications at 10.7% (3/28), 0%, and 92.9% (26/28), respectively. Time-to-results for Rapid Sepsityper®, Sepsityper® extraction, BioFire® BCID2, and Short-term culture were 35, 52, 65, and 306 minutes, respectively. Performance of these platforms can reduce time-to-results and may help effectively treat bloodstream infections faster. Accuracy, time-to-result, and hands-on time are important factors when evaluation diagnostic platforms.
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Affiliation(s)
- Richard D Smith
- Department of Pathology, School of Medicine, University of Maryland, Baltimore, MD, USA; Department of Microbial Pathogenesis, School of Dentistry, University of Maryland, Baltimore, MD, USA.
| | - J Kristie Johnson
- Department of Pathology, School of Medicine, University of Maryland, Baltimore, MD, USA
| | - Robert K Ernst
- Department of Microbial Pathogenesis, School of Dentistry, University of Maryland, Baltimore, MD, USA
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Giannella M, Rinaldi M, Viale P. Antimicrobial Resistance in Organ Transplant Recipients. Infect Dis Clin North Am 2023; 37:515-537. [PMID: 37244806 DOI: 10.1016/j.idc.2023.04.001] [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: 05/29/2023]
Abstract
The overall burden of the main clinically relevant bacterial multidrug-resistant organisms (MDROs) (eg, methicillin-resistant Staphylococcus aureus, vancomycin-resistant enterococci, extended-spectrum β-lactamase producing or extended-spectrum cephalosporin-resistant Enterobacterales, carbapenem-resistant or carbapenemase-producing Enterobacterales, MDR Pseudomonas aeruginosa, and carbapenem-resistant Acinetobacter baumannii) in solid organ transplant (SOT) populations is summarized showing prevalence/incidence, risk factors, and impact on graft/patient outcome according to the type of SOT. The role of such bacteria in donor-derived infections is also reviewed. As for the management, the main prevention strategies and treatment options are discussed. Finally, nonantibiotic-based strategies are considered as future directions for the management of MDRO in SOT setting.
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Affiliation(s)
- Maddalena Giannella
- Infectious Diseases, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italy; Department of Medical and Surgical Sciences, Alma Mater Studiorum University of Bologna, Via Massarenti 11, Bologna 40137, Italy.
| | - Matteo Rinaldi
- Infectious Diseases, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italy; Department of Medical and Surgical Sciences, Alma Mater Studiorum University of Bologna, Via Massarenti 11, Bologna 40137, Italy
| | - Pierluigi Viale
- Infectious Diseases, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italy; Department of Medical and Surgical Sciences, Alma Mater Studiorum University of Bologna, Via Massarenti 11, Bologna 40137, Italy
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27
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Lapin JS, Smith RD, Hornback KM, Johnson JK, Claeys KC. From bottle to bedside: Implementation considerations and antimicrobial stewardship considerations for bloodstream infection rapid diagnostic testing. Pharmacotherapy 2023; 43:847-863. [PMID: 37158053 DOI: 10.1002/phar.2813] [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: 01/31/2023] [Revised: 03/31/2023] [Accepted: 04/03/2023] [Indexed: 05/10/2023]
Abstract
Antimicrobial stewardship (AMS) programs have been quick to adopt novel molecular rapid diagnostic technologies (mRDTs) for bloodstream infections (BSIs) to improve antimicrobial management. As such, most of the literature demonstrating the clinical and economic benefits of mRDTs for BSI is in the presence of active AMS intervention. Leveraging mRDTs to improve antimicrobial therapy for BSI is increasingly integral to AMS program activities. This narrative review discusses available and future mRDTs, the relationship between the clinical microbiology laboratory and AMS programs, and practical considerations for optimizing the use of these tools within a health system. Antimicrobial stewardship programs must work closely with their clinical microbiology laboratories to ensure that mRDTs are used to their fullest benefit while remaining cognizant of their limitations. As more mRDT instruments and panels become available and AMS programs continue to expand, future efforts must consider the expansion beyond traditional settings of large academic medical centers and how combinations of tools can further improve patient care.
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Affiliation(s)
- Jonathan S Lapin
- Department of Pharmacy Practice, University of Maryland Medical Center, Baltimore, Maryland, USA
| | - Richard D Smith
- Department of Pathology, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Krutika M Hornback
- Department of Pharmacy Practice, Medical University of South Carolina (MUSC) Health, Charleston, South Carolina, USA
| | - J Kristie Johnson
- Department of Pathology, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Kimberly C Claeys
- Department of Pharmacy Science and Health Outcomes Research, University of Maryland School of Pharmacy, Baltimore, Maryland, USA
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28
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Ture Z, Güner R, Alp E. Antimicrobial stewardship in the intensive care unit. JOURNAL OF INTENSIVE MEDICINE 2023; 3:244-253. [PMID: 37533805 PMCID: PMC10391567 DOI: 10.1016/j.jointm.2022.10.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Revised: 10/03/2022] [Accepted: 10/10/2022] [Indexed: 08/04/2023]
Abstract
High resistance rates to antimicrobials continue to be a global health threat. The incidence of multidrug-resistant (MDR) microorganisms in intensive care units (ICUs) is quite high compared to in the community and other units in the hospital because ICU patients are generally older, have higher numbers of co-morbidities and immune-suppressed; moreover, the typically high rates of invasive procedures performed in the ICU increase the risk of infection by MDR microorganisms. Antimicrobial stewardship (AMS) refers to the implementation of coordinated interventions to improve and track the appropriate use of antibiotics while offering the best possible antibiotic prescription (according to dose, duration, and route of administration). Broad-spectrum antibiotics are frequently preferred in ICUs because of greater infection severity and colonization and infection by MDR microorganisms. For this reason, a number of studies on AMS in ICUs have increased in recent years. Reducing the use of broad-spectrum antibiotics forms the basis of AMS. For this purpose, parameters such as establishing an AMS team, limiting the use of broad-spectrum antimicrobials, terminating treatments early, using early warning systems, pursuing infection control, and providing education and feedback are used. In this review, current AMS practices in ICUs are discussed.
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Affiliation(s)
- Zeynep Ture
- Department of Infectious Diseases and Clinical Microbiology, Faculty of Medicine, Erciyes University, Kayseri 38039,Turkey
| | - Rahmet Güner
- Department of Infectious Diseases and Clinical Microbiology, Yıldırım Beyazıt University, Ankara 06800, Turkey
| | - Emine Alp
- Department of Infectious Diseases and Clinical Microbiology, Yıldırım Beyazıt University, Ankara 06800, Turkey
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29
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Zhou Y, Shi W, Wen Y, Mao E, Ni T. Comparison of pathogen detection consistency between metagenomic next-generation sequencing and blood culture in patients with suspected bloodstream infection. Sci Rep 2023; 13:9460. [PMID: 37301921 PMCID: PMC10257643 DOI: 10.1038/s41598-023-36681-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Accepted: 06/08/2023] [Indexed: 06/12/2023] Open
Abstract
The application of metagenomic next-generation sequencing (mNGS) has gradually been carried out by clinical practitioner. However, few studies have compared it with blood cultures in patients suffering from suspected bloodstream infections. The purpose of this study was to compare the detection of pathogenic microorganisms by these two assays in patients with suspected bloodstream infection. We retrospectively studied patients with fever, chills, antibiotic use for more than 3 days, suspected bloodstream infection, and admission to the emergency department of Ruijin Hospital from January 2020 to June 2022. All patients had blood drawn on the same day for blood mNGS and blood cultures. Clinical and laboratory parameters were collected on the day blood was drawn. The detection of pathogenic microorganisms by the two methods was compared. Risk factors and in-hospital mortality in patients with bloodstream infections were analysed separately for these two assays. In all 99 patients, the pathogenic microorganisms detection rate in blood mNGS was significantly higher than that in blood culture. Blood mNGS was consistent with blood culture in only 12.00% of all positive bacterial and fungal test results. The level of CRP is related to bacteraemia, fungaemia and viraemia detected by blood mNGS. No clear risk factors could be found in patients with a positive blood culture. In critically ill patients, both tests failed to improve patient outcomes. In patients with suspected bloodstream infection, mNGS is not yet a complete replacement for blood cultures.
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Affiliation(s)
- Yuhua Zhou
- Department of Emergency, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, No. 197, Ruijiner Road, Huangpu District, Shanghai, 200025, China
| | - Wen Shi
- Department of Emergency, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, No. 197, Ruijiner Road, Huangpu District, Shanghai, 200025, China
| | - Yi Wen
- Department of Emergency, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, No. 197, Ruijiner Road, Huangpu District, Shanghai, 200025, China
| | - Enqiang Mao
- Department of Emergency, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, No. 197, Ruijiner Road, Huangpu District, Shanghai, 200025, China.
| | - Tongtian Ni
- Department of Emergency, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, No. 197, Ruijiner Road, Huangpu District, Shanghai, 200025, China.
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30
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Bonaiuto C, Baccani I, Chilleri C, Antonelli A, Giani T, Rossolini GM. Evaluation of the Liquid Colony™ Produced by the FAST System for Shortening the Time of Bacterial Identification and Phenotypic Antimicrobial Susceptibility Testing and Detection of Resistance Mechanisms from Positive Blood Cultures. Diagnostics (Basel) 2023; 13:diagnostics13111849. [PMID: 37296699 DOI: 10.3390/diagnostics13111849] [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: 03/23/2023] [Revised: 05/17/2023] [Accepted: 05/20/2023] [Indexed: 06/12/2023] Open
Abstract
BACKGROUND the aim of this study was to evaluate the performance of the Liquid Colony™ (LC) generated directly from positive blood cultures (PBCs) by the FAST System (Qvella, Richmond Hill, ON, Canada) for rapid identification (ID) and antimicrobial susceptibility testing (AST) compared with the standard of care (SOC) workflow. METHODS Anonymized PBCs were processed in parallel by the FAST System and FAST PBC Prep cartridge (35 min runtime) and SOC. ID was performed by MALDI-ToF mass spectrometry (Bruker, Billerica, MA, USA). AST was performed by reference broth microdilution (Merlin Diagnostika, Bornheim, Germany). Carbapenemase detection was carried out with the lateral flow immunochromatographic assay (LFIA) RESIST-5 O.O.K.N.V. (Coris, Gembloux, Belgium). Polymicrobial PBCs and samples containing yeast were excluded. RESULTS 241 PBCs were evaluated. ID results showed 100% genus-level concordance and 97.8% species-level concordance between LC and SOC. The AST results for Gram-negative bacteria showed a categorical agreement (CA) of 99.1% (1578/1593), with minor error (mE), major error (ME), and very major error (VME) rates of 0.6% (10/1593), 0.3% (3/1122), and 0.4% (2/471), respectively. The results from Gram-positive bacteria showed a CA of 99.6% (1655/1662), with mE, ME, and VME rates of 0.3% (5/1662), 0.2% (2/1279), and 0.0% (0/378), respectively. Bias evaluation revealed acceptable results for both Gram-negatives and Gram-positives (-12.4% and -6.5%, respectively). The LC yielded the detection of 14/18 carbapenemase producers by LFIA. In terms of turnaround time, the ID, AST, and carbapenemase detection results were generally obtained one day earlier with the FAST System compared with the SOC workflow. CONCLUSIONS The ID, AST, and carbapenemase detection results generated with the FAST System LC were highly concordant with the conventional workflow. The LC allowed species ID and carbapenemase detection within around 1 h after blood culture positivity and AST results within approximately 24 h, which is a significant reduction in the turnaround time of the PBC workflow.
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Affiliation(s)
- Chiara Bonaiuto
- Department of Experimental and Clinical Medicine, University of Florence, 50134 Florence, Italy
- Clinical Microbiology and Virology Unit, Careggi University Hospital, 50134 Florence, Italy
| | - Ilaria Baccani
- Department of Experimental and Clinical Medicine, University of Florence, 50134 Florence, Italy
- Clinical Microbiology and Virology Unit, Careggi University Hospital, 50134 Florence, Italy
| | - Chiara Chilleri
- Department of Experimental and Clinical Medicine, University of Florence, 50134 Florence, Italy
- Clinical Microbiology and Virology Unit, Careggi University Hospital, 50134 Florence, Italy
| | - Alberto Antonelli
- Department of Experimental and Clinical Medicine, University of Florence, 50134 Florence, Italy
- Clinical Microbiology and Virology Unit, Careggi University Hospital, 50134 Florence, Italy
| | - Tommaso Giani
- Department of Experimental and Clinical Medicine, University of Florence, 50134 Florence, Italy
- Clinical Microbiology and Virology Unit, Careggi University Hospital, 50134 Florence, Italy
| | - Gian Maria Rossolini
- Department of Experimental and Clinical Medicine, University of Florence, 50134 Florence, Italy
- Clinical Microbiology and Virology Unit, Careggi University Hospital, 50134 Florence, Italy
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Saeki M, Nirasawa S, Aung MS, Ono M, Urushibara N, Kobayashi N, Takahashi S. Detecting the performance of methicillin-resistant Staphylococcus aureus by a molecular diagnostic assay in positive blood culture: Influence of coexistence of mecA-positive bacteria and diversity in orfX-SCCmec junction region in methicillin-susceptible S. aureus. J Infect Chemother 2023:S1341-321X(23)00116-2. [PMID: 37178974 DOI: 10.1016/j.jiac.2023.05.006] [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: 03/01/2023] [Revised: 04/23/2023] [Accepted: 05/02/2023] [Indexed: 05/15/2023]
Abstract
BACKGROUND In blood cultures that test positive for staphylococcal bacteria, rapid identification of methicillin-resistant Staphylococcus aureus (MRSA) or methicillin-susceptible Staphylococcus aureus (MSSA) by molecular assay is useful for appropriate antimicrobial treatment of bloodstream infections. Although the Xpert MRSA/SA BC assay is widely available in clinical settings in Japan, its efficacy has not yet evaluated thoroughly. METHODS We retrospectively studied 100 blood culture cases positive for S. aureus at Sapporo Medical University Hospital between March 2019 to May 2022. Cycle threshold (CT) values for target genes from the Xpert MRSA/SA BC assay were compared to phenotypic results. Genotyping and genetic analysis of the orfX-SCCmec junction region was performed for selected isolates. RESULTS We analyzed 25 and 75 isolates assigned to MRSA and MSSA, respectively, using the Xpert MRSA/SA BC assay. Of these, 99 isolates from agar cultures showed compatible susceptibility to oxacillin. One genetically misidentified case of MRSA was found to be caused by the mixed growth of MSSA and methicillin-resistant S. hominis on agar culture. Of the 73 MSSA with pure growth on agar culture, 45 (61.6%) were found to be orfX-SCCmec-positive, spa-positive, and mecA-negative in this assay. These MSSA belong to diverse spa and coa types. CONCLUSION The Xpert MRSA/SA BC assay accurately identified MRSA and MSSA in positive blood cultures. However, over half of the MSSA isolates showed positive results for orfX-SCCmec, presumably due to genetic diversity in the orfX-associated region of MSSA. Therefore, the coexistence of MSSA and mecA-harboring coagulase-negative staphylococci may cause confusion about identification of MRSA.
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Affiliation(s)
- Masachika Saeki
- Division of Laboratory Medicine, Sapporo Medical University Hospital, Sapporo, Japan
| | - Shinya Nirasawa
- Division of Laboratory Medicine, Sapporo Medical University Hospital, Sapporo, Japan
| | - Meiji Soe Aung
- Department of Hygiene, Sapporo Medical University School of Medicine, Sapporo, Japan
| | - Mayumi Ono
- Division of Laboratory Medicine, Sapporo Medical University Hospital, Sapporo, Japan
| | - Noriko Urushibara
- Department of Hygiene, Sapporo Medical University School of Medicine, Sapporo, Japan
| | - Nobumichi Kobayashi
- Department of Hygiene, Sapporo Medical University School of Medicine, Sapporo, Japan
| | - Satoshi Takahashi
- Division of Laboratory Medicine, Sapporo Medical University Hospital, Sapporo, Japan; Department of Infection Control and Laboratory Medicine, Sapporo Medical University School of Medicine, Sapporo, Japan.
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32
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Kamau E, Yang S. Metagenomic Sequencing of Positive Blood Culture Fluid for Accurate Bacterial and Fungal Species Identification: A Pilot Study. Microorganisms 2023; 11:1259. [PMID: 37317232 DOI: 10.3390/microorganisms11051259] [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: 04/03/2023] [Revised: 04/27/2023] [Accepted: 05/09/2023] [Indexed: 06/16/2023] Open
Abstract
With blood stream infections (BSIs) representing a major cause of mortality and morbidity worldwide, blood cultures play a crucial role in diagnosis, but their clinical application is dampened by the long turn-around time and the detection of only culturable pathogens. In this study, we developed and validated a shotgun metagenomics next-generation sequencing (mNGS) test directly from positive blood culture fluid, allowing for the identification of fastidious or slow growing microorganisms more rapidly. The test was built based on previously validated next-generation sequencing tests, which rely on several key marker genes for bacterial and fungal identification. The new test utilizes an open-source metagenomics CZ-ID platform for the initial analysis to generate the most likely candidate species, which is then used as a reference genome for downstream, confirmatory analysis. This approach is innovative because it takes advantage of an open-source software's agnostic taxonomic calling capability while still relying on the more established and previously validated marker gene-based identification scheme, increasing the confidence in the final results. The test showed high accuracy (100%, 30/30) for both bacterial and fungal microorganisms. We further demonstrated its clinical utility especially for anaerobes and mycobacteria that are either fastidious, slow growing, or unusual. Although applicable in only limited settings, the Positive Blood Culture mNGS test provides an incremental improvement in solving the unmet clinical needs for the diagnosis of challenging BSIs.
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Affiliation(s)
- Edwin Kamau
- Department of Pathology and Laboratory Medicine, UCLA David Geffen School of Medicine, Los Angeles, CA 90095, USA
| | - Shangxin Yang
- Department of Pathology and Laboratory Medicine, UCLA David Geffen School of Medicine, Los Angeles, CA 90095, USA
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Simner PJ, Dien Bard J, Doern C, Kristie Johnson J, Westblade L, Yenokyan G, Patel R, Hanson KE. Reporting of Antimicrobial Resistance from Blood Cultures, an Antibacterial Resistance Leadership Group Survey Summary: Resistance Marker Reporting Practices from Positive Blood Cultures. Clin Infect Dis 2023; 76:1550-1558. [PMID: 36533704 PMCID: PMC10411935 DOI: 10.1093/cid/ciac952] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Revised: 11/23/2022] [Accepted: 12/13/2022] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND We assessed how laboratories use and handle reporting of results of rapid diagnostics performed on positive blood culture broths, with a focus on antimicrobial resistance (AMR) markers. METHODS A survey assembled by the Antibacterial Resistance Leadership Group Diagnostics Committee was circulated from December 2020 to May 2021. The survey was sent to local hospitals, shared on the ClinMicroNet and Division C listservs, and included in a College of American Pathologists proficiency testing survey. RESULTS Ninety-six laboratories of various sizes across the United States (95%) and outside of the United States (5%) participated. Of the laboratories that had at least 1 rapid diagnostic in place (94%), significant heterogeneity in methods used and reporting practices was found across community (52%) and academic (40%) laboratories serving hospitals of various sizes. Respondents had implemented 1 to 6 different panels/platforms for a total of 31 permutations. Methods of reporting rapid organism identification and AMR results varied from listing all targets as "detected"/"not detected" (16-22%) without interpretive guidance, to interpreting results (23-42%), or providing therapeutic guidance comments to patient-facing healthcare teams (3-17%). CONCLUSIONS Current approaches to reporting molecular AMR test results from positive blood culture vary significantly across clinical laboratories. Providing interpretative comments with therapeutic guidance alongside results reported may assist clinicians who are not well-versed in genetic mechanisms of AMR. However, this is currently not being done in all clinical laboratories. Standardized strategies for AMR gene result reporting are needed.
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Affiliation(s)
- Patricia J Simner
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- Department of Medicine, Division of Infectious Diseases, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Jennifer Dien Bard
- Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, Keck School of Medicine, University of Southern California, Los Angeles, California, USA
| | - Christopher Doern
- Department of Pathology, Virginia Commonwealth University Health System, Richmond, Virginia, USA
| | - J Kristie Johnson
- Department of Pathology, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Lars Westblade
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, New York, USA
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, New York, USA
| | - Gayane Yenokyan
- Johns Hopkins Biostatistics Center, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Robin Patel
- Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
- Division of Public Health, Infectious Diseases and Occupational Medicine, Department of Medicine, Mayo Clinic, Rochester, Minnesota, USA
| | - Kimberly E Hanson
- Department of Medicine, Infectious Diseases Division, University of Utah School of Medicine, Salt Lake City, Utah, USA
- Department of Pathology, Clinical Microbiology Division, University of Utah Associated Regional and University Pathologists (ARUP) Laboratories, Salt Lake City, Utah, USA
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Prasetyo DS, Karyanti MR, Yuniar I, Saharman YR, Holiwono L. Application of a sepsis flow chip (SFC) assay for the molecular diagnosis of paediatric sepsis. Access Microbiol 2023; 5:000474.v4. [PMID: 37223064 PMCID: PMC10202402 DOI: 10.1099/acmi.0.000474.v4] [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: 08/11/2022] [Accepted: 02/06/2023] [Indexed: 05/25/2023] Open
Abstract
A delay in detecting sepsis pathogens is a problematic issue for determining definitive antibiotic therapy for the causative pathogens. The gold standard method for sepsis is blood culture but this requires 3 days to detect the definitive pathogen. Molecular methods offer rapid identification of pathogens. We evaluated the use of sepsis flow chip (SFC) assay for identifying pathogens from children with sepsis. Blood samples from children with sepsis were collected and incubated in a culture device. Positive samples were subjected to amplification-hybridization using SFC assay and culture. A total of 94 samples from 47 patients were recovered, from which 25 isolates were recovered, including Klebsiella pneumoniae (11) and Staphylococcus epidermidis (6). From 25 positive blood culture bottles subjected to SFC assay, 24 genus/species and 18 resistance genes were detected. The sensitivity, specificity and conformity was 80, 94.2 and 94.68 % respectively. SFC assay offers promise to identify pathogens from positive blood culture in paediatric patients with sepsis and may support the antimicrobial stewardship programme in hospitals.
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Affiliation(s)
- Dimas Seto Prasetyo
- Clinical Microbiology Medical Staff, Cipto Mangunkusumo General Hospital, Jakarta, Indonesia
- Department of Microbiology Faculty of Medicine, Universitas Indonesia, Jakarta, Indonesia
| | - Mulya Rahma Karyanti
- Pediatric Child Health Medical Staff, Cipto Mangunkusumo General Hospital, Jakarta, Indonesia
- Department of Child Health Faculty of Medicine, Universitas Indonesia, Jakarta, Indonesia
| | - Irene Yuniar
- Pediatric Child Health Medical Staff, Cipto Mangunkusumo General Hospital, Jakarta, Indonesia
- Department of Child Health Faculty of Medicine, Universitas Indonesia, Jakarta, Indonesia
| | - Yulia Rosa Saharman
- Clinical Microbiology Medical Staff, Cipto Mangunkusumo General Hospital, Jakarta, Indonesia
- Department of Microbiology Faculty of Medicine, Universitas Indonesia, Jakarta, Indonesia
| | - Livya Holiwono
- Clinical Microbiology Medical Staff, Cipto Mangunkusumo General Hospital, Jakarta, Indonesia
- Department of Microbiology Faculty of Medicine, Universitas Indonesia, Jakarta, Indonesia
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Zheng H, Chen X, Li W, Lu J, Chen X. Establishment of a Fast Diagnostic Method for Sepsis Pathogens Based on M1 Bead Enrichment. Curr Microbiol 2023; 80:166. [PMID: 37022487 DOI: 10.1007/s00284-023-03280-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2022] [Accepted: 03/21/2023] [Indexed: 04/07/2023]
Abstract
Blood culture-based sepsis diagnostic methods usually cannot obtain positive results in a timely manner. Molecular diagnostic methods, such as real-time PCR without blood culture, would be more time-saving and suitable for pathogenic diagnosis of sepsis, while their sensitivities have always been unsatisfactory for the usually low concentration of pathogens in the blood of sepsis patients. In this study, we established a fast diagnostic method using magnetic beads coated with human recombined mannose-binding lectin that makes it possible to concentrate pathogens from human plasma that have low concentrations of pathogens. With subsequent microculture (MC) and real-time PCR, this method allowed the detection of 1-10 CFUs/ml of Staphylococcus aureus, Group A Streptococcus, Escherichia coli, Pseudomonas aeruginosa, Candida tropicalis, or C. albicans from human plasma within 9.5 h, which was 21-80 h earlier than blood culture. The combination of pathogen enrichment and MC made the detection of sepsis-causing pathogens more time-saving and more sensitive than blood culture or real-time PCR alone.
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Affiliation(s)
- Hao Zheng
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China
| | - Xiaoli Chen
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China
| | - Wenge Li
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China
| | - Jinxing Lu
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China
| | - Xiaoping Chen
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China.
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Kim KJ, Yun SG, Cho Y, Nam MH, Ko YJ, Lee CK. Evaluation of a sterile, filter-based, in-house method for rapid direct bacterial identification and antimicrobial susceptibility testing using positive blood culture. Eur J Clin Microbiol Infect Dis 2023; 42:691-700. [PMID: 37012540 DOI: 10.1007/s10096-023-04592-y] [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: 01/10/2023] [Accepted: 03/24/2023] [Indexed: 04/05/2023]
Abstract
This study aimed to assess the performance of our in-house method for rapid direct bacterial identification (ID) and antimicrobial susceptibility testing (AST) using a positive blood culture (BC) broth. For Gram-negative bacteria, 4 mL of BC broth was aspirated and passed through a Sartorius Minisart syringe filter with a pore size of 5 µm. The filtrate was then centrifuged and washed. A small volume of the pellet was used for ID, using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry, and for AST, using automated broth microdilution. For Gram-positive cocci, 4 mL of BC broth was passed through the Minisart syringe filter. Then, 4 mL of sterile distilled water was injected in the direction opposite to that of the filtration to collect the bacterial residue trapped in the filter. Compared with the conventional method performed with pure colonies on agar plates, 94.0% (234/249) were correctly identified using the in-house method, with rates of 91.4% (127/139) and 97.3% (107/110) for Gram-positive and Gram-negative isolates, respectively. Of 234 correctly identified isolates, 230 were assessed by AST. Categorical agreement and essential agreement were 93.3% and 94.5%, respectively, with a minor error rate of 3.8%, a major error rate of 3.4%, and a very major error rate of 1.6%. Our in-house preparation method showed good performance in rapid direct ID and AST using positive BC broths compared to the conventional method. This simple method can shorten the conventional turnaround time for ID and AST by at least 1 day, potentially contributing to better patient management.
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Affiliation(s)
- Keun Ju Kim
- Department of Laboratory Medicine, College of Medicine, Korea University, Seoul, Korea
| | - Seung Gyu Yun
- Department of Laboratory Medicine, College of Medicine, Korea University, Seoul, Korea
| | - Yunjung Cho
- Department of Laboratory Medicine, College of Medicine, Korea University, Seoul, Korea
| | - Myung-Hyun Nam
- Department of Laboratory Medicine, College of Medicine, Korea University, Seoul, Korea
| | - Young Jin Ko
- Department of Laboratory Medicine, College of Medicine, Chosun University, Gwangju, Korea
| | - Chang Kyu Lee
- Department of Laboratory Medicine, College of Medicine, Korea University, Seoul, Korea.
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Zhu Y, He Z, Jin Y, Zhu S, Xu W, Li B, Nie C, Liu G, Lyu J, Han S. Serum Anion Gap Level Predicts All-Cause Mortality in Septic Patients: A Retrospective Study Based on the MIMIC III Database. J Intensive Care Med 2023; 38:349-357. [PMID: 36066040 DOI: 10.1177/08850666221123483] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
PURPOSE Sepsis is a significant threat in the intensive care unit (ICU) worldwide because it has high morbidity and mortality rates. Early recognition and diagnosis of sepsis are essential for the prevention of adverse outcomes. The present study aimed to quantitatively assess the association between serum anion gap (AG) levels and 30- and 90-day all-cause mortality among sepsis patients. METHODS Clinical data of patients diagnosed with sepsis were extracted from the Medical Information Mart for Intensive Care III (MIMIC III) database. Kaplan-Meier curves and Cox proportional hazards models were used to evaluate the association between serum AG levels and all-cause mortality. A receiver operating characteristic (ROC) curve was drawn to quantify the efficacy of using the serum AG level to predict all-cause mortality. RESULTS A total of 3811 patients were included in the study. The Kaplan-Meier curves showed that patients with higher serum AG levels had a shorter survival time than those with lower levels. Serum AG levels were found to be highly effective in predicting all-cause mortality secondary to sepsis (30-day: AUROC = 0.703; 90-day: AUROC = 0.696). The Cox regression model further indicated that the serum AG level was an independent risk factor for 30- and 90-day mortality in sepsis (HR 3.44, 95% CI 2.97-3.99 for 30-day; HR 3.17, 95% CI 2.76-3.65 for 90-day, P < 0.001 for both). CONCLUSIONS High serum AG may be considered as an alternative parameter for predicting the death risk in sepsis when other variables are not immediately available. Prospective large-scale studies are needed to support its predictive value in the clinic.
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Affiliation(s)
- Yao Zhu
- Department of Neonatology and Pediatrics, The First Affiliated Hospital of Jinan University, Guangzhou, China
| | - Zonglin He
- Department of Neonatology and Pediatrics, The First Affiliated Hospital of Jinan University, Guangzhou, China.,International School, 47885Jinan University, Guangzhou, China.,Division of Life Science, 58207The Hong Kong University of Science and Technology, Hong Kong, China
| | - Ya Jin
- Department of Neonatology and Pediatrics, The First Affiliated Hospital of Jinan University, Guangzhou, China
| | - Sui Zhu
- Department of Public Health and Preventive Medicine, School of Medicine, 47885Jinan University, Guangzhou, China
| | - Weipeng Xu
- Department of Neonatology and Pediatrics, The First Affiliated Hospital of Jinan University, Guangzhou, China
| | - Bingxiao Li
- Department of Neonatology and Pediatrics, The First Affiliated Hospital of Jinan University, Guangzhou, China
| | - Chuan Nie
- Department of Neonatology, 90405Guangdong Women and Children Hospital, Guangzhou, China
| | - Guosheng Liu
- Department of Neonatology and Pediatrics, The First Affiliated Hospital of Jinan University, Guangzhou, China
| | - Jun Lyu
- Department of Clinical Research, The First Affiliated Hospital of Jinan University, Guangzhou, China
| | - Shasha Han
- Department of Neonatology and Pediatrics, The First Affiliated Hospital of Jinan University, Guangzhou, China
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Large-Scale Clinical Evaluation of Rapid Blood Culture Identification Panels for Bloodstream Infections at a Tertiary Hospital. Diagnostics (Basel) 2023; 13:diagnostics13061177. [PMID: 36980485 PMCID: PMC10047266 DOI: 10.3390/diagnostics13061177] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 03/15/2023] [Accepted: 03/17/2023] [Indexed: 03/22/2023] Open
Abstract
The prompt implementation of optimal antibacterial therapy through the rapid identification of the causative organisms is essential for improving outcomes for critically ill patients with bloodstream infections. We evaluated the clinical performance of the FilmArray blood culture identification (BCID) panel for rapidly identifying causative pathogens in the bloodstream using large-scale clinical samples. We analyzed the results of identification using a BCID panel performed on 2005 positive blood culture bottles from September 2019 to June 2022. Pathogen detection efficiency and interval from Gram staining to identification using the BCID panel were compared to those of conventional identification systems—VITEK MS MALDI-TOF Mass Spectrometer and Vitek2—and antibiotic susceptibility testing—Vitek2. We detected 2167 isolates from 2005 positive blood culture bottles. In these isolates, the BCID panel showed 93% full agreement—both organisms and antimicrobial resistance genes were matched, and no off-target organisms were detected. Species-level discordance was found in 0.6% of tests. Sixty-five isolates (3.0%) were only detected by BCID, whereas 22 isolates (1.0%) from the on-target panel were not detected by BCID. This large-scale study demonstrated that the BCID panel was a reliable and rapid identification method for directly identifying bloodstream pathogens in a positive blood culture.
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Arias Ramos D, Alzate JA, Moreno Gómez GA, Hoyos Pulgarín JA, Olaya Gómez JC, Cortés Bonilla I, Vargas Mosquera C. Empirical treatment and mortality in bacteremia due to extended spectrum β-lactamase producing Enterobacterales (ESβL-E), a retrospective cross-sectional study in a tertiary referral hospital from Colombia. Ann Clin Microbiol Antimicrob 2023; 22:13. [PMID: 36797734 PMCID: PMC9933341 DOI: 10.1186/s12941-023-00566-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2022] [Accepted: 02/09/2023] [Indexed: 02/18/2023] Open
Abstract
BACKGROUND Infections caused by extended spectrum β-lactamase (ESβL) producing bacteria are common and problematic. When they cause bloodstream infections, they are associated with significant morbidity and mortality. METHODS A retrospective cross-sectional observational study was conducted in a single center in Pereira, Colombia. It included people hospitalized with bacteremia due to gram-negative bacilli with the extended-spectrum β-lactamase producing phenotype. A logistic regression analysis was constructed. Clinical characteristics and risk factors for death from sepsis were established. RESULTS The prevalence of bacteremia due to Enterobacterales with extended-spectrum β-lactamase producing phenotype was 17%. 110 patients were analyzed. Most patients were men (62%) with a median age of 58 years, hospital mortality was 38%. Admission to intensive care was 45%. The following risk factors for mortality were established: shock requiring vasoactive support, Pitt score > 3 points, and not having an infectious disease consultation (IDC). CONCLUSIONS bacteremia due to Enterobacterales with extended-spectrum β-lactamase producing phenotype have a high mortality. Early recognition of sepsis, identification of risk factors for antimicrobial resistance, and prompt initiation of appropriate empiric antibiotic treatment are important. An infectious disease consultation may help improve outcomes.
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Affiliation(s)
- Deving Arias Ramos
- Universidad Tecnológica de Pereira, Pereira, Colombia. .,Grupo de investigación en Medicina Interna, Universidad Tecnológica de Pereira, Pereira, Colombia.
| | - John Alexander Alzate
- grid.412256.60000 0001 2176 1069Hospital Universitario San Jorge, Pereira, Universidad Tecnológica de Pereira, Pereira, Colombia ,grid.412256.60000 0001 2176 1069Grupo de investigación en Medicina Interna, Universidad Tecnológica de Pereira, Pereira, Colombia
| | - Germán Alberto Moreno Gómez
- grid.412256.60000 0001 2176 1069Universidad Tecnológica de Pereira, Pereira, Colombia ,grid.412256.60000 0001 2176 1069Grupo de investigación en Medicina Interna, Universidad Tecnológica de Pereira, Pereira, Colombia
| | - Julián Andrés Hoyos Pulgarín
- Oncólogos de Occidente, Pereira, Colombia ,grid.412256.60000 0001 2176 1069Grupo de investigación en Medicina Interna, Universidad Tecnológica de Pereira, Pereira, Colombia
| | - Juan Camilo Olaya Gómez
- grid.412256.60000 0001 2176 1069Universidad Tecnológica de Pereira, Pereira, Colombia ,grid.412256.60000 0001 2176 1069Grupo de investigación en Medicina Interna, Universidad Tecnológica de Pereira, Pereira, Colombia
| | - Isabella Cortés Bonilla
- grid.412256.60000 0001 2176 1069Universidad Tecnológica de Pereira, Pereira, Colombia ,grid.412256.60000 0001 2176 1069Grupo de investigación en Medicina Interna, Universidad Tecnológica de Pereira, Pereira, Colombia
| | - Camila Vargas Mosquera
- grid.412256.60000 0001 2176 1069Hospital Universitario San Jorge, Pereira, Universidad Tecnológica de Pereira, Pereira, Colombia ,grid.412256.60000 0001 2176 1069Grupo de investigación en Medicina Interna, Universidad Tecnológica de Pereira, Pereira, Colombia
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Lin K, Zhao Y, Xu B, Yu S, Fu Z, Zhang Y, Wang H, Song J, Fan M, Zhou Y, Ai J, Qiu C, Zhang H, Zhang W. Clinical Diagnostic Performance of Droplet Digital PCR for Suspected Bloodstream Infections. Microbiol Spectr 2023; 11:e0137822. [PMID: 36602351 PMCID: PMC9927361 DOI: 10.1128/spectrum.01378-22] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Accepted: 11/01/2022] [Indexed: 01/06/2023] Open
Abstract
Accurate and timely etiological diagnosis is crucial for bloodstream infections (BSIs) due to their high disability and mortality. We conducted a single-center prospective cohort study to compare the digital droplet PCR (ddPCR) assay with traditional blood culture. A total of 169 blood samples from 122 patients with suspected BSIs were collected, mostly from the department of infectious diseases, the emergency department, and the intensive care units, and the clinical data were also recorded. Nucleic acid was extracted from the blood samples, and a 5-fluorescent-channel droplet digital PCR assay was performed and then fed back with the pathogen and its copies. In BSI patients, ddPCR reported an overall 85.71% (12/14) (95% confidence interval [CI], 56.15 to 97.48%) sensitivity, 100% (7/7) (95% CI, 56.09 to 100.00%) and 71.43% (5/7) (95% CI, 30.26 to 94.89%) sensitivity in patients without empirical treatment and in empirically treated patients, respectively. Compared to traditional blood culture, the overall detection rate of ddPCR was significantly higher, 11.27% (16/142) (95% CI, 6.78 to 17.93%) versus 30.28% (43/142) (95% CI, 23.01 to 38.64%), and the extra detection rate of ddPCR was 19.01% (27/142) (95% CI, 13.11 to 26.63%). Of the ddPCR-positive culture-negative cases, 74.19% (23/31) (95% CI, 55.07 to 87.46%) were consistent with the final clinical diagnosis, including 10 bacteria and fungi. The detection rate of ddPCR was significantly higher in patients with white blood cell (WBC) counts of >10 · 109/L, C-reactive protein (CRP) of >70 mg/L, or procalcitonin (PCT) of >0.9 ng/L. Pathogen loads detected by ddPCR are correlated with WBC, CRP, and especially, PCT levels, precisely and rapidly reflecting clinical disease progression. ddPCR has an important guiding value for the clinical use of antibiotics to achieve the best pathogen coverage and the antibacterial effect. Collectively, ddPCR showed a great diagnostic performance in BSIs and had an overall higher detection rate than blood culture. In addition, ddPCR could be used to dynamically monitor the disease progression and provide medication guidance on antibiotic use. IMPORTANCE ddPCR is a promising method to address the current challenges of BSI diagnosis and precise treatment, as it is highly efficient in DNA detection. It shortens the identification of BSI-related pathogens from several days of traditional bacterial culture to 4 to 5 h. It is extremely sensitive and more tolerant to PCR inhibitors, which may facilitate the amplification and enable the detection of a meager amount of DNA fragments in detecting BSI-related pathogens and drug-resistant genes. It can identify almost 20 pathogens in one reaction, which reduces the usage of clinical blood samples to no more than 2 mL. Additionally, dynamic monitoring, assessment of pathogens, and antibiotic resistance genes in patients could be used to guide timely and precise adjustment of antimicrobial prescription. The short turnaround time of ddPCR may have the potential to guide antimicrobial treatment in the very early stage of sepsis and reduce the mortality and disability rate of sepsis.
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Affiliation(s)
- Ke Lin
- Department of Infectious Disease of Huashan Hospital, National Medical Center for Infectious Diseases and Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, Fudan University, Shanghai, China
| | - Yuanhan Zhao
- Department of Infectious Disease of Huashan Hospital, National Medical Center for Infectious Diseases and Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, Fudan University, Shanghai, China
| | - Bin Xu
- Department of Infectious Disease of Huashan Hospital, National Medical Center for Infectious Diseases and Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, Fudan University, Shanghai, China
| | - Shenglei Yu
- Department of Infectious Disease of Huashan Hospital, National Medical Center for Infectious Diseases and Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, Fudan University, Shanghai, China
| | - Zhangfan Fu
- Department of Infectious Disease of Huashan Hospital, National Medical Center for Infectious Diseases and Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, Fudan University, Shanghai, China
| | - Yi Zhang
- Department of Infectious Disease of Huashan Hospital, National Medical Center for Infectious Diseases and Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, Fudan University, Shanghai, China
| | - Hongyu Wang
- Department of Infectious Disease of Huashan Hospital, National Medical Center for Infectious Diseases and Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, Fudan University, Shanghai, China
| | - Jieyu Song
- Department of Infectious Disease of Huashan Hospital, National Medical Center for Infectious Diseases and Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, Fudan University, Shanghai, China
| | - Mingxiang Fan
- Department of Infectious Disease of Huashan Hospital, National Medical Center for Infectious Diseases and Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, Fudan University, Shanghai, China
| | - Yang Zhou
- Department of Infectious Disease of Huashan Hospital, National Medical Center for Infectious Diseases and Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, Fudan University, Shanghai, China
| | - Jingwen Ai
- Department of Infectious Disease of Huashan Hospital, National Medical Center for Infectious Diseases and Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, Fudan University, Shanghai, China
| | - Chao Qiu
- Department of Infectious Disease of Huashan Hospital, National Medical Center for Infectious Diseases and Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, Fudan University, Shanghai, China
| | - Haocheng Zhang
- Department of Infectious Disease of Huashan Hospital, National Medical Center for Infectious Diseases and Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, Fudan University, Shanghai, China
| | - Wenhong Zhang
- Department of Infectious Disease of Huashan Hospital, National Medical Center for Infectious Diseases and Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, Fudan University, Shanghai, China
- Key Laboratory of Medical Molecular Virology (MOE/MOH) and Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai, China
- State Key Laboratory of Genetic Engineering, School of Life Science, Fudan University, Shanghai, China
- National Clinical Research Centre for Aging and Medicine, Huashan Hospital, Fudan University, Shanghai, China
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Donnars A, Mahieu R, Declerck C, Chenouard R, Lemarié C, Pailhoriès H, Requin J, Kempf M, Eveillard M. BIOFIRE® Blood Culture IDentification 2 (BCID2) panel for early adaptation of antimicrobial therapy in adult patients with bloodstream infections: a real-life experience. Diagn Microbiol Infect Dis 2023; 105:115858. [PMID: 36442386 DOI: 10.1016/j.diagmicrobio.2022.115858] [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: 08/21/2022] [Revised: 10/24/2022] [Accepted: 11/05/2022] [Indexed: 11/13/2022]
Abstract
Our objective was to assess the effectiveness of a multiplex PCR panel for blood culture identification (BCID2) on the implementation of appropriate antimicrobial therapy. We conducted a monocentric pre/post study comparing the time to result from direct microscopic examination (DE) to bacterial identification (BI) in positive blood cultures between 2 different periods: P1 without BCID2 and P2 with BCID2. Appropriate treatments prescribed before DE and after DE / BCID2 and after BI / BCID2 were compared using direct proportion comparison and survival analysis. For mono-microbial bloodstream infections, the proportion of appropriate antimicrobial treatment after DE was 50% in P1 vs. 87.5% after BCID2 in P2 (P < 0.001) for Gram-negative bacteria and 33.0% in P1 vs. 64.4% in P2 (P < 0.01) for Gram-positive bacteria. A significant difference (P = 0.04) was recorded with survival curves for Gram positive bacteria. BCID2 seems effective in reducing the time for prescribing appropriate antimicrobials.
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Affiliation(s)
- Anne Donnars
- Laboratoire de Bactériologie, Département de Biologie des Agents Infectieux, CHU Angers, Angers, France
| | - Rafael Mahieu
- Service des Maladies Infectieuses et Tropicales, CHU Angers, Angers, France; Univ Angers, Nantes Université, CHU Angers, Inserm, CNRS, INCIT, Angers, France
| | - Charles Declerck
- Service des Maladies Infectieuses et Tropicales, CHU Angers, Angers, France
| | - Rachel Chenouard
- Laboratoire de Bactériologie, Département de Biologie des Agents Infectieux, CHU Angers, Angers, France
| | - Carole Lemarié
- Laboratoire de Bactériologie, Département de Biologie des Agents Infectieux, CHU Angers, Angers, France
| | - Hélène Pailhoriès
- Laboratoire de Bactériologie, Département de Biologie des Agents Infectieux, CHU Angers, Angers, France
| | - Jim Requin
- Service des Maladies Infectieuses et Tropicales, CHU Angers, Angers, France
| | - Marie Kempf
- Laboratoire de Bactériologie, Département de Biologie des Agents Infectieux, CHU Angers, Angers, France; Univ Angers, Nantes Université, CHU Angers, Inserm, CNRS, INCIT, Angers, France
| | - Matthieu Eveillard
- Laboratoire de Bactériologie, Département de Biologie des Agents Infectieux, CHU Angers, Angers, France; Univ Angers, Nantes Université, CHU Angers, Inserm, CNRS, INCIT, Angers, France.
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Chirio D, Demonchy E, Le Marechal M, Gaudart A, Lotte R, Carles M, Ruimy R. 24/7 workflow for bloodstream infection diagnostics in microbiology laboratories: the first step to improve clinical management. Clin Chem Lab Med 2023; 61:349-355. [PMID: 36326696 DOI: 10.1515/cclm-2022-0667] [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: 07/11/2022] [Accepted: 10/13/2022] [Indexed: 11/06/2022]
Abstract
OBJECTIVES We aimed to evaluate the impact of an uninterrupted workflow regarding blood cultures on turnaround time and antibiotic prescription. METHODS Monomicrobial episodes of bacteremia were retrospectively evaluated before and after a continuous 24/7 workflow was implemented in our clinical microbiology laboratory (pre- and post-intervention periods; PREIP and POSTIP). Primary outcome was the time from specimen collection to the first change in antibiotic therapy. Secondary outcomes included the time from specimen collection to effective antibiotic therapy and to antibiotic susceptibility testing results (or turnaround time), as well as hospital length of stay and all-cause mortality at 30 days. RESULTS A total of 548 episodes of bacteremia were included in the final analysis. There was no difference in PREIP and POSTIP regarding patient characteristics and causative bacteria. In POSTIP, the mean time to the first change in antibiotic therapy was reduced by 10.4 h (p<0.001). The time to effective antibiotic therapy and the turnaround time were respectively reduced by 4.8 h (p<0.001) and 5.1 h (p=0.006) in POSTIP. There was no difference in mean hospital length of stay or mortality between the two groups. CONCLUSIONS Around the clock processing of blood cultures allows for a reduction in turnaround time, which in turn reduces the delay until effective antibiotic therapy prescription.
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Affiliation(s)
- David Chirio
- Service de Maladies infectieuses et Tropicales, Hôpital l'Archet 1, CHU de Nice, Nice, France
- Université Côte d'Azur, Nice, France
| | - Elisa Demonchy
- Service de Maladies infectieuses et Tropicales, Hôpital l'Archet 1, CHU de Nice, Nice, France
| | - Marion Le Marechal
- Service de Maladies infectieuses et Tropicales, Hôpital l'Archet 1, CHU de Nice, Nice, France
- Département de santé publique, CHU de Nice, Nice, France
| | - Alice Gaudart
- Laboratoire de Bactériologie, CHU de Nice, Hôpital de l'Archet, Nice, France
| | - Romain Lotte
- Université Côte d'Azur, Nice, France
- Laboratoire de Bactériologie, CHU de Nice, Hôpital de l'Archet, Nice, France
- INSERM U1065, C3M, Equipe 6 "Virulence microbienne et signalisation inflammatoire", Bâtiment Universitaire Archimed, Nice, France
| | - Michel Carles
- Service de Maladies infectieuses et Tropicales, Hôpital l'Archet 1, CHU de Nice, Nice, France
- Université Côte d'Azur, Nice, France
| | - Raymond Ruimy
- Université Côte d'Azur, Nice, France
- Laboratoire de Bactériologie, CHU de Nice, Hôpital de l'Archet, Nice, France
- INSERM U1065, C3M, Equipe 6 "Virulence microbienne et signalisation inflammatoire", Bâtiment Universitaire Archimed, Nice, France
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Fast Track Diagnostic Tools for Clinical Management of Sepsis: Paradigm Shift from Conventional to Advanced Methods. Diagnostics (Basel) 2023; 13:diagnostics13020277. [PMID: 36673087 PMCID: PMC9857847 DOI: 10.3390/diagnostics13020277] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2022] [Revised: 12/24/2022] [Accepted: 01/09/2023] [Indexed: 01/15/2023] Open
Abstract
Sepsis is one of the deadliest disorders in the new century due to specific limitations in early and differential diagnosis. Moreover, antimicrobial resistance (AMR) is becoming the dominant threat to human health globally. The only way to encounter the spread and emergence of AMR is through the active detection and identification of the pathogen along with the quantification of resistance. For better management of such disease, there is an essential requirement to approach many suitable diagnostic techniques for the proper administration of antibiotics and elimination of these infectious diseases. The current method employed for the diagnosis of sepsis relies on the conventional culture of blood suspected infection. However, this method is more time consuming and generates results that are false negative in the case of antibiotic pretreated samples as well as slow-growing microbes. In comparison to the conventional method, modern methods are capable of analyzing blood samples, obtaining accurate results from the suspicious patient of sepsis, and giving all the necessary information to identify the pathogens as well as AMR in a short period. The present review is intended to highlight the culture shift from conventional to modern and advanced technologies including their limitations for the proper and prompt diagnosing of bloodstream infections and AMR detection.
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Curtoni A, Ghibaudo D, Veglio C, Imperatore L, Bianco G, Castiglione A, Ciccone G, Scaglione L, Scabini S, Corcione S, De Rosa FG, Costa C, Cavallo R. Light Scattering Technology and MALDI-TOF MS in the microbiological fast-track of bloodstream infections: potential impact on antimicrobial treatment choices in a real-life setting. J Med Microbiol 2023; 72. [PMID: 36748537 DOI: 10.1099/jmm.0.001638] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Introduction. Rapid identification (ID) and antimicrobial susceptibility testing (AST) of bloodstream infections (BSI) pathogens are fundamental to switch from empirical to targeted antibiotic therapy improving patients outcome and reducing antimicrobial resistance spreading.Hypothesis. The adoption of a rapid microbiological protocol (RP) based on Matrix-Assisted Laser Desorption Ionization-Time Of Flight Mass Spectrometry (MALDI-TOF MS) and Light Scattering Technology (LST) for rapid diagnosis of BSI could positively impact on patients' antimicrobial management.Aim. The study aim was to evaluate a RP for BSI microbiological diagnosis in terms of accuracy, turnaround time (TAT) and potential therapeutic impact.Methodology. A prospective observational study was conducted: monomicrobial bacterial blood cultures of septic patients were analysed in parallel by RP and standard protocol (SP). In RP the combination of MALDI-TOF MS and LST was used for rapid ID and AST assessments, respectively. To determine the potential impact of RP on antimicrobial therapy management, clinicians were interviewed on therapeutic decisions based on RP and SP results. RP accuracy, TAT and impact were evaluated in comparison to SP results.Results. A total of 97 patients were enrolled. ID and AST concordance between RP and SP were 96.9 and 94.7 %, respectively. RP technical and real-life TAT were lower than SP (6.4 h vs. 18.4 h; 9.5 vs. 27.1 h). The agreement between RP- and SP-based therapeutic decisions was 90.7 (90 % CI 84.4-95.1). RP results could produce 24/97 correct antibiotic changes with 18/97 possible de-escalations and 25/97 prompt applications of infection control precautions.Conclusion. With the application of RP in BSI management, about one-fourth of patients may safely benefit from early targeted antibiotic therapy and infection control policies with one working day in advance in comparison to conventional methods. This protocol is feasible for clinical use in microbiology laboratories and potentially helpful for Antimicrobial Stewardship.
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Affiliation(s)
- Antonio Curtoni
- Microbiology and Virology Unit, University Hospital Città della Salute e della Scienza di Torino, Turin, Italy
| | - Davide Ghibaudo
- Department of Public Health and Paediatrics, University of Turin, Turin, Italy
| | - Caterina Veglio
- Department of Public Health and Paediatrics, University of Turin, Turin, Italy
| | - Luigi Imperatore
- Internal Medicine Unit, University Hospital Città della Salute e della Scienza di Torino, Turin, Italy
| | - Gabriele Bianco
- Microbiology and Virology Unit, University Hospital Città della Salute e della Scienza di Torino, Turin, Italy
| | - Anna Castiglione
- Unit of Clinical Epidemiology, University Hospital Città della Salute e della Scienza di Torino and CPO Piemonte, Turin, Italy
| | - Giovannino Ciccone
- Unit of Clinical Epidemiology, University Hospital Città della Salute e della Scienza di Torino and CPO Piemonte, Turin, Italy
| | - Luca Scaglione
- Internal Medicine Unit, University Hospital Città della Salute e della Scienza di Torino, Turin, Italy
| | - Silvia Scabini
- Infectious Diseases Unit, University Hospital Città della Salute e della Scienza di Torino, Turin, Italy
| | - Silvia Corcione
- Infectious Diseases Unit, University Hospital Città della Salute e della Scienza di Torino, Turin, Italy.,Department of Medical Sciences, University of Turin, Turin, Italy
| | - Francesco Giuseppe De Rosa
- Infectious Diseases Unit, University Hospital Città della Salute e della Scienza di Torino, Turin, Italy.,Department of Medical Sciences, University of Turin, Turin, Italy
| | - Cristina Costa
- Microbiology and Virology Unit, University Hospital Città della Salute e della Scienza di Torino, Turin, Italy.,Department of Public Health and Paediatrics, University of Turin, Turin, Italy
| | - Rossana Cavallo
- Microbiology and Virology Unit, University Hospital Città della Salute e della Scienza di Torino, Turin, Italy.,Department of Public Health and Paediatrics, University of Turin, Turin, Italy
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45
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Duan R, Wang P. Rapid and Simple Approaches for Diagnosis of Staphylococcus aureus in Bloodstream Infections. Pol J Microbiol 2022; 71:481-489. [PMID: 36476633 PMCID: PMC9944965 DOI: 10.33073/pjm-2022-050] [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: 08/29/2022] [Accepted: 11/01/2022] [Indexed: 12/13/2022] Open
Abstract
Staphylococcus aureus is an important causative pathogen of bloodstream infections. An amplification assay such as real-time PCR is a sensitive, specific technique to detect S. aureus. However, it needs well-trained personnel, and costs are high. A literature review focusing on rapid and simple methods for diagnosing S. aureus was performed. The following methods were included: (a) Hybrisep in situ hybridization test, (b) T2Dx system, (c) BinaxNow Staphylococcus aureus and PBP2a, (d) Gram staining, (e) PNA FISH and QuickFISH, (f) Accelerate PhenoTM system, (g) MALDI-TOF MS, (h) BioFire FilmArray, (i) Xpert MRSA/SA. These rapid and simple methods can rapidly identify S. aureus in positive blood cultures or direct blood samples. Furthermore, BioFire FilmArray and Xpert MRSA/SA identify methicillin-resistant S. aureus (MRSA), and the Accelerate PhenoTM system can also provide antimicrobial susceptibility testing (AST) results. The rapidity and simplicity of results generated by these methods have the potential to improve patient outcomes and aid in the prevention of the emergence and transmission of MRSA.
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Affiliation(s)
- Rui Duan
- Department of Laboratory Medicine and Blood Transfusion, The First People’s Hospital of Jingmen, Jingmen, Hubei Province, China
| | - Pei Wang
- Department of Laboratory Medicine and Blood Transfusion, The First People’s Hospital of Jingmen, Jingmen, Hubei Province, China, E-mail:
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Reddy Banda S, Klapproth H, Smit N, Bednar S, Brandstetter T, Rühe J. An advanced and efficient asymmetric PCR method for microarray applications. Front Bioeng Biotechnol 2022; 10:1045154. [PMID: 36532575 PMCID: PMC9748121 DOI: 10.3389/fbioe.2022.1045154] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Accepted: 11/09/2022] [Indexed: 06/18/2024] Open
Abstract
The sensitivity of a PCR based biochip assay relies on the efficiency of PCR amplicons in binding to the microarray spots. The essential factor determining the sensitivity is the amount of single stranded (ss) amplicons available for biochip hybridization. Asymmetric PCR can generate ss-amplicons depending on the ratio of primers used in the amplification process, but this process is often inefficient. We report a novel variant of PCR called the Asymmetric Exponential and Linear Amplification (AELA) which can overcome these issues and generate large amounts of single stranded amplicons. AELA-PCR introduces an amplification strategy that makes use of both exponential and linear amplification of the target nucleic acid. This is done by specifically designed primers and choice of adequate thermal profiles. In conventional PCR with a classical thermal profile, these specifically designed primers will work normally and contribute to an exponential increase of amplicons. A designed sequence extension of one of the primers and a very specific thermal profile, will result in a situation that the extended primer will be the only functional one for amplification, resulting in a linear phase of the amplification process. That is why during this step only one of the two strands of the target is amplified linearly and no longer exponentially. The result of the whole process is an amplification product enriched very strongly in one of the two single strands of the target. These adaptions in PCR are particularly favorable where the generation of ss-DNA/RNA is required. We demonstrate the higher biochip sensitivity of AELA-PCR compared to conventional amplification methods with an example of the Staphylococcus aureus detection on a DNA oligonucleotide microarray.
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Affiliation(s)
- Suresh Reddy Banda
- Laboratory for Chemistry and Physics of Interfaces, Department of Microsystems Engineering (IMTEK), University of Freiburg, Freiburg, Germany
| | - Holger Klapproth
- Laboratory for Chemistry and Physics of Interfaces, Department of Microsystems Engineering (IMTEK), University of Freiburg, Freiburg, Germany
- Safeguard Biosystems Holding Ltd., London, United Kingdom
| | - Nicolaas Smit
- Safeguard Biosystems Holding Ltd., London, United Kingdom
| | - Sonja Bednar
- Laboratory for Chemistry and Physics of Interfaces, Department of Microsystems Engineering (IMTEK), University of Freiburg, Freiburg, Germany
- Safeguard Biosystems Holding Ltd., London, United Kingdom
| | - Thomas Brandstetter
- Laboratory for Chemistry and Physics of Interfaces, Department of Microsystems Engineering (IMTEK), University of Freiburg, Freiburg, Germany
| | - Jürgen Rühe
- Laboratory for Chemistry and Physics of Interfaces, Department of Microsystems Engineering (IMTEK), University of Freiburg, Freiburg, Germany
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47
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Development of a Multiplex Polymerase Chain Reaction-Based DNA Lateral Flow Assay as a Point-of-Care Diagnostic for Fast and Simultaneous Detection of MRSA and Vancomycin Resistance in Bacteremia. Diagnostics (Basel) 2022; 12:diagnostics12112691. [DOI: 10.3390/diagnostics12112691] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Revised: 10/26/2022] [Accepted: 11/02/2022] [Indexed: 11/06/2022] Open
Abstract
To reduce high mortality and morbidity rates, timely and proper treatment of methicillin-resistant Staphylococcus aureus (MRSA) bloodstream infection is required. A multiplex polymerase reaction (mPCR)-based DNA lateral flow assay (MBDLFA) was developed as a point-of-care diagnostic for simultaneous identification of S. aureus, methicillin resistance, and vancomycin resistance directly from blood or blood cultures. A mPCR was developed to detect nuc, mecA, and vanA/B; its sensitivity, specificity, and limit of detection (LOD) were determined. The developed reaction was further modified for use in MBDLFA and its sensitivity for detection of target genes from artificially inoculated blood samples was checked. The optimized mPCR successfully detected nuc, mecA, and vanA/B from genomic DNA of bacterial colonies with LODs of 107, 107, and 105 CFU/mL, respectively. The reaction was sensitive and specific. The optimized mPCR was used in MBDLFA that detected nuc, mecA, and vanA/B with LODs of 107, 108, and 104 CFU/mL, respectively, directly from artificially inoculated blood. The developed MBDLFA can be used as a rapid, cheap point-of-care diagnostic for detecting S. aureus, MRSA, and vancomycin resistance directly from blood and blood cultures in ~2 h with the naked eye. This will reduce morbidity, mortality, and treatment cost in S. aureus bacteremia.
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Yang L, Lin Y, Zhang X, Wei B, Wang J, Liu B. Predictive Value of Combination of Procalcitonin and Predisposition, Infection, Response, and Organ Dysfunction (PIRO) System in Septic Patients with Positive Blood Cultures in the Emergency Department. Infect Drug Resist 2022; 15:6189-6202. [PMID: 36312440 PMCID: PMC9597669 DOI: 10.2147/idr.s384689] [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: 08/10/2022] [Accepted: 10/13/2022] [Indexed: 11/23/2022] Open
Abstract
Purpose Procalcitonin and predisposition, infection, response, and organ dysfunction (PIRO) system have high predictive value for the prognosis of critically ill patients. There are few studies on the predictive value of patients with positive blood cultures. The aim of the study was to evaluate risk stratification and sepsis-related mortality in patients with positive blood cultures via procalcitonin (PCT) combined with the PIRO system in emergency departments (ED). Methods A total of 1074 patients with positive blood cultures were admitted to Beijing Chao-Yang Hospital ED from December 2017 to October 2020. Their serum PCT was recorded, along with a Sequential Organ Failure Assessment (SOFA) score, Mortality in Emergency Department Sepsis (MEDS) score, Acute Physiology and Chronic Health Evaluation II (APACHE II) score, and PIRO score to predict the prognosis of septic patients with positive blood culture in terms of ICU (intensive care unit) admission, multiple organ dysfunction syndrome (MODS) development, and 28-day mortality. Receiver operating characteristic (ROC) curves and logistic regression analysis were used to assess the prognostic value of the scoring systems. Results A total of 978 patients met the inclusion criteria. PCT, MEDS, APACHE II, and PIRO scores were found to independently predict ICU-admission, MODS development, and 28-day mortality (P<0.05), whereas SOFA did not. The AUC values of the PCT, MEDS, APACHE II, and PIRO scores for ICU-admission were 0.620, 0.740, 0.780, and 0.751, respectively. In the prediction of 28-day mortality, the AUC values of PCT, MEDS, APACHE II, and PIRO were 0.782, 0.745, 0.805, and 0.831, respectively. The AUC values combined PCT and PIRO system in predicting MODS and 28-day mortality were better than when predicting ICU-admission. Conclusion This study indicates that PCT combined with the PIRO scoring system has a higher predictive value and is superior in predicting MODS and 28-day mortality in septic patients with positive blood cultures.
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Affiliation(s)
- Long Yang
- Emergency Medicine Clinical Research Center, Beijing Chao-Yang Hospital, Capital Medical University, & Beijing Key Laboratory of Cardiopulmonary Cerebral Resuscitation, Beijing, 100020, People’s Republic of China
| | - Yue Lin
- Department of Radiology, China-Japan Friendship Hospital, Beijing, 100029, People’s Republic of China
| | - Xiangqun Zhang
- Emergency Medicine Clinical Research Center, Beijing Chao-Yang Hospital, Capital Medical University, & Beijing Key Laboratory of Cardiopulmonary Cerebral Resuscitation, Beijing, 100020, People’s Republic of China
| | - Bing Wei
- Emergency Medicine Clinical Research Center, Beijing Chao-Yang Hospital, Capital Medical University, & Beijing Key Laboratory of Cardiopulmonary Cerebral Resuscitation, Beijing, 100020, People’s Republic of China
| | - Junyu Wang
- Emergency Medicine Clinical Research Center, Beijing Chao-Yang Hospital, Capital Medical University, & Beijing Key Laboratory of Cardiopulmonary Cerebral Resuscitation, Beijing, 100020, People’s Republic of China
| | - Bo Liu
- Emergency Medicine Clinical Research Center, Beijing Chao-Yang Hospital, Capital Medical University, & Beijing Key Laboratory of Cardiopulmonary Cerebral Resuscitation, Beijing, 100020, People’s Republic of China, Correspondence: Bo Liu; Junyu Wang, Emergency Medicine Clinical Research Center, Beijing Chao-Yang Hospital, Capital Medical University, & Beijing Key Laboratory of Cardiopulmonary Cerebral Resuscitation, Beijing, 100020, People’s Republic of China, Tel/Fax +86 10-51718171, Email ;
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Peri AM, Ling W, Furuya-Kanamori L, Harris PNA, Paterson DL. Performance of BioFire Blood Culture Identification 2 Panel (BCID2) for the detection of bloodstream pathogens and their associated resistance markers: a systematic review and meta-analysis of diagnostic test accuracy studies. BMC Infect Dis 2022; 22:794. [PMID: 36266641 PMCID: PMC9585790 DOI: 10.1186/s12879-022-07772-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Accepted: 10/09/2022] [Indexed: 11/10/2022] Open
Abstract
Background Early identification of bloodstream pathogens and their associated antimicrobial resistance may shorten time to optimal therapy in patients with sepsis. The BioFire Blood Culture Identification 2 Panel (BCID2) is a novel multiplex PCR detecting 43 targets directly from positive blood cultures, reducing turnaround times.
Methods We have performed a systematic review and meta-analysis of diagnostic test accuracy studies to assess the BCID2 performance for pathogen identification and resistance markers detection compared to gold standard culture-based methods (including phenotypic and/or genotypic characterization). Results Nine studies were identified reporting data to build 2 × 2 tables for each BCID2 target, including 2005 blood cultures. The pooled specificity of the assay was excellent (> 97%) across most subgroups of targets investigated, with a slightly broader confidence interval for S. epidermidis (98.1%, 95% CI 93.1 to 99.5). Pooled sensitivity was also high for the major determinants of bloodstream infection, including Enterobacterales (98.2%, 95% CI 96.3 to 99.1), S. aureus (96.0%, 95% CI 90.4 to 98.4), Streptococcus spp. (96.7%, 95% CI 92.8 to 98.5), P. aeruginosa (92.7%, 95% CI 83.1 to 97.0), E. faecalis (92.3%, 95% CI 83.5 to 96.6), as well as blaCTX-M (94.9, 95% CI 85.7 to 98.3), carbapenemases (94.9%, 95% CI 83.4 to 98.6) and mecA/C & MREJ (93.9%, 95% CI 83.0 to 98.0). Sensitivity for less common targets was slightly lower, possibly due to their under-representation in the included studies. Conclusions BCID2 showed good performance for detecting major determinants of bloodstream infection and could support early antimicrobial treatment, especially for ESBL or carbapenemase-producing Gram-negative bacilli and methicillin-resistant S. aureus. Supplementary Information The online version contains supplementary material available at 10.1186/s12879-022-07772-x.
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Affiliation(s)
- Anna Maria Peri
- University of Queensland Centre for Clinical Research, Herston, QLD, 4029, Australia.
| | - Weiping Ling
- University of Queensland Centre for Clinical Research, Herston, QLD, 4029, Australia
| | - Luis Furuya-Kanamori
- University of Queensland Centre for Clinical Research, Herston, QLD, 4029, Australia
| | - Patrick N A Harris
- University of Queensland Centre for Clinical Research, Herston, QLD, 4029, Australia.,Central Microbiology, Pathology Queensland, Royal Brisbane and Women's Hospital, Herston, QLD, 4029, Australia
| | - David L Paterson
- University of Queensland Centre for Clinical Research, Herston, QLD, 4029, Australia.,Infectious Diseases Unit, Royal Brisbane and Women's Hospital, Herston, QLD, 4029, Australia
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50
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Bonini A, Carota AG, Poma N, Vivaldi FM, Biagini D, Bottai D, Lenzi A, Tavanti A, Di Francesco F, Lomonaco T. Emerging Biosensing Technologies towards Early Sepsis Diagnosis and Management. BIOSENSORS 2022; 12:894. [PMID: 36291031 PMCID: PMC9599348 DOI: 10.3390/bios12100894] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/24/2022] [Revised: 09/28/2022] [Accepted: 10/13/2022] [Indexed: 06/16/2023]
Abstract
Sepsis is defined as a systemic inflammatory dysfunction strictly associated with infectious diseases, which represents an important health issue whose incidence is continuously increasing worldwide. Nowadays, sepsis is considered as one of the main causes of death that mainly affects critically ill patients in clinical settings, with a higher prevalence in low-income countries. Currently, sepsis management still represents an important challenge, since the use of traditional techniques for the diagnosis does not provide a rapid response, which is crucial for an effective infection management. Biosensing systems represent a valid alternative due to their characteristics such as low cost, portability, low response time, ease of use and suitability for point of care/need applications. This review provides an overview of the infectious agents associated with the development of sepsis and the host biomarkers suitable for diagnosis and prognosis. Special focus is given to the new emerging biosensing technologies using electrochemical and optical transduction techniques for sepsis diagnosis and management.
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Affiliation(s)
- Andrea Bonini
- Department of Chemistry and Industrial Chemistry, University of Pisa, Via G. Moruzzi 13, 56124 Pisa, Italy
- Department of Biology, University of Pisa, Via San Zeno 35-39, 56100 Pisa, Italy
| | - Angela Gilda Carota
- Department of Chemistry and Industrial Chemistry, University of Pisa, Via G. Moruzzi 13, 56124 Pisa, Italy
| | - Noemi Poma
- Department of Biology, University of Pisa, Via San Zeno 35-39, 56100 Pisa, Italy
| | - Federico Maria Vivaldi
- Department of Chemistry and Industrial Chemistry, University of Pisa, Via G. Moruzzi 13, 56124 Pisa, Italy
| | - Denise Biagini
- Department of Chemistry and Industrial Chemistry, University of Pisa, Via G. Moruzzi 13, 56124 Pisa, Italy
| | - Daria Bottai
- Department of Biology, University of Pisa, Via San Zeno 35-39, 56100 Pisa, Italy
| | - Alessio Lenzi
- Department of Chemistry and Industrial Chemistry, University of Pisa, Via G. Moruzzi 13, 56124 Pisa, Italy
| | - Arianna Tavanti
- Department of Biology, University of Pisa, Via San Zeno 35-39, 56100 Pisa, Italy
| | - Fabio Di Francesco
- Department of Chemistry and Industrial Chemistry, University of Pisa, Via G. Moruzzi 13, 56124 Pisa, Italy
| | - Tommaso Lomonaco
- Department of Chemistry and Industrial Chemistry, University of Pisa, Via G. Moruzzi 13, 56124 Pisa, Italy
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